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Acknowledgements

Citation: F. Leonarski, M. Bruckner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matej, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang “Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors” (2023), J. Synchrotron Rad., 30, 227-234 doi:10.1107/S1600577522010268.

The project is supported by :

  • Innosuisse via Innovation Project “NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications” (101.535.1 IP-ENG; Apr 2023 - Sep 2025).

  • ETH Domain via Open Research Data Contribute project (Jan - Dec 2023)

  • AMD University Program with donation of licenses of Ethernet IP cores and Vivado software

This software uses Viridis, Magma and Inferno colormaps from Matplotlib under its BSD-compatible license

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CBOR messages

To communicate between FPGA-equipped receiver system and writers, Jungfraujoch is using binary CBOR encoding with tinycbor library (Intel). The protocol is based on and compatible with DECTRIS Stream2. There are minor differences at the moment:

  • LZ4 alone is not allowed; Bitshuffle+LZ4 and Bitshuffle+Zstandard are allowed

  • Few fields are currently absent

  • Extra fields are present beyond DECTRIS standard

  • There are calibration and metadata messages defined beyond DECTRIS specification

Start message

Field name

Type

Description

Present in DECTRIS format

type

String

value “start”

X

magic_number

uint64

Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver

detector_distance

float

Detector distance [m]

detector_translation

Array(float)

Detector translation vector [m]

X

beam_center_x

float

Beam center in X direction [pixels]

X

beam_center_y

float

Beam center in Y direction [pixels]

X

countrate_correction_enabled

bool

Countrate correction enabled

X

flatfield_enabled

bool

Flatfield enabled

X

number_of_images

uint64

Number of images in the series

X

image_size_x

uint64

Image width [pixels]

X

image_size_y

uint64

Image height [pixels]

X

incident_energy

float

X-ray energy [eV]

X

incident_wavelength

float

X-ray wavelength [Angstrom]

X

frame_time

float

Frame time, if multiple frames per trigger [s]

X

count_time

float

Exposure time [s]

X

saturation_value

int64

Maximum valid sample value

X

error_value

int64 (optional)

Value used in images to describe pixels that are in error state or missing

pixel_size_x

float

Pixel width [m]

X

pixel_size_y

float

Pixel height [m]

X

sensor_thickness

float

Sensor thickness [m]

X

sensor_material

string

Sensor material

X

arm_date

date

Approximate date of arming

X

pixel_mask_enabled

bool

Pixel mask applied on images

X

detector_description

string

Name of the detector

X

detector_serial_number

string

Detector serial number

X

series_unique_id

string

Unique text ID of the series (run_name parameter)

X

series_id

uint64

Unique numeric ID of the series (run_number parameter)

X

fluorescence

object (optional)

X-ray fluorescence spectrum collected at start

- energy

Array(float)

Energy of measuring point [eV]

- data

Array(float)

Fluorescence scan result data [arbitrary units]; must be strictly the same length as energy

goniometer

Map

Definition of rotation axis (optional)

X

- AXIS

string

Rotation axis name (e.g. omega) - only one axis is supported in Jungfraujoch

X

- - increment

float

Rotation axis increment (per image) in degree [deg]

X

- - start

float

Rotation axis start angle [deg]

X

- - axis

Array(float)

Vector for the rotation axis

- - helical_step

Array(float)

Translation for helical scan for 1 image [m]

- - screening_wedge

Array(float)

Wedge for screening [deg] (increment would correspond to difference between screening points)

grid_scan

object

Grid scan definition (optional and exclusive with rotation axis)

- n_fast

uint64

Number of elements along fast axis

- n_slow

uint64

Number of elements along slow axis

- step_x_axis

float

Step along X axis, can be negative [m]

- step_y_axis

float

Step along Y axis, can be negative [m]

- snake_scan

bool

Snake scan (rows alternate direction)

- vertical_scan

bool

Vertical scan (enabled: fast direction = Y, disabled: fast direction = X)

jungfrau_conversion_enabled

bool (optional)

Applying JUNGFRAU pixel conversion (to photons or keV)

jungfrau_conversion_factor

float (optional)

Factor used for JUNGFRAU conversion [eV]

geometry_transformation_enabled

bool (optional)

Transformation from detector module geometry (512x1024) to full detector geometry

pixel_mask

Map(string -> Image)

Pixel mask - multiple in case of storage cells

X

channels

Array(string)

List of image channels

X

max_spot_count

uint64

Maximum number of spots identified in spot finding

storage_cell_number

uint64 (optional)

Number of storage cells used by JUNGFRAU

storage_cell_delay

Rational

Delay of storage cells in JUNGFRAU

threshold_energy

float

Threshold energy for EIGER detector [eV]

image_dtype

string

Pixel bit type (e.g. uint16)

X

unit_cell

object (optional)

Unit cell of the system: a, b, c [angstrom] and alpha, beta, gamma [degree]

az_int_q_bin_count

uint64

Number of azimuthal integration bins in the radial direction

az_int_phi_bin_count

uint64

Number of azimuthal integration bins in the phi angle direction

az_int_bin_to_q

Array(float)

Q value for each azimuthal integration bin [angstrom^-1]

az_int_bin_to_two_theta

Array(float)

Two theta angle value for each azimuthal integration bin [deg]

az_int_bin_to_phi

Array(float)

Phi value for each azimuthal integration bin [deg]

summation

uint64

Factor of frame summation

user_data

string

JSON serialized to string that can contain the following fields (all fields are optional):

X

- file_prefix

string

File prefix

- images_per_file

uint64

Number of images written per file

- images_per_trigger

uint64

Number of images collected per trigger

- source_name

string

Facility name

- source_type

string

Type of X-ray source (use NXsource/type values, for example “Synchrotron X-ray Source” or “Free-Electron Laser”)

- instrument_name

string

Instrument name

- sample_name

string

Name of the sample

- user

any valid JSON

Value of header_appendix provided at collection start to Jungfraujoch

- attenuator_transmission

float

Attenuator transmission []

- total_flux

float

Total flux [ph/s]

- space_group_number

uint64

Space group number

- summation_mode

string

Summation mode (internal|fpga|cpu)

- overwrite

bool

Overwrite existing HDF5 files

- file_format

int

File writer format: 0 = no master file, 1 = soft links, 2 = virtual dataset, 3 = CBF, 4 = TIFF

- roi

Array(object)

ROI configurations; each element is one of:

type “box”: xmin, xmax, ymin, ymax (numbers)

type “circle”: r, x, y (numbers)

type “azim”: qmin, qmax (numbers)

- gain_file_names

Array(string)

Names of JUNGFRAU gain files used for the current detector

- write_master_file

bool

With multiple sockets, it selects which socket will provide master file

- data_reduction_factor_serialmx

uint64

Data reduction factor for serial MX

- experiment_group

string

ID of instrument user, e.g., p-group (SLS/SwissFEL) or proposal number

- jfjoch_release

string

Jungfraujoch release number

- socket_number

uint64

Number of ZeroMQ socket (on jfjoch_broker side) used for transmission

- bit_depth_readout

uint64

Bit depth of the detector readout

- writer_notification_zmq_addr

string

ZeroMQ address to inform jfjoch_broker about writers that finished operation

- xfel_pulse_id

uint64

Pulse IDs are recorded for images

- ring_current_mA

float

Ring current at the start of the measurement

- sample_temperature_K

float

Sample temperature [K]

- detect_ice_rings

bool

Ice ring detection feature is enabled

- indexing_algorithm

string

Indexing algorithm used on-the-fly; allowed values: ffbidx, fft, fftw, none

- geom_refinement_algorithm

string

Post-indexing detector geometry refinement algorithm; allowed values: none, beam_center, beam_center_tetragonal

- poni_rot1

float

Tilt of the detector rot1 according to PyFAI PONI convention [rad]

- poni_rot2

float

Tilt of the detector rot2 according to PyFAI PONI convention [rad]

- poni_rot3

float

Tilt of the detector rot3 according to PyFAI PONI convention [rad]

See DECTRIS documentation for definition of Image as MultiDimArray with optional compression.

Image message

Field name

Type

Description

Present in DECTRIS format

Optional

type

String

value “image”

X

magic_number

uint64

Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver

series_unique_id

string

Unique text ID of the series (run_name parameter)

X

series_id

uint64

Unique numeric ID of the series (run_number parameter)

X

image_id

uint64

Number of image within the series; for MX lossy compression this is sequential excluding removed frames

X

original_image_id

uint64

Number of image within the series; for MX lossy compression this includes removed frames in the count

real_time

Rational

Exposure time

X

start_time

Rational

Exposure start time (highly approximate)

X

end_time

Rational

Exposure end time (highly approximate)

X

spots

Array(object)

Spots:

- x

float

observed position in x (pixels)

- y

float

observed position in y (pixels)

- I

float

intensity (photons)

- maxc

int64

max count (photons)

- ice_ring

bool

spot in resolution range for ice rings

- indexed

bool

indexed solution

reflections

Array(object)

Reflections:

- h

int64

Miller index

- k

int64

Miller index

- l

int64

Miller index

- x

float

position in x (pixels)

- y

float

position in y (pixels)

- d

float

resolution [Angstrom]

- I

float

integrated intensity (photons)

- bkg

float

mean background value (photons)

- sigma

float

standard deviation, estimated from counting statistics (photons)

- image

float

image number (present for each spot)

- dist_ewald

float

distance to Ewald sphere (present only for indexed spots)

- rlp

float

Reciprocal Lorentz and polarization corrections

- partiality

float

Partiality of the reflection

spot_count

uint64

Spot count

spot_count_ice_rings

uint64

Number of spots within identified rings (experimental)

spot_count_low_res

uint64

Number of spots in low resolution (prior to filtering)

spot_count_indexed

uint64

Number of spots which fit indexing solution within a given tolerance

az_int_profile

Array(float)

Azimuthal integration results, use az_int_bin_to_q from start message for legend

NaN is used for empty bins and has to be taken care by the receiver

indexing_result

bool

Indexing successful

indexing_lattice

Array(9 * float)

Indexing result real lattice; present only if indexed

X

indexing_unit_cell

object

Indexing result unit cell: a, b, c [angstrom] and alpha, beta, gamma [degree]; present only if indexed

X

Unit cell is redundant to lattice - yet to simplify downstream programs to analyze results, both are provided

profile_radius

float

Profile radius of the image - describes distance of observed reflections from the Ewald sphere [Angstrom^-1]

mosaicity

float

Angular range of spots in image from a rotation scan [degree]

b_factor

float

Estimated B-factor (Angstrom^2)

indexing_time

float

Time spent on indexing [s]

processing_time

float

Total processing time [s]

xfel_pulse_id

uint64

Bunch ID (for pulsed source, e.g., SwissFEL)

X

xfel_event_code

uint64

Event code (for pulsed source, e.g., SwissFEL)

X

lattice_type

object

Bravais lattice classification of the indexing result (present only if available)

X

- centering

string

One-letter centering code: P, A, B, C, I, F, or R

- niggli_class

int64

Integer identifier for the Niggli-reduced Bravais class

- system

string

Crystal system: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic

jf_info

uint64

Detector info field

receiver_aq_dev_delay

uint64

Receiver internal delay

receiver_free_send_buf

uint64

Receiver internal number of available send buffers

storage_cell

uint64

Storage cell number

saturated_pixel_count

uint64

Saturated pixel count

pixel_sum

uint64

Sum of all pixels, excl. error and saturation

error_pixel_count

uint64

Error pixel count

strong_pixel_count

uint64

Strong pixel count (first stage of spot finding)

min_viable_pixel_value

int64

Minimal pixel value, excl. error and saturation

max_viable_pixel_value

int64

Maximal pixel value, excl. error and saturation

resolution_estimate

float

Diffraction resolution estimation [Angstrom]

X

data_collection_efficiency

float

Image collection efficiency []

packets_expected

uint64

Number of packets expected per image (in units of 2 kB)

packets_received

uint64

Number of packets received per image (in units of 2 kB)

bkg_estimate

float

Mean value for pixels in resolution range from 3.0 to 5.0 A [photons]

beam_center_x

float

Beam center X from post-indexing refinement [pixel]

X

beam_center_y

float

Beam center Y from post-indexing refinement [pixel]

X

beam_corr_x

float

Beam center correction X applied during processing [pixel]

X

beam_corr_y

float

Beam center correction Y applied during processing [pixel]

X

adu_histogram

Array(uint64)

ADU histogram

roi_integrals

object

Results of ROI calculation

X

- sum

int64

Sum of pixels in ROI area [photons]

- sum_square

int64

Sum of squares of pixels in ROI area [photons]

- pixels

uint64

Valid pixels in ROI area

- max_count

int64

Highest count in ROI area [photons]

- x_weighted_sum

int64

ROI pixel X position multiplied by photon count [photons * pixels]

- y_weighted_sum

int64

ROI pixel Y position multiplied by photon count [photons * pixels]

user_data

string

Optional user defined text information - this is image_appendix serialized to JSON format

X

data

Map(string -> Image)

Image

X

Metadata message

Field name

Type

Description

Present in DECTRIS format

Optional

type

String

value “metadata”

X

magic_number

uint64

Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver

series_unique_id

string

Unique text ID of the series (run_name parameter)

X

series_id

uint64

Unique numeric ID of the series (run_number parameter)

X

images

Array(object)

Array of images (order and size of the array are not guaranteed)

X

- image_id

uint64

Number of image within the series; for MX lossy compression this is sequential excluding removed frames

X

- original_image_id

uint64

Number of image within the series; for MX lossy compression this includes removed frames in the count

- real_time

Rational

Exposure time

X

- start_time

Rational

Exposure start time (highly approximate)

X

- end_time

Rational

Exposure end time (highly approximate)

X

- spot_count

uint64

Spot count

- spot_count_ice_rings

uint64

Number of spots within identified rings (experimental)

- az_int_profile

Array(float)

Azimuthal integration results, use az_int_bin_to_q from start message for legend

- indexing_result

bool

Indexing successful

- indexing_lattice

Array(9 * float)

Indexing result real lattice; present only if indexed

X

- indexing_unit_cell

object

Indexing result unit cell: a, b, c [angstrom] and alpha, beta, gamma [degree]; present only if indexed

X

Unit cell is redundant to lattice - yet to simplify downstream programs to analyze results, both are provided

- xfel_pulse_id

uint64

Bunch ID (for pulsed source, e.g., SwissFEL)

X

- xfel_event_code

uint64

Event code (for pulsed source, e.g., SwissFEL)

X

- jf_info

uint64

Detector info field

- receiver_aq_dev_delay

uint64

Receiver internal delay

- receiver_free_send_buf

uint64

Receiver internal number of available send buffers

- storage_cell

uint64

Storage cell number

- saturated_pixel_count

uint64

Saturated pixel count

- error_pixel_count

uint64

Error pixel count

- strong_pixel_count

uint64

Strong pixel count (first stage of spot finding)

- data_collection_efficiency

float

Image collection efficiency []

- bkg_estimate

float

Mean value for pixels in resolution range from 3.0 to 5.0 A [photons] (with solid angle/polarization corrections, if applied)

X

- resolution_estimate

float

Diffraction resolution estimation

X

- adu_histogram

Array(uint64)

ADU histogram

X

- roi_integrals

object

Results of ROI calculation

X

- - sum

int64

Sum of pixels in ROI area [photons]

- - sum_square

int64

Sum of squares of pixels in ROI area [photons]

- - pixels

uint64

Valid pixels in ROI area

- - max_count

int64

Highest count in ROI area [photons]

End message

Field name

Type

Description

Present in DECTRIS format

type

String

value “end”

X

magic_number

uint64

Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver

series_unique_id

string

Unique text ID of the series (run_name parameter)

X

series_id

uint64

Unique numeric ID of the series (run_number parameter)

X

end_date

date

Approximate end date

max_image_number

uint64

Number of image with the highest number (this is counted from 1 - to distinguish zero images and one image)

images_collected

uint64

Number of image collected

images_sent_to_write

uint64

Number of image sent to writer; if writer queues were full, it is possible this is less than images collected

data_collection_efficiency

float

Network packets collected / Network packets expected []

az_int_result

Map(text->Array(float))

Azimuthal integration results, use az_int_bin_to_q from start message for legend

adu_histogram

Map(text->Array(uint64))

ADU values histogram

adu_histogram_bin_width

uint64

Width of bins in the above histogram [ADU]

max_receiver_delay

uint64

Internal performance of Jungfraujoch

bkg_estimate

float

Mean background estimate for the whole run

indexing_rate

float

Mean indexing rate for the whole run

rotation_lattice_type

object

Bravais lattice classification of the total rotation solution over the run (if available); same schema as lattice_type

- centering

string

One-letter centering code: P, A, B, C, I, F, or R

- niggli_class

int64

Integer identifier for the Niggli-reduced Bravais class

- system

string

Crystal system: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic

rotation_lattice

Array(9 * float)

Real-space lattice basis (flattened 3x3 in row-major), corresponding to the rotation indexing result

Calibration message

Field name

Type

Description

Present in DECTRIS format

type

String

value “calibration”

magic_number

uint64

Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver

data

Map(string -> Image)

Calibration map (only single pedestal array per message)

User data

In many cases there is an interest from facilities to forward more metadata, than available explicitly in the Jungfraujoch. For this reason two fields can be provided: header_appendix (sent with start message) and image_appendix (send with image message). To increase flexibility, both appendices can contain any valid JSON message. These appendices are serialized into string and stored in CBOR messages as user_data.

Notably for start message, user_data can contain more information (non-DECTRIS compliant metadata). Therefore user_data is serialized by Jungfraujoch as CBOR object. There is member user which contains header_appendix defined in OpenAPI of Jungfraujoch.

Notes on images and compression

  • Images are encoded as DECTRIS MultiDimArray with typed array tags:

    • For RGB: shape [3, height, width], type: u8

    • For grayscale: shape [height, width], type according to bit depth and sign (e.g., uint16 LE)

  • Compression:

    • Uncompressed: raw CBOR byte string

    • Bitshuffle+LZ4: tag with [“bslz4”, elem_size, bytes]

    • Bitshuffle+Zstandard: tag with [“bszstd”, elem_size, bytes]

\ No newline at end of file diff --git a/CHANGELOG.html b/CHANGELOG.html new file mode 100644 index 00000000..89e2399a --- /dev/null +++ b/CHANGELOG.html @@ -0,0 +1 @@ + Changelog — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

Changelog

1.0.0

1.0.0-rc.126

This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124.

  • jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg.

1.0.0-rc.125

This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124.

  • jfjoch_broker: Improve logic on switching on/off spot finding

  • jfjoch_broker: Increase maximum spot count for FFBIDX to 65536

  • jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD)

  • jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis

  • jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection

  • jfjoch_writer: Save more information about each reflection

1.0.0-rc.124

This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123.

  • jfjoch_broker: Improve refection position prediction and Bragg integration code.

  • jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation.

  • jfjoch_writer: Fix saving mosaicity properly in HDF5 file.

  • jfjoch_viewer: Introduce high-dynamic range mode for images

  • jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%)

  • jfjoch_viewer: Zoom-in numbers have better readability

1.0.0-rc.123

This is an UNSTABLE release.

  • jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility

  • jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M)

  • jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M)

  • jfjoch_viewer: Add more color schemes for better image readability

  • HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable

  • HDF5: suppress warning if path (upstream group) doesn’t exists when checking if leaf exists

1.0.0-rc.122

This is an UNSTABLE release.

  • jfjoch_broker: Add thresholding to prefer shorter vectors after FFT

  • jfjoch_broker: Add experimental mosaicity estimation for rotation experiments (this is work in progress)

  • jfjoch_broker: Update nlohmann::json to 3.12.0

  • jfjoch_viewer: Display file opening errors

  • jfjoch_viewer: When loading files over DBus add retry/back-off till the file is available

1.0.0-rc.121

This is an UNSTABLE release.

  • jfjoch_broker: Report changes in the image buffer, so viewer doesn’t reload constantly

  • jfjoch_viewer: Improve performance of loading images

  • jfjoch_viewer: Auto-throttle image loading in HTTP-sync / movie modes

  • jfjoch_viewer: Auto-foreground calculated with histogram

  • jfjoch_viewer: Fix rare segmentation fault

1.0.0-rc.120

This is an UNSTABLE release.

  • jfjoch_broker: Improve performance of binary plot export

1.0.0-rc.119

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_broker: Add binary export of data analysis plots over OpenAPI

  • jfjoch_broker: Minor fixes to HTTP error handling

  • jfjoch_viewer: Prefer binary plots over JSON plots

  • jfjoch_viewer: Change foreground with F button + wheel

  • jfjoch_viewer: Change way how angles are displayed

  • jfjoch_viewer: Display resolution of the mouse cursor in top left corner

1.0.0-rc.118

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_viewer: Fix issue when HTTP sync silently disconnected when it was enabled when the broker was starting measurement.

  • jfjoch_broker: Add protections on time of geometry optimization and reduce rotation recalculations

1.0.0-rc.117

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_viewer: Add ROI results to the dataset info plots

  • jfjoch_writer: Remove HTTP interface, as it is not needed/used at the moment

1.0.0-rc.116

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_viewer: Add binning options in the context menu

1.0.0-rc.115

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_broker: Default spot finding settings can be configured via config JSON

  • jfjoch_viewer: FFT analysis of data in the dataset plot

1.0.0-rc.114

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_broker: Fix generating JPEG images with resolution estimation

1.0.0-rc.113

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_broker: Improve handling of rotation indexing

  • jfjoch_broker: More information saved in CBOR end message (WIP)

  • jfjoch_writer: Save rotation indexing lattice parameters and Niggli class

  • jfjoch_viewer: Remove (for now) primitive cell information

  • jfjoch_viewer: Use angle for dataset info plot for rotation scans

1.0.0-rc.112

This is an UNSTABLE release and not recommended for production use (please use rc.111 instead).

  • jfjoch_broker: Experimental rotation (3D) indexing

  • jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values

1.0.0-rc.111

This is an UNSTABLE release.

  • jfjoch_viewer: Remove 3D lattice viewer (not really useful at this moment)

  • jfjoch_viewer: Fix auto contrast not refreshing image

1.0.0-rc.110

This is an UNSTABLE release.

  • jfjoch_broker: Add auto-contrast option for preview images

  • Frontend: Add logo image

  • jfjoch_viewer: Add logo image

  • jfjoch_viewer: For image chart allow to set min value to zero

  • jfjoch_viewer: For resolution estimation plots, visualization uses 1/d^2 as measure

  • jfjoch_viewer: Add 3D unit cell visualization (experimental/WIP/not really there)

  • Documentation: Add logo image

1.0.0-rc.109

This is an UNSTABLE release.

  • jfjoch_viewer: Add keyboard shortcuts and option to copy image to clipboard

  • jfjoch_broker: Fix bit-width and exposure time for PSI EIGER detectors

1.0.0-rc.108

This is an UNSTABLE release.

  • jfjoch_viewer: Fix bug when resolution estimation/B-Factor/Profile radius were not set (NaN)

  • jfjoch_viewer: Show spots is off by default, resolution ring mode is enabled by default

  • jfjoch_viewer: Fit to window of image is now default when size of the grid changes

1.0.0-rc.107

This is an UNSTABLE release.

  • jfjoch_viewer: Minor polishing of new functionality

  • jfjoch_broker: User NaN for empty azimuthal bins

1.0.0-rc.106

This is an UNSTABLE release.

  • jfjoch_viewer: Allow for multiple dataset info plots

  • jfjoch_viewer: Highlight current element in grid

1.0.0-rc.105

This is an UNSTABLE release.

  • jfjoch_viewer: Clean-up widgets slightly

  • jfjoch_viewer: Limit right panel to 600 pixels

  • jfjoch_viewer: Parse crystal symmetry type

  • jfjoch_viewer: Grid scan view takes color map and can be fit to zoom

1.0.0-rc.104

This is an UNSTABLE release.

  • jfjoch_writer: Fix and improve the way grid scan geometry is saved (non-NXmx extension makes it way easier)

  • jfjoch_viewer: Display grid scan results in 2D (work in progress)

  • jfjoch_viewer: Improve auto-scaling on start of images (work in progress)

  • jfjoch_viewer: Add B-factor and resolution estimate to the dataset info plots

1.0.0-rc.103

This is an UNSTABLE release.

  • jfjoch_viewer: Minor improvements to the viewer

  • jfjoch_broker: Change behavior for modular detectors: coordinates of 0-th pixel can be now arbitrary and detector will be cropped to the smallest rectangle limited by module coordinates

1.0.0-rc.102

This is an UNSTABLE release.

  • jfjoch_viewer: Minor improvements to the viewer

1.0.0-rc.101

This is an UNSTABLE release.

  • jfjoch_viewer: Auto load is better handling change of states

  • jfjoch_viewer: Fix DBus registration

  • jfjoch_viewer: Handle charts better with vertical lines on hover and status bar update

  • jfjoch_viewer: Calculate ROI in a more efficient way

1.0.0-rc.100

This is an UNSTABLE release.

  • jfjoch_viewer: Fix dbus registration

  • jfjoch_viewer: Remove background slider for diffraction image

  • jfjoch_viewer: Adjustments for 2D azimuthal image viewer

1.0.0-rc.99

This is an UNSTABLE release.

  • jfjoch_broker: Fix output during mask data collection

1.0.0-rc.98

This is an UNSTABLE release and not recommended for production use (please use rc.96 instead).

  • jfjoch_broker: For DECTRIS detectors fix dark data collection during initialization

1.0.0-rc.97

This is an UNSTABLE release and not recommended for production use (please use rc.96 instead).

  • jfjoch_broker: For DECTRIS detectors add dark data collection during initialization for bad pixel mask

  • jfjoch_broker: Refactor of calibration logic for more clear code (likely to introduce problems)

  • jfjoch_viewer: Add option to handle user pixel mask (experimental)

  • jfjoch_viewer: More options for ROI

  • jfjoch_viewer: Add window to display calibration

1.0.0-rc.96

This is an UNSTABLE release.

  • Fixes in CI pipeline

  • jfjoch_broker: Remove PNG preview, no dependency on libpng

  • jfjoch_writer: Fix UTC timestamp being generated wrong (mix between milli- and microseconds)

  • jfjoch_viewer: Show data collection time in dataset tooltip

  • jfjoch_viewer: Allow to choose the calibrant (presets for LaB6 and silver behenate)

  • jfjoch_viewer: Auto foreground value

  • Use external libjpeg-turbo and libtiff: simpler build stack, these are built and linked statically in automated Docker builds

  • Remove OpenBLAS dependency

1.0.0-rc.95

This is an UNSTABLE release.

  • Fixes in CI pipeline

  • Add git-lfs to Rocky8 docker image

Previous releases (91-94) had a wrong FPGA image upload to Gitlab release. This is now solved.

1.0.0-rc.94

This is an UNSTABLE release.

  • FFTIndexer: Add limit on angles to avoid colinear vectors

  • Docker images: Add 3D Qt

  • Gitea: Fixes to the pipeline

1.0.0-rc.93

This is an UNSTABLE release.

  • CI: Fixes to Gitlab based pipeline

  • PCIe driver: Fix PCIe revision being hex number

1.0.0-rc.92

This is an UNSTABLE release.

  • jfjoch_broker: Fix code that predicted Bragg reflections scattering back from the sample.

1.0.0-rc.91

This is an UNSTABLE release. This release introduces new features, which usually means these need more field testing before enough maturity. For production use we recommend waiting for a future bug-fix release.

  • FPGA: Implement high pixel value threshold - pixels above the given value will be considered saturated

  • jfjoch_broker: Spot finding and integration predictions are ported to a GPU

  • jfjoch_broker: Estimate resolution

  • jfjoch_broker: Lattice search

  • jfjoch_broker: Many more improvements in image analysis

1.0.0-rc.90

This is an UNSTABLE release.

  • jfjoch_broker: for indexing min index spots for a viable cells can be changed via OpenAPI

  • jfjoch_viewer: Optional auto-reanalyze images

  • jfjoch_writer: Add option where no files at all are saved

  • Documentation: improvements

1.0.0-rc.89

This is an UNSTABLE release.

  • jfjoch_broker: Fix resolution estimation code

  • jfjoch_broker: Fix Wilson B-factor calculation code

  • jfjoch_viewer: Improve display of plots

  • jfjoch_viewer: Fix segmentation fault

  • jfjoch_viewer: Display missing metadata when using HTTP

  • jfjoch_viewer: Fix bug when opening the same file twice

1.0.0-rc.88

This is an UNSTABLE release.

  • jfjoch_viewer: Add resolution estimation to the image information

  • jfjoch_broker: Minor changes to resolution estimate routine

1.0.0-rc.87

This is an UNSTABLE release.

  • jfjoch_viewer: Display more image metadata (angle / exposure time)

  • jfjoch_viewer: Improve I/sigma and B-factor plots

  • jfjoch_broker: Estimate resolution based on visible spots

1.0.0-rc.86

This is an UNSTABLE release.

  • jfjoch_broker: Update logic when initializing detector to make it a bit more resilient

  • Gitea pipelines have nocuda option for all architectures

1.0.0-rc.85

This is an UNSTABLE release.

  • jfjoch_viewer: When using online view, dataset info plots are not switched back to the first category for each image

  • jfjoch_viewer: Handle spot count better in dataset info plots

  • jfjoch_viewer: Highlight spots in ice ring resolutions in cyan, when detection is enabled

1.0.0-rc.84

This is an UNSTABLE release.

  • jfjoch_broker: Write in log which detector is being initialized

  • Changes to automated build system

1.0.0-rc.83

This is an UNSTABLE release.

  • jfjoch_viewer: Fix in generating preview image for signed data (wrong bit-width was assumed before)

  • CI: Fix script to generate python client

1.0.0-rc.82

This is an UNSTABLE release.

  • jfjoch_viewer: Enable FFTW based indexing in viewer (very slow at the moment)

  • Frontend: Minor fixes

  • Build scripts: Minor fixes to FFTW

1.0.0-rc.81

This is an UNSTABLE release. This release introduces new features, which usually means these need more field testing before enough maturity. For production use we recommend waiting for a future bug-fix release.

  • jfjoch_broker: Add option to detect ice rings, adjust width of ice ring and change of logic to exclude ice rings in indexing

  • jfjoch_broker: Add FFTW based indexer for CPU only indexing

  • jfjoch_broker: Enable saving X-ray fluorescence spectra

  • jfjoch_writer: Write total spot count (before filtering)

  • jfjoch_viewer: Add more information on source, sample, and buttom to show ice rings

  • jfjoch_viewer: Enable data processing inside the viewer

CI: Moving from Gitlab to Gitea at PSI

1.0.0-rc.80

This is an UNSTABLE release.

  • jfjoch_broker: Fix bug when wrong value for a plot (NaN or infinity) would lead to a null in a plot, which cannot be parsed by viewer

1.0.0-rc.79

This is an UNSTABLE release.

  • jfjoch_viewer: Fix bug when loading new dataset was creating a cascade of signals leading to poor performance

  • jfjoch_writer: Save nimages_per_trigger in detectorSpecific

1.0.0-rc.78

This is an UNSTABLE release.

  • jfjoch_viewer: Using a single event loop (reading images is not in dedicated thread anymore)

1.0.0-rc.77

This is an UNSTABLE release.

  • jfjoch_viewer: Display detector and dataset settings with tooltips

  • jfjoch_viewer: Clean excessive HDF5 warnings

  • jfjoch_viewer: Display unit cell

  • jfjoch_extract_hkl: Write a tool to extract reflection intensity from a dataset

1.0.0-rc.76

This is an UNSTABLE release.

  • jfjoch_broker: Increase predicted hkl to 100.0, use lighter math to exclude too-high resolution ones

  • jfjoch_broker: Use standard deviation formula to find profile radius (not the one using median)

  • jfjoch_writer: Save space group number (non-NXmx addition) in addition to name

  • jfjoch_viewer: Fix the bug on reading space_group as string

  • jfjoch_viewer: Add missing resolution labels on rings

  • jfjoch_viewer: Remove Q value from the status bar

1.0.0-rc.75

This is an UNSTABLE release.

  • jfjoch_broker: EIGER2 missing minimum threshold - hardcoded to 2.7 keV for the time being

1.0.0-rc.74

This is an UNSTABLE release.

  • jfjoch_broker: Fix for EIGER UDP port settings (vertical half of the module missing)

  • jfjoch_broker: Detector settings were not applied for EIGER/DECTRIS detector when changed after initialization

1.0.0-rc.73

This is an UNSTABLE release.

  • jfjoch_broker: Space group number treatment in OpenAPI was wrong, zero value is no longer allowed and no longer default

1.0.0-rc.72

This is an UNSTABLE release. This release introduces new features, which usually means these need more field testing before enough maturity. For production use we recommend waiting for a future bug-fix release.

  • jfjoch_broker: Refactor of indexing and geometry refinement code

  • jfjoch_broker: Handle space group/centering in refinement code

  • jfjoch_broker: Replace mosaicity with profile radius: refining the former is difficult with still images

  • jfjoch_broker: There is no longer 0.5 pxl offset for spots-to-reciprocal-space conversion

  • jfjoch_writer: Experimental saving of reflections

  • jfjoch_writer: Save space group name as string

  • jfjoch_viewer: Add profile radius and B-factor

  • jfjoch_viewer: Show 4 digits for wavelength

  • jfjoch_viewer: Match rings between calibrant and observation (will handle missing/wrong rings)

  • FPGA: Use UDP destination port to distinguish between detector modules and data streams

  • FPGA: Add experimental PTP core (PTP over L2, only Sync/Follow_up)

  • FPGA driver: Fix for Linux kernel 6.12+ (thanks to Tim Gruene)

1.0.0-rc.71

This is an UNSTABLE release.

  • jfjoch_broker: Remove resolution estimation via machine learning

  • jfjoch_broker: Harmonize code to analyze spot finding results (indexing/refinement/integration) between CPU and FPGA receivers

  • jfjoch_viewer: Fix error when HDF5 files with indexing results couldn’t be loaded on a machine without GPU

1.0.0-rc.70

This is an UNSTABLE release. This release introduces new features (geometry refinement), which usually means these need more field testing before enough maturity. For production use we recommend waiting for a future bug-fix release.

  • jfjoch_broker: Fix bug when PSI EIGER frame time was not set properly at the start of the measurement

  • jfjoch_broker: Fix PONI rot2 angle rotating detector in a wrong direction (PyFAI convention is for this angle to rotate detector downwards)

  • jfjoch_broker: Enable geometry refinement - first try (work in progress)

  • jfjoch_viewer: Fix deadlock when opening HTTP connections

  • jfjoch_viewer: Display rings as ellipses with detector tilt

  • jfjoch_viewer: Add button to calibrate detector geometry based on LaB6 image

  • jfjoch_writer: Save detector tilt angles (rot1, rot2, rot3)

  • Add Google Ceres a non-linear least-square optimization library to Jungfraujoch

  • Add experimental detector calibration routines (for LaB6)

  • Improve documentation on the ZeroMQ writer notification socket and detector geometry

1.0.0-rc.69

This is an UNSTABLE release.

  • jfjoch_viewer: Metadata can be modified for an open dataset (no option to save)

  • jfjoch_viewer: Refactor multiple issues in the viewer regarding image reading code to allow for further developments

  • jfjoch_viewer: Resolution rings not enabled by default

  • jfjoch_broker: Handle properly PONI rotations in dataset settings though still not updated properly in the HDF5 file

1.0.0-rc.68

This is an UNSTABLE release.

  • jfjoch_broker: Temperature threshold can be changed for JUNGFRAU detector

  • jfjoch_broker: Default detector settings can be configured for each detector separately

  • jfjoch_broker: Refactor spot filtering code, max spot count can be modified for dataset settings

  • jfjoch_broker: Refactor indexing refinement, make it the same for both FFBIDX and FFT indexing

  • jfjoch_broker: Reference unit cell will be taken into account for FFT indexing to filter

  • jfjoch_broker: Review PONI rotation angles and azimuthal angle conventions along with PyFAI

1.0.0-rc.67

This is an UNSTABLE release.

  • jfjoch_broker: Enable SSL

  • jfjoch_broker: Wilson B-factor only provided is fit is relatively OK (R^2 > 0.3); this will be refined much more in the future

1.0.0-rc.66

This is an UNSTABLE release.

  • jfjoch_broker: Indexers operate as thread pool, which is operating

  • jfjoch_viewer: Increase interval between loading images + fix too many verbose messages

1.0.0-rc.65

This is an UNSTABLE release.

  • jfjoch_broker: Print information regarding used image pushers

  • jfjoch_viewer: Allow syncing with Jungfraujoch server

  • OpenAPI: Clarify licensing terms in the file

1.0.0-rc.64

This is an UNSTABLE release.

  • jfjoch_broker: Fix issue in receiver light with very long preparation time for threads

  • jfjoch_broker: Add verbose option

  • jfjoch_broker: Don’t trigger pedestal if critical settings are not changed when loading detector settings

  • jfjoch_broker: Detector left in busy state when detector settings were improper

  • jfjoch_viewer: Modify DBus interface to avoid loading same file and image 0 multiple times

  • jfjoch_lite_perf_test: Add verbose option

1.0.0-rc.63

This is an UNSTABLE release.

  • jfjoch_broker: Save NX/NY for grid scan result

  • jfjoch_broker: Add processing time to CBOR output and plot

  • jfjoch_writer: Add processing time to data file

1.0.0-rc.62

This is an UNSTABLE release.

  • jfjoch_broker: Fix bug where low resolution spots were not counted properly

  • jfjoch_broker: Spot count is provided prior to filtering of spots to max_spot_count

  • jfjoch_broker: Add more spot count information to CBOR

  • jfjoch_viewer: Fix issue with ROI drawing resulting in multiple overlapping rectangles

1.0.0-rc.61

This is an UNSTABLE release.

  • jfjoch_broker: Fix bug where FFT indexing could result in a very short or even zero length vector

  • jfjoch_broker: Ice ring and indexed spot count enabled as plots and saved in grid scan results

  • jfjoch_broker: High resolution limit for low res. spot counting can be adjusted

1.0.0-rc.60

This is an UNSTABLE release.

  • jfjoch_broker: Fix bug when the neural network inference client was busy and this status was never released

  • jfjoch_broker: Revert the indexing threshold with distance from integer for Miller indices

  • jfjoch_broker: Fix bug in scattering vector calculation, resulting in indexing not working outside 1.0 A X-ray wavelength

1.0.0-rc.59

This is an UNSTABLE release.

  • jfjoch_broker: Fix bug when broker was waiting for notification message before sending end message, resulting in deadlock.

  • jfjoch_writer: Verbose option for debugging.

1.0.0-rc.58

This is an UNSTABLE release.

  • jfjoch_viewer: Fix memory leak

  • jfjoch_writer: Add detector_number/serial_number to master file

1.0.0-rc.57

This is an UNSTABLE release.

  • jfjoch_broker: Fix bug when enabling ML resolution estimation was not possible

  • jfjoch_viewer: “Movie” mode

1.0.0-rc.56

This is an UNSTABLE release.

  • jfjoch_broker: Fixing more bugs related to neural network inference for ML estimation

1.0.0-rc.55

This is an UNSTABLE release.

  • jfjoch_broker: Fixing minor bugs related to neural network inference for ML estimation

1.0.0-rc.54

This is an UNSTABLE release.

  • jfjoch_broker: Indexing with AUTO settings (FFBIDX if unit cell provided; FFT if not)

  • jfjoch_broker: Don’t remove shared memory area when deactivating detector

  • jfjoch_writer: Save writer release

  • jfjoch_viewer: Increase time for the messages in the status bar

1.0.0-rc.53

This is an UNSTABLE release.

  • PCIe driver: Imperfect solution for RHEL 9.5+ changes

  • jfjoch_writer: Fix to angle containers for AutoProc compatibility

  • jfjoch_fpga_test: Use consecutive number for devices, not interleaved

1.0.0-rc.52

This is an UNSTABLE release.

  • jfjoch_viewer: Use warmer colors to distinguish from AareGUI

  • jfjoch_viewer: Minor adjustments to DBus setting image number

  • jfjoch_broker: Fix in low resolution spot count plotting

1.0.0-rc.51

This is an UNSTABLE release.

  • jfjoch_broker: Send preview in PNG format

  • jfjoch_broker: Provide count of spots in 50.0 - 5.0 A range

  • jfjoch_broker: Provide ML resolution estimation in scan result

  • jfjoch_broker: Allow removing beam center in web preview

1.0.0-rc.50

This is an UNSTABLE release.

  • The release fixes some of many bugs introduced in recent releases

  • jfjoch_viewer: display predictions for indexed cells

1.0.0-rc.49

This is an UNSTABLE release.

  • jfjoch_broker: Handle sample temperature (K) and ring current (mA) to metadata

  • jfjoch_writer: For angle containers in NXmx add _end dataset, sample temp. and ring current

1.0.0-rc.48

This is an UNSTABLE release.

  • jfjoch_broker: fix the bug when a unit cell was not exported for a scan result.

1.0.0-rc.47

This is an UNSTABLE release.

  • jfjoch_viewer: fix dbus service path

  • jfjoch_writer: fix CBF/TIFF writing

1.0.0-rc.46

This is an UNSTABLE release.

  • jfjoch_viewer: remove dependency on image analysis

1.0.0-rc.45

This is an UNSTABLE release.

  • jfjoch_broker: Detector list returns pixel size (mm)

1.0.0-rc.44

This is an UNSTABLE release.

  • jfjoch_broker: more general definition of scan result export

Braking changes:

  • It removes additions to OpenAPI from 1.0.0-rc.43

  • It makes changes to the “unit_cell” definition in OpenAPI specs. It might be harmless in some languages and may result in errors in other implementations.

1.0.0-rc.43

This is an UNSTABLE release.

  • jfjoch_broker: Export grid scan results into a single data structure

1.0.0-rc.42

This is an UNSTABLE release.

  • jfjoch_broker: Add pixel_sum to CBOR output.

  • jfjoch_broker: Changes to sigma estimation in QuickIntegrate routine

  • jfjoch_writer: Save pixel_sum

1.0.0-rc.41

This is an UNSTABLE release. This release includes multiple new features, it should not be used in production at the moment.

  • jfjoch_broker: Estimate B-factor, mosaicity to evaluate crystal diffraction

  • jfjoch_broker: Export GPU count via OpenAPI

  • jfjoch_broker: Enable 2D azimuthal integration and PONI rotations for detector

  • FPGA: Increase the number of integration bins to 2048

1.0.0-rc.40

This is an UNSTABLE release. This release includes multiple new features, it should not be used in production at the moment.

  • jfjoch_broker: Jungfraujoch supports grid scan metadata, including dedicated plotting schemes and NXmx structures

  • jfjoch_broker: Improve metadata for rotation data collection

  • jfjoch_broker: Better handling of plotting

  • jfjoch_broker: FFT based indexing

  • jfjoch_broker: Integration, first try, results not saved at the moment

  • jfjoch_broker: Internal improvements in image handling

  • jfjoch_writer: Multiple adjustments adapt to changes in this release for new features

  • jfjoch_writer: New state management model to improve clarity of error reporting

  • jfjoch_viewer: Remote control via DBus

  • Frontend: Multiple adjustments for new features

  • Frontend: Grid scan plots

WARNING! OpenAPI contains breaking changes in regard to plotting results, so care has to be taken.

1.0.0-rc.39

  • FPGA: Bugfix for pixel masked for data analysis if summation was on

  • jfjoch_viewer: Fix segmentation fault when cursor was outside of image

1.0.0-rc.38

  • jfjoch_broker: Neural net model is not linked with C++ code due to deployment issues, it is rather distributed as python code, connected via RES

  • jfjoch_broker: Neural net model can use all 4 quadrants of the detector

  • jfjoch_broker: For EIGER image time can be provided through /start

  • jfjoch_viewer: Add image list option

  • jfjoch_viewer: Drawing circular ROIs with shift

  • jfjoch_viewer: Enable image summation

  • jfjoch_viewer: Image reader is significantly reworked, hopefully without affecting the viewer

1.0.0-rc.37

  • jfjoch_broker: Make locking rules more flexible

  • jfjoch_broker: Load mask via SIMPLON interface for DECTRIS detectors

  • jfjoch_viewer: Add status bar

1.0.0-rc.36

This is UNSTABLE release. Wait for new version to use in a production environment.

  • jfjoch_broker: Support for Jungfraujoch Lite is enabled - software-based receiver for DECTRIS detectors (required a lot of refactoring, potentially leading to unstable code)

  • jfjoch_broker: Enable Resonet support (ML-based diffraction resolution estimation)

  • jfjoch_broker: Fix error in compression, where bitshuffle/LZ4 and bitshuffle/Zstd HDF5 headers were wrongly generated for 8-bit and 32-bit data

  • jfjoch_writer: Increase buffering to 1000 images in the receiver

  • jfjoch_writer: Images can be written as CBF or TIFF in addition to HDF5

1.0.0-rc.35

This is UNSTABLE release, not properly tested. Wait for new version for using production.

  • jfjoch_broker: If module is delayed by more than 50 frames versus other modules, it will be ignored and receiver is not waiting.

  • jfjoch_writer: Save EIGER energy threshold

  • jfjoch_writer: Add /entry/sample/goniometer for compatibility with eiger2cbf program

1.0.0-rc.34

This is UNSTABLE release - introducing new features, but not properly tested. Wait for new version for using production.

  • jfjoch_broker: More consistency for file format definition (breaking change in API from 1.0.0-rc.31 for file writer settings)

  • jfjoch_broker: For storage cells mask is logical sum of detector bad pixels for all storage cells

  • jfjoch_broker: Handle situation when detector doesn’t want to gracefully stop (to be tested)

  • jfjoch_broker: Center-of-mass position and mean for ROI is added to available plots

  • jfjoch_viewer: Can extract data analysis results from “legacy” format

  • jfjoch_viewer: Display dataset name

  • FPGA: Pixel mask is used for data analysis part even if it is not applied to pixels

  • FPGA: Add pixel sum to module statistics

  • FPGA: ROI number is reduced to 16, but pixel can belong to every defined ROI

  • FPGA: Spot finder is back to full dynamic range (24-bit)

  • FPGA: More debug features for internal FIFOs

Known issues:

  • ROI count flag was added to firmware. For the time being the flag will be wrongly set to 10 due to mismatch of FPGA build scripts.

  • EIGER data acquisition has an issue that is currently debugged

1.0.0-rc.33

  • jfjoch_broker: Fix issue with EIGER settings being loaded improperly

1.0.0-rc.32

  • jfjoch_broker: Refactor code for azimuthal integration for further improvements

  • jfjoch_broker: Minor fix for EIGER (trim energies are manually set for E9M, to be fixed properly later)

  • jfjoch_writer: Fix too much verbose information

  • FPGA: Minor fixes to spot finder (enable two-pass operation and limit number range to int20)

1.0.0-rc.31

This is UNSTABLE release - introducing many features, but still needs more testing. Expecting soon to put bugfix release.

  • jfjoch_writer: Allow to enable overwriting existing files (not enabled by default)

  • jfjoch_writer: Add new HDF5 master file format, which uses HDF5 virtual data sets and links processing results to data files (not enabled by default)

  • jfjoch_viewer: Image viewer work early test version

  • jfjoch_broker: Fixes to counting packets per dataset/image

  • jfjoch_broker: Image buffer is accessible for outside to check images

  • jfjoch_broker: error/saturated pixels and dedicated ROI “beam” can be tracked online

  • jfjoch_broker: Fix bug in handling pedestal G1/G2 count time for JUNGFRAU

  • jfjoch_broker: Fix bug in applying pixel mask interfering with pedestal calculation

  • jfjoch_broker: Fix bug in EIGER initializing

  • jfjoch_broker: Save maximum pixel value to HDF5 file and export as Web plot

  • PCIe driver: Add PCIe link speed and width

  • FPGA: Improve counting error/saturated/min/max pixels

  • FPGA: Spot finder is gradual column-wise (15 columns up/down) and fixed row-wise (32 pixel boxes); previously it was fixed both column- and row-wise with 32x32 pixel areas

  • FPGA: Require Vivado 2022.2

Warning: There are breaking changes to HDF5 file format, renaming entries regarding image storage cell number and image collection efficiency.

1.0.0-rc.30

  • jfjoch_writer: replace non-blocking with blocking operation on internal queues - less likely to “loose” images within the writer

1.0.0-rc.29

  • jfjoch_broker: refactor logic regarding frame time and count time for more flexibility for EIGER and JUNGFRAU

  • jfjoch_broker: readout time for EIGER is 3 us and JUNGFRAU is 20 us, this can be changed in input file

  • jfjoch_broker: OpenAPI interface includes more ways to provide information on the status (error/warning/info)

  • jfjoch_broker: ROIs handling via OpenAPI and frontend is more user friendly

Warning - two breaking changes to OpenAPI:

  • Handling of ROIs is through /config/roi path only for both circle and box ROIs, path in /roi are no longer accessible

  • broker_status structure introduced in 1.0.0-rc.28 has member message and not error_message to allow handling info/warning messages as well

1.0.0-rc.28

  • jfjoch_broker: save error message for initialization and data collection and provide these with OpenAPI

  • jfjoch_broker: fixed issue when in error state, response to /wait_till_done was not complaint to OpenAPI specs

  • jfjoch_test: remove header that failed when CUDA is absent during compilation

  • frontend: add soft trigger button in data collection tab

  • frontend: show error message when in error state

  • CMake: add option to force compilation without CUDA (-DJFJOCH_USE_CUDA=OFF)

1.0.0-rc.27

  • jfjoch_broker: add option to select electron source in instrument metadata, adapt wavelength calculation

  • jfjoch_broker: update pistache web server version

  • jfjoch_writer: minor changes to republish logic

  • Improvements to documentation

1.0.0-rc.26

  • jfjoch_broker: implement ZeroMQ stream for image metadata information

  • jfjoch_broker: refactor ZeroMQ stream for preview: start/end messages always sent

  • jfjoch_broker: add crystal lattice plots

  • jfjoch_broker: remove empty bins from the plots

  • jfjoch_broker: Fix bugs in ModuleSummation and MXAnalyzer for CPU “long” summation

  • jfjoch_broker: Fix bug when mean background estimation / indexing rate where affected by previous experiment

  • jfjoch_writer: fix missing “-w” parameter

  • jfjoch_writer: temporary files have “.tmp” suffix

  • jfjoch_writer: refactor logic for watermarks

  • jfjoch_writer: report on internal FIFO utilization

  • jfjoch_writer: clean-up naming for azimuthal integration and background estimate

  • jfjoch_writer: write final background estimate and indexing rate in the master file

  • tools/: remove unnecessary tools, make naming consistent

  • CBOR: Add indexing rate and background estimate to end message

  • CBOR: Clean-up documentation

1.0.0-rc.25

  • Updates to documentation

  • License set to GPLv3 / OHL-S

  • Fix bug in DiffractionExperiment::GetDefaultPlotBinning() - resulting in division by 0 if image time longer than 500ms

  • Add information on JUNGFRAU conversion and geometry transformation to CBOR and HDF5

1.0.0-rc.24

New FPGA functionality:

  • EIGER supports 8, 16 and 32-bit data input (for 8-bit mode at half performance; for 32-bit “real” depth is 23-bit + 1-bit signed)

  • Output possible to 8, 16 and 32-bit data

  • Threshold is applied before summation

  • Pixel mask can be applied on FPGA

  • Mark pixels with ADC content = 0 as bad pixels

  • FPGA stores semantic version information (access via /sys/class/misc/jfjoch…/version)

New software functionality:

  • Long summation (above 256 frames) done on CPU

  • Mechanism to save arbitrary data to HDF5 file

  • ZeroMQ preview has option to send start message

  • Rework pixel mask + add statistics displayed in web interface

Bug fixes:

  • Web frontend: Update preview image automatically during data acquisition

  • jfjoch_broker: Error handling if CUDA driver is not installed

  • jfjoch_broker: Correctly update progress during pedestal

  • jfjoch_broker: Provide proper error when uploaded file is not a proper TIFF

  • jfjoch_action_test: enable HLS simulation

Documentation improvement and placement in a dedicated directory

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Algorithms for data analysis

Azimuthal integration

2D azimuthal integration is implemented with a histogram-based algorithm, without split pixels. Solid angle and polarization corrections are available.

Spot finding

Spot finding is implemented with multiple thresholds, rejecting spots based on:

  • signal-to-noise ration of 31x31 pixel rectangle around the spot,

  • pixel intensity,

  • spot resolution,

  • number of pixels.

Finding strong pixels is currently implemented on CPU and FPGA. Combining strong pixels into spots is done with a Connected-component labeling (CCL) algorithm by Arthur Hennequin and coworkers, developed for CERN high-energy physics applications.

Indexing

Two indexing algorithms are implemented:

  • Fast feedback indexer: Algorithm developed by Hans-Christian Stadler (PSI), based on TORO method; requires providing approximate unit cell; implemented on GPUs

  • FFT indexing: implementation on classical M. Rossmann’s FFT algorithm; doesn’t require known unit cell; implemented on both GPUs (with CuFFT) and CPUs (with FFTW)

Both algorithms share the same refinement routine with the least trimmed squares procedure, see TORO papers for details.

Geometry refinement

Geometry refinement is done with the non-linear least squares procedure. Refinement optimizes crystal lattice and beam center in a single run. Solution is implemented with Google Ceres solver, running on CPU. For higher symmetry space groups, refinement imposes constraints on the equality of cell lengths and 90/120 deg. angles.

Bragg integration

Integration is implemented with pure summation (no profile fitting), using a 3-circle method from CrystFEL. Bragg spot predictions are calculated based on a distance from the Ewald sphere, with no explicit use of bandwidth or mosaicity. Maximum distance is estimated as twice of the profile radius. Profile radius is calculated as a mean of distance from the Ewald sphere of indexed spots. Systematic absences are implemented for all systems excluding R-centering.

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Deployment

To deploy Jungfraujoch, one needs to follow four steps:

  1. Install main Jungfraujoch code and frontend web interface

  2. Flash the U55C FPGA card with a proper image and install Linux kernel driver

  3. Install Jungfraujoch writer

  4. Install Python OpenAPI client

Installation procedure depend a lot on the operating system. For RedHat Enterprise Linux 8, Rocky 8, or compatible installation can be done with prebuilt RPMs and is relatively straightforward. For other systems one needs to build software from source. Both ways will be presented.

Install main Jungfraujoch code and frontend web interface

On RHEL 8 systems there is a jfjoch-<version>-1.el8.x86_64.rpm that needs to be installed and contains all the necessary software and web interface.

On other OSes one needs to compile Jungfraujoch from source (from the repo directory):

$ mkdir build
+$ cd build
+$ cmake .. -DCMAKE_INSTALL_PREFIX=<directory to install>
+$ make
+$ sudo make install  
+

For manual installation, we recommend to use non-standard directory (like /opt/jfjoch), to facilitate upgrades and removal. For DKMS to manage kernel module sources it is necessary to copy driver sources to /usr/src/jfjoch-<VERSION> directory. This requires extra flag in cmake -DJFJOCH_INSTALL_DRIVER_SOURCE=ON.

Frontend web user interface has to be built separately with:

$ cd build
+$ make frontend
+

Frontend files (.html and .js) will be placed in frontend/dist (outside of build/ directory!) and has to be copied to a general location, e.g. /usr/local/jfjoch/frontend or /opt/jfjoch/frotend.

Flash the U55C FPGA card with a proper image and install Linux kernel driver.

Firmware flashing

  1. Check that the card is detected by OS with “lspci |grep Xilinx” and check the PCIe bus/device/function (BDF) number, 11:00.0 in this case:

$ lspci |grep Xilinx
+23:00.0 Processing accelerators: Xilinx Corporation Device 3450 (rev 2)
+

Note the device number 3450 that identifies Jungfraujoch device (Jungfraujoch pass is 3450 m above sea level) and rev 2 identifying release of the firmware.

  1. Check the speed of the card, that it is detected as PCIe Gen4x8 device (needs to be done as root, otherwise configuration details are not given):

$ sudo lspci -vv -s <PCIe slot number>
+23:00.0 Processing accelerators: Xilinx Corporation Device 3450
+(...)
+LnkSta:     Speed 16GT/s (ok), Width x8 (ok)
+(...)
+

  1. Download the MCS image from release files or build it using Vivado (WARNING! building time can be about 8 hours and doesn’t allways reach correct timing).

  2. Flash the card with xbflash.qspi tool (part of Jungfraujoch). For fresh card use:

sudo xbflash.qspi --primary <path to MCS file> --card <PCIe slot from above> --bar-offset 0x1f06000 
+

For card that was already flashed with Jungfraujoch images:

sudo xbflash.qspi --primary <path to MCS file> --card <PCIe slot from above>
+

It is necessary to confirm the operation by pressing Y key or one can add --force option to avoid confirmation. It is safe to run multiple flashing processes in parallel for different cards, for example in separate screen sessions.

  1. Cold reboot:

sudo ipmitool chassis power cycle
+

Install PCIe driver

For first run it is though recommended to try the driver without installing to the kernel directory:

$ cd fpga/pcie_driver
+$ make
+$ sudo insmod jfjoch.ko
+

Check with dmesg that the device was properly found:

$ dmesg |grep jfjoch
+[  431.624933] jfjoch 0000:23:00.0: enabling device (0140 -> 0142)
+[  431.919147] misc jfjoch0: Jungfraujoch FPGA loaded with FW build: 5610030a
+

If things work, it is recommended to install the driver with DKMS, so it is rebuilt for kernel updates. On RHEL 8 you can install prebuilt RPM provided in the Gitlab package registry. On other systems follow procedure in PCIe driver.

NOTE: Driver installation procedure on non-RHEL 8 systems is not well understood/optimized at the moment.

NOTE: In case driver is included in the init RAM-disk image, it is necessary to rebuild the RAM-disk if driver is updated:

$ sudo dracut -f
+

Configure network

Configure switch according to FPGA network guide - specifically set manual speed and turn off auto-negotiation for the port used to connect U55C card and connect card to switch.

Running Jungfraujoch software

Main Jungfraujoch service is called jfjoch_broker. It is responsible for handling data from FPGAs, doing processing, analysis, compression and sending images on ZeroMQ output. It is recommended to run the service as systemd service.

jfjoch_broker takes two parameters: JSON configuration file and HTTP port (default is 5232). Example JSON files are placed in etc/ folder. JSON file format is also explained in the OpenAPI definition, as jfjoch_settings data structure.

When running the service can be accessed via HTTP interface from a web browser for configuration and monitoring.

To prepare the configuration file one also needs to reference calibration files: gain files for PSI JUNGFRAU and trim-bit files for PSI EIGER. These need to be obtained from the PSI Detector Group.

Card verification

To test that FPGA board is working properly without access to a JUNGFRAU detector, you can use jfjoch_fpga_test tool. For example to simulate 10M pixel system with 4 FPGA cards and 200k images on a 2 CPU system with 2 GPUs:

jfjoch_fpga_test ~/nextgendcu/ -m20 -s4 -i 200000 -Pn2g2
+

Or 1M pixel system with one FPGA card:

jfjoch_fpga_test ~/nextgendcu/ -m2 -s1 -i 200000
+

Install Jungfraujoch writer

Jungfraujoch writer is an additional service, that can connect to jfjoch_broker ZeroMQ interface and writes files according to NeXus/NXmx HDF5 standard.

At the moment it is better to have a separate machine, with access to distributed file system, for writing images.

Writer can be installed with a dedicated RPM file or compiled from source. For compilation, you can use the following commands:

mkdir build
+cd build
+cmake -DJFJOCH_WRITER_ONLY=ON -DCMAKE_INSTALL_PREFIX=<directory to install> ..
+make jfjoch
+

Install Jungfraujoch image viewer

Jungfraujoch viewer is X-ray diffraction image viewer, that is optimized to open Jungfraujoch HDF5 files.

The viewer is a Qt application and it requires recent version of the library, therefore it is an optional dependency.

To include it in the building of Jungfraujoch use -DJFJOCH_VIEWER_BUILD=ON directive for CMake:

mkdir build
+cd build
+cmake -DJFJOCH_VIEWER_BUILD=ON -DCMAKE_INSTALL_PREFIX=<directory to install> ..
+make jfjoch
+

Install Jungfraujoch Python client

Use pip:

pip install jfjoch-client
+
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Supported detectors

PSI detectors

Jungfraujoch supports PSI JUNGFRAU and PSI EIGER detectors. Jungfruajoch controls the detector via statically compiled slsDetectorPackage into its source code. It is important that detector firmware has to match slsDetectorPackage version used in Jungfraujoch (8.0.2 at the moment). See PSI Detector group website for details.

DECTRIS detectors

Jungfraujoch can be used with DECTRIS detectors, as a data analysis tool. In this solution Jungfraujoch controls the Detector Control Unit (DCU) of the detector, and handles output data stream of the DCU. This mode, called “lite” mode, doesn’t use FPGA boards, but mostly CPUs and GPUs for indexing. The mode is currently experimental and intended for low data rates (100 Hz).

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Detector geometry

At the moment Jungfraujoch supports solely flat detectors. The default option is to place modules in their actual location vs. detector frame. It is not recommended to place detector modules stacked.

The simplest case is detector perpendicular to the beam. In this case it is enough to provide beam center, detector distance and wavelength.

For more complex case, one can provide tilt of the detector rotation in PyFAI convention. This convention uses Point Of Nominal Interaction (PONI) definition. Beam X and Y would correspond to the location on the detector, where beam from the sample is perpendicular to the detector surface and not to the actual direct beam location. Then tilt of the detector is defined with three rotation angles: rot1 (rotating detector right), rot2 (rotating detector downwards), rot3 (rotating detector clockwise). See PyFAI documentation for more details.

Macromolecular crystallography convention for the vertical direction

One place of confusion is the convention to have point (0,0) of the detector in the top left corner of the detector, with Y values increasing downwards. This is also consistent with computer image formats.

However, other techniques (as well as internal operation of PSI X-ray detectors) might follow convention, for point (0,0) being in the bottom left corner and Y values increasing upwards. Such a convention is used, for example, by PyFAI.

In general, convention is controlled in Jungfraujoch with a setting in the JSON configuration file, which allows mirroring detector in Y.

Extra care has to be taken by the user to ensure that no errors are made.

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FPGA smartNIC

See separate document for installation instructions.

Hardware

Currently supported FPGA is only Xilinx Alveo U55C.

See AMD/Xilinx webpage for card user guide (UG1469). According to the user guide:

Alveo data center accelerator cards are designed to be installed into a data center server, where controlled air flow provides direct cooling.
+

Card needs to be placed in PCI Express (PCIe) Gen4 x8 slot, though mechanically slot has to accommodate x16 card. There is no need to connect additional power cable, as power of the card is not exceeding 75 W load available from PCIe edge connector. Current power estimation is about 30 W when idle and 45 W in operation. The card has built-in protection, which will cut power to the card if HBM temperature is above 120°C.

Two variants of the card are available:

  • 100g - this variant operates one port in 100 Gbit/s mode and should be used when connecting detector via a switch.

  • 8x10g - this variant operates both QSFP ports at 4x10 Gbit/s. QSFP+ (40 Gbit/s) transceivers and MTO/MTP harness cables are necessary. It is designed for detector directly connected to the Jungfraujoch server, without switch.

See network documentation for details of network.

Building firmware

Xilinx Vivado version has to precisely match version described in [the system requirements](../README.md. only when vivado and vitis_hls are detected in the path.

Xilinx Vivado

The following procedures require having AMD (Xilinx) Vivado and Vitis HLS toolsets version 2022.2 installed on the machine. Due to the nature of TCL scripts used to generate board designs Vivado version has to exactly match one provided above - specifically newer versions of Vivado will not work.

In additional to Intellectual Property (IP) cores included in Vivado, two additional licenses are necessary:

  • Non-cost license for Ultrascale+ 100G core has to be requested from AMD/Xilinx website, see Xilinx website, to build 100g design.

  • Paid 10G/25G Subsystem for Ultrascale+ to build 8x10g design. PSI received non-cost licenses from Xilinx University Program for the latter cores. Therefore, usage of bitstreams generated by PSI continuous integration pipeline for 8x10g is only allowed for non-commercial use.

HLS compilation

Make HLS routines:

mkdir build
+cd build
+cmake ..
+make hls
+

Synthesis

Create PCIe 100g bitstream with the following command:

mkdir build
+cd build
+cmake ..
+make pcie_100g
+

and 8x10g:

mkdir build
+cd build
+cmake ..
+make pcie_8x10g
+

When Vivado is not present

During CMake execution, the following executables: vivado and vitis_hls must be present in the path. If not, build targets will not be generated, and such or similar error message will show up:

$ make pcie_100g
+make: *** No rule to make target 'pcie_100g'.  Stop.
+

Gitlab CI

If Gitlab CI is properly set-up, firmware will be automatically built for every commit that starts with FPGA. Built firmware should be downloaded as MCS files.

Frame generator

Jungfraujoch card is equipped with frame generator. It allows to simulate JUNGFRAU detector without having access to such system. It is placed in parallel to Ethernet MAC - so it is placed before the network stack and before any processing happening on the card. In the future a redirection will be possible to send the simulated stream through the 100G TX network link. Frame generator is written in HLS and controlled with AXI-Lite.

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FPGA data analysis

Jungfraujoch FPGA design has incorporated X-ray diffraction image analysis capabilities.

Pixel mask

Pixels can be masked. For each module a 32-bit map of pixels is loaded to FPGA, with non-zero value meaning masked pixels. According to this map, pixels will be assigned a special value (minimum number for signed types and maximum number for non-signed types) and will be excluded from a subsequent analysis.

ADU histogram

Before conversion to photons/energy, an ADU histogram can be calculated for a module. This allows to preserve some signature of unconverted values. This is done on a module-basis and works with bins with 32 ADU width.

For EIGER this can be used as just a histogram procedure.

JUNGFRAU conversion

For JUNGFRAU module images are converted from ADUs to energy value and divided by a given number to keV units. Result of the operation is rounded to integers.

Pixel thresholding

Pixel range can be specified. Pixels below a minimum threshold will be assigned zero. Pixels above a maximum threshold will be assigned saturated pixel value (the largest number for a given bit-width and sign type). This is specifically designed to operate on unsummed frames, so frame-specific parameters (overload/noise) can be handled.

Frame summation

Frames can be summed together (on a per-module basis) in Jungfraujoch, with a limit of 256 frames added together.

Azimuthal integration

To implement azimuthal integration, FPGA is able to sum pixels based on a provided integration map and per-pixel corrections. This way Jungfraujoch implements azimuthal integration with solid angle and polarization corrections. Corrections were implemented according to formulas developed by Jensen et al. (J. Synchr. Rad., 29, 1420-1428, 2022).

Given FPGA limitations, split-pixels cannot be implemented and number of bins is limited as 1024 per detector module. This way 2D azimuthal integration, as needed for example by SAS-TT, cannot be currently implemented with the FPGA card and needs to be done on a CPU. One needs to be careful with per-pixel corrections - their acceptable range is constrained by 16-bit pixed point integer implementation and is tuned for standard SAXS/WAXS range.

Spot finding

Jungfraujoch FPGA implements a built-in spot finder. Spot finder allows to apply the following criteria for finding strong pixels:

  1. Resolution criterion - pixels only within a provided resolution range can be considered as strong pixels (calculating resolution map needs to happen on CPU before data collection run).

  2. Bad pixels - pixels marked as bad, as well as chip edges and module edges are excluded from spot finding,

  3. Overloads - pixels marked as overloads on JUNGFRAU are always included in the strong pixel output, but are excluded for signal-to-noise ratio calculation,

  4. Pixel value - pixels above certain threshold value can be marked as strong,

  5. Signal-to-noise (SNR) ratio - pixels with SNR above a threshold can be marked as strong,

  6. Connected pixels - strong pixels can be discarded if they are “alone”, so their 8 directly neighboring pixels are not counted as strong pixels.

While besides bad pixels criterion, all the above are optional (can be turned off), only pixels that fulfill all enabled criteria are selected as strong pixels.

SNR ratio calculation

Signal-to-noise ratio is calculated for a rectangular area. In horizontal direction the area is fixed - line of 1024 pixels is divided into 32 areas each of 32 pixels. This is dictated by the data flow within the FPGA. In vertical direction the area is flexible - it is 15 lines above and below of the given pixel. Given very large box size, approximation are made, for example that N ≈ N-1 in calculating standard deviation.

Region-of-interest (ROI) integration

Each pixel in a module can be assigned to one of 64 ROIs. For each ROIs, sum, sum of squares, max count, and number of valid pixels will be calculated. Jungfraujoch also calculates X and Y values weighted by pixel values, though this feature is not properly tested at the moment and not integrated in downstream analysis.

Pixel statisitics

The following statistics are collected for each module:

  • Number of masked pixels

  • Number of saturated pixels (excl.masked)

  • Number of error pixels (excl. masked)

  • Sum of valid pixels in the module

  • Minimum value of valid pixels in the module

  • Maximum value of valid pixels in the module Valid pixels are not masked, not saturated, not error pixels.

Square root compression

Jungfraujoch FPGA includes lossy compression preserving counting statistic properties of X-ray image, while reducing bit width of an image. Scheme was described in Wakonig et al., J. Appl. Cryst., 53, 574-586, 2020. Pixel value X is replaced with sqrt(N*X), where N is integer constant in range 1 to 16.

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FPGA data flow

The following steps are performed on FPGA (in the order of operation):

  1. UDP header decoding

  2. SLS detector header decoding

  3. State machine that controls data acquisition (start/stop/cancel)

  4. High-bandwidth memory cache to buffer network packets and reorder them to form full modules

  5. ADU histogram for JUNGFRAU

  6. Mask pixels from missing packets with special value

  7. Reorder lines for EIGER to form a proper module

  8. Mask pixels based on provided pixel mask

  9. JUNGFRAU conversion with gain and pedestal corrections

  10. Threshold to zero pixels below certain count value

  11. Integration according to predefined map (e.g., 1D azimuthal integration)

  12. Spot finding

  13. ROI calculation

  14. Image lossy compression using N*sqrt(pixel) values

  15. Send images, analysis results and metadata to host memory via PCI Express

Each step has dedicated core, written in the high-level synthesis. Exact operation of cores for data analysis is explained in dedicated document.

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FPGA license

FPGA components of Jungfraujoch are licensed using OHL-S license. See full text below. The license is equivalent of GNU Public License with adaptations for hardware. See OHL webpage for details and FAQs.

CERN Open Hardware Licence Version 2 - Strongly Reciprocal

Preamble

CERN has developed this licence to promote collaboration among hardware designers and to provide a legal tool which supports the freedom to use, study, modify, share and distribute hardware designs and products based on those designs. Version 2 of the CERN Open Hardware Licence comes in three variants: CERN-OHL-P (permissive); and two reciprocal licences: CERN-OHL-W (weakly reciprocal) and this licence, CERN-OHL-S (strongly reciprocal).

The CERN-OHL-S is copyright CERN 2020. Anyone is welcome to use it, in unmodified form only.

Use of this Licence does not imply any endorsement by CERN of any Licensor or their designs nor does it imply any involvement by CERN in their development.

1 Definitions

1.1 ‘Licence’ means this CERN-OHL-S.

1.2 ‘Compatible Licence’ means

a) any earlier version of the CERN Open Hardware licence, or

b) any version of the CERN-OHL-S, or

c) any licence which permits You to treat the Source to which it applies as licensed under CERN-OHL-S provided that on Conveyance of any such Source, or any associated Product You treat the Source in question as being licensed under CERN-OHL-S.

1.3 ‘Source’ means information such as design materials or digital code which can be applied to Make or test a Product or to prepare a Product for use, Conveyance or sale, regardless of its medium or how it is expressed. It may include Notices.

1.4 ‘Covered Source’ means Source that is explicitly made available under this Licence.

1.5 ‘Product’ means any device, component, work or physical object, whether in finished or intermediate form, arising from the use, application or processing of Covered Source.

1.6 ‘Make’ means to create or configure something, whether by manufacture, assembly, compiling, loading or applying Covered Source or another Product or otherwise.

1.7 ‘Available Component’ means any part, sub-assembly, library or code which:

a) is licensed to You as Complete Source under a Compatible Licence; or

b) is available, at the time a Product or the Source containing it is first Conveyed, to You and any other prospective licensees

i) as a physical part with sufficient rights and information (including any configuration and programming files and information about its characteristics and interfaces) to enable it either to be Made itself, or to be sourced and used to Make the Product; or ii) as part of the normal distribution of a tool used to design or Make the Product.

1.8 ‘Complete Source’ means the set of all Source necessary to Make a Product, in the preferred form for making modifications, including necessary installation and interfacing information both for the Product, and for any included Available Components. If the format is proprietary, it must also be made available in a format (if the proprietary tool can create it) which is viewable with a tool available to potential licensees and licensed under a licence approved by the Free Software Foundation or the Open Source Initiative. Complete Source need not include the Source of any Available Component, provided that You include in the Complete Source sufficient information to enable a recipient to Make or source and use the Available Component to Make the Product.

1.9 ‘Source Location’ means a location where a Licensor has placed Covered Source, and which that Licensor reasonably believes will remain easily accessible for at least three years for anyone to obtain a digital copy.

1.10 ‘Notice’ means copyright, acknowledgement and trademark notices, Source Location references, modification notices (subsection 3.3(b)) and all notices that refer to this Licence and to the disclaimer of warranties that are included in the Covered Source.

1.11 ‘Licensee’ or ‘You’ means any person exercising rights under this Licence.

1.12 ‘Licensor’ means a natural or legal person who creates or modifies Covered Source. A person may be a Licensee and a Licensor at the same time.

1.13 ‘Convey’ means to communicate to the public or distribute.

2 Applicability

2.1 This Licence governs the use, copying, modification, Conveying of Covered Source and Products, and the Making of Products. By exercising any right granted under this Licence, You irrevocably accept these terms and conditions.

2.2 This Licence is granted by the Licensor directly to You, and shall apply worldwide and without limitation in time.

2.3 You shall not attempt to restrict by contract or otherwise the rights granted under this Licence to other Licensees.

2.4 This Licence is not intended to restrict fair use, fair dealing, or any other similar right.

3 Copying, Modifying and Conveying Covered Source

3.1 You may copy and Convey verbatim copies of Covered Source, in any medium, provided You retain all Notices.

3.2 You may modify Covered Source, other than Notices, provided that You irrevocably undertake to make that modified Covered Source available from a Source Location should You Convey a Product in circumstances where the recipient does not otherwise receive a copy of the modified Covered Source. In each case subsection 3.3 shall apply.

  You may only delete Notices if they are no longer applicable to
+  the corresponding Covered Source as modified by You and You may
+  add additional Notices applicable to Your modifications.
+  Including Covered Source in a larger work is modifying the
+  Covered Source, and the larger work becomes modified Covered
+  Source.
+

3.3 You may Convey modified Covered Source (with the effect that You shall also become a Licensor) provided that You:

a) retain Notices as required in subsection 3.2;

b) add a Notice to the modified Covered Source stating that You have modified it, with the date and brief description of how You have modified it;

c) add a Source Location Notice for the modified Covered Source if You Convey in circumstances where the recipient does not otherwise receive a copy of the modified Covered Source; and

d) license the modified Covered Source under the terms and conditions of this Licence (or, as set out in subsection 8.3, a later version, if permitted by the licence of the original Covered Source). Such modified Covered Source must be licensed as a whole, but excluding Available Components contained in it, which remain licensed under their own applicable licences.

4 Making and Conveying Products

You may Make Products, and/or Convey them, provided that You either provide each recipient with a copy of the Complete Source or ensure that each recipient is notified of the Source Location of the Complete Source. That Complete Source is Covered Source, and You must accordingly satisfy Your obligations set out in subsection 3.3. If specified in a Notice, the Product must visibly and securely display the Source Location on it or its packaging or documentation in the manner specified in that Notice.

5 Research and Development

You may Convey Covered Source, modified Covered Source or Products to a legal entity carrying out development, testing or quality assurance work on Your behalf provided that the work is performed on terms which prevent the entity from both using the Source or Products for its own internal purposes and Conveying the Source or Products or any modifications to them to any person other than You. Any modifications made by the entity shall be deemed to be made by You pursuant to subsection 3.2.

6 DISCLAIMER AND LIABILITY

6.1 DISCLAIMER OF WARRANTY – The Covered Source and any Products are provided ‘as is’ and any express or implied warranties, including, but not limited to, implied warranties of merchantability, of satisfactory quality, non-infringement of third party rights, and fitness for a particular purpose or use are disclaimed in respect of any Source or Product to the maximum extent permitted by law. The Licensor makes no representation that any Source or Product does not or will not infringe any patent, copyright, trade secret or other proprietary right. The entire risk as to the use, quality, and performance of any Source or Product shall be with You and not the Licensor. This disclaimer of warranty is an essential part of this Licence and a condition for the grant of any rights granted under this Licence.

6.2 EXCLUSION AND LIMITATION OF LIABILITY – The Licensor shall, to the maximum extent permitted by law, have no liability for direct, indirect, special, incidental, consequential, exemplary, punitive or other damages of any character including, without limitation, procurement of substitute goods or services, loss of use, data or profits, or business interruption, however caused and on any theory of contract, warranty, tort (including negligence), product liability or otherwise, arising in any way in relation to the Covered Source, modified Covered Source and/or the Making or Conveyance of a Product, even if advised of the possibility of such damages, and You shall hold the Licensor(s) free and harmless from any liability, costs, damages, fees and expenses, including claims by third parties, in relation to such use.

7 Patents

7.1 Subject to the terms and conditions of this Licence, each Licensor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in subsections 7.2 and 8.4) patent licence to Make, have Made, use, offer to sell, sell, import, and otherwise transfer the Covered Source and Products, where such licence applies only to those patent claims licensable by such Licensor that are necessarily infringed by exercising rights under the Covered Source as Conveyed by that Licensor.

7.2 If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Covered Source or a Product constitutes direct or contributory patent infringement, or You seek any declaration that a patent licensed to You under this Licence is invalid or unenforceable then any rights granted to You under this Licence shall terminate as of the date such process is initiated.

8 General

8.1 If any provisions of this Licence are or subsequently become invalid or unenforceable for any reason, the remaining provisions shall remain effective.

8.2 You shall not use any of the name (including acronyms and abbreviations), image, or logo by which the Licensor or CERN is known, except where needed to comply with section 3, or where the use is otherwise allowed by law. Any such permitted use shall be factual and shall not be made so as to suggest any kind of endorsement or implication of involvement by the Licensor or its personnel.

8.3 CERN may publish updated versions and variants of this Licence which it considers to be in the spirit of this version, but may differ in detail to address new problems or concerns. New versions will be published with a unique version number and a variant identifier specifying the variant. If the Licensor has specified that a given variant applies to the Covered Source without specifying a version, You may treat that Covered Source as being released under any version of the CERN-OHL with that variant. If no variant is specified, the Covered Source shall be treated as being released under CERN-OHL-S. The Licensor may also specify that the Covered Source is subject to a specific version of the CERN-OHL or any later version in which case You may apply this or any later version of CERN-OHL with the same variant identifier published by CERN.

8.4 This Licence shall terminate with immediate effect if You fail to comply with any of its terms and conditions.

8.5 However, if You cease all breaches of this Licence, then Your Licence from any Licensor is reinstated unless such Licensor has terminated this Licence by giving You, while You remain in breach, a notice specifying the breach and requiring You to cure it within 30 days, and You have failed to come into compliance in all material respects by the end of the 30 day period. Should You repeat the breach after receipt of a cure notice and subsequent reinstatement, this Licence will terminate immediately and permanently. Section 6 shall continue to apply after any termination.

8.6 This Licence shall not be enforceable except by a Licensor acting as such, and third party beneficiary rights are specifically excluded.

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FPGA network

The U55C card is equipped with two network connectors - QSFP0 is the upper port and QSFP1 is lower port (when PCIe connector is on the bottom). The card FPGA design is offered in two variants 100g and 8x10g. These have different behavior regarding the network:

100g this variant operates QSFP0 port in 100 Gbit/s mode and should be used when connecting detector via a switch. QSFP28 transceivers are necessary.

8x10g this variant operates both QSFP ports at 4x10 Gbit/s. QSFP+ (40 Gbit/s) transceivers and MTO/MTP harness cables are necessary. It is designed for detector directly connected to the Jungfraujoch server, without switch.

Transceivers

AMD doesn’t provide transceiver compatibility matrix for Alveo U55C. In our experience operating the card we haven’t seen issues with transceivers from various providers (FS.com, Mellanox, Finnisar). We have also successfully operated card with correct direct attach cables instead of fiber optics. Given the card doesn’t support link training functionality of 100 Gbit/s ethernet, it could result in performance problems with copper cables, though we haven’t encountered such a situation.

Switch configuration

Special care has to be taken for switch operation, given the FPGA core doesn’t support auto-negotiation. It is necessary to configure switch port to fixed speed (100 Gbit/s or 10 Gbit/s) and to disable auto-negotiation. It is also necessary to enable jumbo frames (MTU of 9000).

Network LEDs

Each QSFP connector is equipped with green and orange LEDs. These LEDs are connected to Ethernet physical layer status port (rx_status). LED on corresponds to having a physical connection to a switch/computer/detector on the other side of the network. For 100 Gbit/s only green is used, for 8x10 Gbit/s green LEDs means all ports connected, orange LEDs at least one of the ports connected.

Network stack

Each Ethernet link has its own basic network stack. Functionality for Ethernet/ARP/IPv4/ICMP is therefore separately handled for each port. Each link will get dedicated MAC address, and IPv4 addresses can be also assigned independently if needed.

The card will send gratuitous ARP messages every 5 seconds to keep its entry in switch MAC table. The card will also reply to ARP requests for its IP and to ICMP ping requests sent with the card IPv4 address. The card won’t respond to broadcast ICMP pings.

Each link can be put in direct mode. In this case destination Ethernet MAC and IPv4 addresses are not enforced for incoming UDP packets. This settings should be used for connecting detector modules directly to the FPGA card, so any detector module can be connected to any 10 Gbit/s link on the same card. Currently direct mode is turned OFF for 100g design and ON for 8x10g design. This can be manually adjusted for each link.

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FPGA PCIe driver

Compilation

To compile kernel module type:

make
+

Installation

To install kernel module, you need to have root permissions and run:

sudo make install
+

Loading driver into kernel

After installing the kernel driver, it should be possible to insert it into the kernel via:

modprobe jfjoch
+

Ownership of the character devices

By default, character devices /dev/jfjoch<device number> are owned by root (user/group) and are not accessible by others. This means that jfjoch_broker must be running as superuser, which might not be optimal for security reasons in most cases. The behavior can be changed by creating udev rules. Create a file called /etc/udev/rules.d/99-jfjoch.rules with the following content:

KERNEL=="jfjoch*" OWNER="<UNIX username>" GROUP="<UNIX group>"
+

It is OK to provide only group, for example to make the devices accessible by group jungfrau:

KERNEL=="jfjoch*" GROUP="jungfrau"
+

DKMS

To avoid problems with updating the kernel, it is possible to use DKMS to autobuild Jungfraujoch kernel module, when new kernel is installed. For RHEL 8 it is well tested to use the RPM module built automatically from Jungfraujoch source. For other systems, it is necessary to follow the procedure below, though it is not well tested.

This first requires to install DKMS - for RHEL it is available via EPEL repository:

sudo dnf install dkms
+

Then use script provided in the driver directory to copy driver code to DKMS directory:

./install_dkms.sh
+

If upgrading the driver, please first remove current driver from DKMS system:

dkms remove jfjoch -v <version> --all
+

Driver parameters

Currently, there is one driver parameter nbuffers, that defines count of exchange buffers (see below). This can be adjusted in the modprobe operation, for example:

modprobe jfjoch nbuffers=1024
+

Exchange buffers

The parameter defines number of buffers used to exchange data between card and host application. Each buffer can hold one detector module (1024x512) in 16-bit or 32-bit mode + associated processing results and metadata. These buffers are used by both card-to-host and host-to-card operations.

Buffers use special allocation, as they are continuous in physical address space, which helps the FPGA card to transfer all data associated with detector module in two DMA transfers (one data, one metadata). Useful buffer size is a bit more than 2 MiB, but given that kernel allocates physical memory in power of two, 4 MiB is safe number for one buffer size. Buffer can be mapped into user space, but performing mmap system call on the /dev/jfjoch<number of device> character device.

Buffer count can be adjusted by setting nbuffers parameter. There are two considerations for setting optimal value:

  1. For card-to-host transfers, minimal value is roughly <number of threads in receiver> * <number of modules processed by thread; usually equal to number of modules per card>, this way each thread can have enough data for operation. Default thread count for Jungfraujoch receiver is 64.

  2. For host-to-card transfers, full detector calibration has to fit into memory and one buffer accommodates one calibration set for one module. So minimal count is <number of modules> * (3 + 3 * <number of storage cells>).

Based on both rules, optimal number is 512 buffers (2 GiB), though this can be adjusted for particular system and configuration.

Known problems

To avoid inconsistent behavior, this driver won’t load if release number differs between the kernel driver and FPGA card.

CMake file

While CMake file is present in the driver directory, it is only for the purpose of proper detection of the files in CLion IDE. It is not made for actual compilation of the kernel driver and should not be used for that purpose.

Character device access

For each FPGA device a character device is created called /dev/jfjoch<number of device>. When device is opened two operations are possible: mmap() to map exchange buffers ioctl() to communicate with the cards Interfacing should be done through the JungfraujochDevice class in fpga/host_library directory.

Sysfs access

Certain performance counters can be read through sysfs mechanism in the kernel. One needs to cat files in /sys/class/misc/jfjoch<number of device>/ directory.

RHEL 9.5+ issue

RedHat Enterprise Linux 9.5 backported modification to settings virtual memory flags from Linux kernel 6.3, while still operating kernel version 5.14. It is complicated to come up with a single rule to select when newer functions should be used, so it works with RHEL 9.5+, while still being compatible with other Linux distributions. It is even more complex given not all RHEL compatible distributions adopted the change at the same version. For the moment the quick fix is to define an environment variable HAVE_VM_FLAGS_SET before making the kernel.

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FPGA advanced reference

Register map

FPGA setup can be done via registers:

Address

Bits

Meaning

Mode

Notes

0x000000 - 0x00FFFF

Reserved (in case using MicroBlaze in the future, this has to be reserved for internal memory)

0x010000

32

Action Control Register

Bit 0 - Action start

R/W

Bit 1 - Action idle

R

Bit 2 - Action cancel

R/W

cleared on reset or action start

Bit 3 - Clear network counters

R/W

cleared on reset

Bit 12:4 - Debug signals (see action_config.v for details)

R

Bit 16 - AXI Mailbox interrupt 0

R

0x010004

32

Reserved

-

0x010008

32

Reserved

-

0x01000C

32

GIT SHA1

R

0x010010

32

Reserved

R

0x010014

32

Reserved

R

0x010018

32

Jungfraujoch FPGA variant

R

0x01001C

32

Reserved

R

0x010020

32

Max. number supported detector modules

R

constant

0x010024

32

Reserved

R

constant

0x010028

64

Pipeline stalls before writing to host memory

R

reset on action start

0x010030

64

Pipeline stalls before accessing HBM

R

reset on action start

0x010038

32

FIFO status (see action_config.v for details)

R

0x01003C

32

Size of single HBM channel in bytes (default value for the particular card)

R/W

should not be altered for standard operation

0x010040

64

Packets processed by the action

R

cleared on reset or action start

0x010048

64

Valid ethernet packets

R

cleared on reset

0x010050

64

Valid ICMP packets

R

cleared on reset

0x010058

64

Valid UDP packets

R

cleared on reset

0x010060

64

Valid detector packets processed by the card

R

cleared on reset

0x010068

64

Packets flagged as errors by CMAC

R

cleared on reset

0x010070

64

Pipeline stalls before data processing

R

reset on action start

0x010078

64

AXI-beats before accessing HBM

R

reset on action start

0x010080

64

AXI-beats before data processing

R

reset on action start

0x010088

64

AXI-beats before host writer

R

reset on action start

0x010090

64

Last encountered SwissFEL pulse ID

R

cleared on reset

0x010100

32

Spot finder photon count threshold

R/W

0x010104

32

Spot finder signal-to-noise ratio threshold (single-precision float)

R/W

0x010200

64

MAC address source for internal frame generator

R/W

network byte order

0x010208

32

IPv4 address source for internal frame generator

R/W

network byte order

0x01020C

32

Number of detector modules (value minus one: 0 => 1 module, 1 => 2 modules, etc.)

R/W

0x010210

32

Data collection mode

R/W

Bit 0 - Conversion to photons

Bit 1 - Output extend to 32-bit

Bit 2 - Output is unsigned integer

Bit 3 - Use sq. root lossy compression

Bit 7 - JUNGFRAU fixed G1 mode

Bit 8 - Set to zero values below threshold

Bit 16:31 - Data collection ID (carried with completions)

0x010214

32

Photon energy in keV (single-precision float)

R/W

0x010218

32

Number of frames expected in the data collection (defines termination condition)

R/W

0x01021C

32

Number of storage cells

R/W

0x010220

32

Summation on card (value minus one: 0 => summation of 1, 1 => summation of 2, etc.)

R/W

0x010224

32

Coefficient for sq. root compression (need to set bit in data collection mode to apply)

R/W

0x010225

32

Threshold; set values below set to zero (need to set bit in data collection mode to apply)

R/W

0x030000 - 0x03FFFF

AXI Mailbox for Work Request / Work Completion

See Xilinx PG114 for register map

0x040000 - 0x04FFFF

QuadSPI flash

See Xilinx PG153 for register map

0x050000 - 0x05FFFF

Interrupt controller

See Xilinx PG099 for register map

0x060000 - 0x06FFFF

Load calibration (HLS)

0x070000 - 0x07FFFF

AXI Firewall

See Xilinx PG293 for register map

0x080000 - 0x08FFFF

Frame generator (HLS)

0x090000 - 0x09FFFF

PCIe DMA control

See Xilinx PG195 for register map

0x0A0000 - 0x0AFFFF

I2C clock generator

See Xilinx PG195 for register map

0x0C0000 - 0x0FFFFF

Xilinx Card Management Solution Subsystem management subsystem

See Xilinx PG348 for register map

0x100000 - 0x10FFFF

MAC 10G / CMAC 100G

See Xilinx PG210/PG203 for register map

0x110000 - 0x11FFFF

MAC 10G

See Xilinx PG210 for register map

0x120000 - 0x12FFFF

MAC 10G

See Xilinx PG210 for register map

0x130000 - 0x13FFFF

MAC 10G

See Xilinx PG210 for register map

0x140000 - 0x14FFFF

MAC 10G

See Xilinx PG210 for register map

0x150000 - 0x15FFFF

MAC 10G

See Xilinx PG210 for register map

0x160000 - 0x16FFFF

MAC 10G

See Xilinx PG210 for register map

0x170000 - 0x17FFFF

MAC 10G

See Xilinx PG210 for register map

0x200000 - 0x20FFFF

Eth/IPv4 network stack for interface #0

0x210000 - 0x21FFFF

Eth/IPv4 network stack for interface #1

0x220000 - 0x22FFFF

Eth/IPv4 network stack for interface #2

0x230000 - 0x23FFFF

Eth/IPv4 network stack for interface #3

0x240000 - 0x24FFFF

Eth/IPv4 network stack for interface #4

0x250000 - 0x25FFFF

Eth/IPv4 network stack for interface #5

0x260000 - 0x26FFFF

Eth/IPv4 network stack for interface #6

0x270000 - 0x27FFFF

Eth/IPv4 network stack for interface #7

0x400000 - 0x47FFFF

64

Address table: decodes handles used by load_calibration and host_writer to DMA addresses

AXI Mailbox

AXI mailbox is used to send work request from host to action, and receive work completions. Messages are exchanged through AXI Mailbox IP from Xilinx (see Xilinx PG114).

Work request has the following structure:

Bit start

Bit end

Meaning

0

15

Work request ID (handle)

Work completion has the following structure:

Bit start

Bit end

Meaning

0

15

Work request ID (handle)

Special values:

65534 - start of data collection

65535 - end of data collection

15

31

Data collection ID

HBM memory

Interface number

Core

Meaning

0-1

jf_conversion

Gain factor G0

2-3

jf_conversion

Gain factor G1

4-5

jf_conversion

Gain factor G2

6-7

jf_conversion

Pedestal G0

8-9

jf_conversion

Pedestal G1

10-11

jf_conversion

Pedestal G2

12-13

integration

Integration map

14-15

integration

Integration weights

16-17

spot_finder_mask

Spot finder resolution

18-19

roi_calc

ROI calculation

20-21

frame_generator

Frame generator

22-27

load_from_hbm

Frame summation

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Hardware requirements

Operating Jungfraujoch requires the following:

  1. High performance server

  2. FPGA board(s) installed in the server

  3. (optionally) GPU boards

  4. (optionally) 100G switch to connect FPGA and the detector

Unfortunately, at the moment it is not possible to purchase server configuration from a major vendor that would include AMD FPGA boards. Therefore, the two has to be purchases separately. This might have impact on the warranty for the hardware and has to be clarified with the vendor. PSI only supports the system on the best effort basis and doesn’t take any responsibility for warranty limitations for operating FPGA boards in the server. Having said this - we didn’t encounter any hardware issues so far.

High performance server

PSI is using HPE DL380 Gen11 servers are the moment to operate Jungfraujoch systems. However, this is because of general preference for this vendor, there is no Jungfraujoch-specific reason to buy from this vendor. We do expect that system from any other vendor with similar specification should work as well.

At PSI, we use the following configuration of HPE DL380 Gen11 to operate 9M pixel detectors at 2 kHz is as follows:

  • 2 x Intel Xeon 8558P

  • 512 GB RAM

  • 2 x Nvidia L4 GPU (for indexing)

  • 1 x Nvidia Connect-X 6 200G ethernet/IB network (for outgoing traffic; this can be substituted according to facility needs)

  • Copper 1G/10G network

PCI slots

When ordering the system it is important to ensure enough PCIe cards can be accommodated in the system. In case of our system we need to put at least seven PCIe cards: 4 x FPGA, 2x GPU, 1x network

Note - for FPGA x8 lane electrically/x16 lane mechanically PCIe slots are OK.

FPGA

Jungfraujoch is built for AMD/Xilinx U55C (A-U55C-P00G-PQ-G) card. Other FPGA cards are currently not supported.

Single U55C card supports roughly 5 detector modules (2.5M pixels) at 2 kHz and 10 detector modules (5M pixels) at 1 kHz. For detectors operating at lower frame rates (e.g., 100 Hz) larger detectors can be supported by a single U55C card, though it requires using TX delay functionality in the detector.

GPUs

Operating fast-feedback indexer code requires operation of a graphic processing unit from Nvidia. For practical reasons, i.e. power consumption and cost, we choose inference grade card Nvidia L4. In the past we have also used T4 cards. So, in principle any recent CUDA compatible GPU should work.

Network switch

Small detectors (up to 4M pixel) can be in principle operated without switch. In this case one needs 8x10g variant of the Jungfraujoch FPGA image, which allows to directly connect 4 JUNGFRAU modules to one U55C card.

Such configuration is however impractical for larger systems or more complex deployments, like multiple detectors operated from one Jungfraujochs server. In this case one needs a network switch.

We currently use Nvidia/Mellanox SN2100 switch, though there is no reason not to use other models/other vendors. For switches with only 100G ports it is important to ensure, that these can be split into 4x10G ports to connect the detector.

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jfjoch_broker

jfjoch_broker is the main service for the Jungfraujoch application. It is responsible for:

  • Providing user interface via HTTP and OpenAPI

  • Configuring FPGA firmware

  • Building images from FPGA output and forwarding the results over ZeroMQ

External interfaces

Broker operates four external interfaces.

Image stream ZeroMQ PULL socket with CBOR serialization is used to send images, metadata and processing results for writing or downstream processing. See details here.

Preview stream ZeroMQ PUB socket, as above but limited to subset of frames (1 image/s by default). See details here.

Metadata stream ZeroMQ PUB socket, contains metadata for all the images, with bundling. See details here.

Configuration, status and results interface HTTP/REST interface described in the OpenAPI format. Description of the API is presented in the OpenAPI description.

Broker configuration

jfjoch_broker requires JSON configuration files. The file is described by OpenAPI structure jfjoch_settings defined in jfjoch_api.yaml file. It is recommended to go through example files in the etc/.

Example with all fields:

{
+  "pcie": [
+    {
+      "blk": "/dev/jfjoch0",
+      "ipv4": "10.1.1.7"
+    },
+    {
+      "blk": "/dev/jfjoch1",
+      "ipv4": "10.1.1.8"
+    }
+  ],
+  "zeromq": {
+    "send_watermark": 100,
+    "send_buffer_size": 1024,
+    "image_socket": [
+      "tcp://1.2.3.4:5000",
+      "tcp://1.2.3.4:5001"
+    ],
+    "writer_notification_socket": "tcp://1.3.4.6:7000"
+  },
+  "instrument": {
+    "source_name": "Swiss Light Source",
+    "source_type": "Synchrotron X-ray Source",
+    "instrument_name": "X06SA",
+    "pulsed_source": false,
+    "electron_source": false
+  },
+  "detector": [
+    {
+      "description": "EIGER 1M",
+      "serial_number": "E1M-01",
+      "type": "EIGER",
+      "high_voltage_V": 150,
+      "udp_interface_count": 1,
+      "module_sync": true,
+      "sensor_thickness_um": 320,
+      "calibration_file": [
+        "gainMaps.bin"
+      ],
+      "hostname": [
+        "e1m-01",
+        "e1m-02"
+      ],
+      "readout_time_us": 3,
+      "sensor_material": "Si",
+      "tx_delay": [
+        0,1
+      ],
+      "base_data_ipv4_address": "10.10.10.50",
+      "standard_geometry": {
+        "nmodules": 1,
+        "gap_x": 8,
+        "gap_y": 36,
+        "modules_in_row": 1
+      },
+      "custom_geometry": [
+        {
+          "x0": 0,
+          "y0": 0,
+          "fast_axis": "Xp",
+          "slow_axis": "Xp"
+        }
+      ],
+      "mirror_y": true
+    }
+  ],
+  "detector_settings": {
+    "frame_time_us": 450,
+    "count_time_us": 0,
+    "internal_frame_generator": false,
+    "internal_frame_generator_images": 1,
+    "detector_trigger_delay_ns": 0,
+    "timing": "auto",
+    "eiger_threshold_keV": 6.0,
+    "jungfrau_pedestal_g0_frames": 2000,
+    "jungfrau_pedestal_g1_frames": 300,
+    "jungfrau_pedestal_g2_frames": 300,
+    "jungfrau_pedestal_g0_rms_limit": 100,
+    "jungfrau_pedestal_min_image_count": 128,
+    "jungfrau_storage_cell_count": 1,
+    "jungfrau_storage_cell_delay_ns": 5000,
+    "jungfrau_fixed_gain_g1": false,
+    "jungfrau_use_gain_hg0": false
+  },
+  "azim_int": {
+    "polarization_factor": -1,
+    "solid_angle_corr": true,
+    "high_q_recipA": 0,
+    "low_q_recipA": 0,
+    "q_spacing": 0
+  },
+  "image_format": {
+    "summation": true,
+    "geometry_transform": true,
+    "jungfrau_conversion": true,
+    "jungfrau_conversion_factor_keV": 0.001,
+    "bit_depth_image": 16,
+    "signed_output": true,
+    "mask_module_edges": true,
+    "mask_chip_edges": true
+  },
+  "image_buffer_MiB": 2048,
+  "receiver_threads": 64,
+  "numa_policy": "n2g2",
+  "frontend_directory": "/usr/share/jfjoch/frontend",
+  "image_pusher": "ZeroMQ",
+  "zeromq_metadata": {
+    "enabled": true,
+    "period_ms": 1000,
+    "socket_address": "tcp://0.0.0.0:4357"
+  },
+  "zeromq_preview": {
+    "enabled": true,
+    "period_ms": 1000,
+    "socket_address": "tcp://0.0.0.0:4356"
+  }
+}
+

Setting up a local test for Jungfraujoch

For development, it is possible to set up a local installation of Jungfraujoch. This will work without FPGA installed in the computer and allows to test Jungfraujoch software layer, including ZeroMQ streaming and file writing.

The workflow simulates FPGA behavior, by running high-level synthesis code on the CPU - the performance is therefore very low, as fixed-point calculations have large performance penalty on CPU. In the CPU simulation mode, one can simulate using only a single FPGA device.

To run the test:

Compile Jungfraujoch with frontend

mkdir build
+cd build
+cmake ..
+make jfjoch
+make frontend
+

Alternatively, for RHEL8 system, you can use RPM generated by automated pipeline. Solely jfjoch one is enough. In this case - it is necessary to update etc/broker_local.json file with frontend path in /usr/share/jfjoch/frontend.

Start service

Start broker:

cd build/broker
+./jfjoch_broker ../../etc/broker_local.json 5232
+

Run tests

To run test a Python script is provided:

cd tests/test_data
+python jfjoch_broker_test.py
+

The script will initialize Jungfraujoch, import test image and start data collection.

Expected result

You can observe online data analysis by opening the following web page: http://localhost:5232. Also, a dataset with images should be written in the build/broker directory.

\ No newline at end of file diff --git a/JFJOCH_WRITER.html b/JFJOCH_WRITER.html new file mode 100644 index 00000000..daf2837b --- /dev/null +++ b/JFJOCH_WRITER.html @@ -0,0 +1,70 @@ + jfjoch_writer — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

jfjoch_writer

jfjoch_writer is NeXus compliant HDF5 file writer.

Acknowledgements

  • Zdenek Matej (MAX IV)

  • Felix Engelmann (MAX IV) for testing and multiple improvement suggestions.

Running directory

Writer needs to be running in base directory for writing files - file_prefix will be always relative in regard to writer running directory. Writer detects and protects for basic security issues, like file_prefix starting with a slash, or starting with ../, or containing /../.

Usage

Writer needs to be started as a background service, with the following command:

jfjoch_writer {options} <address to connect via ZeroMQ to DCU>
+
+Options:
+-R<int> | --root_dir=<int>           Root directory for file writing
+-H<int> | --http_port=<int>          HTTP port for statistics
+-r<int> | --zmq_repub_port=<int>     ZeroMQ port for PUSH socket to republish images
+-f<int> | --zmq_file_port=<int>      ZeroMQ port for PUB socket for notifications on finalized files
+-w<int> | --rcv_watermark=<int>      Receiving ZeroMQ socket watermark (default = 100)
+-W<int> | --repub_watermark=<int>    Republish ZeroMQ socket watermark (default = 1000)
+

for example:

jfjoch_writer -H5234 tcp://dcu-address:5400 
+

HTTP interface

Writer has dedicated status interface via HTTP. It allows for two operations:

  • check state of the writer to check if the writer is properly synchronized with DCU (e.g., that file_prefix agrees with what was set on the DCU) and monitor progress.

  • cancel writing this will close all the HDF5 files being written and restart writer - the option should be used only if DCU process was terminated or disconnected, it SHOULD NOT be used as standard cancellation procedure (when DCU received cancel command it should properly finish writing as well)

Republish

Republish creates a PULL socket on the writer, where all the messages are republished for further use by data analysis pipeline. Republish is non-blocking, so if there is no receiver on other end or the sending queue is full - images won’t be republished. In case of START/END messages republishing will attempt sending for 100 ms, but if send times out it won’t be retried.

Republish functionality is optional, if republish port number is omitted this functionality is not enabled.

Overwriting files

When jfjoch_writer creates a HDF5 file, it first adds suffix .<random>.tmp. Random value depends on current time-stamp and likely will be different from each file of the particular series. After file is all saved and closed, it is renamed to remove the suffix. By default, renaming won’t happen if this would overwrite existing file. However, this behavior can be changed by setting overwrite parameter to true in the file writer configuration.

Finalized files information

Creates PUB socket to inform about finalized data files. For each closed file, the socket will send a JSON message, with the following structure:

{
+  "filename": <string>: HDF5 data file name (relative to writer root directory),
+  "nimages": <int> number of images in the file (counting from 1!),
+  "file_number": <int> number of file within the acquisition,
+  "sample_name": <string> name of sample,
+  "run_name": <string> name of run,
+  "run_number": <int> number of run,
+  "experiment_group": <string> number of p-group / proposal (optional),
+  "user_data": <any json> user_data,
+  "beam_x_pxl": <float> beam center (X) in pixels,
+  "beam_y_pxl": <float> beam center (Y) in pixels,
+  "detector_distance_m": <float> detector distance (X) in m,
+  "detector_height_pxl": <int> detector size (X) in pixels,
+  "detector_width_pxl": <int> detector size (Y) in pixels,
+  "incident_energy_eV": <float> photon energy of the X-ray beam,
+  "pixel_size_m": <float> pixel size in meter (assuming pixel X == Y),
+  "saturation": <int> this count and higher mean saturation,
+  "space_group_number": <int> space group number (optional),
+  "underload": <int> pixels with this count should be excluded,
+  "unit_cell": <optinal> unit cell dimensions in Angstrom/degree {
+    "a": <float>, "b": <float>, "c": <float>,
+    "alpha": <float>, "beta": <float>, "gamma": <float>
+  },
+}
+

user_data is defined as header_appendix in the /start operation in the jfjoch_broker. Other metadata are also carried over from /start operation.

If the header_appendix is a string with valid JSON meaning, it will be embedded as JSON, otherwise it will be escaped as string. For example header_appendix of {"param1": "test1", "param2": ["test1", "test2"]}, than example message will look as follows:

{
+  "filename": "dataset_name_data_000001.h5",
+  "nimages": 1000,
+  "file_number": 0,
+  "sample_name": "lysozyme",
+  "run_name": "lyso_cryo",
+  "run_number": 25,
+  "experiment_group": "p00001",
+  "beam_x_pxl": 1200,
+  "beam_y_pxl": 1500,
+  "detector_distance_m": 0.155,
+  "detector_height_pxl": 2164,
+  "detector_width_pxl": 2068,
+  "image_time_s": 0.001,
+  "nimages": 2,
+  "incident_energy_eV": 12400.0,
+  "pixel_size_m": 7.5e-05,
+  "saturation": 32766,
+  "space_group_number": 96,
+  "underload": -32768,
+  "unit_cell": {
+    "a": 78.0,
+    "alpha": 90.0,
+    "b": 78.0,
+    "beta": 90.0,
+    "c": 39.0,
+    "gamma": 90.0
+  },
+  "user_data": {
+    "param1": "test1", 
+    "param2": ["test1", "test2"]
+  }
+}
+

Notifications for finalized files are optional, if notification port number is omitted this functionality is not enabled.

HDF5 file structure

Jungfraujoch aims to generate files compliant with NXmx format.

Master file

There are custom extension to NXmx format. These will be documented in the future.

Specifically, if data collection was configured with header_appendix having key equal to hdf5 and value as JSON object with number and string values. These will be added to /entry/user.

There are two versions of master file possible.

By default, legacy version is used. This version is compatible with DECTRIS file writer version 1.0 format. This ensures the file compatibility of Neggia and Durin XDS plugins, as well as DECTRIS Albula viewer version 4.0. Distinct feature is that if images are split into data files, there will be multiple links in /entry/data, each corresponding to a data file. Yet, certain new HDF5 features, like virtual datasets, are not possible in this format since it has to be compatible with HDF5 1.8 features.

Therefore, we have enabled format VDS version. This will link to all data files via a single virtual dataset /entry/data/data. The same way spot finding, azimuthal integration and others, will be linked between master and data files. This format allows to display processing results in currently developed Jungfraujoch Viewer. For the time being it only works with Durin XDS plugin, and require DECTRIS Albula viewer version 4.1+.

Data file

Data file has the following structure:

Location

Description

Optional

Linked in master file v. 2

/entry/data/data

Images

X

/entry/detector/timestamp

Timestamp of the image

/entry/detector/exptime

Exposure time of the image

/entry/detector/number

Image number; if image rejection was used this will be the original image number

/entry/detector/det_info

Debug field of the JF detector

X

/entry/detector/storage_cell_image

Storage cell number

X

X *

/entry/detector/rcv_delay

Receiver delay for the image (Jungfraujoch debugging)

X

/entry/detector/rcv_free_send_buffers

Receiver number of free send buffers at the time of sending the image (Jungfraujoch debugging)

X

/entry/detector/data_collection_efficiency_image

Ratio of received and expected UDP packets

X

X *

/entry/detector/packets_expected

Number of UDP packets expected for the image

X

/entry/detector/packets_received

Number of UDP packets received for the image

X

/entry/image/max_value

Max viable value of the image (excl. overloads, etc.)

X

/entry/azint/bin_to_q

Azimuthal integration - bin-to-Q mapping

X

/entry/azint/image

Azimuthal integration - per image

X

X

/entry/MX/peakXPosRaw

Peak position X (see CXI format)

X

X

/entry/MX/peakYPosRaw

Peak position Y (see CXI format)

X

X

/entry/MX/peakTotalIntensity

Peak total intensity (see CXI format)

X

X

/entry/MX/peakH

Miller index h for each detected (indexed) peak

X

X

/entry/MX/peakK

Miller index k for each detected (indexed) peak

X

X

/entry/MX/peakL

Miller index l for each detected (indexed) peak

X

X

/entry/MX/peakDistEwaldSphere

Distance of the peak from the Ewald sphere (prediction)

X

X

/entry/MX/nPeaks

Number of peaks per image (see CXI format)

X

X

/entry/MX/strongPixels

Number of strong pixel per image

X

X

/entry/MX/nPeaksRingFiltered

Number of peaks not belonging to rings

X

X

/entry/MX/imageIndexed

Image is successfully indexed

X

X

/entry/MX/profileRadius

Crystal profile radius for indexed images

X

X

/entry/MX/latticeIndexed

Crystal lattice for the image, assuming it is indexed

X

X

/entry/MX/bkgEstimate

Mean value of pixels in the radius of 3-5 A

X

X

/entry/MX/resolutionEstimate

Resolution estimate based on on-the-fly integration

X

X

/entry/MX/beam_corr_x

Beam center correction applied during processing (X) [pixel]

X

X

/entry/MX/beam_corr_y

Beam center correction applied during processing (Y) [pixel]

X

X

/entry/MX/niggli_class

Niggli class identifier of the indexed Bravais lattice (per image) - see International Tables for Crystallography A (2016). Vol. A, Table 3.1.3.1

X

X

/entry/MX/bravais_lattice

Bravais lattice short code (per image), e.g., aP, mC, oF, tI, hP, hR, cF

X

X

/entry/roi/{roi_name}/max

Max pixel value for roi named {roi_name}

X

X

/entry/roi/{roi_name}/sum

Sum pixel value for roi named {roi_name}

X

X

/entry/roi/{roi_name}/sum_sq

Sum pixel values squared for roi named {roi_name}

X

X

/entry/roi/{roi_name}/npixel

Number of valid pixel for roi named {roi_name}

X

X

/entry/roi/{roi_name}/x

Weighted X-coordinate for roi named {roi_name}

X

X

/entry/roi/{roi_name}/y

Weighted Y-coordinate for roi named {roi_name}

X

X

/entry/xfel/pulseID

Pulse ID (for XFEL only)

X

X

/entry/xfel/eventCode

Event code (for XFEL only)

X

X

* - Datasets from /entry/detector in data file are mapped to /entry/instrument/detector/detectorSpecific in master file.

If spot finding is enabled, spots are written in the CXI format and are recognized by CrystFEL. The following has to be added to the CrystFEL geometry file:

peak_list = /opt/MX
+peak_list_type = cxi
+

Other formats (CBF and TIFF)

In addition to HDF5 format, Jungfraujoch allows to save images in the Crystallographic Binary File (CBF) format. CBF files are written according to miniCBF format, with only basic header, and always with 32-bit signed integer format. Dynamic range is reduced to max 2^24, negative numbers are zeroed, and masked, and/or bad pixels are set to -1.

Also writing to TIFF files is possible, though no metadata are saved in this case.

No file option(s)

There are two options to disable writing of files by the writer:

  • Setting file_prefix to empty string - this will disable sending files on ZeroMQ image socket.

  • Setting file format to NoFile - files are streamed over ZeroMQ socket, but jfjoch_writer will not write anything. This can be useful for debugging purposes, or if you only rely on republishing functionality of the jfjoch_writer

\ No newline at end of file diff --git a/LICENSE.html b/LICENSE.html new file mode 100644 index 00000000..aff8bc00 --- /dev/null +++ b/LICENSE.html @@ -0,0 +1,20 @@ + License — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

License

Jungfraujoch software is licensed with GPLv3 license. Jungfraujoch FPGA is licensed with CERN OHL-S license (see FPGA license).

GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

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If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).

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Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.

  1. Additional Terms.

“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.

When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.

Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:

a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or

b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or

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All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.

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Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.

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You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).

However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.

Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.

Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.

  1. Acceptance Not Required for Having Copies.

You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.

  1. Automatic Licensing of Downstream Recipients.

Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.

An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party’s predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.

You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.

  1. Patents.

A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor’s “contributor version”.

A contributor’s “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.

Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.

In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.

If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. “Knowingly relying” means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient’s use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.

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Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.

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  1. Revised Versions of this License.

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  1. Interpretation of Sections 15 and 16.

If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

END OF TERMS AND CONDITIONS

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

<one line to give the program's name and a brief idea of what it does.>
+Copyright (C) <year>  <name of author>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:

<program>  Copyright (C) <year>  <name of author>
+This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type `show c' for details.
+

The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.

You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see https://www.gnu.org/licenses/.

The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read https://www.gnu.org/licenses/why-not-lgpl.html.

Jungfraujoch exceptions to GPL

As a special exception, we specifically permit linking Jungfraujoch code with Nvidia CUDA libraries.

We also permit to link Jungfraujoch software (GPLv3) with Jungfraujoch high-level synthesis code (CERN OHL 2.0) for the purpose of simulating FPGA design on CPU.

If OpenAPI definition file (jfjoch_api.yaml) is solely used to generate client code or to interact with the Jungfraujoch API it may be distributed under terms of your choosing without being subject to GPL requirements.

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OpenAPI

OpenAPI specs

See document with detailed OpenAPI specs.

Python client

Jungfraujoch is controlled with HTTP/REST interface defined with an OpenAPI specification. For convenience, we provide Python client as jfjoch-client PyPi package. To install the client you can use pip tool:

pip install jfjoch-client
+

See API reference from the OpenAPI generator.

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OpenAPI specification

See document with detailed OpenAPI specs generated with Redocly.

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Pixel mask

Mask format

Jungfraujoch follows generally NXmx format format for pixel mask. Pixel mask is described as 32-bit unsigned integer array of size the same as the image. Conditions to mask pixel are described by setting a particular bit to one. This way it is possible to encode reason why pixel is included in the pixel mask, also for one pixel there can be multiple reasons encoded at the same time.

Bit values are set as follows:

Bit 0 - gap (pixel with no sensor)

Bit 1 - error pixel (for PSI JUNGFRAU: pixel doesn’t set proper gain during pedestal, for DECTRIS: pixel is part of detector pixel mask)

Bit 4 - noisy pixel (for PSI JUNGFRAU: pixel pedestal G0 RMS is over threshold, for DECTRIS: pixel was flagged with signal during dark data collection at initialization)

Bit 8 - user defined mask

Bit 30 - module edge (only for PSI systems)

Bit 31 - chip edge interpolated pixel (multipixel)

Custom user mask

Jungfraujoch allows to upload custom user mask. This happens in two steps. First create mask in TIFF format:

import numpy as np
+import tifffile as tiff
+
+# Create a 2068x2164 numpy array filled with zeros, with 32-bit unsigned integers
+array = np.zeros((2068, 2164), dtype=np.uint32)
+
+# Mark the pixel (300, 400) with the value 1
+array[300, 400] = 1
+
+# Save the array as a TIFF file
+tiff.imwrite('mask.tiff', array)
+

Pixels with non-zero value in the TIFF file will be marked as belonging to the user mask (bit 8).

Then upload the mask to Jungfraujoch server:

curl -v http://<jfjoch_broker http address>/config/user_mask.tiff -XPUT --data-binary @mask.tiff
+
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Linux package repositories

For convenience, we are providing package repositories. With versions including and excluding CUDA linking. We recommend to install Jungfraujoch viewer from nocuda repository and remaining packages from cuda12/cuda13 repository.

RHEL based systems

For RHEL systems we provide the following repositories:

RHEL version

CUDA

Repository file

8.x

12.x

https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo

8.x

-

https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda.repo

9.x

13.x

https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda13.repo

9.x

-

https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-nocuda.repo

To install the repository, run:

dnf config-manager --add-repo https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo
+

Currently signing of RPMs is not supported, so the repository file needs to be manually modified to set gpgcheck=0 or installation must run with --nogpgcheck.

We provide the following packages in the repository:

  • jfjoch

  • jfjoch-driver

  • jfjoch-writer

  • jfjoch-viewer

Ubuntu based systems

For Ubuntu systems, we also provide the following repositories:

sudo curl https://gitea.psi.ch/api/packages/mx/debian/repository.key -o /etc/apt/keyrings/gitea-mx.asc
+echo "deb [signed-by=/etc/apt/keyrings/gitea-mx.asc] https://gitea.psi.ch/api/packages/mx/debian $distribution $component" | sudo tee -a /etc/apt/sources.list.d/gitea.list
+sudo apt update
+

$distribution uses Ubuntu names jammy (22.04) and noble (24.04). $component can be set to cuda13 and nocuda.

We provide the following packages in the repository:

  • jfjoch-jfjoch

  • jfjoch-driver

  • jfjoch-writer

  • jfjoch-viewer

Ubuntu packages are currently only going through a very limited testing.

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Software requirements

Operating system

Recommended operating system is Red Hat Enterprise Linux (RHEL) / Rocky Linux versions 8 or 9. For this operating systems we provide RPMs with pre-built binaries to simplify deployment. On experimental basis we also build repositories for Ubuntu 22.04 and 24.04.

Running Jungfraujoch on Red Hat Enterprise Linux 7 is currently not tested and not recommended, but likely possible with providing some packages from external repositories.

Software dependencies

Required:

Optional:

  • CUDA compiler version 11 or newer - required for MX fast feedback indexer

  • FFTW library - for indexing if GPU/CUDA is absent

  • NUMA library - to pin threads to nodes/CPUs

  • Node.js - to make frontend

  • Qt version 6 (for jfjoch_viewer)

Automatically downloaded by CMake and statically linked:

Please follow the link provided above to check for LICENSE file. Building code with dependencies above requires access from the build system to github.com.

Directly included in the repository:

For license check LICENSE file in respective directory

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Tests

Automated test routine is then accessible as tests/jfjoch_test. There are also benchmark routines:

  • jfjoch_hdf5_test to measure HDF5 dataset writing speed (single threaded)

  • jfjoch_offline_process to apply spot finding and indexing routines in Jungfraujoch to an example dataset - this is equivalent to FPGA spot finding algorithm, but NOT performance equivalent as it is particularly not-efficient

  • jfjoch_fpga_test to test quality/performance of FPGA card(s) and software routines

In addition, tests are executed to verify that datasets written by Jungfraujoch are readable with XDS Durin plugin, XDS Neggia plygin and CrystFEL. Input files for these programs are placed in xds_durin, xds_neggia and crystfel folders. See .gitlab-ci.yml for details.

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Tools

jfjoch_pcie_status

Prints detailed status information about the card. Execute by adding device path, e.g.:

./jfjoch_pcie_status /dev/jfjoch0
+

The program is safe to execute during a running data collection.

jfjoch_pcie_clear_net_counters

Network counters in the card give information about Ethernet, UDP and ICMP packets encountered by the network stack prior to Jungfraujoch logic. These counters are running from the moment card is powered on. They can be reset by running the program with device name, e.g.:

./jfjoch_pcie_clear_net_counters /dev/jfjoch0
+

jfjoch_pcie_net_cfg

Network configuration can be retrieved and modified with jfjoch_pcie_net_cfg tool. Usage:

jfjoch_pcie_net_cfg <device name>
+     Read configuration for all network interface of a device
+jfjoch_pcie_net_cfg <device name> <if number>|fgen
+     Read configuration for a particular network interface / internal frame generator"
+jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
+     Set IPv4 address for a particular network interface / internal frame generator
+jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
+     Set direct mode for a particular network interface / internal frame generator
+jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
+     Clear Ethernet counter for a particular network interface / internal frame generator
+

jfjoch_hdf5_tools

Tool to test single threaded HDF5 writer performance

jfjoch_offline_process

Tool to run offline processing on existing HDF5 dataset

jfjoch_udp_simulator

UDP simulator to test Jungfraujoch FPGA

jfjoch_pcie_read_register

Tool to read verbatim Jungfraujoch FPGA registers

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Semantic versioning

Jungfraujoch is following semantic versioning. For this purpose we define public API as following:

  • OpenAPI configuration interface

  • CBOR serialization ZeroMQ stream

  • HDF5 file format

This means that changes in the format of thereof must be accompanied by version change - major version in case of breaking changes, minor version in case of feature expansion.

NOTE: FPGA design, PCIe driver, and internal libraries are not part of the public API and are considered internals of Jungfraujoch. Breaking changes in these components can happen without incrementing major version of the whole package. It will be marked in changelog.

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Web frontend

Jungfraujoch is equipped with React-based web frontend for user-friendly experience. Frontend has the following options:

  • Presenting current state of the detector

  • Plotting results of online quality calculations

  • Showing live view images from the detector

  • JUNGFRAU calibration numbers

  • Configuring the detector, as well as pedestal/initialization operations

Frontend is written in TypeScript. For details see frontend/ directory.

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ZeroMQ socket

Jungfraujoch process (jfjoch_broker) operates three ZeroMQ outputs. All three can be operated/enabled independently. These are:

  • Image - all the images including metadata (PUSH socket)

  • Preview - images with metadata at a reduced frame rate (PUB socket)

  • Metadata - only metadata for all the images, bundled into packages (PUB socket)

Image stream

Images (with metadata) are serialized as CBOR image message. The stream will also include CBOR start message, calibration messages and end message with run metadata.

Image stream can be split into multiple sockets to increase performance, in this case images will be split according to file number to which the image belongs. All sockets will forward start and end messages. Only first socket will forward calibration messages and will be marked to write master file.

This is using PUSH ZeroMQ socket(s). It should be strictly avoided to have multiple receivers connected to one PUSH ZeroMQ socket. ZeroMQ will send the images in a round-robin basis to the receivers. In this case start and end messages will end up only with one receiver. Instead, Jungfraujoch feature of multiple sockets should be used.

Image stream can be replaced with direct HDF5 writer and CBOR dump image pushers, it can be disabled by select “None” image pusher for all the measurements.

If file_prefix is not provided for a data collection, images won’t be sent to image stream (or its HDF5/CBOR replacements).

Behavior is as following:

  • Start message is sent with timeout of 5s. If within the time the message cannot be put in the outgoing queue or there is no connected puller exception is thrown - stop data collection with error due to absence of a writer.

  • Images are sent in non-blocking way and without timeout.

  • End message is sent with timeout of 5s. No error is reported.

Writer notification socket

Normally ZeroMQ is asynchronous. When jfjoch_broker is sending messages via ZeroMQ image stream, it doesn’t know if these were properly handled downstream, e.g., written to disk. For this reason a writer notification socket is introduced. It allows to downstream processing code to notify ‘jfjoch_broker’ that all images were handled properly.

To use writer notification socket, it has to be first enabled in the JSON configuration file of broker with writer_notification_socket entry:

{
+  "writer_notification_socket":"tcp://192.168.0.1:*"
+}
+

Such entry will create PULL socket on 192.168.0.1 network interface listening on one, random TCP port. When data processing is started, the image stream will send CBOR start message. This message will include information on writer_notification_zmq_addr, which needs to be used by downstream code. Since the start message must reference the address of jfjoch_broker host, notification socket should always listen on a particular network interface, and should not be configured with placeholder address 0.0.0.0. It is, however, OK to use placeholder :* for network port, as it will be substituted for the one chosen by ZeroMQ.

For every image stream, downstream code must send the following message to the PULL socket:

{
+  "run_number":135,
+  "run_name": "lysozyme_1",
+  "socket_number": 1,
+  "processed_images":250,
+  "ok": true
+}
+

Here run_number, run_name and socket_number must match information from the start message. ok is boolean confirming if the writing process was OK. processed_images is number of images that were written/processed, this is to track how many images were ignored by non-blocking ZeroMQ procedures. If not, it is possible to include error message:

{
+  "run_number":135,
+  "run_name": "lysozyme_1",
+  "socket_number": 1,
+  "processed_images": 0,
+  "ok": false,
+  "error": "Permission error"
+}
+

This way errors from the downstream code are propagated to jfjoch_broker.

If writer notification socket is configured, but downstream code doesn’t send proper notification, jfjoch_broker will time out after 60 seconds producing an error message.

Preview stream

Jungfraujoch can also send images (with metadata) at a reduced frame rate for preview purpose. Images are serialized as CBOR image message. The stream will also include CBOR start message and end message with run metadata. Only start and image messages are sent.

This is using PUB socket with conflate option. I.e., only the last message is kept by ZeroMQ, so if receiver cannot cope with the messages, it will always receive the last generated message (no backlog). For this reason it is also recommended to use the same option on receiver side.

Given PUB socket properties, it is possible to connect multiple viewers to a single socket — all the viewers should receive all the images sent.

Metadata stream

Jungfrajoch can also send pure metadata for the purpose of archiving such information. Metadata are serialized as CBOR metadata message. This is very similar as image message, but excludes the actual image array and spot positions. As metadata are relatively small, to avoid large number of messages, Jungfraujoch bundles metadata of many images in one message. Order of images within bundle, as well a size of the bundle, are not guaranteed The stream will also include CBOR start message and end message with run metadata.

This is using PUB socket with watermark, so there is some queuing of messages with ZeroMQ. Multiple receivers can be connected.

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API docs by Redocly

Jungfraujoch (1.0.0-rc.126)

Download OpenAPI specification:

Filip Leonarski (Paul Scherrer Institute): filip.leonarski@psi.ch License: GPL-3.0

API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). +Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. +Jungfraujoch uses FPGA boards to acquire data at high data rates.

+

License Clarification

While this API definition is licensed under GPL-3.0, the GPL copyleft provisions do not apply +when this file is used solely to generate OpenAPI clients or when implementing applications that +interact with the API. Generated client code and applications using this API definition are not +subject to the GPL license requirements and may be distributed under terms of your choosing.

+

This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and +the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that +user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not +derivative works of the kernel and are not subject to the terms of the GPL.

+

This exception is intended to allow wider use of this API specification without imposing GPL +requirements on applications that merely interact with the API, regardless of whether they +communicate through network calls or other mechanisms.

+

Initialize detector and data acquisition

Should be used in two cases:

+
    +
  • Detector is in Inactive state
    • +
  • Detector is in Error state +X-ray shutter must be closed. +This operation will reconfigure network interface of the detector. +During operation of the detector it is recommended to use the POST /pedestal operation instead. +If storage cells are used, the execution time might be few minutes.
    • +
+

This is async function - one needs to use POST /wait_till_done to ensure operation is done.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Collect dark current for the detector

Updates calibration of the JUNGFRAU detector. Must be in Idle state.

+

X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).

+

This is async function - one needs to use POST /wait_till_done to ensure operation is done.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Start detector

Start data acquisition. +Detector must be in Idle state. +Doesn't run calibration procedure. +When the function returns, detector is ready to accept soft/TTL triggers.

+
Request Body schema: application/json
images_per_trigger
integer <int64> >= 1
Default: 1

For standard synchrotron data collection - this is number of images collected per one TTL trigger +For XFEL (pulsed source) - this number is ignored and set to 1 +For storage cell mode - this number is ignored and set to number of storage cells

+
ntrigger
integer <int64> >= 1
Default: 1

Number of TTL trigger that the detector is expected to receive during data collection

+
image_time_us
integer <int64> >= 0

Image time. +If not provided (or zero value) the frame time is assumed as default. +For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.
In XFEL mode: summation happens for frames collected with multiple triggers. +Ignored for storage cells and if raw data are saved.

+
beam_x_pxl
required
number <float>

/entry/detector/beam_center_x in NXmx +Beam center in X direction [pixels]

+
beam_y_pxl
required
number <float>

/entry/detector/beam_center_y in NXmx +Beam center in X direction [pixels]

+
detector_distance_mm
required
number <float> >= 0

/entry/detector/distance in NXmx Detector distance [mm]

+
incident_energy_keV
required
number <float> [ 0.001 .. 500 ]

Used to calculate /entry/beam/incident_wavelength in NXmx +Incident particle (photon, electron) energy in keV

+
file_prefix
string
Default: ""

Prefix for filenames. If left empty, no file will be saved.

+
images_per_file
integer <int64> >= 0
Default: 1000

Number of files in a single HDF5 data file (0 = write all images to a single data file).

+
space_group_number
integer <int64> [ 1 .. 194 ]

Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.

+
sample_name
string
Default: ""

/entry/sample/name in NXmx +Sample name

+
compression
string
Default: "bslz4"
Enum: "bslz4" "bszstd" "bszstd_rle" "none"

Compression type for the images transferred over ZeroMQ and saved to HDF5 file.

+
total_flux
number <float>

/entry/beam/total_flux in NXmx +Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]

+
transmission
number <float> [ 0 .. 1 ]

/entry/instrument/attenuator/attenuator_transmission +Transmission of attenuator (filter) [no units]

+
object (rotation_axis)

Definition of a crystal rotation axis

+
object (grid_scan)

Definition of a grid scan (mutually exclusive with rotation_axis)

+
header_appendix
any

Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) +In general, it is not saved in HDF5 file.

+

However, if values are placed in "hdf5" object, jfjoch_writer will write them in /entry/data of the HDF5 file. +This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. +For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.

+
image_appendix
any

Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) +Not saved in HDF5 file

+
data_reduction_factor_serialmx
number <float> [ 0 .. 1 ]
Default: 1

Rate at which non-indexed images are accepted to be forwarded to writer. +Value of 1.0 (default) means that all images are written. +Values below zero mean that non-indexed images will be accepted with a given probability.

+
pixel_value_low_threshold
integer <int64> >= 0

Set all counts lower than the value to zero. +When the value is set, negative numbers other than error pixel value are always set to zero. +Setting to zero is equivalent to turning the option off.

+
run_number
integer <int64> >= 0

Number of run within an experimental session. +Transferred over CBOR stream as "series ID", though not saved in HDF5 file. +It is highly recommended to keep this number unique for each data collection during experimental series. +If not provided, the number will be automatically incremented.

+
run_name
string

Unique ID of run. +Transferred over CBOR stream as "unique series ID", though not saved in HDF5 file. +It is highly recommended to keep this name unique for each data collection during experimental series. +If not provided, the name will be automatically generated as number + colon + file_prefix.

+
experiment_group
string

Name of group owning the data (e.g. p-group or proposal number). +Transferred over CBOR stream, though not saved in HDF5 file.

+
poisson_compression
integer <int64> [ 0 .. 16 ]

Enable lossy compression of pixel values that preserves Poisson statistics. +Requires to provide a numerical factor SQ. +Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer. +Compression is turned off if the value is missing or it is set to zero.

+
write_nxmx_hdf5_master
boolean
Default: true

Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments +and to turn off for other experiments.

+
save_calibration
boolean

Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer. +If parameter is not provided calibration will be saved only if more than 4 images are recorded.

+
polarization_factor
number <float> [ -1 .. 1 ]

Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization

+
ring_current_mA
number <float> >= 0

Ring current at the beginning of the data collection

+
sample_temperature_K
number <float> >= 0

Sample temperature in Kelvin

+
poni_rot1_rad
number <float> [ -6.28318530718 .. 6.28318530718 ]
Default: 0

PONI angle rot1 (see PyFAI documentation for details) in radians

+
poni_rot2_rad
number <float> [ -6.28318530718 .. 6.28318530718 ]
Default: 0

PONI angle rot2 (see PyFAI documentation for details) in radians

+
poni_rot3_rad
number <float> [ -6.28318530718 .. 6.28318530718 ]
Default: 0

PONI angle rot3 (see PyFAI documentation for details) in radians

+
object (unit_cell)

Unit cell parameters. Necessary to run indexing. Units of angstrom and degree

+
spot_finding
boolean
Default: true

Enable spot finding and save spots

+
max_spot_count
integer [ 10 .. 2000 ]
Default: 250

Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected

+
detect_ice_rings
boolean

Flag spots as ice rings and reduce their effect on indexing

+
object

Responses

Request samples

Content type
application/json
{
  • "images_per_trigger": 1,
  • "ntrigger": 1,
  • "image_time_us": 0,
  • "beam_x_pxl": 0.1,
  • "beam_y_pxl": 0.1,
  • "detector_distance_mm": 0.1,
  • "incident_energy_keV": 0.001,
  • "file_prefix": "",
  • "images_per_file": 1000,
  • "space_group_number": 1,
  • "sample_name": "",
  • "compression": "bslz4",
  • "total_flux": 0.1,
  • "transmission": 1,
  • "goniometer": {
    },
  • "grid_scan": {
    },
  • "header_appendix": null,
  • "image_appendix": null,
  • "data_reduction_factor_serialmx": 1,
  • "pixel_value_low_threshold": 0,
  • "run_number": 0,
  • "run_name": "string",
  • "experiment_group": "string",
  • "poisson_compression": 16,
  • "write_nxmx_hdf5_master": true,
  • "save_calibration": true,
  • "polarization_factor": -1,
  • "ring_current_mA": 0.1,
  • "sample_temperature_K": 0.1,
  • "poni_rot1_rad": 0,
  • "poni_rot2_rad": 0,
  • "poni_rot3_rad": 0,
  • "unit_cell": {
    },
  • "spot_finding": true,
  • "max_spot_count": 250,
  • "detect_ice_rings": true,
  • "xray_fluorescence_spectrum": {
    }
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Wait for acquisition done

Block execution of external script till initialization, data collection or pedestal is finished. +Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.

+

To not block web server for a indefinite period of time, the procedure is provided with a timeout. +Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.

+
query Parameters
timeout
integer [ 0 .. 3600 ]
Default: 60

Timeout in seconds (0 == immediate response)

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Send soft trigger to the detector

Generate soft trigger

+

Responses

Cancel running data collection

Command will inform FPGA network card to stop pedestal or data collection at the current stage. +Any frame that is currently being processed by CPU will be finished and sent to writer. +Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to Idle state.

+

If data collection is not running, the command has no effect.

+

Responses

Prepare detector to turn off

Should be in Idle or Error state. +Command deactivates data acquisition and turns off detector high voltage and ASIC. +Should be used always before turning off power from the detector.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Change detector configuration

Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings. +This can only be done when detector is Idle, Error or Inactive states. +If detector is in Idle state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation. +If detector is in Inactive or Error states, new settings will be saved, but no calibration will be executed.

+
Request Body schema: application/json
frame_time_us
required
integer <int64> >= 1

Interval between consecutive frames. +This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number. +For EIGER detector this is default frame time, not used otherwise

+
count_time_us
integer <int64>

Integration time of the detector. +If not provided count time will be set to maximum value for a given frame time.

+
internal_frame_generator
boolean
Default: false

Use internal frame generator in FPGA instead of getting data from a real detector

+
internal_frame_generator_images
integer <int64> [ 1 .. 64 ]
Default: 1

Number of images stored in the internal frame generator.

+
detector_trigger_delay_ns
integer <int64> >= 0
Default: 0

Delay between TTL trigger and acquisition start [ns]

+
timing
string (detector_timing)
Default: "trigger"
Enum: "auto" "trigger" "burst" "gated"
eiger_threshold_keV
number <float> [ 1 .. 100 ]

Threshold for the PSI EIGER detector and all DECTRIS detectors. +If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy. +If value is not provided, threshold will be determined on start of acquisition as half of incident energy. +This might lead to increased start time.

+
eiger_bit_depth
integer <int64>
Enum: 8 16 32

Bit depth of PSI EIGER read-out. This is
If value is not provided, depth will be determined based on the image time:

+
    +
  • Exposure time < 500 microseconds depth of 8 bit will be used,
    • +
  • 500 <= exposure time < 2622 microseconds depth of 16 bit will be used
    • +
  • Exposure time >= 2622 microseconds depth of 32 bit will be used.
    • +
+
jungfrau_pedestal_g0_frames
integer <int64> >= 0
Default: 2000
jungfrau_pedestal_g1_frames
integer <int64> >= 0
Default: 300
jungfrau_pedestal_g2_frames
integer <int64> >= 0
Default: 300
jungfrau_pedestal_min_image_count
integer <int64> >= 32
Default: 128

Minimum number of collected images for pedestal to consider it viable

+
jungfrau_storage_cell_count
integer <int64> [ 1 .. 16 ]
Default: 1
jungfrau_storage_cell_delay_ns
integer <int64> >= 2100
Default: 5000

Delay between two storage cells [ns]

+
jungfrau_fixed_gain_g1
boolean
Default: false

Fix gain to G1 (can be useful for storage cells)

+
jungfrau_use_gain_hg0
boolean
Default: false

Use high G0 (for low energy applications)

+

Responses

Request samples

Content type
application/json
{
  • "frame_time_us": 1,
  • "count_time_us": 0,
  • "internal_frame_generator": false,
  • "internal_frame_generator_images": 1,
  • "detector_trigger_delay_ns": 0,
  • "timing": "auto",
  • "eiger_threshold_keV": 1,
  • "eiger_bit_depth": 8,
  • "jungfrau_pedestal_g0_frames": 2000,
  • "jungfrau_pedestal_g1_frames": 300,
  • "jungfrau_pedestal_g2_frames": 300,
  • "jungfrau_pedestal_min_image_count": 128,
  • "jungfrau_storage_cell_count": 1,
  • "jungfrau_storage_cell_delay_ns": 5000,
  • "jungfrau_fixed_gain_g1": false,
  • "jungfrau_use_gain_hg0": false
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get detector configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "frame_time_us": 1,
  • "count_time_us": 0,
  • "internal_frame_generator": false,
  • "internal_frame_generator_images": 1,
  • "detector_trigger_delay_ns": 0,
  • "timing": "auto",
  • "eiger_threshold_keV": 1,
  • "eiger_bit_depth": 8,
  • "jungfrau_pedestal_g0_frames": 2000,
  • "jungfrau_pedestal_g1_frames": 300,
  • "jungfrau_pedestal_g2_frames": 300,
  • "jungfrau_pedestal_min_image_count": 128,
  • "jungfrau_storage_cell_count": 1,
  • "jungfrau_storage_cell_delay_ns": 5000,
  • "jungfrau_fixed_gain_g1": false,
  • "jungfrau_use_gain_hg0": false
}

Change indexing algorithm settings

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
algorithm
required
string (indexing_algorithm)
Default: "FFBIDX"
Enum: "FFBIDX" "FFT" "FFTW" "Auto" "None"

Selection of an indexing algorithm used by Jungfraujoch

+
fft_max_unit_cell_A
required
number <float> [ 50 .. 500 ]
Default: 250

Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT

+
fft_min_unit_cell_A
required
number <float> [ 5 .. 40 ]
Default: 10

Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT

+
fft_high_resolution_A
required
number <float> [ 0.5 .. 6 ]
Default: 2

Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT. +There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.

+
fft_num_vectors
required
integer <int64> >= 128
Default: 16384

Number of search directions for the FFT algorithm; parameter value affects execution time of FFT.

+
tolerance
required
number <float> [ 0 .. 0.5 ]

Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted

+
thread_count
required
integer <int64> [ 1 .. 64 ]

Thread count for indexing algorithm

+
geom_refinement_algorithm
required
string (geom_refinement_algorithm)
Enum: "BeamCenter" "None"

Selection of an post-indexing detector geometry refinement algorithm used by Jungfraujoch. +This option is using non-linear least squares optimization to find unit cell and beam center.

+
unit_cell_dist_tolerance
required
number <float> [ 0.0001 .. 0.2001 ]
Default: 0.05

Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored

+
viable_cell_min_spots
required
integer <int64> >= 5
Default: 10

Minimum number of indexed spots required for a cell to be considered viable

+
index_ice_rings
required
boolean
Default: false

Include spots marked as ice rings in the indexing run. +If dataset_settings doesn't have detect_ice_rings on, this option will have no effect on processing.

+
rotation_indexing
required
boolean
Default: false
rotation_indexing_min_angular_range_deg
required
number <float> >= 1
Default: 20
rotation_indexing_angular_stride_deg
required
number <float> >= 0
Default: 0.5

Responses

Request samples

Content type
application/json
{
  • "algorithm": "FFBIDX",
  • "fft_max_unit_cell_A": 250,
  • "fft_min_unit_cell_A": 10,
  • "fft_high_resolution_A": 2,
  • "fft_num_vectors": 16384,
  • "tolerance": 0.5,
  • "thread_count": 1,
  • "geom_refinement_algorithm": "BeamCenter",
  • "unit_cell_dist_tolerance": 0.05,
  • "viable_cell_min_spots": 10,
  • "index_ice_rings": false,
  • "rotation_indexing": false,
  • "rotation_indexing_min_angular_range_deg": 20,
  • "rotation_indexing_angular_stride_deg": 0.5
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get indexing configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "algorithm": "FFBIDX",
  • "fft_max_unit_cell_A": 250,
  • "fft_min_unit_cell_A": 10,
  • "fft_high_resolution_A": 2,
  • "fft_num_vectors": 16384,
  • "tolerance": 0.5,
  • "thread_count": 1,
  • "geom_refinement_algorithm": "BeamCenter",
  • "unit_cell_dist_tolerance": 0.05,
  • "viable_cell_min_spots": 10,
  • "index_ice_rings": false,
  • "rotation_indexing": false,
  • "rotation_indexing_min_angular_range_deg": 20,
  • "rotation_indexing_angular_stride_deg": 0.5
}

Change file writer settings

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
overwrite
boolean
Default: false

Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.

+
format
string (file_writer_format)
Default: "NXmxLegacy"
Enum: "None" "NXmxLegacy" "NXmxVDS" "CBF" "TIFF" "NoFileWritten"

None - no master file written +NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling

+

Responses

Request samples

Content type
application/json
{
  • "overwrite": false,
  • "format": "None"
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get file writer settings

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "overwrite": false,
  • "format": "None"
}

Change instrument metadata

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
source_name
required
string
source_type
string
Default: ""

Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. +https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource +NXsource allows the following:

+

Spallation Neutron Source +Pulsed Reactor Neutron Source +Reactor Neutron Source +Synchrotron X-ray Source +Pulsed Muon Source +Rotating Anode X-ray +Fixed Tube X-ray +UV Laser +Free-Electron Laser +Optical Laser +Ion Source +UV Plasma Source +Metal Jet X-ray

+
instrument_name
required
string
pulsed_source
boolean
Default: false

Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)

+
electron_source
boolean
Default: false

Settings specific to electron source (e.g., wavelength definition)

+

Responses

Request samples

Content type
application/json
{
  • "source_name": "Swiss Light Source",
  • "source_type": "Synchrotron X-ray Source",
  • "instrument_name": "CristallinaMX",
  • "pulsed_source": false,
  • "electron_source": false
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get instrument metadata

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "source_name": "Swiss Light Source",
  • "source_type": "Synchrotron X-ray Source",
  • "instrument_name": "CristallinaMX",
  • "pulsed_source": false,
  • "electron_source": false
}

Change image output format

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
summation
required
boolean

Enable summation of images to a given image_time +If disabled images are saved according to original detector speed, but image count is adjusted

+
geometry_transform
required
boolean

Place module read-out into their location on composed detector and extend multipixels

+
jungfrau_conversion
required
boolean

Convert pixel value in ADU to photon counts/energy +Only affects JUNGFRAU detector

+
jungfrau_conversion_factor_keV
number <float> [ 0.001 .. 500 ]

Used to convert energy deposited into pixel to counts +If not provided incident_energy_keV is used

+
bit_depth_image
integer <int64>
Enum: 8 16 32

Bit depth of resulting image (it doesn't affect the detector read-out value) +If not provided value is adjusted automatically

+
signed_output
boolean

Controls if pixels have signed output +If not provided value is adjusted automatically

+
mask_module_edges
required
boolean
Default: true

Mask 1 pixel on the module boundary

+
mask_chip_edges
required
boolean
Default: true

Mask multipixels on chip boundary

+
jungfrau_mask_pixels_without_g0
boolean
Default: true

JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1. +This should be turned off for cases, where detector is operated at room temperature with long exposure time.

+
apply_mask
required
boolean
Default: false

Masked pixels are set to special value in the images produced by Jungfraujoch

+
jungfrau_pedestal_g0_rms_limit
integer <int64> >= 0
Default: 100

Pixels with pedestal G0 RMS above the threshold are marked as masked pixels

+

Responses

Request samples

Content type
application/json
{
  • "summation": true,
  • "geometry_transform": true,
  • "jungfrau_conversion": true,
  • "jungfrau_conversion_factor_keV": 0.001,
  • "bit_depth_image": 8,
  • "signed_output": true,
  • "mask_module_edges": true,
  • "mask_chip_edges": true,
  • "jungfrau_mask_pixels_without_g0": true,
  • "apply_mask": false,
  • "jungfrau_pedestal_g0_rms_limit": 100
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get image output format

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "summation": true,
  • "geometry_transform": true,
  • "jungfrau_conversion": true,
  • "jungfrau_conversion_factor_keV": 0.001,
  • "bit_depth_image": 8,
  • "signed_output": true,
  • "mask_module_edges": true,
  • "mask_chip_edges": true,
  • "jungfrau_mask_pixels_without_g0": true,
  • "apply_mask": false,
  • "jungfrau_pedestal_g0_rms_limit": 100
}

Configure format for raw data collection

This can only be done when detector is Idle, Error or Inactive states.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Configure format for data collection with full conversion

This can only be done when detector is Idle, Error or Inactive states.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Configure spot finding

Can be done anytime, also while data collection is running

+
Request Body schema: application/json
enable
required
boolean
Default: true

Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. +Even if disabled spot finding information will still be send and written, though always with zero spots.

+
indexing
required
boolean
Default: true

Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.

+
signal_to_noise_threshold
required
number <float> >= 0
photon_count_threshold
required
integer <int64> >= 0
min_pix_per_spot
required
integer <int64> >= 1
max_pix_per_spot
required
integer <int64> >= 1
high_resolution_limit
required
number <float>

High resolution limit for spot finding [Angstrom]

+
low_resolution_limit
required
number <float>

Low resolution limit for spot finding [Angstrom]

+
high_resolution_limit_for_spot_count_low_res
required
number <float> [ 2 .. 8 ]

High resolution threshold to consider spot "low resolution" [Angstrom]

+
quick_integration
required
boolean
Default: false

Quick integration of Bragg spots in diffraction images. +If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate. +(experimental feature)

+
ice_ring_width_q_recipA
required
number <float> [ 0 .. 1 ]
Default: 0.02

Width of ice ring in q-space in reciprocal space

+
high_res_gap_Q_recipA
number <float> [ 0.1 .. 5 ]
Default: 1.5

This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector. +If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter. +This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.

+

Responses

Request samples

Content type
application/json
{
  • "enable": true,
  • "indexing": true,
  • "signal_to_noise_threshold": 0.1,
  • "photon_count_threshold": 0,
  • "min_pix_per_spot": 1,
  • "max_pix_per_spot": 1,
  • "high_resolution_limit": 0.1,
  • "low_resolution_limit": 0.1,
  • "high_resolution_limit_for_spot_count_low_res": 2,
  • "quick_integration": false,
  • "ice_ring_width_q_recipA": 0.02,
  • "high_res_gap_Q_recipA": 1.5
}

Get data processing configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "enable": true,
  • "indexing": true,
  • "signal_to_noise_threshold": 0.1,
  • "photon_count_threshold": 0,
  • "min_pix_per_spot": 1,
  • "max_pix_per_spot": 1,
  • "high_resolution_limit": 0.1,
  • "low_resolution_limit": 0.1,
  • "high_resolution_limit_for_spot_count_low_res": 2,
  • "quick_integration": false,
  • "ice_ring_width_q_recipA": 0.02,
  • "high_res_gap_Q_recipA": 1.5
}

Configure azimuthal integration

Can be done when detector is Inactive or Idle

+
Request Body schema: application/json
polarization_corr
required
boolean
Default: true

Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)

+
solid_angle_corr
required
boolean
Default: true

Apply solid angle correction for azimuthal integration

+
high_q_recipA
required
number <float>
low_q_recipA
required
number <float>
q_spacing
required
number <float>
azimuthal_bins
integer <int64> [ 1 .. 256 ]
Default: 1

Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration

+

Responses

Request samples

Content type
application/json
{
  • "polarization_corr": true,
  • "solid_angle_corr": true,
  • "high_q_recipA": 0.1,
  • "low_q_recipA": 0.1,
  • "q_spacing": 0.1,
  • "azimuthal_bins": 1
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get azimuthal integration configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "polarization_corr": true,
  • "solid_angle_corr": true,
  • "high_q_recipA": 0.1,
  • "low_q_recipA": 0.1,
  • "q_spacing": 0.1,
  • "azimuthal_bins": 1
}

Load binary image for internal FPGA generator

Load image for internal FPGA generator. This can only happen in Idle state of the detector. +Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates +(depending on detector settings).

+
query Parameters
id
integer <int64> [ 0 .. 127 ]

Image id to upload

+
Request Body schema: application/octet-stream
string <binary>

Responses

Load TIFF image for internal FPGA generator

Load image for internal FPGA generator. This can only happen in Idle state of the detector. +Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates +(depending on detector settings).

+
query Parameters
id
integer [ 0 .. 127 ]

Image ID to upload

+
Request Body schema: image/tiff
string <binary>

Responses

Select detector

Jungfraujoch allows to control multiple detectors and/or region-of-interests. +The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response). +Changing detector will set detector to Inactive state and will require reinitialization.

+
Request Body schema: application/json
id
required
integer <int64>

Responses

Request samples

Content type
application/json
{
  • "id": 1
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

List available detectors

Configured detectors that can be selected by used

+

Responses

Response samples

Content type
application/json
{
  • "detectors": [
    ],
  • "current_id": 0
}

Set ZeroMQ preview settings

Jungfraujoch can generate preview message stream on ZeroMQ SUB socket. +Here settings of the socket can be adjusted. +While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request. +Options set with this PUT request have no effect on HTTP based preview.

+
Request Body schema: application/json
enabled
required
boolean
Default: true

ZeroMQ preview socket is enabled.

+
period_ms
required
integer <int64>
Default: 1000

Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. +If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection). +This has no effect on HTTP based preview, which updates always at rate of 1 second.

+
socket_address
string

PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate. +Images are serialized using CBOR. +Address follows ZeroMQ convention for sockets - in practice ipc:// and tcp://: sockets are OK. +0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

+

Responses

Request samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get ZeroMQ preview settings

Responses

Response samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Set ZeroMQ metadata settings

Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images. +Here settings of the socket can be adjusted. +While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.

+
Request Body schema: application/json
enabled
required
boolean
Default: true

ZeroMQ metadata socket is enabled.

+
period_ms
required
integer <int64> >= 1
Default: 1000

Period for generating metadata package sent to the ZeroMQ interface in milliseconds.

+
socket_address
string

PUB ZeroMQ socket for image metadata information. +Image metadata are serialized using CBOR. +Address follows ZeroMQ convention for sockets - in practice ipc:// and tcp://: sockets are OK. +0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

+

Responses

Request samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get ZeroMQ metadata socket settings

Responses

Response samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Set configuration for dark data collection to calculate mask

This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point. +This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
detector_threshold_keV
required
number <float> [ 2.5 .. 100 ]
Default: 3.5

Energy threshold for dark image collection

+
frame_time_us
required
integer <int64> [ 500 .. 100000 ]
Default: 10000

Time between frames for dark image collection

+
number_of_frames
required
integer <int64> >= 0
Default: 1000

Number of frames for dark image collection; zero means no dark collection

+
max_allowed_pixel_count
required
integer <int64> >= 0
Default: 1

Maximum count in a pixel considered normal (not-masked)

+
max_frames_with_signal
required
integer <int64> >= 0
Default: 10

Maximum number of frames with signal in a pixel considered normal (not-masked)

+

Responses

Request samples

Content type
application/json
{
  • "detector_threshold_keV": 3.5,
  • "frame_time_us": 10000,
  • "number_of_frames": 1000,
  • "max_allowed_pixel_count": 1,
  • "max_frames_with_signal": 10
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get settings for dark data collection to calculate mask

Responses

Response samples

Content type
application/json
{
  • "detector_threshold_keV": 3.5,
  • "frame_time_us": 10000,
  • "number_of_frames": 1000,
  • "max_allowed_pixel_count": 1,
  • "max_frames_with_signal": 10
}

Get Jungfraujoch status

Status of the data acquisition

+

Responses

Response samples

Content type
application/json
{
  • "state": "Inactive",
  • "progress": 1,
  • "message": "string",
  • "message_severity": "success",
  • "gpu_count": 0
}

Get status of FPGA devices

Responses

Response samples

Content type
application/json
[
  • {
    }
]

Return XFEL pulse IDs for the current data acquisition

Return array of XFEL pulse IDs - (-1) if image not recorded

+

Responses

Response samples

Content type
application/json
[
  • 0
]

Return XFEL event codes for the current data acquisition

Return array of XFEL event codes

+

Responses

Response samples

Content type
application/json
[
  • 0
]

Get detector status

Status of the JUNGFRAU detector

+

Responses

Response samples

Content type
application/json
{
  • "state": "Idle",
  • "powerchip": "PowerOn",
  • "server_version": "string",
  • "number_of_triggers_left": 0,
  • "fpga_temp_degC": [
    ],
  • "high_voltage_V": [
    ]
}

Get ROI definitions

Responses

Response samples

Content type
application/json
{
  • "box": {
    },
  • "circle": {
    },
  • "azim": {
    }
}

Upload ROI definitions

Request Body schema: application/json
required
object (roi_box_list)

List of box ROIs

+
required
object (roi_circle_list)

List of circular ROIs

+
required
object (roi_azim_list)

List of azimuthal ROIs

+

Responses

Request samples

Content type
application/json
{
  • "box": {
    },
  • "circle": {
    },
  • "azim": {
    }
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get general statistics

query Parameters
compression
boolean
Default: false

Enable DEFLATE compression of output data.

+

Responses

Response samples

Content type
application/json
{
  • "detector": {
    },
  • "detector_list": {
    },
  • "detector_settings": {
    },
  • "image_format_settings": {
    },
  • "instrument_metadata": {
    },
  • "file_writer_settings": {
    },
  • "data_processing_settings": {
    },
  • "measurement": {
    },
  • "broker": {
    },
  • "fpga": [
    ],
  • "calibration": [
    ],
  • "zeromq_preview": {
    },
  • "zeromq_metadata": {
    },
  • "dark_mask": {
    },
  • "pixel_mask": {
    },
  • "roi": {
    },
  • "az_int": {
    },
  • "buffer": {
    },
  • "indexing": {
    }
}

Get data collection statistics

Results of the last data collection

+

Responses

Response samples

Content type
application/json
{
  • "file_prefix": "string",
  • "run_number": 0,
  • "experiment_group": "string",
  • "images_expected": 0,
  • "images_collected": 0,
  • "images_sent": 0,
  • "images_discarded_lossy_compression": 0,
  • "max_image_number_sent": 0,
  • "collection_efficiency": 1,
  • "compression_ratio": 5.3,
  • "cancelled": true,
  • "max_receiver_delay": 0,
  • "indexing_rate": 0.1,
  • "detector_width": 0,
  • "detector_height": 0,
  • "detector_pixel_depth": 2,
  • "bkg_estimate": 0.1,
  • "unit_cell": "string",
  • "error_pixels": 0.1,
  • "saturated_pixels": 0.1,
  • "roi_beam_pixels": 0.1,
  • "roi_beam_sum": 0.1
}

Get calibration statistics

Statistics are provided for each module/storage cell separately

+

Responses

Response samples

Content type
application/json
[
  • {
    }
]

Get mask of the detector (binary)

Detector must be Initialized. +Get full pixel mask of the detector. +See NXmx standard for meaning of pixel values.

+

Responses

Detector must be Initialized. +Get user mask of the detector (binary) +

Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked

+

Responses

Upload user mask of the detector (binary)

Should be in Idle state. +Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. +If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. +In the latter case - module gaps are ignored and don't need to be assigned value. +Mask is expected as binary array (4-byte; unsigned). +0 - good pixel, other value - masked +User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.

+
Request Body schema: application/octet-stream
string <binary>

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get mask of the detector (TIFF)

Should be in Idle state. +Get full pixel mask of the detector +See NXmx standard for meaning of pixel values

+

Responses

Detector must be Initialized. +Get user mask of the detector (TIFF) +

Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked

+

Responses

Upload user mask of the detector

Should be in Idle state. +Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. +If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. +In the latter case - module gaps are ignored and don't need to be assigned value. +Mask is expected as TIFF (4-byte; unsigned). +0 - good pixel, other value - masked +User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. +User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.

+
Request Body schema: image/tiff
string <binary>

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get pedestal in TIFF format

query Parameters
gain_level
required
integer

Gain level (0, 1, 2)

+
sc
integer

Storage cell number

+

Responses

Generate 1D plot from Jungfraujoch

query Parameters
binning
integer
Default: 1

Binning of frames for the plot (0 = default binning)

+
compression
boolean
Default: false

Enable DEFLATE compression of output data.

+
type
required
string
Enum: "bkg_estimate" "azint" "azint_1d" "spot_count" "spot_count_low_res" "spot_count_indexed" "spot_count_ice" "indexing_rate" "indexing_time" "indexing_unit_cell_length" "indexing_unit_cell_angle" "profile_radius" "mosaicity" "b_factor" "error_pixels" "saturated_pixels" "image_collection_efficiency" "receiver_delay" "receiver_free_send_buf" "strong_pixels" "roi_sum" "roi_mean" "roi_max_count" "roi_pixels" "roi_weighted_x" "roi_weighted_y" "packets_received" "max_pixel_value" "resolution_estimate" "pixel_sum" "processing_time" "beam_center_x" "beam_center_y"

Type of requested plot

+
fill
number <float>

Fill value for elements that were missed during data collection

+
experimental_coord
boolean
Default: false

If measurement has goniometer axis defined, plot X-axis will represent rotation angle +If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value +For still measurement the number is ignored

+
azint_unit
string
Default: "Q_recipA"
Enum: "Q_recipA" "d_A" "two_theta_deg"

Unit used for azim int.

+

Responses

Response samples

Content type
application/json
{
  • "title": "string",
  • "unit_x": "image_number",
  • "size_x": 0.1,
  • "size_y": 0.1,
  • "plot": [
    ]
}

Generate 1D plot from Jungfraujoch and send in raw binary format. +Data are provided as (32-bit) float binary array. +This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. +

query Parameters
type
required
string
Enum: "bkg_estimate" "azint" "azint_1d" "spot_count" "spot_count_low_res" "spot_count_indexed" "spot_count_ice" "indexing_rate" "indexing_time" "indexing_unit_cell_length" "indexing_unit_cell_angle" "profile_radius" "mosaicity" "b_factor" "error_pixels" "saturated_pixels" "image_collection_efficiency" "receiver_delay" "receiver_free_send_buf" "strong_pixels" "roi_sum" "roi_mean" "roi_max_count" "roi_pixels" "roi_weighted_x" "roi_weighted_y" "packets_received" "max_pixel_value" "resolution_estimate" "pixel_sum" "processing_time" "beam_center_x" "beam_center_y"

Type of requested plot

+
roi
string non-empty

Name of ROI for which plot is requested

+

Responses

Get full scan result

Responses

Response samples

Content type
application/json
{
  • "file_prefix": "string",
  • "rotation_unit_cell": {
    },
  • "rotation_crystal_lattice": [
    ],
  • "images": [
    ]
}

Get Start message in CBOR format

Contains metadata for a dataset (e.g., experimental geometry)

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get image message in CBOR format

Contains full image data and metadata. The image must come from the latest data collection.

+
query Parameters
id
integer <int64> >= -2
Default: -1

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get preview image in JPEG format using custom settings

query Parameters
id
integer <int64> >= -2
Default: -1

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

+
show_user_mask
boolean
Default: false

Show user mask

+
show_roi
boolean
Default: false

Show ROI areas on the image

+
show_spots
boolean
Default: true

Show spot finding results on the image

+
show_beam_center
boolean
Default: true

Show beam center on the image

+
saturation
number <float> [ -32767 .. 32767 ]

Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used

+
jpeg_quality
integer <int64> [ 0 .. 100 ]
Default: 100

Quality of JPEG image (100 - highest; 0 - lowest)

+
show_res_ring
number <float> [ 0.1 .. 100 ]
Default: 0.1

Show resolution ring, provided in Angstrom

+
color
string
Default: "indigo"
Enum: "indigo" "viridis" "bw" "wb" "green" "heat" "magma" "inferno"

Color scale for preview image

+
show_res_est
boolean
Default: false

Show resolution estimation as a ring

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get preview image in TIFF format

query Parameters
id
integer <int64> >= -2
Default: -1

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

+

Responses

Clear image buffer

Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get status of the image buffers

Can be run at any stage of Jungfraujoch operation, including during data collection. +The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots, +then image might be replaced in the buffer between calling /images and /image.cbor.

+

Responses

Response samples

Content type
application/json
{
  • "min_image_number": 0,
  • "max_image_number": 0,
  • "image_numbers": [
    ],
  • "total_slots": 0,
  • "available_slots": 0,
  • "current_counter": 0
}

Get Jungfraujoch version of jfjoch_broker

Responses

+ + + + diff --git a/_images/jfjoch.png b/_images/jfjoch.png new file mode 100644 index 00000000..aa75a7ea Binary files /dev/null and b/_images/jfjoch.png differ diff --git a/_sources/ACKNOWLEDGEMENT.md.txt b/_sources/ACKNOWLEDGEMENT.md.txt new file mode 100644 index 00000000..56807b32 --- /dev/null +++ b/_sources/ACKNOWLEDGEMENT.md.txt @@ -0,0 +1,10 @@ +# Acknowledgements + +Citation: F. Leonarski, M. Bruckner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matej, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad., 30, 227-234 [doi:10.1107/S1600577522010268](https://doi.org/10.1107/S1600577522010268). + +The project is supported by : +* Innosuisse via Innovation Project "NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications" (101.535.1 IP-ENG; Apr 2023 - Sep 2025). +* ETH Domain via Open Research Data Contribute project (Jan - Dec 2023) +* AMD University Program with donation of licenses of Ethernet IP cores and Vivado software + +This software uses Viridis, Magma and Inferno colormaps from Matplotlib under its BSD-compatible license diff --git a/_sources/CBOR.md.txt b/_sources/CBOR.md.txt new file mode 100644 index 00000000..4e0c6735 --- /dev/null +++ b/_sources/CBOR.md.txt @@ -0,0 +1,292 @@ +# CBOR messages + +To communicate between FPGA-equipped receiver system and writers, +Jungfraujoch is using binary CBOR encoding with tinycbor library (Intel). +The protocol is based on and compatible with [DECTRIS Stream2](https://github.com/dectris/documentation/tree/main/stream_v2). +There are minor differences at the moment: + +* LZ4 alone is not allowed; Bitshuffle+LZ4 and Bitshuffle+Zstandard are allowed +* Few fields are currently absent +* Extra fields are present beyond DECTRIS standard +* There are calibration and metadata messages defined beyond DECTRIS specification + +## Start message + +| Field name | Type | Description | Present in DECTRIS format | +|----------------------------------|----------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:| +| type | String | value "start" | X | +| magic_number | uint64 | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver | | +| detector_distance | float | Detector distance \[m\] | | +| detector_translation | Array(float) | Detector translation vector \[m\] | X | +| beam_center_x | float | Beam center in X direction \[pixels\] | X | +| beam_center_y | float | Beam center in Y direction \[pixels\] | X | +| countrate_correction_enabled | bool | Countrate correction enabled | X | +| flatfield_enabled | bool | Flatfield enabled | X | +| number_of_images | uint64 | Number of images in the series | X | +| image_size_x | uint64 | Image width \[pixels\] | X | +| image_size_y | uint64 | Image height \[pixels\] | X | +| incident_energy | float | X-ray energy \[eV\] | X | +| incident_wavelength | float | X-ray wavelength \[Angstrom\] | X | +| frame_time | float | Frame time, if multiple frames per trigger \[s\] | X | +| count_time | float | Exposure time \[s\] | X | +| saturation_value | int64 | Maximum valid sample value | X | +| error_value | int64 (optional) | Value used in images to describe pixels that are in error state or missing | | +| pixel_size_x | float | Pixel width \[m\] | X | +| pixel_size_y | float | Pixel height \[m\] | X | +| sensor_thickness | float | Sensor thickness \[m\] | X | +| sensor_material | string | Sensor material | X | +| arm_date | date | Approximate date of arming | X | +| pixel_mask_enabled | bool | Pixel mask applied on images | X | +| detector_description | string | Name of the detector | X | +| detector_serial_number | string | Detector serial number | X | +| series_unique_id | string | Unique text ID of the series (run_name parameter) | X | +| series_id | uint64 | Unique numeric ID of the series (run_number parameter) | X | +| fluorescence | object (optional) | X-ray fluorescence spectrum collected at start | | +| - energy | Array(float) | Energy of measuring point \[eV\] | | +| - data | Array(float) | Fluorescence scan result `data` \[arbitrary units\]; must be strictly the same length as energy | | +| goniometer | Map | Definition of rotation axis (optional) | X | +| - `AXIS` | string | Rotation axis name (e.g. omega) - only one axis is supported in Jungfraujoch | X | +| - - increment | float | Rotation axis increment (per image) in degree \[deg\] | X | +| - - start | float | Rotation axis start angle \[deg\] | X | +| - - axis | Array(float) | Vector for the rotation axis | | +| - - helical_step | Array(float) | Translation for helical scan for 1 image \[m\] | | +| - - screening_wedge | Array(float) | Wedge for screening \[deg\] (increment would correspond to difference between screening points) | | +| grid_scan | object | Grid scan definition (optional and exclusive with rotation axis) | | +| - n_fast | uint64 | Number of elements along fast axis | | +| - n_slow | uint64 | Number of elements along slow axis | | +| - step_x_axis | float | Step along X axis, can be negative \[m\] | | +| - step_y_axis | float | Step along Y axis, can be negative \[m\] | | +| - snake_scan | bool | Snake scan (rows alternate direction) | | +| - vertical_scan | bool | Vertical scan (enabled: fast direction = Y, disabled: fast direction = X) | | +| jungfrau_conversion_enabled | bool (optional) | Applying JUNGFRAU pixel conversion (to photons or keV) | | +| jungfrau_conversion_factor | float (optional) | Factor used for JUNGFRAU conversion \[eV\] | | +| geometry_transformation_enabled | bool (optional) | Transformation from detector module geometry (512x1024) to full detector geometry | | +| pixel_mask | Map(string -> Image) | Pixel mask - multiple in case of storage cells | X | +| channels | Array(string) | List of image channels | X | +| max_spot_count | uint64 | Maximum number of spots identified in spot finding | | +| storage_cell_number | uint64 (optional) | Number of storage cells used by JUNGFRAU | | +| storage_cell_delay | Rational | Delay of storage cells in JUNGFRAU | | +| threshold_energy | float | Threshold energy for EIGER detector \[eV\] | | +| image_dtype | string | Pixel bit type (e.g. uint16) | X | +| unit_cell | object (optional) | Unit cell of the system: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\] | | +| az_int_q_bin_count | uint64 | Number of azimuthal integration bins in the radial direction | | +| az_int_phi_bin_count | uint64 | Number of azimuthal integration bins in the phi angle direction | | +| az_int_bin_to_q | Array(float) | Q value for each azimuthal integration bin \[angstrom^-1\] | | +| az_int_bin_to_two_theta | Array(float) | Two theta angle value for each azimuthal integration bin \[deg\] | | +| az_int_bin_to_phi | Array(float) | Phi value for each azimuthal integration bin \[deg\] | | +| summation | uint64 | Factor of frame summation | | +| user_data | string | JSON serialized to string that can contain the following fields (all fields are optional): | X | +| - file_prefix | string | File prefix | | +| - images_per_file | uint64 | Number of images written per file | | +| - images_per_trigger | uint64 | Number of images collected per trigger | | +| - source_name | string | Facility name | | +| - source_type | string | Type of X-ray source (use NXsource/type values, for example "Synchrotron X-ray Source" or "Free-Electron Laser") | | +| - instrument_name | string | Instrument name | | +| - sample_name | string | Name of the sample | | +| - user | any valid JSON | Value of header_appendix provided at collection start to Jungfraujoch | | +| - attenuator_transmission | float | Attenuator transmission \[\] | | +| - total_flux | float | Total flux \[ph/s\] | | +| - space_group_number | uint64 | Space group number | | +| - summation_mode | string | Summation mode (internal\|fpga\|cpu) | | +| - overwrite | bool | Overwrite existing HDF5 files | | +| - file_format | int | File writer format: 0 = no master file, 1 = soft links, 2 = virtual dataset, 3 = CBF, 4 = TIFF | | +| - roi | Array(object) | ROI configurations; each element is one of: | | +| | | type "box": xmin, xmax, ymin, ymax (numbers) | | +| | | type "circle": r, x, y (numbers) | | +| | | type "azim": qmin, qmax (numbers) | | +| - gain_file_names | Array(string) | Names of JUNGFRAU gain files used for the current detector | | +| - write_master_file | bool | With multiple sockets, it selects which socket will provide master file | | +| - data_reduction_factor_serialmx | uint64 | Data reduction factor for serial MX | | +| - experiment_group | string | ID of instrument user, e.g., p-group (SLS/SwissFEL) or proposal number | | +| - jfjoch_release | string | Jungfraujoch release number | | +| - socket_number | uint64 | Number of ZeroMQ socket (on `jfjoch_broker` side) used for transmission | | +| - bit_depth_readout | uint64 | Bit depth of the detector readout | | +| - writer_notification_zmq_addr | string | ZeroMQ address to inform `jfjoch_broker` about writers that finished operation | | +| - xfel_pulse_id | uint64 | Pulse IDs are recorded for images | | +| - ring_current_mA | float | Ring current at the start of the measurement | | +| - sample_temperature_K | float | Sample temperature \[K\] | | +| - detect_ice_rings | bool | Ice ring detection feature is enabled | | +| - indexing_algorithm | string | Indexing algorithm used on-the-fly; allowed values: ffbidx, fft, fftw, none | | +| - geom_refinement_algorithm | string | Post-indexing detector geometry refinement algorithm; allowed values: none, beam_center, beam_center_tetragonal | | +| - poni_rot1 | float | Tilt of the detector rot1 according to PyFAI PONI convention \[rad\] | | +| - poni_rot2 | float | Tilt of the detector rot2 according to PyFAI PONI convention \[rad\] | | +| - poni_rot3 | float | Tilt of the detector rot3 according to PyFAI PONI convention \[rad\] | | + +See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/stream_v2) for definition of Image as MultiDimArray with optional compression. + +## Image message + +| Field name | Type | Description | Present in DECTRIS format | Optional | +|----------------------------|----------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:|:--------:| +| type | String | value "image" | X | | +| magic_number | uint64 | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver | | | +| series_unique_id | string | Unique text ID of the series (run_name parameter) | X | | +| series_id | uint64 | Unique numeric ID of the series (run_number parameter) | X | | +| image_id | uint64 | Number of image within the series; for MX lossy compression this is sequential excluding removed frames | X | | +| original_image_id | uint64 | Number of image within the series; for MX lossy compression this includes removed frames in the count | | | +| real_time | Rational | Exposure time | X | | +| start_time | Rational | Exposure start time (highly approximate) | X | | +| end_time | Rational | Exposure end time (highly approximate) | X | | +| spots | Array(object) | Spots: | | | +| - x | float | observed position in x (pixels) | | | +| - y | float | observed position in y (pixels) | | | +| - I | float | intensity (photons) | | | +| - maxc | int64 | max count (photons) | | | +| - ice_ring | bool | spot in resolution range for ice rings | | | +| - indexed | bool | indexed solution | | | +| reflections | Array(object) | Reflections: | | | +| - h | int64 | Miller index | | | +| - k | int64 | Miller index | | | +| - l | int64 | Miller index | | | +| - x | float | position in x (pixels) | | | +| - y | float | position in y (pixels) | | | +| - d | float | resolution \[Angstrom\] | | | +| - I | float | integrated intensity (photons) | | | +| - bkg | float | mean background value (photons) | | | +| - sigma | float | standard deviation, estimated from counting statistics (photons) | | | +| - image | float | image number (present for each spot) | | | +| - dist_ewald | float | distance to Ewald sphere (present only for indexed spots) | | | +| - rlp | float | Reciprocal Lorentz and polarization corrections | | | +| - partiality | float | Partiality of the reflection | | | +| spot_count | uint64 | Spot count | | | +| spot_count_ice_rings | uint64 | Number of spots within identified rings (experimental) | | | +| spot_count_low_res | uint64 | Number of spots in low resolution (prior to filtering) | | | +| spot_count_indexed | uint64 | Number of spots which fit indexing solution within a given tolerance | | | +| az_int_profile | Array(float) | Azimuthal integration results, use az_int_bin_to_q from start message for legend | | | +| | | NaN is used for empty bins and has to be taken care by the receiver | | | +| indexing_result | bool | Indexing successful | | | +| indexing_lattice | Array(9 * float) | Indexing result real lattice; present only if indexed | | X | +| indexing_unit_cell | object | Indexing result unit cell: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]; present only if indexed | | X | +| | | Unit cell is redundant to lattice - yet to simplify downstream programs to analyze results, both are provided | | | +| profile_radius | float | Profile radius of the image - describes distance of observed reflections from the Ewald sphere \[Angstrom^-1\] | | | +| mosaicity | float | Angular range of spots in image from a rotation scan \[degree\] | | | +| b_factor | float | Estimated B-factor (Angstrom^2) | | | +| indexing_time | float | Time spent on indexing \[s\] | | | +| processing_time | float | Total processing time \[s\] | | | +| xfel_pulse_id | uint64 | Bunch ID (for pulsed source, e.g., SwissFEL) | | X | +| xfel_event_code | uint64 | Event code (for pulsed source, e.g., SwissFEL) | | X | +| lattice_type | object | Bravais lattice classification of the indexing result (present only if available) | | X | +| - centering | string | One-letter centering code: P, A, B, C, I, F, or R | | | +| - niggli_class | int64 | Integer identifier for the Niggli-reduced Bravais class | | | +| - system | string | Crystal system: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic | | | +| jf_info | uint64 | Detector info field | | | +| receiver_aq_dev_delay | uint64 | Receiver internal delay | | | +| receiver_free_send_buf | uint64 | Receiver internal number of available send buffers | | | +| storage_cell | uint64 | Storage cell number | | | +| saturated_pixel_count | uint64 | Saturated pixel count | | | +| pixel_sum | uint64 | Sum of all pixels, excl. error and saturation | | | +| error_pixel_count | uint64 | Error pixel count | | | +| strong_pixel_count | uint64 | Strong pixel count (first stage of spot finding) | | | +| min_viable_pixel_value | int64 | Minimal pixel value, excl. error and saturation | | | +| max_viable_pixel_value | int64 | Maximal pixel value, excl. error and saturation | | | +| resolution_estimate | float | Diffraction resolution estimation \[Angstrom\] | | X | +| data_collection_efficiency | float | Image collection efficiency \[\] | | | +| packets_expected | uint64 | Number of packets expected per image (in units of 2 kB) | | | +| packets_received | uint64 | Number of packets received per image (in units of 2 kB) | | | +| bkg_estimate | float | Mean value for pixels in resolution range from 3.0 to 5.0 A \[photons\] | | | +| beam_center_x | float | Beam center X from post-indexing refinement \[pixel\] | | X | +| beam_center_y | float | Beam center Y from post-indexing refinement \[pixel\] | | X | +| beam_corr_x | float | Beam center correction X applied during processing \[pixel\] | | X | +| beam_corr_y | float | Beam center correction Y applied during processing \[pixel\] | | X | +| adu_histogram | Array(uint64) | ADU histogram | | | +| roi_integrals | object | Results of ROI calculation | | X | +| - sum | int64 | Sum of pixels in ROI area \[photons\] | | | +| - sum_square | int64 | Sum of squares of pixels in ROI area \[photons\] | | | +| - pixels | uint64 | Valid pixels in ROI area | | | +| - max_count | int64 | Highest count in ROI area \[photons\] | | | +| - x_weighted_sum | int64 | ROI pixel X position multiplied by photon count \[photons * pixels\] | | | +| - y_weighted_sum | int64 | ROI pixel Y position multiplied by photon count \[photons * pixels\] | | | +| user_data | string | Optional user defined text information - this is image_appendix serialized to JSON format | X | | +| data | Map(string -> Image) | Image | X | | + +## Metadata message + +| Field name | Type | Description | Present in DECTRIS format | Optional | +|------------------------------|------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:|:--------:| +| type | String | value "metadata" | X | | +| magic_number | uint64 | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver | | | +| series_unique_id | string | Unique text ID of the series (run_name parameter) | X | | +| series_id | uint64 | Unique numeric ID of the series (run_number parameter) | X | | +| images | Array(object) | Array of images (order and size of the array are not guaranteed) | X | | +| - image_id | uint64 | Number of image within the series; for MX lossy compression this is sequential excluding removed frames | X | | +| - original_image_id | uint64 | Number of image within the series; for MX lossy compression this includes removed frames in the count | | | +| - real_time | Rational | Exposure time | X | | +| - start_time | Rational | Exposure start time (highly approximate) | X | | +| - end_time | Rational | Exposure end time (highly approximate) | X | | +| - spot_count | uint64 | Spot count | | | +| - spot_count_ice_rings | uint64 | Number of spots within identified rings (experimental) | | | +| - az_int_profile | Array(float) | Azimuthal integration results, use az_int_bin_to_q from start message for legend | | | +| - indexing_result | bool | Indexing successful | | | +| - indexing_lattice | Array(9 * float) | Indexing result real lattice; present only if indexed | | X | +| - indexing_unit_cell | object | Indexing result unit cell: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]; present only if indexed | | X | +| | | Unit cell is redundant to lattice - yet to simplify downstream programs to analyze results, both are provided | | | +| - xfel_pulse_id | uint64 | Bunch ID (for pulsed source, e.g., SwissFEL) | | X | +| - xfel_event_code | uint64 | Event code (for pulsed source, e.g., SwissFEL) | | X | +| - jf_info | uint64 | Detector info field | | | +| - receiver_aq_dev_delay | uint64 | Receiver internal delay | | | +| - receiver_free_send_buf | uint64 | Receiver internal number of available send buffers | | | +| - storage_cell | uint64 | Storage cell number | | | +| - saturated_pixel_count | uint64 | Saturated pixel count | | | +| - error_pixel_count | uint64 | Error pixel count | | | +| - strong_pixel_count | uint64 | Strong pixel count (first stage of spot finding) | | | +| - data_collection_efficiency | float | Image collection efficiency \[\] | | | +| - bkg_estimate | float | Mean value for pixels in resolution range from 3.0 to 5.0 A \[photons\] (with solid angle/polarization corrections, if applied) | | X | +| - resolution_estimate | float | Diffraction resolution estimation | | X | +| - adu_histogram | Array(uint64) | ADU histogram | | X | +| - roi_integrals | object | Results of ROI calculation | | X | +| - - sum | int64 | Sum of pixels in ROI area \[photons\] | | | +| - - sum_square | int64 | Sum of squares of pixels in ROI area \[photons\] | | | +| - - pixels | uint64 | Valid pixels in ROI area | | | +| - - max_count | int64 | Highest count in ROI area \[photons\] | | | + +## End message + +| Field name | Type | Description | Present in DECTRIS format | +|----------------------------|--------------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:| +| type | String | value "end" | X | +| magic_number | uint64 | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver | | +| series_unique_id | string | Unique text ID of the series (run_name parameter) | X | +| series_id | uint64 | Unique numeric ID of the series (run_number parameter) | X | +| end_date | date | Approximate end date | | +| max_image_number | uint64 | Number of image with the highest number (this is counted from 1 - to distinguish zero images and one image) | | +| images_collected | uint64 | Number of image collected | | +| images_sent_to_write | uint64 | Number of image sent to writer; if writer queues were full, it is possible this is less than images collected | | +| data_collection_efficiency | float | Network packets collected / Network packets expected \[\] | | +| az_int_result | Map(text->Array(float)) | Azimuthal integration results, use az_int_bin_to_q from start message for legend | | +| adu_histogram | Map(text->Array(uint64)) | ADU values histogram | | +| adu_histogram_bin_width | uint64 | Width of bins in the above histogram \[ADU\] | | +| max_receiver_delay | uint64 | Internal performance of Jungfraujoch | | +| bkg_estimate | float | Mean background estimate for the whole run | | +| indexing_rate | float | Mean indexing rate for the whole run | | +| rotation_lattice_type | object | Bravais lattice classification of the total rotation solution over the run (if available); same schema as `lattice_type` | | +| - centering | string | One-letter centering code: P, A, B, C, I, F, or R | | +| - niggli_class | int64 | Integer identifier for the Niggli-reduced Bravais class | | +| - system | string | Crystal system: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic | | +| rotation_lattice | Array(9 * float) | Real-space lattice basis (flattened 3x3 in row-major), corresponding to the rotation indexing result | | + +## Calibration message + +| Field name | Type | Description | Present in DECTRIS format | +|--------------|----------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:| +| type | String | value "calibration" | | +| magic_number | uint64 | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver | | +| data | Map(string -> Image) | Calibration map (only single pedestal array per message) | | + +## User data +In many cases there is an interest from facilities to forward more metadata, than available explicitly in the Jungfraujoch. +For this reason two fields can be provided: `header_appendix` (sent with start message) and `image_appendix` (send with image message). +To increase flexibility, both appendices can contain any valid JSON message. +These appendices are serialized into string and stored in CBOR messages as `user_data`. + +Notably for start message, `user_data` can contain more information (non-DECTRIS compliant metadata). +Therefore `user_data` is serialized by Jungfraujoch as CBOR object. There is member `user` which contains `header_appendix` defined in OpenAPI of Jungfraujoch. + +### Notes on images and compression + +- Images are encoded as DECTRIS MultiDimArray with typed array tags: + - For RGB: shape \[3, height, width\], type: u8 + - For grayscale: shape \[height, width\], type according to bit depth and sign (e.g., uint16 LE) +- Compression: + - Uncompressed: raw CBOR byte string + - Bitshuffle+LZ4: tag with \["bslz4", elem_size, bytes\] + - Bitshuffle+Zstandard: tag with \["bszstd", elem_size, bytes\] \ No newline at end of file diff --git a/_sources/CHANGELOG.md.txt b/_sources/CHANGELOG.md.txt new file mode 100644 index 00000000..56999e16 --- /dev/null +++ b/_sources/CHANGELOG.md.txt @@ -0,0 +1,811 @@ +# Changelog +## 1.0.0 +### 1.0.0-rc.126 +This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. + +* jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg. + +### 1.0.0-rc.125 +This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. +If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. + +* jfjoch_broker: Improve logic on switching on/off spot finding +* jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 +* jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) +* jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis +* jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection +* jfjoch_writer: Save more information about each reflection + +### 1.0.0-rc.124 +This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, +especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. + +* jfjoch_broker: Improve refection position prediction and Bragg integration code. +* jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. +* jfjoch_writer: Fix saving mosaicity properly in HDF5 file. +* jfjoch_viewer: Introduce high-dynamic range mode for images +* jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) +* jfjoch_viewer: Zoom-in numbers have better readability + +### 1.0.0-rc.123 +This is an UNSTABLE release. + +* jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility +* jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) +* jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) +* jfjoch_viewer: Add more color schemes for better image readability +* HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable +* HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists + +### 1.0.0-rc.122 +This is an UNSTABLE release. + +* jfjoch_broker: Add thresholding to prefer shorter vectors after FFT +* jfjoch_broker: Add experimental mosaicity estimation for rotation experiments (this is work in progress) +* jfjoch_broker: Update nlohmann::json to 3.12.0 +* jfjoch_viewer: Display file opening errors +* jfjoch_viewer: When loading files over DBus add retry/back-off till the file is available + +### 1.0.0-rc.121 +This is an UNSTABLE release. + +* jfjoch_broker: Report changes in the image buffer, so viewer doesn't reload constantly +* jfjoch_viewer: Improve performance of loading images +* jfjoch_viewer: Auto-throttle image loading in HTTP-sync / movie modes +* jfjoch_viewer: Auto-foreground calculated with histogram +* jfjoch_viewer: Fix rare segmentation fault + +### 1.0.0-rc.120 +This is an UNSTABLE release. + +* jfjoch_broker: Improve performance of binary plot export + +### 1.0.0-rc.119 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_broker: Add binary export of data analysis plots over OpenAPI +* jfjoch_broker: Minor fixes to HTTP error handling +* jfjoch_viewer: Prefer binary plots over JSON plots +* jfjoch_viewer: Change foreground with F button + wheel +* jfjoch_viewer: Change way how angles are displayed +* jfjoch_viewer: Display resolution of the mouse cursor in top left corner + +### 1.0.0-rc.118 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_viewer: Fix issue when HTTP sync silently disconnected when it was enabled when the broker was starting measurement. +* jfjoch_broker: Add protections on time of geometry optimization and reduce rotation recalculations + +### 1.0.0-rc.117 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_viewer: Add ROI results to the dataset info plots +* jfjoch_writer: Remove HTTP interface, as it is not needed/used at the moment + +### 1.0.0-rc.116 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_viewer: Add binning options in the context menu + +### 1.0.0-rc.115 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_broker: Default spot finding settings can be configured via config JSON +* jfjoch_viewer: FFT analysis of data in the dataset plot + +### 1.0.0-rc.114 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_broker: Fix generating JPEG images with resolution estimation + +### 1.0.0-rc.113 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_broker: Improve handling of rotation indexing +* jfjoch_broker: More information saved in CBOR end message (WIP) +* jfjoch_writer: Save rotation indexing lattice parameters and Niggli class +* jfjoch_viewer: Remove (for now) primitive cell information +* jfjoch_viewer: Use angle for dataset info plot for rotation scans + +### 1.0.0-rc.112 +This is an UNSTABLE release and not recommended for production use (please use rc.111 instead). + +* jfjoch_broker: Experimental rotation (3D) indexing +* jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values + +### 1.0.0-rc.111 +This is an UNSTABLE release. + +* jfjoch_viewer: Remove 3D lattice viewer (not really useful at this moment) +* jfjoch_viewer: Fix auto contrast not refreshing image + +### 1.0.0-rc.110 +This is an UNSTABLE release. + +* jfjoch_broker: Add auto-contrast option for preview images +* Frontend: Add logo image +* jfjoch_viewer: Add logo image +* jfjoch_viewer: For image chart allow to set min value to zero +* jfjoch_viewer: For resolution estimation plots, visualization uses 1/d^2 as measure +* jfjoch_viewer: Add 3D unit cell visualization (experimental/WIP/not really there) +* Documentation: Add logo image + +### 1.0.0-rc.109 +This is an UNSTABLE release. + +* jfjoch_viewer: Add keyboard shortcuts and option to copy image to clipboard +* jfjoch_broker: Fix bit-width and exposure time for PSI EIGER detectors + +### 1.0.0-rc.108 +This is an UNSTABLE release. + +* jfjoch_viewer: Fix bug when resolution estimation/B-Factor/Profile radius were not set (NaN) +* jfjoch_viewer: Show spots is off by default, resolution ring mode is enabled by default +* jfjoch_viewer: Fit to window of image is now default when size of the grid changes + +### 1.0.0-rc.107 +This is an UNSTABLE release. + +* jfjoch_viewer: Minor polishing of new functionality +* jfjoch_broker: User NaN for empty azimuthal bins + +### 1.0.0-rc.106 +This is an UNSTABLE release. + +* jfjoch_viewer: Allow for multiple dataset info plots +* jfjoch_viewer: Highlight current element in grid + +### 1.0.0-rc.105 +This is an UNSTABLE release. + +* jfjoch_viewer: Clean-up widgets slightly +* jfjoch_viewer: Limit right panel to 600 pixels +* jfjoch_viewer: Parse crystal symmetry type +* jfjoch_viewer: Grid scan view takes color map and can be fit to zoom + +### 1.0.0-rc.104 +This is an UNSTABLE release. + +* jfjoch_writer: Fix and improve the way grid scan geometry is saved (non-NXmx extension makes it way easier) +* jfjoch_viewer: Display grid scan results in 2D (work in progress) +* jfjoch_viewer: Improve auto-scaling on start of images (work in progress) +* jfjoch_viewer: Add B-factor and resolution estimate to the dataset info plots + +### 1.0.0-rc.103 +This is an UNSTABLE release. + +* jfjoch_viewer: Minor improvements to the viewer +* jfjoch_broker: Change behavior for modular detectors: coordinates of 0-th pixel can be now arbitrary and detector will be cropped to the smallest rectangle limited by module coordinates + +### 1.0.0-rc.102 +This is an UNSTABLE release. + +* jfjoch_viewer: Minor improvements to the viewer + +### 1.0.0-rc.101 +This is an UNSTABLE release. + +* jfjoch_viewer: Auto load is better handling change of states +* jfjoch_viewer: Fix DBus registration +* jfjoch_viewer: Handle charts better with vertical lines on hover and status bar update +* jfjoch_viewer: Calculate ROI in a more efficient way + +### 1.0.0-rc.100 +This is an UNSTABLE release. + +* jfjoch_viewer: Fix dbus registration +* jfjoch_viewer: Remove background slider for diffraction image +* jfjoch_viewer: Adjustments for 2D azimuthal image viewer + +### 1.0.0-rc.99 +This is an UNSTABLE release. + +* jfjoch_broker: Fix output during mask data collection + +### 1.0.0-rc.98 +This is an UNSTABLE release and not recommended for production use (please use rc.96 instead). + +* jfjoch_broker: For DECTRIS detectors fix dark data collection during initialization + +### 1.0.0-rc.97 +This is an UNSTABLE release and not recommended for production use (please use rc.96 instead). + +* jfjoch_broker: For DECTRIS detectors add dark data collection during initialization for bad pixel mask +* jfjoch_broker: Refactor of calibration logic for more clear code (likely to introduce problems) +* jfjoch_viewer: Add option to handle user pixel mask (experimental) +* jfjoch_viewer: More options for ROI +* jfjoch_viewer: Add window to display calibration + +### 1.0.0-rc.96 +This is an UNSTABLE release. + +* Fixes in CI pipeline +* jfjoch_broker: Remove PNG preview, no dependency on libpng +* jfjoch_writer: Fix UTC timestamp being generated wrong (mix between milli- and microseconds) +* jfjoch_viewer: Show data collection time in dataset tooltip +* jfjoch_viewer: Allow to choose the calibrant (presets for LaB6 and silver behenate) +* jfjoch_viewer: Auto foreground value +* Use external libjpeg-turbo and libtiff: simpler build stack, these are built and linked statically in automated Docker builds +* Remove OpenBLAS dependency + +### 1.0.0-rc.95 +This is an UNSTABLE release. + +* Fixes in CI pipeline +* Add git-lfs to Rocky8 docker image + +Previous releases (91-94) had a wrong FPGA image upload to Gitlab release. This is now solved. + +### 1.0.0-rc.94 +This is an UNSTABLE release. + +* FFTIndexer: Add limit on angles to avoid colinear vectors +* Docker images: Add 3D Qt +* Gitea: Fixes to the pipeline + +### 1.0.0-rc.93 +This is an UNSTABLE release. + +* CI: Fixes to Gitlab based pipeline +* PCIe driver: Fix PCIe revision being hex number + +### 1.0.0-rc.92 +This is an UNSTABLE release. + +* jfjoch_broker: Fix code that predicted Bragg reflections scattering back from the sample. + +### 1.0.0-rc.91 +This is an UNSTABLE release. This release introduces new features, which usually means these need more field testing before enough maturity. +For production use we recommend waiting for a future bug-fix release. + +* FPGA: Implement high pixel value threshold - pixels above the given value will be considered saturated +* jfjoch_broker: Spot finding and integration predictions are ported to a GPU +* jfjoch_broker: Estimate resolution +* jfjoch_broker: Lattice search +* jfjoch_broker: Many more improvements in image analysis + +### 1.0.0-rc.90 +This is an UNSTABLE release. + +* jfjoch_broker: for indexing min index spots for a viable cells can be changed via OpenAPI +* jfjoch_viewer: Optional auto-reanalyze images +* jfjoch_writer: Add option where no files at all are saved +* Documentation: improvements + +### 1.0.0-rc.89 +This is an UNSTABLE release. + +* jfjoch_broker: Fix resolution estimation code +* jfjoch_broker: Fix Wilson B-factor calculation code +* jfjoch_viewer: Improve display of plots +* jfjoch_viewer: Fix segmentation fault +* jfjoch_viewer: Display missing metadata when using HTTP +* jfjoch_viewer: Fix bug when opening the same file twice + +### 1.0.0-rc.88 +This is an UNSTABLE release. + +* jfjoch_viewer: Add resolution estimation to the image information +* jfjoch_broker: Minor changes to resolution estimate routine + +### 1.0.0-rc.87 +This is an UNSTABLE release. + +* jfjoch_viewer: Display more image metadata (angle / exposure time) +* jfjoch_viewer: Improve I/sigma and B-factor plots +* jfjoch_broker: Estimate resolution based on visible spots + +### 1.0.0-rc.86 +This is an UNSTABLE release. + +* jfjoch_broker: Update logic when initializing detector to make it a bit more resilient +* Gitea pipelines have nocuda option for all architectures + +### 1.0.0-rc.85 +This is an UNSTABLE release. + +* jfjoch_viewer: When using online view, dataset info plots are not switched back to the first category for each image +* jfjoch_viewer: Handle spot count better in dataset info plots +* jfjoch_viewer: Highlight spots in ice ring resolutions in cyan, when detection is enabled + +### 1.0.0-rc.84 +This is an UNSTABLE release. + +* jfjoch_broker: Write in log which detector is being initialized +* Changes to automated build system + +### 1.0.0-rc.83 +This is an UNSTABLE release. + +* jfjoch_viewer: Fix in generating preview image for signed data (wrong bit-width was assumed before) +* CI: Fix script to generate python client + +### 1.0.0-rc.82 +This is an UNSTABLE release. + +* jfjoch_viewer: Enable FFTW based indexing in viewer (very slow at the moment) +* Frontend: Minor fixes +* Build scripts: Minor fixes to FFTW + +### 1.0.0-rc.81 +This is an UNSTABLE release. This release introduces new features, which usually means these need more field testing before enough maturity. +For production use we recommend waiting for a future bug-fix release. + +* jfjoch_broker: Add option to detect ice rings, adjust width of ice ring and change of logic to exclude ice rings in indexing +* jfjoch_broker: Add FFTW based indexer for CPU only indexing +* jfjoch_broker: Enable saving X-ray fluorescence spectra +* jfjoch_writer: Write total spot count (before filtering) +* jfjoch_viewer: Add more information on source, sample, and buttom to show ice rings +* jfjoch_viewer: Enable data processing inside the viewer + +CI: Moving from Gitlab to Gitea at PSI + +### 1.0.0-rc.80 +This is an UNSTABLE release. + +* jfjoch_broker: Fix bug when wrong value for a plot (NaN or infinity) would lead to a null in a plot, which cannot be parsed by viewer + +### 1.0.0-rc.79 +This is an UNSTABLE release. + +* jfjoch_viewer: Fix bug when loading new dataset was creating a cascade of signals leading to poor performance +* jfjoch_writer: Save nimages_per_trigger in detectorSpecific + +### 1.0.0-rc.78 +This is an UNSTABLE release. + +* jfjoch_viewer: Using a single event loop (reading images is not in dedicated thread anymore) + +### 1.0.0-rc.77 +This is an UNSTABLE release. + +* jfjoch_viewer: Display detector and dataset settings with tooltips +* jfjoch_viewer: Clean excessive HDF5 warnings +* jfjoch_viewer: Display unit cell +* jfjoch_extract_hkl: Write a tool to extract reflection intensity from a dataset + +### 1.0.0-rc.76 +This is an UNSTABLE release. + +* jfjoch_broker: Increase predicted hkl to 100.0, use lighter math to exclude too-high resolution ones +* jfjoch_broker: Use standard deviation formula to find profile radius (not the one using median) +* jfjoch_writer: Save space group number (non-NXmx addition) in addition to name +* jfjoch_viewer: Fix the bug on reading space_group as string +* jfjoch_viewer: Add missing resolution labels on rings +* jfjoch_viewer: Remove Q value from the status bar + +### 1.0.0-rc.75 +This is an UNSTABLE release. + +* jfjoch_broker: EIGER2 missing minimum threshold - hardcoded to 2.7 keV for the time being + +### 1.0.0-rc.74 +This is an UNSTABLE release. + +* jfjoch_broker: Fix for EIGER UDP port settings (vertical half of the module missing) +* jfjoch_broker: Detector settings were not applied for EIGER/DECTRIS detector when changed after initialization + +### 1.0.0-rc.73 +This is an UNSTABLE release. + +* jfjoch_broker: Space group number treatment in OpenAPI was wrong, zero value is no longer allowed and no longer default + +### 1.0.0-rc.72 +This is an UNSTABLE release. +This release introduces new features, which usually means these need more field testing before enough maturity. +For production use we recommend waiting for a future bug-fix release. + +* jfjoch_broker: Refactor of indexing and geometry refinement code +* jfjoch_broker: Handle space group/centering in refinement code +* jfjoch_broker: Replace mosaicity with profile radius: refining the former is difficult with still images +* jfjoch_broker: There is no longer 0.5 pxl offset for spots-to-reciprocal-space conversion +* jfjoch_writer: Experimental saving of reflections +* jfjoch_writer: Save space group name as string +* jfjoch_viewer: Add profile radius and B-factor +* jfjoch_viewer: Show 4 digits for wavelength +* jfjoch_viewer: Match rings between calibrant and observation (will handle missing/wrong rings) +* FPGA: Use UDP destination port to distinguish between detector modules and data streams +* FPGA: Add experimental PTP core (PTP over L2, only Sync/Follow_up) +* FPGA driver: Fix for Linux kernel 6.12+ (thanks to Tim Gruene) + +### 1.0.0-rc.71 +This is an UNSTABLE release. + +* jfjoch_broker: Remove resolution estimation via machine learning +* jfjoch_broker: Harmonize code to analyze spot finding results (indexing/refinement/integration) between CPU and FPGA receivers +* jfjoch_viewer: Fix error when HDF5 files with indexing results couldn't be loaded on a machine without GPU + +### 1.0.0-rc.70 +This is an UNSTABLE release. +This release introduces new features (geometry refinement), which usually means these need more field testing before enough maturity. +For production use we recommend waiting for a future bug-fix release. + +* jfjoch_broker: Fix bug when PSI EIGER frame time was not set properly at the start of the measurement +* jfjoch_broker: Fix PONI rot2 angle rotating detector in a wrong direction (PyFAI convention is for this angle to rotate detector downwards) +* jfjoch_broker: Enable geometry refinement - first try (work in progress) +* jfjoch_viewer: Fix deadlock when opening HTTP connections +* jfjoch_viewer: Display rings as ellipses with detector tilt +* jfjoch_viewer: Add button to calibrate detector geometry based on LaB6 image +* jfjoch_writer: Save detector tilt angles (rot1, rot2, rot3) + +* Add Google Ceres a non-linear least-square optimization library to Jungfraujoch +* Add experimental detector calibration routines (for LaB6) +* Improve documentation on the ZeroMQ writer notification socket and detector geometry + +### 1.0.0-rc.69 +This is an UNSTABLE release. + +* jfjoch_viewer: Metadata can be modified for an open dataset (no option to save) +* jfjoch_viewer: Refactor multiple issues in the viewer regarding image reading code to allow for further developments +* jfjoch_viewer: Resolution rings not enabled by default +* jfjoch_broker: Handle properly PONI rotations in dataset settings though still not updated properly in the HDF5 file + +### 1.0.0-rc.68 +This is an UNSTABLE release. + +* jfjoch_broker: Temperature threshold can be changed for JUNGFRAU detector +* jfjoch_broker: Default detector settings can be configured for each detector separately +* jfjoch_broker: Refactor spot filtering code, max spot count can be modified for dataset settings +* jfjoch_broker: Refactor indexing refinement, make it the same for both FFBIDX and FFT indexing +* jfjoch_broker: Reference unit cell will be taken into account for FFT indexing to filter +* jfjoch_broker: Review PONI rotation angles and azimuthal angle conventions along with PyFAI + +### 1.0.0-rc.67 +This is an UNSTABLE release. + +* jfjoch_broker: Enable SSL +* jfjoch_broker: Wilson B-factor only provided is fit is relatively OK (R^2 > 0.3); this will be refined much more in the future + +### 1.0.0-rc.66 +This is an UNSTABLE release. + +* jfjoch_broker: Indexers operate as thread pool, which is operating +* jfjoch_viewer: Increase interval between loading images + fix too many verbose messages + +### 1.0.0-rc.65 +This is an UNSTABLE release. + +* jfjoch_broker: Print information regarding used image pushers +* jfjoch_viewer: Allow syncing with Jungfraujoch server +* OpenAPI: Clarify licensing terms in the file + +### 1.0.0-rc.64 +This is an UNSTABLE release. + +* jfjoch_broker: Fix issue in receiver light with very long preparation time for threads +* jfjoch_broker: Add verbose option +* jfjoch_broker: Don't trigger pedestal if critical settings are not changed when loading detector settings +* jfjoch_broker: Detector left in busy state when detector settings were improper +* jfjoch_viewer: Modify DBus interface to avoid loading same file and image 0 multiple times +* jfjoch_lite_perf_test: Add verbose option + +### 1.0.0-rc.63 +This is an UNSTABLE release. + +* jfjoch_broker: Save NX/NY for grid scan result +* jfjoch_broker: Add processing time to CBOR output and plot +* jfjoch_writer: Add processing time to data file + +### 1.0.0-rc.62 +This is an UNSTABLE release. + +* jfjoch_broker: Fix bug where low resolution spots were not counted properly +* jfjoch_broker: Spot count is provided prior to filtering of spots to max_spot_count +* jfjoch_broker: Add more spot count information to CBOR +* jfjoch_viewer: Fix issue with ROI drawing resulting in multiple overlapping rectangles + +### 1.0.0-rc.61 +This is an UNSTABLE release. + +* jfjoch_broker: Fix bug where FFT indexing could result in a very short or even zero length vector +* jfjoch_broker: Ice ring and indexed spot count enabled as plots and saved in grid scan results +* jfjoch_broker: High resolution limit for low res. spot counting can be adjusted + +### 1.0.0-rc.60 +This is an UNSTABLE release. + +* jfjoch_broker: Fix bug when the neural network inference client was busy and this status was never released +* jfjoch_broker: Revert the indexing threshold with distance from integer for Miller indices +* jfjoch_broker: Fix bug in scattering vector calculation, resulting in indexing not working outside 1.0 A X-ray wavelength + +### 1.0.0-rc.59 +This is an UNSTABLE release. + +* jfjoch_broker: Fix bug when broker was waiting for notification message before sending end message, resulting in deadlock. +* jfjoch_writer: Verbose option for debugging. + +### 1.0.0-rc.58 +This is an UNSTABLE release. + +* jfjoch_viewer: Fix memory leak +* jfjoch_writer: Add detector_number/serial_number to master file + +### 1.0.0-rc.57 +This is an UNSTABLE release. + +* jfjoch_broker: Fix bug when enabling ML resolution estimation was not possible +* jfjoch_viewer: "Movie" mode + +### 1.0.0-rc.56 +This is an UNSTABLE release. + +* jfjoch_broker: Fixing more bugs related to neural network inference for ML estimation + +### 1.0.0-rc.55 +This is an UNSTABLE release. + +* jfjoch_broker: Fixing minor bugs related to neural network inference for ML estimation + +### 1.0.0-rc.54 +This is an UNSTABLE release. + +* jfjoch_broker: Indexing with AUTO settings (FFBIDX if unit cell provided; FFT if not) +* jfjoch_broker: Don't remove shared memory area when deactivating detector +* jfjoch_writer: Save writer release +* jfjoch_viewer: Increase time for the messages in the status bar + +### 1.0.0-rc.53 +This is an UNSTABLE release. + +* PCIe driver: Imperfect solution for RHEL 9.5+ changes +* jfjoch_writer: Fix to angle containers for AutoProc compatibility +* jfjoch_fpga_test: Use consecutive number for devices, not interleaved + +### 1.0.0-rc.52 +This is an UNSTABLE release. + +* jfjoch_viewer: Use warmer colors to distinguish from AareGUI +* jfjoch_viewer: Minor adjustments to DBus setting image number +* jfjoch_broker: Fix in low resolution spot count plotting + +### 1.0.0-rc.51 +This is an UNSTABLE release. + +* jfjoch_broker: Send preview in PNG format +* jfjoch_broker: Provide count of spots in 50.0 - 5.0 A range +* jfjoch_broker: Provide ML resolution estimation in scan result +* jfjoch_broker: Allow removing beam center in web preview + +### 1.0.0-rc.50 +This is an UNSTABLE release. + +* The release fixes some of many bugs introduced in recent releases +* jfjoch_viewer: display predictions for indexed cells + +### 1.0.0-rc.49 +This is an UNSTABLE release. + +* jfjoch_broker: Handle sample temperature (K) and ring current (mA) to metadata +* jfjoch_writer: For angle containers in NXmx add _end dataset, sample temp. and ring current + +### 1.0.0-rc.48 +This is an UNSTABLE release. + +* jfjoch_broker: fix the bug when a unit cell was not exported for a scan result. + +### 1.0.0-rc.47 +This is an UNSTABLE release. + +* jfjoch_viewer: fix dbus service path +* jfjoch_writer: fix CBF/TIFF writing + +### 1.0.0-rc.46 +This is an UNSTABLE release. + +* jfjoch_viewer: remove dependency on image analysis + +### 1.0.0-rc.45 +This is an UNSTABLE release. + +* jfjoch_broker: Detector list returns pixel size (mm) + +### 1.0.0-rc.44 +This is an UNSTABLE release. + +* jfjoch_broker: more general definition of scan result export + +Braking changes: +* It removes additions to OpenAPI from 1.0.0-rc.43 +* It makes changes to the "unit_cell" definition in OpenAPI specs. It might be harmless in some languages and may result in errors in other implementations. + +### 1.0.0-rc.43 +This is an UNSTABLE release. + +* jfjoch_broker: Export grid scan results into a single data structure + +### 1.0.0-rc.42 +This is an UNSTABLE release. + +* jfjoch_broker: Add pixel_sum to CBOR output. +* jfjoch_broker: Changes to sigma estimation in QuickIntegrate routine +* jfjoch_writer: Save pixel_sum + +### 1.0.0-rc.41 +This is an UNSTABLE release. This release includes multiple new features, it should not be used in production at the moment. + +* jfjoch_broker: Estimate B-factor, mosaicity to evaluate crystal diffraction +* jfjoch_broker: Export GPU count via OpenAPI +* jfjoch_broker: Enable 2D azimuthal integration and PONI rotations for detector + +* FPGA: Increase the number of integration bins to 2048 + +### 1.0.0-rc.40 +This is an UNSTABLE release. This release includes multiple new features, it should not be used in production at the moment. + +* jfjoch_broker: Jungfraujoch supports grid scan metadata, including dedicated plotting schemes and NXmx structures +* jfjoch_broker: Improve metadata for rotation data collection +* jfjoch_broker: Better handling of plotting +* jfjoch_broker: FFT based indexing +* jfjoch_broker: Integration, first try, results not saved at the moment +* jfjoch_broker: Internal improvements in image handling + +* jfjoch_writer: Multiple adjustments adapt to changes in this release for new features +* jfjoch_writer: New state management model to improve clarity of error reporting + +* jfjoch_viewer: Remote control via DBus + +* Frontend: Multiple adjustments for new features +* Frontend: Grid scan plots + +WARNING! OpenAPI contains breaking changes in regard to plotting results, so care has to be taken. + +### 1.0.0-rc.39 +* FPGA: Bugfix for pixel masked for data analysis if summation was on +* jfjoch_viewer: Fix segmentation fault when cursor was outside of image + +### 1.0.0-rc.38 +* jfjoch_broker: Neural net model is not linked with C++ code due to deployment issues, it is rather distributed as python code, connected via RES +* jfjoch_broker: Neural net model can use all 4 quadrants of the detector +* jfjoch_broker: For EIGER image time can be provided through /start +* jfjoch_viewer: Add image list option +* jfjoch_viewer: Drawing circular ROIs with shift +* jfjoch_viewer: Enable image summation +* jfjoch_viewer: Image reader is significantly reworked, hopefully without affecting the viewer + +### 1.0.0-rc.37 +* jfjoch_broker: Make locking rules more flexible +* jfjoch_broker: Load mask via SIMPLON interface for DECTRIS detectors +* jfjoch_viewer: Add status bar + +### 1.0.0-rc.36 +This is UNSTABLE release. Wait for new version to use in a production environment. + +* jfjoch_broker: Support for Jungfraujoch Lite is enabled - software-based receiver for DECTRIS detectors (required a lot of refactoring, potentially leading to unstable code) +* jfjoch_broker: Enable Resonet support (ML-based diffraction resolution estimation) +* jfjoch_broker: Fix error in compression, where bitshuffle/LZ4 and bitshuffle/Zstd HDF5 headers were wrongly generated for 8-bit and 32-bit data +* jfjoch_writer: Increase buffering to 1000 images in the receiver +* jfjoch_writer: Images can be written as CBF or TIFF in addition to HDF5 + +### 1.0.0-rc.35 +This is UNSTABLE release, not properly tested. Wait for new version for using production. + +* jfjoch_broker: If module is delayed by more than 50 frames versus other modules, it will be ignored and receiver is not waiting. +* jfjoch_writer: Save EIGER energy threshold +* jfjoch_writer: Add `/entry/sample/goniometer` for compatibility with `eiger2cbf` program + +### 1.0.0-rc.34 +This is UNSTABLE release - introducing new features, but not properly tested. Wait for new version for using production. + +* jfjoch_broker: More consistency for file format definition (breaking change in API from 1.0.0-rc.31 for file writer settings) +* jfjoch_broker: For storage cells mask is logical sum of detector bad pixels for all storage cells +* jfjoch_broker: Handle situation when detector doesn't want to gracefully stop (to be tested) +* jfjoch_broker: Center-of-mass position and mean for ROI is added to available plots +* jfjoch_viewer: Can extract data analysis results from "legacy" format +* jfjoch_viewer: Display dataset name +* FPGA: Pixel mask is used for data analysis part even if it is not applied to pixels +* FPGA: Add pixel sum to module statistics +* FPGA: ROI number is reduced to 16, but pixel can belong to every defined ROI +* FPGA: Spot finder is back to full dynamic range (24-bit) +* FPGA: More debug features for internal FIFOs + +Known issues: +* ROI count flag was added to firmware. For the time being the flag will be wrongly set to 10 due to mismatch of FPGA build scripts. +* EIGER data acquisition has an issue that is currently debugged + +### 1.0.0-rc.33 +* jfjoch_broker: Fix issue with EIGER settings being loaded improperly + +### 1.0.0-rc.32 +* jfjoch_broker: Refactor code for azimuthal integration for further improvements +* jfjoch_broker: Minor fix for EIGER (trim energies are manually set for E9M, to be fixed properly later) +* jfjoch_writer: Fix too much verbose information +* FPGA: Minor fixes to spot finder (enable two-pass operation and limit number range to int20) + +### 1.0.0-rc.31 +This is UNSTABLE release - introducing many features, but still needs more testing. +Expecting soon to put bugfix release. + +* jfjoch_writer: Allow to enable overwriting existing files (not enabled by default) +* jfjoch_writer: Add new HDF5 master file format, which uses HDF5 virtual data sets and links processing results to data files (not enabled by default) +* jfjoch_viewer: Image viewer work early test version +* jfjoch_broker: Fixes to counting packets per dataset/image +* jfjoch_broker: Image buffer is accessible for outside to check images +* jfjoch_broker: error/saturated pixels and dedicated ROI "beam" can be tracked online +* jfjoch_broker: Fix bug in handling pedestal G1/G2 count time for JUNGFRAU +* jfjoch_broker: Fix bug in applying pixel mask interfering with pedestal calculation +* jfjoch_broker: Fix bug in EIGER initializing +* jfjoch_broker: Save maximum pixel value to HDF5 file and export as Web plot +* PCIe driver: Add PCIe link speed and width +* FPGA: Improve counting error/saturated/min/max pixels +* FPGA: Spot finder is gradual column-wise (15 columns up/down) and fixed row-wise (32 pixel boxes); previously it was fixed both column- and row-wise with 32x32 pixel areas +* FPGA: Require Vivado 2022.2 + +Warning: +There are breaking changes to HDF5 file format, renaming entries regarding image storage cell number and image collection efficiency. + +### 1.0.0-rc.30 +* jfjoch_writer: replace non-blocking with blocking operation on internal queues - less likely to "loose" images within the writer + +### 1.0.0-rc.29 +* jfjoch_broker: refactor logic regarding frame time and count time for more flexibility for EIGER and JUNGFRAU +* jfjoch_broker: readout time for EIGER is 3 us and JUNGFRAU is 20 us, this can be changed in input file +* jfjoch_broker: OpenAPI interface includes more ways to provide information on the status (error/warning/info) +* jfjoch_broker: ROIs handling via OpenAPI and frontend is more user friendly + +Warning - two breaking changes to OpenAPI: +* Handling of ROIs is through `/config/roi` path only for both circle and box ROIs, path in `/roi` are no longer accessible +* `broker_status` structure introduced in 1.0.0-rc.28 has member `message` and not `error_message` to allow +handling info/warning messages as well + +### 1.0.0-rc.28 +* jfjoch_broker: save error message for initialization and data collection and provide these with OpenAPI +* jfjoch_broker: fixed issue when in error state, response to /wait_till_done was not complaint to OpenAPI specs +* jfjoch_test: remove header that failed when CUDA is absent during compilation +* frontend: add soft trigger button in data collection tab +* frontend: show error message when in error state +* CMake: add option to force compilation without CUDA (-DJFJOCH_USE_CUDA=OFF) + +### 1.0.0-rc.27 +* jfjoch_broker: add option to select electron source in instrument metadata, adapt wavelength calculation +* jfjoch_broker: update pistache web server version +* jfjoch_writer: minor changes to republish logic +* Improvements to documentation + +### 1.0.0-rc.26 +* jfjoch_broker: implement ZeroMQ stream for image metadata information +* jfjoch_broker: refactor ZeroMQ stream for preview: start/end messages always sent +* jfjoch_broker: add crystal lattice plots +* jfjoch_broker: remove empty bins from the plots +* jfjoch_broker: Fix bugs in ModuleSummation and MXAnalyzer for CPU "long" summation +* jfjoch_broker: Fix bug when mean background estimation / indexing rate where affected by previous experiment +* jfjoch_writer: fix missing "-w" parameter +* jfjoch_writer: temporary files have ".tmp" suffix +* jfjoch_writer: refactor logic for watermarks +* jfjoch_writer: report on internal FIFO utilization +* jfjoch_writer: clean-up naming for azimuthal integration and background estimate +* jfjoch_writer: write final background estimate and indexing rate in the master file +* tools/: remove unnecessary tools, make naming consistent +* CBOR: Add indexing rate and background estimate to end message +* CBOR: Clean-up documentation + +### 1.0.0-rc.25 + +* Updates to documentation +* License set to GPLv3 / OHL-S +* Fix bug in DiffractionExperiment::GetDefaultPlotBinning() - resulting in division by 0 if image time longer than 500ms +* Add information on JUNGFRAU conversion and geometry transformation to CBOR and HDF5 + +### 1.0.0-rc.24 + +New FPGA functionality: +* EIGER supports 8, 16 and 32-bit data input (for 8-bit mode at half performance; for 32-bit "real" depth is 23-bit + 1-bit signed) +* Output possible to 8, 16 and 32-bit data +* Threshold is applied before summation +* Pixel mask can be applied on FPGA +* Mark pixels with ADC content = 0 as bad pixels +* FPGA stores semantic version information (access via /sys/class/misc/jfjoch.../version) + +New software functionality: +* Long summation (above 256 frames) done on CPU +* Mechanism to save arbitrary data to HDF5 file +* ZeroMQ preview has option to send start message +* Rework pixel mask + add statistics displayed in web interface + +Bug fixes: +* Web frontend: Update preview image automatically during data acquisition +* jfjoch_broker: Error handling if CUDA driver is not installed +* jfjoch_broker: Correctly update progress during pedestal +* jfjoch_broker: Provide proper error when uploaded file is not a proper TIFF +* jfjoch_action_test: enable HLS simulation + +Documentation improvement and placement in a dedicated directory \ No newline at end of file diff --git a/_sources/CPU_DATA_ANALYSIS.md.txt b/_sources/CPU_DATA_ANALYSIS.md.txt new file mode 100644 index 00000000..84994c57 --- /dev/null +++ b/_sources/CPU_DATA_ANALYSIS.md.txt @@ -0,0 +1,46 @@ +# Algorithms for data analysis + +## Azimuthal integration +2D azimuthal integration is implemented with a histogram-based algorithm, without split pixels. +Solid angle and polarization corrections are available. + +## Spot finding +Spot finding is implemented with multiple thresholds, rejecting spots based on: + +* signal-to-noise ration of 31x31 pixel rectangle around the spot, +* pixel intensity, +* spot resolution, +* number of pixels. + +Finding strong pixels is currently implemented on CPU and FPGA. +Combining strong pixels into spots is done with a Connected-component labeling (CCL) algorithm by Arthur Hennequin and coworkers, developed for CERN high-energy physics applications. + +## Indexing +Two indexing algorithms are implemented: +* Fast feedback indexer: Algorithm developed by Hans-Christian Stadler (PSI), based on TORO method; requires providing approximate unit cell; implemented on GPUs +* FFT indexing: implementation on classical M. Rossmann's FFT algorithm; doesn't require known unit cell; implemented on both GPUs (with CuFFT) and CPUs (with FFTW) + +Both algorithms share the same refinement routine with the least trimmed squares procedure, see TORO papers for details. + +## Lattice search +If the user provides the space group number in the measurement start call, lattice symmetry is taken for granted for the further refinement. + +Otherwise, Jungfraujoch will search for an optimal Bravais lattice. First it performs Niggli reduction and calculates G6 metric tensor, +using the routine implemented in the Gemmi library. Next, it goes through Niggli classes and selects the highest symmetry one, according to +[Table 3.1.3.1](https://onlinelibrary.wiley.com/iucr/itc/Ac/ch3o1v0001/table3o1o3o1/) by P. M. de Wolff +in the International Tables for Crystallography (2016). Vol. A. It is assumed that the lattice is matching Niggli class +if distance is within 3% difference and angles are within three deg. tolerance. Niggli class 43 (mI) is not implemented. + +Note: In case of special cases, where no lattice search is expected, it is necessary to set the space group number as 1 (P1). + +## Geometry refinement +Geometry refinement is done with the non-linear least squares procedure. +Refinement optimizes crystal lattice and beam center in a single run. +Solution is implemented with Google Ceres solver, running on CPU. +For higher symmetry space groups, refinement imposes constraints on the equality of cell lengths and 90/120 deg. angles. + +## Bragg integration +Integration is implemented with pure summation (no profile fitting), using a 3-circle method from CrystFEL. +Bragg spot predictions are calculated based on a distance from the Ewald sphere, with no explicit use of bandwidth or mosaicity. +Maximum distance is estimated as twice of the profile radius. Profile radius is calculated as a mean of distance from the Ewald sphere of indexed spots. +Systematic absences are implemented for all systems excluding R-centering. \ No newline at end of file diff --git a/_sources/DEPLOYMENT.md.txt b/_sources/DEPLOYMENT.md.txt new file mode 100644 index 00000000..fb91982c --- /dev/null +++ b/_sources/DEPLOYMENT.md.txt @@ -0,0 +1,159 @@ +# Deployment + +To deploy Jungfraujoch, one needs to follow four steps: + +1. Install main Jungfraujoch code and frontend web interface +2. Flash the U55C FPGA card with a proper image and install Linux kernel driver +3. Install Jungfraujoch writer +4. Install Python OpenAPI client + +Installation procedure depend a lot on the operating system. For RedHat Enterprise Linux 8, Rocky 8, or compatible +installation can be done with prebuilt RPMs and is relatively straightforward. For other systems one needs to build +software from source. Both ways will be presented. + + +## Install main Jungfraujoch code and frontend web interface + +On RHEL 8 systems there is a `jfjoch--1.el8.x86_64.rpm` that needs to be installed and contains all the necessary software and web interface. + +On other OSes one needs to compile Jungfraujoch from source (from the repo directory): +``` +$ mkdir build +$ cd build +$ cmake .. -DCMAKE_INSTALL_PREFIX= +$ make +$ sudo make install +``` +For manual installation, we recommend to use non-standard directory (like `/opt/jfjoch`), to facilitate upgrades and removal. +For DKMS to manage kernel module sources it is necessary to copy driver sources to `/usr/src/jfjoch-` directory. This requires extra flag in cmake `-DJFJOCH_INSTALL_DRIVER_SOURCE=ON`. + +Frontend web user interface has to be built separately with: +``` +$ cd build +$ make frontend +``` +Frontend files (.html and .js) will be placed in `frontend/dist` (outside of `build/` directory!) and has to be copied to a general location, e.g. `/usr/local/jfjoch/frontend` or `/opt/jfjoch/frotend`. + +## Flash the U55C FPGA card with a proper image and install Linux kernel driver. + +### Firmware flashing +1. Check that the card is detected by OS with "lspci |grep Xilinx" and check the PCIe bus/device/function (BDF) number, `11:00.0` in this case: +``` +$ lspci |grep Xilinx +23:00.0 Processing accelerators: Xilinx Corporation Device 3450 (rev 2) +``` +Note the device number `3450` that identifies Jungfraujoch device (Jungfraujoch pass is 3450 m above sea level) and `rev 2` identifying release of the firmware. + +2. Check the speed of the card, that it is detected as PCIe Gen4x8 device (needs to be done as root, otherwise configuration details are not given): +``` +$ sudo lspci -vv -s +23:00.0 Processing accelerators: Xilinx Corporation Device 3450 +(...) +LnkSta: Speed 16GT/s (ok), Width x8 (ok) +(...) +``` + +3. Download the MCS image from release files or build it using Vivado (WARNING! building time can be about 8 hours and doesn't allways reach correct timing). +4. Flash the card with `xbflash.qspi` tool (part of Jungfraujoch). For fresh card use: +``` +sudo xbflash.qspi --primary --card --bar-offset 0x1f06000 +``` +For card that was already flashed with Jungfraujoch images: + +``` +sudo xbflash.qspi --primary --card +``` +It is necessary to confirm the operation by pressing `Y` key or one can add `--force` option to avoid confirmation. +It is safe to run multiple flashing processes in parallel for different cards, for example in separate screen sessions. + +5. Cold reboot: +``` +sudo ipmitool chassis power cycle +``` + +### Install PCIe driver + +For first run it is though recommended to try the driver without installing to the kernel directory: +``` +$ cd fpga/pcie_driver +$ make +$ sudo insmod jfjoch.ko +``` + +Check with `dmesg` that the device was properly found: +``` +$ dmesg |grep jfjoch +[ 431.624933] jfjoch 0000:23:00.0: enabling device (0140 -> 0142) +[ 431.919147] misc jfjoch0: Jungfraujoch FPGA loaded with FW build: 5610030a +``` + +If things work, it is recommended to install the driver with DKMS, so it is rebuilt for kernel updates. +On RHEL 8 you can install prebuilt RPM provided in the Gitlab package registry. On other systems follow procedure in +[PCIe driver](FPGA_PCIE_DRIVER.md). + +NOTE: Driver installation procedure on non-RHEL 8 systems is not well understood/optimized at the moment. + +NOTE: In case driver is included in the init RAM-disk image, it is necessary to rebuild the RAM-disk if driver is updated: +``` +$ sudo dracut -f +``` +### Configure network +Configure switch according to [FPGA network guide](FPGA_NETWORK.md) - specifically set manual speed and turn off auto-negotiation +for the port used to connect U55C card and connect card to switch. + +### Running Jungfraujoch software +Main Jungfraujoch service is called `jfjoch_broker`. It is responsible for handling data from FPGAs, doing processing, analysis, compression and sending images on ZeroMQ output. +It is recommended to run the service as `systemd` service. + +`jfjoch_broker` takes two parameters: JSON configuration file and HTTP port (default is 5232). +Example JSON files are placed in `etc/` folder. JSON file format is also explained in the OpenAPI definition, as `jfjoch_settings` data structure. + +When running the service can be accessed via HTTP interface from a web browser for configuration and monitoring. + +To prepare the configuration file one also needs to reference calibration files: gain files for PSI JUNGFRAU and trim-bit files for PSI EIGER. +These need to be obtained from the PSI Detector Group. + +### Card verification + +To test that FPGA board is working properly without access to a JUNGFRAU detector, you can use `jfjoch_fpga_test` tool. +For example to simulate 10M pixel system with 4 FPGA cards and 200k images on a 2 CPU system with 2 GPUs: +``` +jfjoch_fpga_test ~/nextgendcu/ -m20 -s4 -i 200000 -Pn2g2 +``` +Or 1M pixel system with one FPGA card: +``` +jfjoch_fpga_test ~/nextgendcu/ -m2 -s1 -i 200000 +``` + +## Install Jungfraujoch writer +Jungfraujoch writer is an additional service, that can connect to `jfjoch_broker` ZeroMQ interface and writes files according to NeXus/NXmx HDF5 standard. + +At the moment it is better to have a separate machine, with access to distributed file system, for writing images. + +Writer can be installed with a dedicated RPM file or compiled from source. For compilation, you can use the following commands: +``` +mkdir build +cd build +cmake -DJFJOCH_WRITER_ONLY=ON -DCMAKE_INSTALL_PREFIX= .. +make jfjoch +``` + +## Install Jungfraujoch image viewer +Jungfraujoch viewer is X-ray diffraction image viewer, that is optimized to open Jungfraujoch HDF5 files. + +The viewer is a Qt application and it requires recent version of the library, therefore it is an optional dependency. + +To include it in the building of Jungfraujoch use `-DJFJOCH_VIEWER_BUILD=ON` directive for CMake: +``` +mkdir build +cd build +cmake -DJFJOCH_VIEWER_BUILD=ON -DCMAKE_INSTALL_PREFIX= .. +make jfjoch +``` + + +## Install Jungfraujoch Python client +Use pip: +```shell +pip install jfjoch-client +``` \ No newline at end of file diff --git a/_sources/DETECTORS.md.txt b/_sources/DETECTORS.md.txt new file mode 100644 index 00000000..4e817fe3 --- /dev/null +++ b/_sources/DETECTORS.md.txt @@ -0,0 +1,13 @@ +# Supported detectors + +## PSI detectors +Jungfraujoch supports PSI JUNGFRAU and PSI EIGER detectors. Jungfruajoch controls the detector via statically compiled `slsDetectorPackage` into its source code. +It is important that detector firmware has to match `slsDetectorPackage` version used in Jungfraujoch (8.0.2 at the moment). +See [PSI Detector group website](https://www.psi.ch/en/lxn/software-releases) for details. + +# DECTRIS detectors + +Jungfraujoch can be used with DECTRIS detectors, as a data analysis tool. +In this solution Jungfraujoch controls the Detector Control Unit (DCU) of the detector, and handles output data stream of the DCU. +This mode, called "lite" mode, doesn't use FPGA boards, but mostly CPUs and GPUs for indexing. +The mode is currently experimental and intended for low data rates (100 Hz). diff --git a/_sources/DETECTOR_GEOMETRY.md.txt b/_sources/DETECTOR_GEOMETRY.md.txt new file mode 100644 index 00000000..15534556 --- /dev/null +++ b/_sources/DETECTOR_GEOMETRY.md.txt @@ -0,0 +1,24 @@ +# Detector geometry + +At the moment Jungfraujoch supports solely flat detectors. The default option is to place modules in their actual location +vs. detector frame. It is not recommended to place detector modules stacked. + +The simplest case is detector perpendicular to the beam. In this case it is enough to provide beam center, detector distance +and wavelength. + +For more complex case, one can provide tilt of the detector rotation in PyFAI convention. +This convention uses Point Of Nominal Interaction (PONI) definition. Beam X and Y would correspond to the location on the detector, +where beam from the sample is perpendicular to the detector surface and not to the actual direct beam location. Then tilt of the detector +is defined with three rotation angles: `rot1` (rotating detector right), `rot2` (rotating detector downwards), `rot3` (rotating detector clockwise). +See [PyFAI documentation](https://pyfai.readthedocs.io/en/stable/) for more details. + +## Macromolecular crystallography convention for the vertical direction +One place of confusion is the convention to have point (0,0) of the detector in the top left corner of the detector, +with Y values increasing downwards. This is also consistent with computer image formats. + +However, other techniques (as well as internal operation of PSI X-ray detectors) might follow convention, for point (0,0) +being in the bottom left corner and Y values increasing upwards. Such a convention is used, for example, by PyFAI. + +In general, convention is controlled in Jungfraujoch with a setting in the JSON configuration file, which allows mirroring detector in Y. + +Extra care has to be taken by the user to ensure that no errors are made. \ No newline at end of file diff --git a/_sources/FPGA.md.txt b/_sources/FPGA.md.txt new file mode 100644 index 00000000..61a4fcc7 --- /dev/null +++ b/_sources/FPGA.md.txt @@ -0,0 +1,81 @@ +# FPGA smartNIC + +See separate document for [installation instructions](DEPLOYMENT.md). + +## Hardware +Currently supported FPGA is only **Xilinx Alveo U55C**. + +See AMD/Xilinx webpage for [card user guide (UG1469)](https://docs.xilinx.com/r/en-US/ug1469-alveo-u55c). +According to the user guide: +``` +Alveo data center accelerator cards are designed to be installed into a data center server, where controlled air flow provides direct cooling. +``` + +Card needs to be placed in PCI Express (PCIe) Gen4 x8 slot, though mechanically slot has to accommodate x16 card. +There is no need to connect additional power cable, as power of the card is not exceeding 75 W load available from PCIe edge connector. +Current power estimation is about 30 W when idle and 45 W in operation. The card has built-in protection, which will cut power to the card if HBM temperature is above 120°C. + +Two variants of the card are available: +* `100g` - this variant operates one port in 100 Gbit/s mode and should be used when connecting detector via a switch. +* `8x10g` - this variant operates both QSFP ports at 4x10 Gbit/s. QSFP+ (40 Gbit/s) transceivers and MTO/MTP harness cables +are necessary. It is designed for detector directly connected to the Jungfraujoch server, without switch. + +See [network documentation](FPGA_NETWORK.md) for details of network. + +## Building firmware +Xilinx Vivado version has to precisely match version described in [the system requirements](../README.md. +only when `vivado` and `vitis_hls` are detected in the path. + +### Xilinx Vivado +The following procedures require having AMD (Xilinx) Vivado and Vitis HLS toolsets version **2022.2** installed on the machine. +Due to the nature of TCL scripts used to generate board designs Vivado version has to exactly match one provided above - +specifically newer versions of Vivado will not work. + +In additional to Intellectual Property (IP) cores included in Vivado, two additional licenses are necessary: +* Non-cost license for Ultrascale+ 100G core has to be requested from AMD/Xilinx website, see [Xilinx website](https://www.xilinx.com/products/intellectual-property/cmac_usplus.html), to build `100g` design. +* Paid 10G/25G Subsystem for Ultrascale+ to build `8x10g` design. +PSI received non-cost licenses from Xilinx University Program for the latter cores. Therefore, usage of bitstreams +generated by PSI continuous integration pipeline for `8x10g` is only allowed for non-commercial use. +### HLS compilation +Make HLS routines: +``` +mkdir build +cd build +cmake .. +make hls +``` + +### Synthesis +Create PCIe `100g` bitstream with the following command: +``` +mkdir build +cd build +cmake .. +make pcie_100g +``` +and `8x10g`: +``` +mkdir build +cd build +cmake .. +make pcie_8x10g +``` +### When Vivado is not present + +During CMake execution, the following executables: `vivado` and `vitis_hls` must be present in the path. +If not, build targets will not be generated, and such or similar error message will show up: +``` +$ make pcie_100g +make: *** No rule to make target 'pcie_100g'. Stop. +``` + +### Gitlab CI +If Gitlab CI is properly set-up, firmware will be automatically built for every commit that starts with FPGA. +Built firmware should be downloaded as MCS files. + +### Frame generator + +Jungfraujoch card is equipped with frame generator. It allows to simulate JUNGFRAU detector without having access to such system. +It is placed in parallel to Ethernet MAC - so it is placed before the network stack and before any processing happening on the card. +In the future a redirection will be possible to send the simulated stream through the 100G TX network link. +Frame generator is written in HLS and controlled with AXI-Lite. \ No newline at end of file diff --git a/_sources/FPGA_DATA_ANALYSIS.md.txt b/_sources/FPGA_DATA_ANALYSIS.md.txt new file mode 100644 index 00000000..493ca232 --- /dev/null +++ b/_sources/FPGA_DATA_ANALYSIS.md.txt @@ -0,0 +1,74 @@ +# FPGA data analysis + +Jungfraujoch FPGA design has incorporated X-ray diffraction image analysis capabilities. + +## Pixel mask +Pixels can be masked. For each module a 32-bit map of pixels is loaded to FPGA, with non-zero value meaning masked pixels. +According to this map, pixels will be assigned a special value (minimum number for signed types and maximum number for non-signed types) +and will be excluded from a subsequent analysis. + +## ADU histogram +Before conversion to photons/energy, an ADU histogram can be calculated for a module. This allows to preserve some signature +of unconverted values. This is done on a module-basis and works with bins with 32 ADU width. + +For EIGER this can be used as just a histogram procedure. + +## JUNGFRAU conversion +For JUNGFRAU module images are converted from ADUs to energy value and divided by a given number to keV units. +Result of the operation is rounded to integers. + +## Pixel thresholding +Pixel range can be specified. +Pixels below a minimum threshold will be assigned zero. +Pixels above a maximum threshold will be assigned saturated pixel value (the largest number for a given bit-width and sign type). +This is specifically designed to operate on unsummed frames, so frame-specific parameters (overload/noise) can be handled. + +## Frame summation +Frames can be summed together (on a per-module basis) in Jungfraujoch, with a limit of 256 frames added together. + +## Azimuthal integration +To implement azimuthal integration, FPGA is able to sum pixels based on a provided integration map and per-pixel corrections. +This way Jungfraujoch implements azimuthal integration with solid angle and polarization corrections. +Corrections were implemented according to formulas developed by [Jensen et al. (J. Synchr. Rad., 29, 1420-1428, 2022)](https://journals.iucr.org/s/issues/2022/06/00/fv5148/). + +Given FPGA limitations, split-pixels cannot be implemented and number of bins is limited as 1024 per detector module. +This way 2D azimuthal integration, as needed for example by SAS-TT, cannot be currently implemented with the FPGA card and needs to be done on a CPU. +One needs to be careful with per-pixel corrections - their acceptable range is constrained by 16-bit pixed point integer implementation +and is tuned for standard SAXS/WAXS range. + +## Spot finding +Jungfraujoch FPGA implements a built-in spot finder. Spot finder allows to apply the following criteria for finding strong pixels: +1. Resolution criterion - pixels only within a provided resolution range can be considered as strong pixels (calculating resolution map needs to happen on CPU before data collection run). +2. Bad pixels - pixels marked as bad, as well as chip edges and module edges are excluded from spot finding, +3. Overloads - pixels marked as overloads on JUNGFRAU are always included in the strong pixel output, but are excluded for signal-to-noise ratio calculation, +4. Pixel value - pixels above certain threshold value can be marked as strong, +5. Signal-to-noise (SNR) ratio - pixels with SNR above a threshold can be marked as strong, +6. Connected pixels - strong pixels can be discarded if they are "alone", so their 8 directly neighboring pixels are not counted as strong pixels. + +While besides bad pixels criterion, all the above are optional (can be turned off), only pixels that fulfill all enabled criteria are selected as strong pixels. + +### SNR ratio calculation +Signal-to-noise ratio is calculated for a rectangular area. +In horizontal direction the area is fixed - line of 1024 pixels is divided into 32 areas each of 32 pixels. +This is dictated by the data flow within the FPGA. +In vertical direction the area is flexible - it is 15 lines above and below of the given pixel. +Given very large box size, approximation are made, for example that `N ≈ N-1` in calculating standard deviation. + +## Region-of-interest (ROI) integration +Each pixel in a module can be assigned to one of 64 ROIs. For each ROIs, sum, sum of squares, max count, and number of valid pixels will be calculated. +Jungfraujoch also calculates X and Y values weighted by pixel values, though this feature is not properly tested at the moment and not integrated in downstream analysis. + +## Pixel statisitics +The following statistics are collected for each module: +* Number of masked pixels +* Number of saturated pixels (excl.masked) +* Number of error pixels (excl. masked) +* Sum of valid pixels in the module +* Minimum value of valid pixels in the module +* Maximum value of valid pixels in the module +Valid pixels are not masked, not saturated, not error pixels. + +## Square root compression +Jungfraujoch FPGA includes lossy compression preserving counting statistic properties of X-ray image, while reducing bit width of an image. +Scheme was described in [Wakonig et al., J. Appl. Cryst., 53, 574-586, 2020](https://doi.org/10.1107/S1600576720001776). +Pixel value `X` is replaced with `sqrt(N*X)`, where `N` is integer constant in range 1 to 16. diff --git a/_sources/FPGA_DESIGN.md.txt b/_sources/FPGA_DESIGN.md.txt new file mode 100644 index 00000000..56cd1c19 --- /dev/null +++ b/_sources/FPGA_DESIGN.md.txt @@ -0,0 +1,21 @@ +# FPGA data flow + +The following steps are performed on FPGA (in the order of operation): + +1. UDP header decoding +2. SLS detector header decoding +3. State machine that controls data acquisition (start/stop/cancel) +4. High-bandwidth memory cache to buffer network packets and reorder them to form full modules +5. ADU histogram for JUNGFRAU +6. Mask pixels from missing packets with special value +7. Reorder lines for EIGER to form a proper module +8. Mask pixels based on provided pixel mask +9. JUNGFRAU conversion with gain and pedestal corrections +10. Threshold to zero pixels below certain count value +11. Integration according to predefined map (e.g., 1D azimuthal integration) +12. Spot finding +13. ROI calculation +14. Image lossy compression using N*sqrt(pixel) values +15. Send images, analysis results and metadata to host memory via PCI Express + +Each step has dedicated core, written in the high-level synthesis. Exact operation of cores for data analysis is explained in dedicated [document](FPGA_DATA_ANALYSIS.md). \ No newline at end of file diff --git a/_sources/FPGA_LICENSE.md.txt b/_sources/FPGA_LICENSE.md.txt new file mode 100644 index 00000000..540a9605 --- /dev/null +++ b/_sources/FPGA_LICENSE.md.txt @@ -0,0 +1,295 @@ +# FPGA license + +FPGA components of Jungfraujoch are licensed using OHL-S license. See full text below. +The license is equivalent of GNU Public License with adaptations for hardware. +See [OHL webpage](https://ohwr.org/project/cernohl/-/wikis/Documents/CERN-OHL-version-2) for details and FAQs. + +## CERN Open Hardware Licence Version 2 - Strongly Reciprocal + + +Preamble + +CERN has developed this licence to promote collaboration among +hardware designers and to provide a legal tool which supports the +freedom to use, study, modify, share and distribute hardware designs +and products based on those designs. Version 2 of the CERN Open +Hardware Licence comes in three variants: CERN-OHL-P (permissive); and +two reciprocal licences: CERN-OHL-W (weakly reciprocal) and this +licence, CERN-OHL-S (strongly reciprocal). + +The CERN-OHL-S is copyright CERN 2020. Anyone is welcome to use it, in +unmodified form only. + +Use of this Licence does not imply any endorsement by CERN of any +Licensor or their designs nor does it imply any involvement by CERN in +their development. + + +1 Definitions + +1.1 'Licence' means this CERN-OHL-S. + +1.2 'Compatible Licence' means + +a) any earlier version of the CERN Open Hardware licence, or + +b) any version of the CERN-OHL-S, or + +c) any licence which permits You to treat the Source to which + it applies as licensed under CERN-OHL-S provided that on + Conveyance of any such Source, or any associated Product You + treat the Source in question as being licensed under + CERN-OHL-S. + +1.3 'Source' means information such as design materials or digital +code which can be applied to Make or test a Product or to +prepare a Product for use, Conveyance or sale, regardless of its +medium or how it is expressed. It may include Notices. + +1.4 'Covered Source' means Source that is explicitly made available +under this Licence. + +1.5 'Product' means any device, component, work or physical object, +whether in finished or intermediate form, arising from the use, +application or processing of Covered Source. + +1.6 'Make' means to create or configure something, whether by +manufacture, assembly, compiling, loading or applying Covered +Source or another Product or otherwise. + +1.7 'Available Component' means any part, sub-assembly, library or +code which: + +a) is licensed to You as Complete Source under a Compatible + Licence; or + +b) is available, at the time a Product or the Source containing + it is first Conveyed, to You and any other prospective + licensees + +i) as a physical part with sufficient rights and + information (including any configuration and + programming files and information about its + characteristics and interfaces) to enable it either to + be Made itself, or to be sourced and used to Make the + Product; or +ii) as part of the normal distribution of a tool used to + design or Make the Product. + +1.8 'Complete Source' means the set of all Source necessary to Make +a Product, in the preferred form for making modifications, +including necessary installation and interfacing information +both for the Product, and for any included Available Components. +If the format is proprietary, it must also be made available in +a format (if the proprietary tool can create it) which is +viewable with a tool available to potential licensees and +licensed under a licence approved by the Free Software +Foundation or the Open Source Initiative. Complete Source need +not include the Source of any Available Component, provided that +You include in the Complete Source sufficient information to +enable a recipient to Make or source and use the Available +Component to Make the Product. + +1.9 'Source Location' means a location where a Licensor has placed +Covered Source, and which that Licensor reasonably believes will +remain easily accessible for at least three years for anyone to +obtain a digital copy. + +1.10 'Notice' means copyright, acknowledgement and trademark notices, +Source Location references, modification notices (subsection +3.3(b)) and all notices that refer to this Licence and to the +disclaimer of warranties that are included in the Covered +Source. + +1.11 'Licensee' or 'You' means any person exercising rights under +this Licence. + +1.12 'Licensor' means a natural or legal person who creates or +modifies Covered Source. A person may be a Licensee and a +Licensor at the same time. + +1.13 'Convey' means to communicate to the public or distribute. + + +2 Applicability + +2.1 This Licence governs the use, copying, modification, Conveying +of Covered Source and Products, and the Making of Products. By +exercising any right granted under this Licence, You irrevocably +accept these terms and conditions. + +2.2 This Licence is granted by the Licensor directly to You, and +shall apply worldwide and without limitation in time. + +2.3 You shall not attempt to restrict by contract or otherwise the +rights granted under this Licence to other Licensees. + +2.4 This Licence is not intended to restrict fair use, fair dealing, +or any other similar right. + + +3 Copying, Modifying and Conveying Covered Source + +3.1 You may copy and Convey verbatim copies of Covered Source, in +any medium, provided You retain all Notices. + +3.2 You may modify Covered Source, other than Notices, provided that +You irrevocably undertake to make that modified Covered Source +available from a Source Location should You Convey a Product in +circumstances where the recipient does not otherwise receive a +copy of the modified Covered Source. In each case subsection 3.3 +shall apply. + + You may only delete Notices if they are no longer applicable to + the corresponding Covered Source as modified by You and You may + add additional Notices applicable to Your modifications. + Including Covered Source in a larger work is modifying the + Covered Source, and the larger work becomes modified Covered + Source. + +3.3 You may Convey modified Covered Source (with the effect that You +shall also become a Licensor) provided that You: + +a) retain Notices as required in subsection 3.2; + +b) add a Notice to the modified Covered Source stating that You + have modified it, with the date and brief description of how + You have modified it; + +c) add a Source Location Notice for the modified Covered Source + if You Convey in circumstances where the recipient does not + otherwise receive a copy of the modified Covered Source; and + +d) license the modified Covered Source under the terms and + conditions of this Licence (or, as set out in subsection + 8.3, a later version, if permitted by the licence of the + original Covered Source). Such modified Covered Source must + be licensed as a whole, but excluding Available Components + contained in it, which remain licensed under their own + applicable licences. + + +4 Making and Conveying Products + +You may Make Products, and/or Convey them, provided that You either +provide each recipient with a copy of the Complete Source or ensure +that each recipient is notified of the Source Location of the Complete +Source. That Complete Source is Covered Source, and You must +accordingly satisfy Your obligations set out in subsection 3.3. If +specified in a Notice, the Product must visibly and securely display +the Source Location on it or its packaging or documentation in the +manner specified in that Notice. + + +5 Research and Development + +You may Convey Covered Source, modified Covered Source or Products to +a legal entity carrying out development, testing or quality assurance +work on Your behalf provided that the work is performed on terms which +prevent the entity from both using the Source or Products for its own +internal purposes and Conveying the Source or Products or any +modifications to them to any person other than You. Any modifications +made by the entity shall be deemed to be made by You pursuant to +subsection 3.2. + + +6 DISCLAIMER AND LIABILITY + +6.1 DISCLAIMER OF WARRANTY -- The Covered Source and any Products +are provided 'as is' and any express or implied warranties, +including, but not limited to, implied warranties of +merchantability, of satisfactory quality, non-infringement of +third party rights, and fitness for a particular purpose or use +are disclaimed in respect of any Source or Product to the +maximum extent permitted by law. The Licensor makes no +representation that any Source or Product does not or will not +infringe any patent, copyright, trade secret or other +proprietary right. The entire risk as to the use, quality, and +performance of any Source or Product shall be with You and not +the Licensor. This disclaimer of warranty is an essential part +of this Licence and a condition for the grant of any rights +granted under this Licence. + +6.2 EXCLUSION AND LIMITATION OF LIABILITY -- The Licensor shall, to +the maximum extent permitted by law, have no liability for +direct, indirect, special, incidental, consequential, exemplary, +punitive or other damages of any character including, without +limitation, procurement of substitute goods or services, loss of +use, data or profits, or business interruption, however caused +and on any theory of contract, warranty, tort (including +negligence), product liability or otherwise, arising in any way +in relation to the Covered Source, modified Covered Source +and/or the Making or Conveyance of a Product, even if advised of +the possibility of such damages, and You shall hold the +Licensor(s) free and harmless from any liability, costs, +damages, fees and expenses, including claims by third parties, +in relation to such use. + + +7 Patents + +7.1 Subject to the terms and conditions of this Licence, each +Licensor hereby grants to You a perpetual, worldwide, +non-exclusive, no-charge, royalty-free, irrevocable (except as +stated in subsections 7.2 and 8.4) patent licence to Make, have +Made, use, offer to sell, sell, import, and otherwise transfer +the Covered Source and Products, where such licence applies only +to those patent claims licensable by such Licensor that are +necessarily infringed by exercising rights under the Covered +Source as Conveyed by that Licensor. + +7.2 If You institute patent litigation against any entity (including +a cross-claim or counterclaim in a lawsuit) alleging that the +Covered Source or a Product constitutes direct or contributory +patent infringement, or You seek any declaration that a patent +licensed to You under this Licence is invalid or unenforceable +then any rights granted to You under this Licence shall +terminate as of the date such process is initiated. + + +8 General + +8.1 If any provisions of this Licence are or subsequently become +invalid or unenforceable for any reason, the remaining +provisions shall remain effective. + +8.2 You shall not use any of the name (including acronyms and +abbreviations), image, or logo by which the Licensor or CERN is +known, except where needed to comply with section 3, or where +the use is otherwise allowed by law. Any such permitted use +shall be factual and shall not be made so as to suggest any kind +of endorsement or implication of involvement by the Licensor or +its personnel. + +8.3 CERN may publish updated versions and variants of this Licence +which it considers to be in the spirit of this version, but may +differ in detail to address new problems or concerns. New +versions will be published with a unique version number and a +variant identifier specifying the variant. If the Licensor has +specified that a given variant applies to the Covered Source +without specifying a version, You may treat that Covered Source +as being released under any version of the CERN-OHL with that +variant. If no variant is specified, the Covered Source shall be +treated as being released under CERN-OHL-S. The Licensor may +also specify that the Covered Source is subject to a specific +version of the CERN-OHL or any later version in which case You +may apply this or any later version of CERN-OHL with the same +variant identifier published by CERN. + +8.4 This Licence shall terminate with immediate effect if You fail +to comply with any of its terms and conditions. + +8.5 However, if You cease all breaches of this Licence, then Your +Licence from any Licensor is reinstated unless such Licensor has +terminated this Licence by giving You, while You remain in +breach, a notice specifying the breach and requiring You to cure +it within 30 days, and You have failed to come into compliance +in all material respects by the end of the 30 day period. Should +You repeat the breach after receipt of a cure notice and +subsequent reinstatement, this Licence will terminate +immediately and permanently. Section 6 shall continue to apply +after any termination. + +8.6 This Licence shall not be enforceable except by a Licensor +acting as such, and third party beneficiary rights are +specifically excluded. \ No newline at end of file diff --git a/_sources/FPGA_NETWORK.md.txt b/_sources/FPGA_NETWORK.md.txt new file mode 100644 index 00000000..cad5e8d4 --- /dev/null +++ b/_sources/FPGA_NETWORK.md.txt @@ -0,0 +1,39 @@ +# FPGA network + +The U55C card is equipped with two network connectors - QSFP0 is the upper port and QSFP1 is lower port (when PCIe connector is on the bottom). +The card FPGA design is offered in two variants `100g` and `8x10g`. These have different behavior regarding the network: + +`100g` this variant operates QSFP0 port in 100 Gbit/s mode and should be used when connecting detector via a **switch**. +QSFP28 transceivers are necessary. + +`8x10g` this variant operates both QSFP ports at 4x10 Gbit/s. QSFP+ (40 Gbit/s) transceivers and MTO/MTP harness cables + are necessary. It is designed for **detector directly connected** to the Jungfraujoch server, without switch. + +## Transceivers +AMD doesn't provide transceiver compatibility matrix for Alveo U55C. +In our experience operating the card we haven't seen issues with transceivers from various providers (FS.com, Mellanox, Finnisar). +We have also successfully operated card with correct direct attach cables instead of fiber optics. Given the card doesn't +support link training functionality of 100 Gbit/s ethernet, it could result in performance problems with copper cables, though we haven't +encountered such a situation. + +## Switch configuration +Special care has to be taken for switch operation, given the FPGA core doesn't support auto-negotiation. It is necessary to configure switch port +to fixed speed (100 Gbit/s or 10 Gbit/s) and to disable auto-negotiation. It is also necessary to enable jumbo frames (MTU of 9000). + +## Network LEDs +Each QSFP connector is equipped with green and orange LEDs. These LEDs are connected to Ethernet physical layer status port (rx_status). +LED on corresponds to having a physical connection to a switch/computer/detector on the other side of the network. +For 100 Gbit/s only green is used, for 8x10 Gbit/s green LEDs means all ports connected, orange LEDs at least one of the ports connected. + +## Network stack +Each Ethernet link has its own basic network stack. Functionality for Ethernet/ARP/IPv4/ICMP is therefore separately handled for each port. +Each link will get dedicated MAC address, and IPv4 addresses can be also assigned independently if needed. + +The card will send gratuitous ARP messages every 5 seconds to keep its entry in switch MAC table. +The card will also reply to ARP requests for its IP and to ICMP ping requests sent with the card IPv4 address. +The card won't respond to broadcast ICMP pings. + +Each link can be put in `direct` mode. In this case destination Ethernet MAC and IPv4 addresses are not enforced for incoming UDP packets. +This settings should be used for connecting detector modules directly to the FPGA card, so any detector module can be connected to any +10 Gbit/s link on the same card. Currently `direct` mode is turned OFF for `100g` design and ON for `8x10g` design. +This can be manually adjusted for each link. \ No newline at end of file diff --git a/_sources/FPGA_PCIE_DRIVER.md.txt b/_sources/FPGA_PCIE_DRIVER.md.txt new file mode 100644 index 00000000..743d7f24 --- /dev/null +++ b/_sources/FPGA_PCIE_DRIVER.md.txt @@ -0,0 +1,100 @@ +# FPGA PCIe driver + +## Compilation +To compile kernel module type: +``` +make +``` + +## Installation +To install kernel module, you need to have root permissions and run: +``` +sudo make install +``` + +## Loading driver into kernel +After installing the kernel driver, it should be possible to insert it into the kernel via: +``` +modprobe jfjoch +``` + +## Ownership of the character devices +By default, character devices `/dev/jfjoch` are owned by root (user/group) and are not accessible by others. +This means that `jfjoch_broker` must be running as superuser, which might not be optimal for security reasons in most cases. +The behavior can be changed by creating `udev` rules. Create a file called `/etc/udev/rules.d/99-jfjoch.rules` +with the following content: +``` +KERNEL=="jfjoch*" OWNER="" GROUP="" +``` +It is OK to provide only group, for example to make the devices accessible by group `jungfrau`: +``` +KERNEL=="jfjoch*" GROUP="jungfrau" +``` + +## DKMS +To avoid problems with updating the kernel, it is possible to use DKMS to autobuild Jungfraujoch kernel +module, when new kernel is installed. For RHEL 8 it is well tested to use the RPM module built automatically from Jungfraujoch source. +For other systems, it is necessary to follow the procedure below, though it is not well tested. + +This first requires to install DKMS - for RHEL it is available via EPEL repository: +``` +sudo dnf install dkms +``` +Then use script provided in the driver directory to copy driver code to DKMS directory: +``` +./install_dkms.sh +``` +If upgrading the driver, please first remove current driver from DKMS system: +``` +dkms remove jfjoch -v --all +``` + +## Driver parameters +Currently, there is one driver parameter `nbuffers`, that defines count of exchange buffers (see below). +This can be adjusted in the modprobe operation, for example: +``` +modprobe jfjoch nbuffers=1024 +``` + +## Exchange buffers +The parameter defines number of buffers used to exchange data between card and host application. +Each buffer can hold one detector module (1024x512) in 16-bit or 32-bit mode + associated processing results and metadata. +These buffers are used by both card-to-host and host-to-card operations. + +Buffers use special allocation, as they are continuous in physical address space, which helps the FPGA card to transfer all +data associated with detector module in two DMA transfers (one data, one metadata). +Useful buffer size is a bit more than 2 MiB, but given that kernel allocates physical memory in power of two, **4 MiB** is safe number for one buffer size. +Buffer can be mapped into user space, but performing `mmap` system call on the `/dev/jfjoch` character device. + +Buffer count can be adjusted by setting `nbuffers` parameter. There are two considerations for setting optimal value: +1. For card-to-host transfers, minimal value is roughly +` * `, +this way each thread can have enough data for operation. Default thread count for Jungfraujoch receiver is 64. +2. For host-to-card transfers, full detector calibration has to fit into memory and one buffer accommodates one calibration set for one module. +So minimal count is ` * (3 + 3 * )`. + +Based on both rules, optimal number is 512 buffers (2 GiB), though this can be adjusted for particular system and configuration. + +## Known problems +To avoid inconsistent behavior, this driver won't load if release number differs between the kernel driver and FPGA card. + +## CMake file +While CMake file is present in the driver directory, it is only for the purpose of proper detection of the files in CLion IDE. +It is not made for actual compilation of the kernel driver and should not be used for that purpose. + +## Character device access +For each FPGA device a character device is created called `/dev/jfjoch`. +When device is opened two operations are possible: +mmap() to map exchange buffers +ioctl() to communicate with the cards +Interfacing should be done through the JungfraujochDevice class in `fpga/host_library` directory. + +## Sysfs access +Certain performance counters can be read through sysfs mechanism in the kernel. +One needs to `cat` files in `/sys/class/misc/jfjoch/` directory. + +## RHEL 9.5+ issue +RedHat Enterprise Linux 9.5 backported modification to settings virtual memory flags from Linux kernel 6.3, while still operating kernel version 5.14. +It is complicated to come up with a single rule to select when newer functions should be used, so it works with RHEL 9.5+, +while still being compatible with other Linux distributions. It is even more complex given not all RHEL compatible distributions adopted the change at the same version. +For the moment the quick fix is to define an environment variable `HAVE_VM_FLAGS_SET` before making the kernel. diff --git a/_sources/FPGA_SETTINGS.md.txt b/_sources/FPGA_SETTINGS.md.txt new file mode 100644 index 00000000..b5e7bce0 --- /dev/null +++ b/_sources/FPGA_SETTINGS.md.txt @@ -0,0 +1,121 @@ +# FPGA advanced reference +## Register map +FPGA setup can be done via registers: + +| Address | Bits | Meaning | Mode | Notes | +|---------------------|------|------------------------------------------------------------------------------------------------|:-----|----------------------------------------------| +| 0x000000 - 0x00FFFF | | Reserved (in case using MicroBlaze in the future, this has to be reserved for internal memory) | | | +| 0x010000 | 32 | Action Control Register | | | +| | | Bit 0 - Action start | R/W | | +| | | Bit 1 - Action idle | R | | +| | | Bit 2 - Action cancel | R/W | cleared on reset or action start | +| | | Bit 3 - Clear network counters | R/W | cleared on reset | +| | | Bit 12:4 - Debug signals (see action_config.v for details) | R | | +| | | Bit 16 - AXI Mailbox interrupt 0 | R | | +| 0x010004 | 32 | Reserved | - | | +| 0x010008 | 32 | Reserved | - | | +| 0x01000C | 32 | GIT SHA1 | R | | +| 0x010010 | 32 | Reserved | R | | +| 0x010014 | 32 | Reserved | R | | +| 0x010018 | 32 | Jungfraujoch FPGA variant | R | | +| 0x01001C | 32 | Reserved | R | | +| 0x010020 | 32 | Max. number supported detector modules | R | constant | +| 0x010024 | 32 | Reserved | R | constant | +| 0x010028 | 64 | Pipeline stalls before writing to host memory | R | reset on action start | +| 0x010030 | 64 | Pipeline stalls before accessing HBM | R | reset on action start | +| 0x010038 | 32 | FIFO status (see action_config.v for details) | R | | +| 0x01003C | 32 | Size of single HBM channel in bytes (default value for the particular card) | R/W | should not be altered for standard operation | +| 0x010040 | 64 | Packets processed by the action | R | cleared on reset or action start | +| 0x010048 | 64 | Valid ethernet packets | R | cleared on reset | +| 0x010050 | 64 | Valid ICMP packets | R | cleared on reset | +| 0x010058 | 64 | Valid UDP packets | R | cleared on reset | +| 0x010060 | 64 | Valid detector packets processed by the card | R | cleared on reset | +| 0x010068 | 64 | Packets flagged as errors by CMAC | R | cleared on reset | +| 0x010070 | 64 | Pipeline stalls before data processing | R | reset on action start | +| 0x010078 | 64 | AXI-beats before accessing HBM | R | reset on action start | +| 0x010080 | 64 | AXI-beats before data processing | R | reset on action start | +| 0x010088 | 64 | AXI-beats before host writer | R | reset on action start | +| 0x010090 | 64 | Last encountered SwissFEL pulse ID | R | cleared on reset | +| 0x010100 | 32 | Spot finder photon count threshold | R/W | | +| 0x010104 | 32 | Spot finder signal-to-noise ratio threshold (single-precision float) | R/W | | +| 0x010200 | 64 | MAC address source for internal frame generator | R/W | network byte order | +| 0x010208 | 32 | IPv4 address source for internal frame generator | R/W | network byte order | +| 0x01020C | 32 | Number of detector modules (value minus one: 0 => 1 module, 1 => 2 modules, etc.) | R/W | | +| 0x010210 | 32 | Data collection mode | R/W | | +| | | Bit 0 - Conversion to photons | | | +| | | Bit 1 - Output extend to 32-bit | | | +| | | Bit 2 - Output is unsigned integer | | | +| | | Bit 3 - Use sq. root lossy compression | | | +| | | Bit 7 - JUNGFRAU fixed G1 mode | | | +| | | Bit 8 - Set to zero values below threshold | | | +| | | Bit 16:31 - Data collection ID (carried with completions) | | | +| 0x010214 | 32 | Photon energy in keV (single-precision float) | R/W | | +| 0x010218 | 32 | Number of frames expected in the data collection (defines termination condition) | R/W | | +| 0x01021C | 32 | Number of storage cells | R/W | | +| 0x010220 | 32 | Summation on card (value minus one: 0 => summation of 1, 1 => summation of 2, etc.) | R/W | | +| 0x010224 | 32 | Coefficient for sq. root compression (need to set bit in data collection mode to apply) | R/W | | +| 0x010225 | 32 | Threshold; set values below set to zero (need to set bit in data collection mode to apply) | R/W | | +| 0x030000 - 0x03FFFF | | AXI Mailbox for Work Request / Work Completion | | See Xilinx PG114 for register map | +| 0x040000 - 0x04FFFF | | QuadSPI flash | | See Xilinx PG153 for register map | +| 0x050000 - 0x05FFFF | | Interrupt controller | | See Xilinx PG099 for register map | +| 0x060000 - 0x06FFFF | | Load calibration (HLS) | | | +| 0x070000 - 0x07FFFF | | AXI Firewall | | See Xilinx PG293 for register map | +| 0x080000 - 0x08FFFF | | Frame generator (HLS) | | | +| 0x090000 - 0x09FFFF | | PCIe DMA control | | See Xilinx PG195 for register map | +| 0x0A0000 - 0x0AFFFF | | I2C clock generator | | See Xilinx PG195 for register map | +| 0x0C0000 - 0x0FFFFF | | Xilinx Card Management Solution Subsystem management subsystem | | See Xilinx PG348 for register map | +| 0x100000 - 0x10FFFF | | MAC 10G / CMAC 100G | | See Xilinx PG210/PG203 for register map | +| 0x110000 - 0x11FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x120000 - 0x12FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x130000 - 0x13FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x140000 - 0x14FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x150000 - 0x15FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x160000 - 0x16FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x170000 - 0x17FFFF | | MAC 10G | | See Xilinx PG210 for register map | +| 0x200000 - 0x20FFFF | | Eth/IPv4 network stack for interface #0 | | | +| 0x210000 - 0x21FFFF | | Eth/IPv4 network stack for interface #1 | | | +| 0x220000 - 0x22FFFF | | Eth/IPv4 network stack for interface #2 | | | +| 0x230000 - 0x23FFFF | | Eth/IPv4 network stack for interface #3 | | | +| 0x240000 - 0x24FFFF | | Eth/IPv4 network stack for interface #4 | | | +| 0x250000 - 0x25FFFF | | Eth/IPv4 network stack for interface #5 | | | +| 0x260000 - 0x26FFFF | | Eth/IPv4 network stack for interface #6 | | | +| 0x270000 - 0x27FFFF | | Eth/IPv4 network stack for interface #7 | | | +| 0x400000 - 0x47FFFF | 64 | Address table: decodes handles used by load_calibration and host_writer to DMA addresses | | | + +## AXI Mailbox + +AXI mailbox is used to send work request from host to action, and receive work completions. +Messages are exchanged through AXI Mailbox IP from Xilinx (see Xilinx PG114). + +Work request has the following structure: + +| Bit start | Bit end | Meaning | +|-----------|---------|----------------------------------------------------| +| 0 | 15 | Work request ID (handle) | + +Work completion has the following structure: + +| Bit start | Bit end | Meaning | +|-----------|---------|----------------------------------| +| 0 | 15 | Work request ID (handle) | +| | | Special values: | +| | | 65534 - start of data collection | +| | | 65535 - end of data collection | +| 15 | 31 | Data collection ID | + +## HBM memory + +| Interface number | Core | Meaning | +|------------------|------------------|---------------------------------------------| +| 0-1 | jf_conversion | Gain factor G0 | +| 2-3 | jf_conversion | Gain factor G1 | +| 4-5 | jf_conversion | Gain factor G2 | +| 6-7 | jf_conversion | Pedestal G0 | +| 8-9 | jf_conversion | Pedestal G1 | +| 10-11 | jf_conversion | Pedestal G2 | +| 12-13 | integration | Integration map | +| 14-15 | integration | Integration weights | +| 16-17 | spot_finder_mask | Spot finder resolution | +| 18-19 | roi_calc | ROI calculation | +| 20-21 | frame_generator | Frame generator | +| 22-27 | load_from_hbm | Frame summation | diff --git a/_sources/HARDWARE.md.txt b/_sources/HARDWARE.md.txt new file mode 100644 index 00000000..527c2844 --- /dev/null +++ b/_sources/HARDWARE.md.txt @@ -0,0 +1,55 @@ +# Hardware requirements +Operating Jungfraujoch requires the following: + +1. High performance server +2. FPGA board(s) installed in the server +3. (optionally) GPU boards +4. (optionally) 100G switch to connect FPGA and the detector + +Unfortunately, at the moment it is not possible to purchase server configuration from a major vendor that would include +AMD FPGA boards. Therefore, the two has to be purchases separately. This might have impact on the warranty for the hardware +and has to be clarified with the vendor. PSI only supports the system on the best effort basis and doesn't take any responsibility +for warranty limitations for operating FPGA boards in the server. Having said this - we didn't encounter any hardware issues so far. + +## High performance server +PSI is using HPE DL380 Gen11 servers are the moment to operate Jungfraujoch systems. However, this is because of general +preference for this vendor, there is no Jungfraujoch-specific reason to buy from this vendor. We do expect that system +from any other vendor with similar specification should work as well. + +At PSI, we use the following configuration of HPE DL380 Gen11 to operate 9M pixel detectors at 2 kHz is as follows: +* 2 x Intel Xeon 8558P +* 512 GB RAM +* 2 x Nvidia L4 GPU (for indexing) +* 1 x Nvidia Connect-X 6 200G ethernet/IB network (for outgoing traffic; this can be substituted according to facility needs) +* Copper 1G/10G network + +### PCI slots +When ordering the system it is important to ensure enough PCIe cards can be accommodated in the system. +In case of our system we need to put at least seven PCIe cards: 4 x FPGA, 2x GPU, 1x network + +Note - for FPGA x8 lane electrically/x16 lane mechanically PCIe slots are OK. + +## FPGA +Jungfraujoch is built for [AMD/Xilinx U55C](https://www.amd.com/en/products/accelerators/alveo/u55c/a-u55c-p00g-pq-g.html) +(A-U55C-P00G-PQ-G) card. Other FPGA cards are currently not supported. + +Single U55C card supports roughly 5 detector modules (2.5M pixels) at 2 kHz and 10 detector modules (5M pixels) at 1 kHz. +For detectors operating at lower frame rates (e.g., 100 Hz) larger detectors can be supported by a single U55C card, though it requires +using TX delay functionality in the detector. + +## GPUs +Operating fast-feedback indexer code requires operation of a graphic processing unit from Nvidia. +For practical reasons, i.e. power consumption and cost, we choose inference grade card Nvidia L4. +In the past we have also used T4 cards. So, in principle any recent CUDA compatible GPU should work. + +## Network switch +Small detectors (up to 4M pixel) can be in principle operated without switch. In this case one needs `8x10g` variant +of the Jungfraujoch FPGA image, which allows to directly connect 4 JUNGFRAU modules to one U55C card. + +Such configuration is however +impractical for larger systems or more complex deployments, like multiple detectors operated from one Jungfraujochs server. +In this case one needs a network switch. + +We currently use Nvidia/Mellanox SN2100 switch, though there is no reason not to use other models/other vendors. +For switches with only 100G ports it is important to ensure, that these can be split into 4x10G ports to connect the detector. + diff --git a/_sources/JFJOCH_BROKER.md.txt b/_sources/JFJOCH_BROKER.md.txt new file mode 100644 index 00000000..073c32fb --- /dev/null +++ b/_sources/JFJOCH_BROKER.md.txt @@ -0,0 +1,189 @@ +# jfjoch_broker + +`jfjoch_broker` is the main service for the Jungfraujoch application. It is responsible for: + +* Providing user interface via HTTP and OpenAPI +* Configuring FPGA firmware +* Building images from FPGA output and forwarding the results over ZeroMQ + +## External interfaces +Broker operates four external interfaces. + +**Image stream** ZeroMQ PULL socket with CBOR serialization is used to send images, metadata and processing results for writing or downstream +processing. See details [here](ZEROMQ_STREAM.md#image-stream). + +**Preview stream** ZeroMQ PUB socket, as above but limited to subset of frames (1 image/s by default). See details [here](ZEROMQ_STREAM.md#preview-stream). + +**Metadata stream** ZeroMQ PUB socket, contains metadata for all the images, with bundling. See details [here](ZEROMQ_STREAM.md#metadata-stream). + +**Configuration, status and results interface** HTTP/REST interface described in the OpenAPI format. +Description of the API is presented in the [OpenAPI description](../broker/redoc-static.html). + +## Broker configuration +`jfjoch_broker` requires JSON configuration files. The file is described by OpenAPI structure `jfjoch_settings` defined in `jfjoch_api.yaml` file. +It is recommended to go through example files in the `etc/`. + +Example with all fields: + +```json +{ + "pcie": [ + { + "blk": "/dev/jfjoch0", + "ipv4": "10.1.1.7" + }, + { + "blk": "/dev/jfjoch1", + "ipv4": "10.1.1.8" + } + ], + "zeromq": { + "send_watermark": 100, + "send_buffer_size": 1024, + "image_socket": [ + "tcp://1.2.3.4:5000", + "tcp://1.2.3.4:5001" + ], + "writer_notification_socket": "tcp://1.3.4.6:7000" + }, + "instrument": { + "source_name": "Swiss Light Source", + "source_type": "Synchrotron X-ray Source", + "instrument_name": "X06SA", + "pulsed_source": false, + "electron_source": false + }, + "detector": [ + { + "description": "EIGER 1M", + "serial_number": "E1M-01", + "type": "EIGER", + "high_voltage_V": 150, + "udp_interface_count": 1, + "module_sync": true, + "sensor_thickness_um": 320, + "calibration_file": [ + "gainMaps.bin" + ], + "hostname": [ + "e1m-01", + "e1m-02" + ], + "readout_time_us": 3, + "sensor_material": "Si", + "tx_delay": [ + 0,1 + ], + "base_data_ipv4_address": "10.10.10.50", + "standard_geometry": { + "nmodules": 1, + "gap_x": 8, + "gap_y": 36, + "modules_in_row": 1 + }, + "custom_geometry": [ + { + "x0": 0, + "y0": 0, + "fast_axis": "Xp", + "slow_axis": "Xp" + } + ], + "mirror_y": true + } + ], + "detector_settings": { + "frame_time_us": 450, + "count_time_us": 0, + "internal_frame_generator": false, + "internal_frame_generator_images": 1, + "detector_trigger_delay_ns": 0, + "timing": "auto", + "eiger_threshold_keV": 6.0, + "jungfrau_pedestal_g0_frames": 2000, + "jungfrau_pedestal_g1_frames": 300, + "jungfrau_pedestal_g2_frames": 300, + "jungfrau_pedestal_g0_rms_limit": 100, + "jungfrau_pedestal_min_image_count": 128, + "jungfrau_storage_cell_count": 1, + "jungfrau_storage_cell_delay_ns": 5000, + "jungfrau_fixed_gain_g1": false, + "jungfrau_use_gain_hg0": false + }, + "azim_int": { + "polarization_factor": -1, + "solid_angle_corr": true, + "high_q_recipA": 0, + "low_q_recipA": 0, + "q_spacing": 0 + }, + "image_format": { + "summation": true, + "geometry_transform": true, + "jungfrau_conversion": true, + "jungfrau_conversion_factor_keV": 0.001, + "bit_depth_image": 16, + "signed_output": true, + "mask_module_edges": true, + "mask_chip_edges": true + }, + "image_buffer_MiB": 2048, + "receiver_threads": 64, + "numa_policy": "n2g2", + "frontend_directory": "/usr/share/jfjoch/frontend", + "image_pusher": "ZeroMQ", + "zeromq_metadata": { + "enabled": true, + "period_ms": 1000, + "socket_address": "tcp://0.0.0.0:4357" + }, + "zeromq_preview": { + "enabled": true, + "period_ms": 1000, + "socket_address": "tcp://0.0.0.0:4356" + } +} +``` + +## Setting up a local test for Jungfraujoch +For development, it is possible to set up a local installation of Jungfraujoch. +This will work without FPGA installed in the computer and allows to test Jungfraujoch software layer, including +ZeroMQ streaming and file writing. + +The workflow simulates FPGA behavior, by running high-level synthesis code on the CPU - the performance is therefore +very low, as fixed-point calculations have large performance penalty on CPU. In the CPU simulation mode, one can simulate +using only a single FPGA device. + +To run the test: + +### Compile Jungfraujoch with frontend +``` +mkdir build +cd build +cmake .. +make jfjoch +make frontend +``` +Alternatively, for RHEL8 system, you can use RPM generated by automated pipeline. +Solely `jfjoch` one is enough. +In this case - it is necessary to update `etc/broker_local.json` file with frontend path in `/usr/share/jfjoch/frontend`. + +### Start service +Start broker: +``` +cd build/broker +./jfjoch_broker ../../etc/broker_local.json 5232 +``` + +### Run tests +To run test a Python script is provided: +``` +cd tests/test_data +python jfjoch_broker_test.py +``` +The script will initialize Jungfraujoch, import test image and start data collection. + +### Expected result +You can observe online data analysis by opening the following web page: [http://localhost:5232](http://localhost:5232). +Also, a dataset with images should be written in the `build/broker` directory. + diff --git a/_sources/JFJOCH_WRITER.md.txt b/_sources/JFJOCH_WRITER.md.txt new file mode 100644 index 00000000..9ffd2b64 --- /dev/null +++ b/_sources/JFJOCH_WRITER.md.txt @@ -0,0 +1,213 @@ +# jfjoch_writer + +`jfjoch_writer` is NeXus compliant HDF5 file writer. + +## Acknowledgements +* Zdenek Matej (MAX IV) +* Felix Engelmann (MAX IV) +for testing and multiple improvement suggestions. + +## Running directory +Writer needs to be running in base directory for writing files - `file_prefix` will be always relative in regard to writer running directory. +Writer detects and protects for basic security issues, like `file_prefix` starting with a slash, or starting with `../`, or containing `/../`. + +## Usage +Writer needs to be started as a background service, with the following command: +``` +jfjoch_writer {options}
+ +Options: +-R | --root_dir= Root directory for file writing +-H | --http_port= HTTP port for statistics +-r | --zmq_repub_port= ZeroMQ port for PUSH socket to republish images +-f | --zmq_file_port= ZeroMQ port for PUB socket for notifications on finalized files +-w | --rcv_watermark= Receiving ZeroMQ socket watermark (default = 100) +-W | --repub_watermark= Republish ZeroMQ socket watermark (default = 1000) +``` +for example: +``` +jfjoch_writer -H5234 tcp://dcu-address:5400 +``` + +## HTTP interface +Writer has dedicated status interface via HTTP. It allows for two operations: +* ***check state of the writer*** to check if the writer is properly synchronized with DCU (e.g., that `file_prefix` agrees with what was set on the DCU) and monitor progress. +* ***cancel writing*** this will close all the HDF5 files being written and restart writer - the option should be used only if DCU process was terminated or disconnected, it SHOULD NOT be used as standard cancellation procedure (when DCU received cancel command it should properly finish writing as well) + +## Republish +Republish creates a PULL socket on the writer, where all the messages are republished for further use by data analysis pipeline. +Republish is non-blocking, so if there is no receiver on other end or the sending queue is full - images won't be republished. +In case of START/END messages republishing will attempt sending for 100 ms, but if send times out it won't be retried. + +Republish functionality is optional, if republish port number is omitted this functionality is not enabled. + +## Overwriting files +When `jfjoch_writer` creates a HDF5 file, it first adds suffix `..tmp`. +Random value depends on current time-stamp and likely will be different from each file of the particular series. +After file is all saved and closed, it is renamed to remove the suffix. +By default, renaming won't happen if this would overwrite existing file. +However, this behavior can be changed by setting `overwrite` parameter to true in the file writer configuration. + +## Finalized files information +Creates PUB socket to inform about finalized data files. For each closed file, the socket will send a JSON message, with the following structure: + +``` +{ + "filename": : HDF5 data file name (relative to writer root directory), + "nimages": number of images in the file (counting from 1!), + "file_number": number of file within the acquisition, + "sample_name": name of sample, + "run_name": name of run, + "run_number": number of run, + "experiment_group": number of p-group / proposal (optional), + "user_data": user_data, + "beam_x_pxl": beam center (X) in pixels, + "beam_y_pxl": beam center (Y) in pixels, + "detector_distance_m": detector distance (X) in m, + "detector_height_pxl": detector size (X) in pixels, + "detector_width_pxl": detector size (Y) in pixels, + "incident_energy_eV": photon energy of the X-ray beam, + "pixel_size_m": pixel size in meter (assuming pixel X == Y), + "saturation": this count and higher mean saturation, + "space_group_number": space group number (optional), + "underload": pixels with this count should be excluded, + "unit_cell": unit cell dimensions in Angstrom/degree { + "a": , "b": , "c": , + "alpha": , "beta": , "gamma": + }, +} +``` +`user_data` is defined as `header_appendix` in the `/start` operation in the `jfjoch_broker`. +Other metadata are also carried over from `/start` operation. + +If the `header_appendix` is a string with valid JSON meaning, it will be embedded as JSON, otherwise it will be escaped as string. +For example `header_appendix` of `{"param1": "test1", "param2": ["test1", "test2"]}`, than example message will look as follows: +```json +{ + "filename": "dataset_name_data_000001.h5", + "nimages": 1000, + "file_number": 0, + "sample_name": "lysozyme", + "run_name": "lyso_cryo", + "run_number": 25, + "experiment_group": "p00001", + "beam_x_pxl": 1200, + "beam_y_pxl": 1500, + "detector_distance_m": 0.155, + "detector_height_pxl": 2164, + "detector_width_pxl": 2068, + "image_time_s": 0.001, + "nimages": 2, + "incident_energy_eV": 12400.0, + "pixel_size_m": 7.5e-05, + "saturation": 32766, + "space_group_number": 96, + "underload": -32768, + "unit_cell": { + "a": 78.0, + "alpha": 90.0, + "b": 78.0, + "beta": 90.0, + "c": 39.0, + "gamma": 90.0 + }, + "user_data": { + "param1": "test1", + "param2": ["test1", "test2"] + } +} +``` + +Notifications for finalized files are optional, if notification port number is omitted this functionality is not enabled. + +## HDF5 file structure +Jungfraujoch aims to generate files compliant with NXmx format. + +### Master file + +There are custom extension to NXmx format. These will be documented in the future. + +Specifically, if data collection was configured with `header_appendix` having key equal to `hdf5` and value as JSON +object with number and string values. These will be added to `/entry/user`. + +There are two versions of master file possible. + +By default, *legacy version* is used. This version is compatible with DECTRIS file writer version 1.0 format. +This ensures the file compatibility of Neggia and Durin XDS plugins, as well as DECTRIS Albula viewer version 4.0. +Distinct feature is that if images are split into data files, there will be multiple links in `/entry/data`, +each corresponding to a data file. +Yet, certain new HDF5 features, like virtual datasets, are not possible in this format since it has to be compatible with HDF5 1.8 features. + +Therefore, we have enabled format *VDS version*. This will link to all data files via a single virtual dataset `/entry/data/data`. +The same way spot finding, azimuthal integration and others, will be linked between master and data files. +This format allows to display processing results in currently developed Jungfraujoch Viewer. +For the time being it only works with Durin XDS plugin, and require DECTRIS Albula viewer version 4.1+. + +### Data file + +Data file has the following structure: + +| Location | Description | Optional | Linked in master file v. 2 | +|--------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------:|:--------------------------:| +| /entry/data/data | Images | | X | +| /entry/detector/timestamp | Timestamp of the image | | | +| /entry/detector/exptime | Exposure time of the image | | | +| /entry/detector/number | Image number; if image rejection was used this will be the original image number | | | +| /entry/detector/det_info | Debug field of the JF detector | X | | +| /entry/detector/storage_cell_image | Storage cell number | X | X * | +| /entry/detector/rcv_delay | Receiver delay for the image (Jungfraujoch debugging) | X | | +| /entry/detector/rcv_free_send_buffers | Receiver number of free send buffers at the time of sending the image (Jungfraujoch debugging) | X | | +| /entry/detector/data_collection_efficiency_image | Ratio of received and expected UDP packets | X | X * | +| /entry/detector/packets_expected | Number of UDP packets expected for the image | X | | +| /entry/detector/packets_received | Number of UDP packets received for the image | X | | +| /entry/image/max_value | Max viable value of the image (excl. overloads, etc.) | X | | +| /entry/azint/bin_to_q | Azimuthal integration - bin-to-Q mapping | X | | +| /entry/azint/image | Azimuthal integration - per image | X | X | +| /entry/MX/peakXPosRaw | Peak position X (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/peakYPosRaw | Peak position Y (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/peakTotalIntensity | Peak total intensity (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/peakH | Miller index h for each detected (indexed) peak | X | X | +| /entry/MX/peakK | Miller index k for each detected (indexed) peak | X | X | +| /entry/MX/peakL | Miller index l for each detected (indexed) peak | X | X | +| /entry/MX/peakDistEwaldSphere | Distance of the peak from the Ewald sphere (prediction) | X | X | +| /entry/MX/nPeaks | Number of peaks per image (see [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf)) | X | X | +| /entry/MX/strongPixels | Number of strong pixel per image | X | X | +| /entry/MX/nPeaksRingFiltered | Number of peaks not belonging to rings | X | X | +| /entry/MX/imageIndexed | Image is successfully indexed | X | X | +| /entry/MX/profileRadius | Crystal profile radius for indexed images | X | X | +| /entry/MX/latticeIndexed | Crystal lattice for the image, assuming it is indexed | X | X | +| /entry/MX/bkgEstimate | Mean value of pixels in the radius of 3-5 A | X | X | +| /entry/MX/resolutionEstimate | Resolution estimate based on on-the-fly integration | X | X | +| /entry/MX/beam_corr_x | Beam center correction applied during processing (X) [pixel] | X | X | +| /entry/MX/beam_corr_y | Beam center correction applied during processing (Y) [pixel] | X | X | +| /entry/MX/niggli_class | Niggli class identifier of the indexed Bravais lattice (per image) - see [International Tables for Crystallography A (2016). Vol. A, Table 3.1.3.1](https://onlinelibrary.wiley.com/iucr/itc/Ac/ch3o1v0001/table3o1o3o1.pdf) | X | X | +| /entry/MX/bravais_lattice | Bravais lattice short code (per image), e.g., aP, mC, oF, tI, hP, hR, cF | X | X | +| /entry/roi/{roi_name}/max | Max pixel value for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/sum | Sum pixel value for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/sum_sq | Sum pixel values squared for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/npixel | Number of valid pixel for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/x | Weighted X-coordinate for roi named {roi_name} | X | X | +| /entry/roi/{roi_name}/y | Weighted Y-coordinate for roi named {roi_name} | X | X | +| /entry/xfel/pulseID | Pulse ID (for XFEL only) | X | X | +| /entry/xfel/eventCode | Event code (for XFEL only) | X | X | + +\* - Datasets from `/entry/detector` in data file are mapped to `/entry/instrument/detector/detectorSpecific` in master file. + +If spot finding is enabled, spots are written in the [CXI format](https://raw.githubusercontent.com/cxidb/CXI/master/cxi_file_format.pdf) and are recognized by CrystFEL. The following has to be added to the CrystFEL geometry file: +``` +peak_list = /opt/MX +peak_list_type = cxi +``` + +## Other formats (CBF and TIFF) +In addition to HDF5 format, Jungfraujoch allows to save images in the Crystallographic Binary File (CBF) format. +CBF files are written according to miniCBF format, with only basic header, and always with 32-bit signed integer format. +Dynamic range is reduced to max 2^24, negative numbers are zeroed, and masked, and/or bad pixels are set to -1. + +Also writing to TIFF files is possible, though no metadata are saved in this case. + +## No file option(s) +There are two options to disable writing of files by the writer: +* Setting `file_prefix` to empty string - this will disable sending files on ZeroMQ image socket. +* Setting file format to `NoFile` - files are streamed over ZeroMQ socket, but `jfjoch_writer` will not write anything. +This can be useful for debugging purposes, or if you only rely on republishing functionality of the `jfjoch_writer` \ No newline at end of file diff --git a/_sources/LICENSE.md.txt b/_sources/LICENSE.md.txt new file mode 100644 index 00000000..8b19c24c --- /dev/null +++ b/_sources/LICENSE.md.txt @@ -0,0 +1,690 @@ +# License + +Jungfraujoch software is licensed with GPLv3 license. +Jungfraujoch FPGA is licensed with CERN OHL-S license (see [FPGA license](FPGA_LICENSE.md)). + +## GNU GENERAL PUBLIC LICENSE +Version 3, 29 June 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. +Everyone is permitted to copy and distribute verbatim copies +of this license document, but changing it is not allowed. + +### Preamble + +The GNU General Public License is a free, copyleft license for +software and other kinds of works. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w` and `show c` should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + +You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + +The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. + + +## Jungfraujoch exceptions to GPL + +As a special exception, we specifically permit linking Jungfraujoch code with Nvidia CUDA libraries. + +We also permit to link Jungfraujoch software (GPLv3) with Jungfraujoch high-level synthesis code (CERN OHL 2.0) for the purpose +of simulating FPGA design on CPU. + +If OpenAPI definition file (jfjoch_api.yaml) is solely used to generate client code or to interact with the Jungfraujoch +API it may be distributed under terms of your choosing without being subject to GPL requirements. diff --git a/_sources/OPENAPI.md.txt b/_sources/OPENAPI.md.txt new file mode 100644 index 00000000..a13a3280 --- /dev/null +++ b/_sources/OPENAPI.md.txt @@ -0,0 +1,13 @@ +# OpenAPI +## OpenAPI specs + +See document with detailed [OpenAPI specs](OPENAPI_SPECS.rst). + +## Python client +Jungfraujoch is controlled with HTTP/REST interface defined with an OpenAPI specification. +For convenience, we provide Python client as [jfjoch-client](https://pypi.org/project/jfjoch-client/) PyPi package. +To install the client you can use `pip` tool: +``` +pip install jfjoch-client +``` +See [API reference from the OpenAPI generator](python_client/README.md). \ No newline at end of file diff --git a/_sources/OPENAPI_SPECS.rst.txt b/_sources/OPENAPI_SPECS.rst.txt new file mode 100644 index 00000000..15bf4e7f --- /dev/null +++ b/_sources/OPENAPI_SPECS.rst.txt @@ -0,0 +1,4 @@ +OpenAPI specification +===================== + +See document with detailed `OpenAPI specs <_static/redoc-static.html>`_ generated with Redocly. \ No newline at end of file diff --git a/_sources/PIXEL_MASK.md.txt b/_sources/PIXEL_MASK.md.txt new file mode 100644 index 00000000..143f0fd5 --- /dev/null +++ b/_sources/PIXEL_MASK.md.txt @@ -0,0 +1,46 @@ +# Pixel mask + +## Mask format + +Jungfraujoch follows generally [NXmx format](https://manual.nexusformat.org/classes/applications/NXmx.html) format for pixel mask. +Pixel mask is described as 32-bit unsigned integer array of size the same as the image. +Conditions to mask pixel are described by setting a particular bit to one. This way it is possible to encode reason why pixel is included in the pixel mask, also for one pixel there can be multiple reasons encoded at the same time. + +Bit values are set as follows: + +Bit 0 - gap (pixel with no sensor) + +Bit 1 - error pixel (for PSI JUNGFRAU: pixel doesn't set proper gain during pedestal, for DECTRIS: pixel is part of detector pixel mask) + +Bit 4 - noisy pixel (for PSI JUNGFRAU: pixel pedestal G0 RMS is over threshold, for DECTRIS: pixel was flagged with signal during dark data collection at initialization) + +Bit 8 - user defined mask + +Bit 30 - module edge (only for PSI systems) + +Bit 31 - chip edge interpolated pixel (multipixel) + +## Custom user mask + +Jungfraujoch allows to upload custom user mask. This happens in two steps. First create mask in TIFF format: + +```python +import numpy as np +import tifffile as tiff + +# Create a 2068x2164 numpy array filled with zeros, with 32-bit unsigned integers +array = np.zeros((2068, 2164), dtype=np.uint32) + +# Mark the pixel (300, 400) with the value 1 +array[300, 400] = 1 + +# Save the array as a TIFF file +tiff.imwrite('mask.tiff', array) +``` + +Pixels with non-zero value in the TIFF file will be marked as belonging to the user mask (bit 8). + +Then upload the mask to Jungfraujoch server: +```shell +curl -v http:///config/user_mask.tiff -XPUT --data-binary @mask.tiff +``` diff --git a/_sources/REPOSITORIES.md.txt b/_sources/REPOSITORIES.md.txt new file mode 100644 index 00000000..b03b211f --- /dev/null +++ b/_sources/REPOSITORIES.md.txt @@ -0,0 +1,47 @@ +# Linux package repositories +For convenience, we are providing package repositories. With versions including and excluding CUDA linking. +We recommend to install Jungfraujoch viewer from `nocuda` repository and remaining packages from `cuda12`/`cuda13` repository. + +## RHEL based systems + +For RHEL systems we provide the following repositories: + +| RHEL version | CUDA | Repository file | +|--------------|------|-------------------------------------------------------------------------| +| 8.x | 12.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo | +| 8.x | - | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda.repo | +| 9.x | 13.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda13.repo | +| 9.x | - | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-nocuda.repo | + +To install the repository, run: + +```bash +dnf config-manager --add-repo https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo +``` +Currently signing of RPMs is not supported, so the repository file needs to be manually modified to set `gpgcheck=0` +or installation must run with `--nogpgcheck`. + +We provide the following packages in the repository: +* jfjoch +* jfjoch-driver +* jfjoch-writer +* jfjoch-viewer + +## Ubuntu based systems + +For Ubuntu systems, we also provide the following repositories: +``` +sudo curl https://gitea.psi.ch/api/packages/mx/debian/repository.key -o /etc/apt/keyrings/gitea-mx.asc +echo "deb [signed-by=/etc/apt/keyrings/gitea-mx.asc] https://gitea.psi.ch/api/packages/mx/debian $distribution $component" | sudo tee -a /etc/apt/sources.list.d/gitea.list +sudo apt update +``` + +`$distribution` uses Ubuntu names `jammy` (22.04) and `noble` (24.04). `$component` can be set to `cuda13` and `nocuda`. + +We provide the following packages in the repository: +* jfjoch-jfjoch +* jfjoch-driver +* jfjoch-writer +* jfjoch-viewer + +Ubuntu packages are currently only going through a very limited testing. \ No newline at end of file diff --git a/_sources/SOFTWARE.md.txt b/_sources/SOFTWARE.md.txt new file mode 100644 index 00000000..3f783c2d --- /dev/null +++ b/_sources/SOFTWARE.md.txt @@ -0,0 +1,53 @@ +# Software requirements +## Operating system +Recommended operating system is Red Hat Enterprise Linux (RHEL) / Rocky Linux versions 8 or 9. +For this operating systems we provide RPMs with pre-built binaries to simplify deployment. +On experimental basis we also build repositories for Ubuntu 22.04 and 24.04. + +Running Jungfraujoch on Red Hat Enterprise Linux 7 is currently not tested and not recommended, +but likely possible with providing some packages from external repositories. + + +## Software dependencies +Required: +* C++20 compiler and C++20 standard library; recommended GCC 11+ or clang 14+ (Intel OneAPI, AMD AOCC) +* CMake version 3.21 or newer + GNU make tool +* zlib compression library +* EIGEN library (only on a compilation system) +* HDF5 library version 1.10 or newer - see [github.com/HDFGroup/hdf5](https://github.com/HDFGroup/hdf5) +* TIFF library - see [gitlab.com/libtiff/libtiff](https://gitlab.com/libtiff/libtiff) +* JPEG library (preferably jpeg-turbo) - see [github.com/libjpeg-turbo/libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo) + +Optional: +* CUDA compiler version 11 or newer - required for MX fast feedback indexer +* FFTW library - for indexing if GPU/CUDA is absent +* NUMA library - to pin threads to nodes/CPUs +* Node.js - to make frontend +* Qt version 6 (for jfjoch_viewer) + +Automatically downloaded by CMake and statically linked: +* SLS Detector Package - see [github.com/slsdetectorgroup/slsDetectorPackage](https://github.com/slsdetectorgroup/slsDetectorPackage) +* Zstandard (Facebook) - see [github.com/facebook/zstd](https://github.com/facebook/zstd) +* Pistache webserver - see [github.com/pistacheio/pistache](https://github.com/pistacheio/pistache) +* Fast feedback indexer (Hans-Christian Stadler, PSI) - see [github.com/paulscherrerinstitute/fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) +* Catch2 testing library - see [github.com/catchorg/Catch2](https://github.com/catchorg/Catch2) +* Ceres Solver library for least square optimization - see [http://ceres-solver.org/] + +Please follow the link provided above to check for LICENSE file. Building code with dependencies above requires access from the build system to github.com. + +Directly included in the repository: +* JSON parser/writer from N. Lohmann - see [github.com/nlohmann/json](https://github.com/nlohmann/json) +* Xilinx arbitrary precision arithmetic headers - see [github.com/Xilinx/HLS_arbitrary_Precision_Types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) +* Bitshuffle filter from K. Masui - see [github.com/kiyo-masui/bitshuffle](https://github.com/kiyo-masui/bitshuffle) +* Fast replacement for Bitshuffle pre-compression filter (Kal Cutter, DECTRIS) - see [github.com/kalcutter/bitshuffle](https://github.com/kalcutter/bitshuffle) +* Tinycbor (Intel) - see [github.com/intel/tinycbor](https://github.com/intel/tinycbor) +* LZ4 compression by Y.Collet - see [github.com/lz4/lz4](https://github.com/lz4/lz4) +* Spdlog logging library - see [github.com/gabime/spdlog](https://github.com/gabime/spdlog) +* ZeroMQ library (through slsDetectorPackage) - see [github.com/zeromq/libzmq](https://github.com/zeromq/libzmq) +* Cpp-http library for HTTP - see [github.com/yhirose/cpp-httplib](https://github.com/yhirose/cpp-httplib) +* Base64 decoder/encoder - see [gist.github.com/tomykaira](https://gist.github.com/tomykaira/f0fd86b6c73063283afe550bc5d77594) +* GEMMI library by Global Phasing - see [github.com/project-gemmi/gemmi](https://github.com/project-gemmi/gemmi) + +For license check LICENSE file in respective directory + + diff --git a/_sources/TESTS.md.txt b/_sources/TESTS.md.txt new file mode 100644 index 00000000..89042e6a --- /dev/null +++ b/_sources/TESTS.md.txt @@ -0,0 +1,10 @@ +# Tests + +Automated test routine is then accessible as `tests/jfjoch_test`. There are also benchmark routines: + +* `jfjoch_hdf5_test` to measure HDF5 dataset writing speed (single threaded) +* `jfjoch_offline_process` to apply spot finding and indexing routines in Jungfraujoch to an example dataset - this is equivalent to FPGA spot finding algorithm, but NOT performance equivalent as it is particularly not-efficient +* `jfjoch_fpga_test` to test quality/performance of FPGA card(s) and software routines + +In addition, tests are executed to verify that datasets written by Jungfraujoch are readable with XDS Durin plugin, XDS Neggia plygin and CrystFEL. +Input files for these programs are placed in `xds_durin`, `xds_neggia` and `crystfel` folders. See `.gitlab-ci.yml` for details. diff --git a/_sources/TOOLS.md.txt b/_sources/TOOLS.md.txt new file mode 100644 index 00000000..d567125f --- /dev/null +++ b/_sources/TOOLS.md.txt @@ -0,0 +1,47 @@ +# Tools + +## jfjoch_pcie_status +Prints detailed status information about the card. Execute by adding device path, e.g.: +``` +./jfjoch_pcie_status /dev/jfjoch0 +``` +The program is safe to execute during a running data collection. + +## jfjoch_pcie_clear_net_counters +Network counters in the card give information about Ethernet, UDP and ICMP packets encountered by the network stack prior to Jungfraujoch logic. +These counters are running from the moment card is powered on. They can be reset by running the program with device name, e.g.: +``` +./jfjoch_pcie_clear_net_counters /dev/jfjoch0 +``` + +## jfjoch_pcie_net_cfg +Network configuration can be retrieved and modified with `jfjoch_pcie_net_cfg` tool. Usage: + +``` +jfjoch_pcie_net_cfg + Read configuration for all network interface of a device +jfjoch_pcie_net_cfg |fgen + Read configuration for a particular network interface / internal frame generator" +jfjoch_pcie_net_cfg |fgen ipv4 + Set IPv4 address for a particular network interface / internal frame generator +jfjoch_pcie_net_cfg |fgen direct 0|1 + Set direct mode for a particular network interface / internal frame generator +jfjoch_pcie_net_cfg |fgen clear + Clear Ethernet counter for a particular network interface / internal frame generator +``` + +## jfjoch_hdf5_tools + +Tool to test single threaded HDF5 writer performance + +## jfjoch_offline_process + +Tool to run offline processing on existing HDF5 dataset + +## jfjoch_udp_simulator + +UDP simulator to test Jungfraujoch FPGA + +## jfjoch_pcie_read_register + +Tool to read verbatim Jungfraujoch FPGA registers \ No newline at end of file diff --git a/_sources/VERSIONING.md.txt b/_sources/VERSIONING.md.txt new file mode 100644 index 00000000..aac81542 --- /dev/null +++ b/_sources/VERSIONING.md.txt @@ -0,0 +1,13 @@ +# Semantic versioning + +Jungfraujoch is following semantic versioning. For this purpose we define public API as following: + +* OpenAPI configuration interface +* CBOR serialization ZeroMQ stream +* HDF5 file format + +This means that changes in the format of thereof must be accompanied by version change - major version in case of breaking changes, minor version in case of feature expansion. + +NOTE: FPGA design, PCIe driver, and internal libraries are not part of the public API and are considered internals of Jungfraujoch. +Breaking changes in these components can happen without incrementing major version of the whole package. +It will be marked in changelog. \ No newline at end of file diff --git a/_sources/WEB_FRONTEND.md.txt b/_sources/WEB_FRONTEND.md.txt new file mode 100644 index 00000000..51cf14d0 --- /dev/null +++ b/_sources/WEB_FRONTEND.md.txt @@ -0,0 +1,9 @@ +# Web frontend +Jungfraujoch is equipped with React-based web frontend for user-friendly experience. Frontend has the following options: +* Presenting current state of the detector +* Plotting results of online quality calculations +* Showing live view images from the detector +* JUNGFRAU calibration numbers +* Configuring the detector, as well as pedestal/initialization operations + +Frontend is written in TypeScript. For details see `frontend/` directory. \ No newline at end of file diff --git a/_sources/ZEROMQ_STREAM.md.txt b/_sources/ZEROMQ_STREAM.md.txt new file mode 100644 index 00000000..be0dda95 --- /dev/null +++ b/_sources/ZEROMQ_STREAM.md.txt @@ -0,0 +1,98 @@ +# ZeroMQ socket + +Jungfraujoch process (`jfjoch_broker`) operates three ZeroMQ outputs. +All three can be operated/enabled independently. +These are: +* **Image** - all the images including metadata (PUSH socket) +* **Preview** - images with metadata at a reduced frame rate (PUB socket) +* **Metadata** - only metadata for all the images, bundled into packages (PUB socket) + +## Image stream +Images (with metadata) are serialized as CBOR [image message](CBOR.md#image-message). +The stream will also include CBOR [start message](CBOR.md#start-message), [calibration messages](CBOR.md#calibration-message) and [end message](CBOR.md#end-message) with run metadata. + +Image stream can be split into multiple sockets to increase performance, in this case images will be split according to file number to which the image belongs. +All sockets will forward start and end messages. +Only first socket will forward calibration messages and will be marked to write master file. + +This is using PUSH ZeroMQ socket(s). +It should be strictly avoided to have multiple receivers connected to one PUSH ZeroMQ socket. +ZeroMQ will send the images in a round-robin basis to the receivers. +In this case start and end messages will end up only with one receiver. +Instead, Jungfraujoch feature of multiple sockets should be used. + +Image stream can be replaced with direct HDF5 writer and CBOR dump image pushers, it can be disabled by select "None" image pusher for all the measurements. + +If `file_prefix` is not provided for a data collection, images won't be sent to image stream (or its HDF5/CBOR replacements). + +Behavior is as following: +* Start message is sent with timeout of 5s. If within the time the message cannot be put in the outgoing queue or there is no connected puller exception is thrown - stop data collection with error due to absence of a writer. +* Images are sent in non-blocking way and without timeout. +* End message is sent with timeout of 5s. No error is reported. + +## Writer notification socket +Normally ZeroMQ is asynchronous. When `jfjoch_broker` is sending messages via ZeroMQ image stream, it doesn't know +if these were properly handled downstream, e.g., written to disk. For this reason a writer notification socket is introduced. +It allows to downstream processing code to notify 'jfjoch_broker' that all images were handled properly. + +To use writer notification socket, it has to be first enabled in the JSON configuration file of broker with `writer_notification_socket` entry: +```json +{ + "writer_notification_socket":"tcp://192.168.0.1:*" +} +``` +Such entry will create PULL socket on `192.168.0.1` network interface listening on one, random TCP port. When data processing is started, the +image stream will send CBOR [start message](CBOR.md#start-message). This message will include information on `writer_notification_zmq_addr`, +which needs to be used by downstream code. Since the start message must reference the address of `jfjoch_broker` host, notification +socket should always listen on a particular network interface, and should not be configured with placeholder address `0.0.0.0`. It is, however, OK +to use placeholder `:*` for network port, as it will be substituted for the one chosen by ZeroMQ. + +For every image stream, downstream code must send the following message to the PULL socket: +```json +{ + "run_number":135, + "run_name": "lysozyme_1", + "socket_number": 1, + "processed_images":250, + "ok": true +} +``` +Here `run_number`, `run_name` and `socket_number` must match information from the start message. +`ok` is boolean confirming if the writing process was OK. +`processed_images` is number of images that were written/processed, this is to track how many images were ignored by non-blocking ZeroMQ procedures. +If not, it is possible to include error message: +```json +{ + "run_number":135, + "run_name": "lysozyme_1", + "socket_number": 1, + "processed_images": 0, + "ok": false, + "error": "Permission error" +} +``` +This way errors from the downstream code are propagated to `jfjoch_broker`. + +If writer notification socket is configured, but downstream code doesn't send proper notification, `jfjoch_broker` will time out after 60 seconds producing an error message. + +## Preview stream +Jungfraujoch can also send images (with metadata) at a reduced frame rate for preview purpose. +Images are serialized as CBOR [image message](CBOR.md#image-message). +The stream will also include CBOR [start message](CBOR.md#start-message) and [end message](CBOR.md#end-message) with run metadata. +Only start and image messages are sent. + +This is using PUB socket with conflate option. I.e., only the last message is kept by ZeroMQ, so if receiver cannot cope +with the messages, it will always receive the last generated message (no backlog). +For this reason it is also recommended to use the same option on receiver side. + +Given PUB socket properties, it is possible to connect multiple viewers to a single socket --- all the viewers should receive all the images sent. + +## Metadata stream +Jungfrajoch can also send pure metadata for the purpose of archiving such information. +Metadata are serialized as CBOR [metadata message](CBOR.md#metadata-message). +This is very similar as image message, but excludes the actual image array and spot positions. +As metadata are relatively small, to avoid large number of messages, Jungfraujoch bundles metadata of many images in one message. +Order of images within bundle, as well a size of the bundle, are not guaranteed +The stream will also include CBOR [start message](CBOR.md#start-message) and [end message](CBOR.md#end-message) with run metadata. + +This is using PUB socket with watermark, so there is some queuing of messages with ZeroMQ. Multiple receivers can be connected. diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 00000000..9d4e4a8e --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,66 @@ +.. image:: jfjoch.png + :width: 256 + :align: left + +PSI Jungfraujoch +================ + +Jungfraujoch is data acquisition and on-the-fly analysis system developed by the `Paul Scherrer Institut `__. + +It can be currently used with PSI and DECTRIS detectors. + +Jungfraujoch is distributed under the GPLv3 license. + +.. toctree:: + :maxdepth: 1 + :caption: General + + ACKNOWLEDGEMENT + LICENSE + DETECTORS + HARDWARE + SOFTWARE + VERSIONING + DEPLOYMENT + CHANGELOG + +.. toctree:: + :maxdepth: 1 + :caption: Software + + JFJOCH_BROKER + JFJOCH_WRITER + TOOLS + +.. toctree:: + :maxdepth: 1 + :caption: FPGA + + FPGA + FPGA_LICENSE + FPGA_DESIGN + FPGA_NETWORK + FPGA_PCIE_DRIVER + FPGA_SETTINGS + FPGA_DATA_ANALYSIS + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + DETECTOR_GEOMETRY + CPU_DATA_ANALYSIS + OPENAPI + OPENAPI_SPECS + CBOR + ZEROMQ_STREAM + PIXEL_MASK + WEB_FRONTEND + TESTS + +.. toctree:: + :maxdepth: 1 + :caption: OpenAPI Python client + + python_client/README + python_client/docs/DefaultApi \ No newline at end of file diff --git a/_sources/python_client/README.md.txt b/_sources/python_client/README.md.txt new file mode 100644 index 00000000..c7b9be75 --- /dev/null +++ b/_sources/python_client/README.md.txt @@ -0,0 +1,235 @@ +# jfjoch-client +API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). +Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. +Jungfraujoch uses FPGA boards to acquire data at high data rates. + +# License Clarification + +While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** +when this file is used solely to generate OpenAPI clients or when implementing applications that +interact with the API. Generated client code and applications using this API definition are not +subject to the GPL license requirements and may be distributed under terms of your choosing. + +This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and +the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that +user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not +derivative works of the kernel and are not subject to the terms of the GPL. + +This exception is intended to allow wider use of this API specification without imposing GPL +requirements on applications that merely interact with the API, regardless of whether they +communicate through network calls or other mechanisms. + + +This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project: + +- API version: 1.0.0-rc.126 +- Package version: 1.0.0-rc.126 +- Generator version: 7.20.0 +- Build package: org.openapitools.codegen.languages.PythonClientCodegen + +## Requirements. + +Python 3.9+ + +## Installation & Usage +### pip install + +If the python package is hosted on a repository, you can install directly using: + +```sh +pip install git+https://git.psi.ch/jungfraujoch/jungfraujoch.git +``` +(you may need to run `pip` with root permission: `sudo pip install git+https://git.psi.ch/jungfraujoch/jungfraujoch.git`) + +Then import the package: +```python +import jfjoch_client +``` + +### Setuptools + +Install via [Setuptools](http://pypi.python.org/pypi/setuptools). + +```sh +python setup.py install --user +``` +(or `sudo python setup.py install` to install the package for all users) + +Then import the package: +```python +import jfjoch_client +``` + +### Tests + +Execute `pytest` to run the tests. + +## Getting Started + +Please follow the [installation procedure](#installation--usage) and then run the following: + +```python + +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Cancel running data collection + api_instance.cancel_post() + except ApiException as e: + print("Exception when calling DefaultApi->cancel_post: %s\n" % e) + +``` + +## Documentation for API Endpoints + +All URIs are relative to *http://localhost:5232* + +Class | Method | HTTP request | Description +------------ | ------------- | ------------- | ------------- +*DefaultApi* | [**cancel_post**](docs/DefaultApi.md#cancel_post) | **POST** /cancel | Cancel running data collection +*DefaultApi* | [**config_azim_int_get**](docs/DefaultApi.md#config_azim_int_get) | **GET** /config/azim_int | Get azimuthal integration configuration +*DefaultApi* | [**config_azim_int_put**](docs/DefaultApi.md#config_azim_int_put) | **PUT** /config/azim_int | Configure azimuthal integration +*DefaultApi* | [**config_dark_mask_get**](docs/DefaultApi.md#config_dark_mask_get) | **GET** /config/dark_mask | Get settings for dark data collection to calculate mask +*DefaultApi* | [**config_dark_mask_put**](docs/DefaultApi.md#config_dark_mask_put) | **PUT** /config/dark_mask | Set configuration for dark data collection to calculate mask +*DefaultApi* | [**config_detector_get**](docs/DefaultApi.md#config_detector_get) | **GET** /config/detector | Get detector configuration +*DefaultApi* | [**config_detector_put**](docs/DefaultApi.md#config_detector_put) | **PUT** /config/detector | Change detector configuration +*DefaultApi* | [**config_file_writer_get**](docs/DefaultApi.md#config_file_writer_get) | **GET** /config/file_writer | Get file writer settings +*DefaultApi* | [**config_file_writer_put**](docs/DefaultApi.md#config_file_writer_put) | **PUT** /config/file_writer | Change file writer settings +*DefaultApi* | [**config_image_format_conversion_post**](docs/DefaultApi.md#config_image_format_conversion_post) | **POST** /config/image_format/conversion | Configure format for data collection with full conversion +*DefaultApi* | [**config_image_format_get**](docs/DefaultApi.md#config_image_format_get) | **GET** /config/image_format | Get image output format +*DefaultApi* | [**config_image_format_put**](docs/DefaultApi.md#config_image_format_put) | **PUT** /config/image_format | Change image output format +*DefaultApi* | [**config_image_format_raw_post**](docs/DefaultApi.md#config_image_format_raw_post) | **POST** /config/image_format/raw | Configure format for raw data collection +*DefaultApi* | [**config_indexing_get**](docs/DefaultApi.md#config_indexing_get) | **GET** /config/indexing | Get indexing configuration +*DefaultApi* | [**config_indexing_put**](docs/DefaultApi.md#config_indexing_put) | **PUT** /config/indexing | Change indexing algorithm settings +*DefaultApi* | [**config_instrument_get**](docs/DefaultApi.md#config_instrument_get) | **GET** /config/instrument | Get instrument metadata +*DefaultApi* | [**config_instrument_put**](docs/DefaultApi.md#config_instrument_put) | **PUT** /config/instrument | Change instrument metadata +*DefaultApi* | [**config_internal_generator_image_put**](docs/DefaultApi.md#config_internal_generator_image_put) | **PUT** /config/internal_generator_image | Load binary image for internal FPGA generator +*DefaultApi* | [**config_internal_generator_image_tiff_put**](docs/DefaultApi.md#config_internal_generator_image_tiff_put) | **PUT** /config/internal_generator_image.tiff | Load TIFF image for internal FPGA generator +*DefaultApi* | [**config_mask_get**](docs/DefaultApi.md#config_mask_get) | **GET** /config/mask | Get mask of the detector (binary) +*DefaultApi* | [**config_mask_tiff_get**](docs/DefaultApi.md#config_mask_tiff_get) | **GET** /config/mask.tiff | Get mask of the detector (TIFF) +*DefaultApi* | [**config_roi_get**](docs/DefaultApi.md#config_roi_get) | **GET** /config/roi | Get ROI definitions +*DefaultApi* | [**config_roi_put**](docs/DefaultApi.md#config_roi_put) | **PUT** /config/roi | Upload ROI definitions +*DefaultApi* | [**config_select_detector_get**](docs/DefaultApi.md#config_select_detector_get) | **GET** /config/select_detector | List available detectors +*DefaultApi* | [**config_select_detector_put**](docs/DefaultApi.md#config_select_detector_put) | **PUT** /config/select_detector | Select detector +*DefaultApi* | [**config_spot_finding_get**](docs/DefaultApi.md#config_spot_finding_get) | **GET** /config/spot_finding | Get data processing configuration +*DefaultApi* | [**config_spot_finding_put**](docs/DefaultApi.md#config_spot_finding_put) | **PUT** /config/spot_finding | Configure spot finding +*DefaultApi* | [**config_user_mask_get**](docs/DefaultApi.md#config_user_mask_get) | **GET** /config/user_mask | Detector must be Initialized. Get user mask of the detector (binary) +*DefaultApi* | [**config_user_mask_put**](docs/DefaultApi.md#config_user_mask_put) | **PUT** /config/user_mask | Upload user mask of the detector (binary) +*DefaultApi* | [**config_user_mask_tiff_get**](docs/DefaultApi.md#config_user_mask_tiff_get) | **GET** /config/user_mask.tiff | Detector must be Initialized. Get user mask of the detector (TIFF) +*DefaultApi* | [**config_user_mask_tiff_put**](docs/DefaultApi.md#config_user_mask_tiff_put) | **PUT** /config/user_mask.tiff | Upload user mask of the detector +*DefaultApi* | [**config_zeromq_metadata_get**](docs/DefaultApi.md#config_zeromq_metadata_get) | **GET** /config/zeromq_metadata | Get ZeroMQ metadata socket settings +*DefaultApi* | [**config_zeromq_metadata_put**](docs/DefaultApi.md#config_zeromq_metadata_put) | **PUT** /config/zeromq_metadata | Set ZeroMQ metadata settings +*DefaultApi* | [**config_zeromq_preview_get**](docs/DefaultApi.md#config_zeromq_preview_get) | **GET** /config/zeromq_preview | Get ZeroMQ preview settings +*DefaultApi* | [**config_zeromq_preview_put**](docs/DefaultApi.md#config_zeromq_preview_put) | **PUT** /config/zeromq_preview | Set ZeroMQ preview settings +*DefaultApi* | [**deactivate_post**](docs/DefaultApi.md#deactivate_post) | **POST** /deactivate | Prepare detector to turn off +*DefaultApi* | [**detector_status_get**](docs/DefaultApi.md#detector_status_get) | **GET** /detector/status | Get detector status +*DefaultApi* | [**fpga_status_get**](docs/DefaultApi.md#fpga_status_get) | **GET** /fpga_status | Get status of FPGA devices +*DefaultApi* | [**image_buffer_clear_post**](docs/DefaultApi.md#image_buffer_clear_post) | **POST** /image_buffer/clear | Clear image buffer +*DefaultApi* | [**image_buffer_image_cbor_get**](docs/DefaultApi.md#image_buffer_image_cbor_get) | **GET** /image_buffer/image.cbor | Get image message in CBOR format +*DefaultApi* | [**image_buffer_image_jpeg_get**](docs/DefaultApi.md#image_buffer_image_jpeg_get) | **GET** /image_buffer/image.jpeg | Get preview image in JPEG format using custom settings +*DefaultApi* | [**image_buffer_image_tiff_get**](docs/DefaultApi.md#image_buffer_image_tiff_get) | **GET** /image_buffer/image.tiff | Get preview image in TIFF format +*DefaultApi* | [**image_buffer_start_cbor_get**](docs/DefaultApi.md#image_buffer_start_cbor_get) | **GET** /image_buffer/start.cbor | Get Start message in CBOR format +*DefaultApi* | [**image_buffer_status_get**](docs/DefaultApi.md#image_buffer_status_get) | **GET** /image_buffer/status | Get status of the image buffers +*DefaultApi* | [**initialize_post**](docs/DefaultApi.md#initialize_post) | **POST** /initialize | Initialize detector and data acquisition +*DefaultApi* | [**pedestal_post**](docs/DefaultApi.md#pedestal_post) | **POST** /pedestal | Collect dark current for the detector +*DefaultApi* | [**preview_pedestal_tiff_get**](docs/DefaultApi.md#preview_pedestal_tiff_get) | **GET** /preview/pedestal.tiff | Get pedestal in TIFF format +*DefaultApi* | [**preview_plot_bin_get**](docs/DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. +*DefaultApi* | [**preview_plot_get**](docs/DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch +*DefaultApi* | [**result_scan_get**](docs/DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result +*DefaultApi* | [**start_post**](docs/DefaultApi.md#start_post) | **POST** /start | Start detector +*DefaultApi* | [**statistics_calibration_get**](docs/DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics +*DefaultApi* | [**statistics_data_collection_get**](docs/DefaultApi.md#statistics_data_collection_get) | **GET** /statistics/data_collection | Get data collection statistics +*DefaultApi* | [**statistics_get**](docs/DefaultApi.md#statistics_get) | **GET** /statistics | Get general statistics +*DefaultApi* | [**status_get**](docs/DefaultApi.md#status_get) | **GET** /status | Get Jungfraujoch status +*DefaultApi* | [**trigger_post**](docs/DefaultApi.md#trigger_post) | **POST** /trigger | Send soft trigger to the detector +*DefaultApi* | [**version_get**](docs/DefaultApi.md#version_get) | **GET** /version | Get Jungfraujoch version of jfjoch_broker +*DefaultApi* | [**wait_till_done_post**](docs/DefaultApi.md#wait_till_done_post) | **POST** /wait_till_done | Wait for acquisition done +*DefaultApi* | [**xfel_event_code_get**](docs/DefaultApi.md#xfel_event_code_get) | **GET** /xfel/event_code | Return XFEL event codes for the current data acquisition +*DefaultApi* | [**xfel_pulse_id_get**](docs/DefaultApi.md#xfel_pulse_id_get) | **GET** /xfel/pulse_id | Return XFEL pulse IDs for the current data acquisition + + +## Documentation For Models + + - [AzimIntSettings](docs/AzimIntSettings.md) + - [BrokerStatus](docs/BrokerStatus.md) + - [CalibrationStatisticsInner](docs/CalibrationStatisticsInner.md) + - [DarkMaskSettings](docs/DarkMaskSettings.md) + - [DatasetSettings](docs/DatasetSettings.md) + - [DatasetSettingsXrayFluorescenceSpectrum](docs/DatasetSettingsXrayFluorescenceSpectrum.md) + - [Detector](docs/Detector.md) + - [DetectorList](docs/DetectorList.md) + - [DetectorListElement](docs/DetectorListElement.md) + - [DetectorModule](docs/DetectorModule.md) + - [DetectorModuleDirection](docs/DetectorModuleDirection.md) + - [DetectorPowerState](docs/DetectorPowerState.md) + - [DetectorSelection](docs/DetectorSelection.md) + - [DetectorSettings](docs/DetectorSettings.md) + - [DetectorState](docs/DetectorState.md) + - [DetectorStatus](docs/DetectorStatus.md) + - [DetectorTiming](docs/DetectorTiming.md) + - [DetectorType](docs/DetectorType.md) + - [ErrorMessage](docs/ErrorMessage.md) + - [FileWriterFormat](docs/FileWriterFormat.md) + - [FileWriterSettings](docs/FileWriterSettings.md) + - [FpgaStatusInner](docs/FpgaStatusInner.md) + - [GeomRefinementAlgorithm](docs/GeomRefinementAlgorithm.md) + - [GridScan](docs/GridScan.md) + - [ImageBufferStatus](docs/ImageBufferStatus.md) + - [ImageFormatSettings](docs/ImageFormatSettings.md) + - [ImagePusherType](docs/ImagePusherType.md) + - [IndexingAlgorithm](docs/IndexingAlgorithm.md) + - [IndexingSettings](docs/IndexingSettings.md) + - [InstrumentMetadata](docs/InstrumentMetadata.md) + - [JfjochSettings](docs/JfjochSettings.md) + - [JfjochSettingsSsl](docs/JfjochSettingsSsl.md) + - [JfjochStatistics](docs/JfjochStatistics.md) + - [MeasurementStatistics](docs/MeasurementStatistics.md) + - [PcieDevicesInner](docs/PcieDevicesInner.md) + - [PixelMaskStatistics](docs/PixelMaskStatistics.md) + - [Plot](docs/Plot.md) + - [PlotUnitX](docs/PlotUnitX.md) + - [Plots](docs/Plots.md) + - [RoiAzimList](docs/RoiAzimList.md) + - [RoiAzimuthal](docs/RoiAzimuthal.md) + - [RoiBox](docs/RoiBox.md) + - [RoiBoxList](docs/RoiBoxList.md) + - [RoiCircle](docs/RoiCircle.md) + - [RoiCircleList](docs/RoiCircleList.md) + - [RoiDefinitions](docs/RoiDefinitions.md) + - [RotationAxis](docs/RotationAxis.md) + - [ScanResult](docs/ScanResult.md) + - [ScanResultImagesInner](docs/ScanResultImagesInner.md) + - [SpotFindingSettings](docs/SpotFindingSettings.md) + - [StandardDetectorGeometry](docs/StandardDetectorGeometry.md) + - [UnitCell](docs/UnitCell.md) + - [ZeromqMetadataSettings](docs/ZeromqMetadataSettings.md) + - [ZeromqPreviewSettings](docs/ZeromqPreviewSettings.md) + - [ZeromqSettings](docs/ZeromqSettings.md) + + + +## Documentation For Authorization + +Endpoints do not require authorization. + + +## Author + +filip.leonarski@psi.ch + + diff --git a/_sources/python_client/docs/AzimIntSettings.md.txt b/_sources/python_client/docs/AzimIntSettings.md.txt new file mode 100644 index 00000000..da7c1aae --- /dev/null +++ b/_sources/python_client/docs/AzimIntSettings.md.txt @@ -0,0 +1,34 @@ +# AzimIntSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**polarization_corr** | **bool** | Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings) | [default to True] +**solid_angle_corr** | **bool** | Apply solid angle correction for azimuthal integration | [default to True] +**high_q_recip_a** | **float** | | +**low_q_recip_a** | **float** | | +**q_spacing** | **float** | | +**azimuthal_bins** | **int** | Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration | [optional] [default to 1] + +## Example + +```python +from jfjoch_client.models.azim_int_settings import AzimIntSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of AzimIntSettings from a JSON string +azim_int_settings_instance = AzimIntSettings.from_json(json) +# print the JSON string representation of the object +print(AzimIntSettings.to_json()) + +# convert the object into a dict +azim_int_settings_dict = azim_int_settings_instance.to_dict() +# create an instance of AzimIntSettings from a dict +azim_int_settings_from_dict = AzimIntSettings.from_dict(azim_int_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/BrokerStatus.md.txt b/_sources/python_client/docs/BrokerStatus.md.txt new file mode 100644 index 00000000..0d772274 --- /dev/null +++ b/_sources/python_client/docs/BrokerStatus.md.txt @@ -0,0 +1,33 @@ +# BrokerStatus + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**state** | **str** | | +**progress** | **float** | Progress of data collection (only available if receiving is running) | [optional] +**message** | **str** | Message to display besides state of the jfjoch_broker; mostly used for errors and warnings This matters especially for async functions (start/initialize), where API won't return reason for the error during async operation. | [optional] +**message_severity** | **str** | Level of the message to display | [optional] [default to 'error'] +**gpu_count** | **int** | Number of installed GPUs | [optional] + +## Example + +```python +from jfjoch_client.models.broker_status import BrokerStatus + +# TODO update the JSON string below +json = "{}" +# create an instance of BrokerStatus from a JSON string +broker_status_instance = BrokerStatus.from_json(json) +# print the JSON string representation of the object +print(BrokerStatus.to_json()) + +# convert the object into a dict +broker_status_dict = broker_status_instance.to_dict() +# create an instance of BrokerStatus from a dict +broker_status_from_dict = BrokerStatus.from_dict(broker_status_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/CalibrationStatisticsInner.md.txt b/_sources/python_client/docs/CalibrationStatisticsInner.md.txt new file mode 100644 index 00000000..e6c03dd0 --- /dev/null +++ b/_sources/python_client/docs/CalibrationStatisticsInner.md.txt @@ -0,0 +1,37 @@ +# CalibrationStatisticsInner + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**module_number** | **int** | | +**storage_cell_number** | **int** | | +**pedestal_g0_mean** | **float** | | +**pedestal_g1_mean** | **float** | | +**pedestal_g2_mean** | **float** | | +**gain_g0_mean** | **float** | | +**gain_g1_mean** | **float** | | +**gain_g2_mean** | **float** | | +**masked_pixels** | **int** | | + +## Example + +```python +from jfjoch_client.models.calibration_statistics_inner import CalibrationStatisticsInner + +# TODO update the JSON string below +json = "{}" +# create an instance of CalibrationStatisticsInner from a JSON string +calibration_statistics_inner_instance = CalibrationStatisticsInner.from_json(json) +# print the JSON string representation of the object +print(CalibrationStatisticsInner.to_json()) + +# convert the object into a dict +calibration_statistics_inner_dict = calibration_statistics_inner_instance.to_dict() +# create an instance of CalibrationStatisticsInner from a dict +calibration_statistics_inner_from_dict = CalibrationStatisticsInner.from_dict(calibration_statistics_inner_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ColorScale.md.txt b/_sources/python_client/docs/ColorScale.md.txt new file mode 100644 index 00000000..51ad5d79 --- /dev/null +++ b/_sources/python_client/docs/ColorScale.md.txt @@ -0,0 +1,16 @@ +# ColorScale + + +## Enum + +* `INDIGO` (value: `'Indigo'`) + +* `VIRIDIS` (value: `'Viridis'`) + +* `BLACKWHITE` (value: `'BlackWhite'`) + +* `HEAT` (value: `'Heat'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DarkMaskSettings.md.txt b/_sources/python_client/docs/DarkMaskSettings.md.txt new file mode 100644 index 00000000..58102d94 --- /dev/null +++ b/_sources/python_client/docs/DarkMaskSettings.md.txt @@ -0,0 +1,34 @@ +# DarkMaskSettings + +Settings for collection of dark images to be used for mask calculation + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**detector_threshold_ke_v** | **float** | Energy threshold for dark image collection | [default to 3.5] +**frame_time_us** | **int** | Time between frames for dark image collection | [default to 10000] +**number_of_frames** | **int** | Number of frames for dark image collection; zero means no dark collection | [default to 1000] +**max_allowed_pixel_count** | **int** | Maximum count in a pixel considered normal (not-masked) | [default to 1] +**max_frames_with_signal** | **int** | Maximum number of frames with signal in a pixel considered normal (not-masked) | [default to 10] + +## Example + +```python +from jfjoch_client.models.dark_mask_settings import DarkMaskSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of DarkMaskSettings from a JSON string +dark_mask_settings_instance = DarkMaskSettings.from_json(json) +# print the JSON string representation of the object +print(DarkMaskSettings.to_json()) + +# convert the object into a dict +dark_mask_settings_dict = dark_mask_settings_instance.to_dict() +# create an instance of DarkMaskSettings from a dict +dark_mask_settings_from_dict = DarkMaskSettings.from_dict(dark_mask_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DatasetSettings.md.txt b/_sources/python_client/docs/DatasetSettings.md.txt new file mode 100644 index 00000000..fe7a1895 --- /dev/null +++ b/_sources/python_client/docs/DatasetSettings.md.txt @@ -0,0 +1,65 @@ +# DatasetSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**images_per_trigger** | **int** | For standard synchrotron data collection - this is number of images collected per one TTL trigger For XFEL (pulsed source) - this number is ignored and set to 1 For storage cell mode - this number is ignored and set to number of storage cells | [optional] [default to 1] +**ntrigger** | **int** | Number of TTL trigger that the detector is expected to receive during data collection | [optional] [default to 1] +**image_time_us** | **int** | Image time. If not provided (or zero value) the frame time is assumed as default. For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time. In XFEL mode: summation happens for frames collected with multiple triggers. Ignored for storage cells and if raw data are saved. | [optional] +**beam_x_pxl** | **float** | /entry/detector/beam_center_x in NXmx Beam center in X direction [pixels] | +**beam_y_pxl** | **float** | /entry/detector/beam_center_y in NXmx Beam center in X direction [pixels] | +**detector_distance_mm** | **float** | /entry/detector/distance in NXmx Detector distance [mm] | +**incident_energy_ke_v** | **float** | Used to calculate /entry/beam/incident_wavelength in NXmx Incident particle (photon, electron) energy in keV | +**file_prefix** | **str** | Prefix for filenames. If left empty, no file will be saved. | [optional] [default to ''] +**images_per_file** | **int** | Number of files in a single HDF5 data file (0 = write all images to a single data file). | [optional] [default to 1000] +**space_group_number** | **int** | Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch. | [optional] +**sample_name** | **str** | /entry/sample/name in NXmx Sample name | [optional] [default to ''] +**compression** | **str** | Compression type for the images transferred over ZeroMQ and saved to HDF5 file. | [optional] [default to 'bslz4'] +**total_flux** | **float** | /entry/beam/total_flux in NXmx Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s] | [optional] +**transmission** | **float** | /entry/instrument/attenuator/attenuator_transmission Transmission of attenuator (filter) [no units] | [optional] +**goniometer** | [**RotationAxis**](RotationAxis.md) | | [optional] +**grid_scan** | [**GridScan**](GridScan.md) | | [optional] +**header_appendix** | **object** | Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file. However, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/data of the HDF5 file. This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2. | [optional] +**image_appendix** | **object** | Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) Not saved in HDF5 file | [optional] +**data_reduction_factor_serialmx** | **float** | Rate at which non-indexed images are accepted to be forwarded to writer. Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability. | [optional] [default to 1.0] +**pixel_value_low_threshold** | **int** | Set all counts lower than the value to zero. When the value is set, negative numbers other than error pixel value are always set to zero. Setting to zero is equivalent to turning the option off. | [optional] +**run_number** | **int** | Number of run within an experimental session. Transferred over CBOR stream as \"series ID\", though not saved in HDF5 file. It is highly recommended to keep this number unique for each data collection during experimental series. If not provided, the number will be automatically incremented. | [optional] +**run_name** | **str** | Unique ID of run. Transferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file. It is highly recommended to keep this name unique for each data collection during experimental series. If not provided, the name will be automatically generated as number + colon + file_prefix. | [optional] +**experiment_group** | **str** | Name of group owning the data (e.g. p-group or proposal number). Transferred over CBOR stream, though not saved in HDF5 file. | [optional] +**poisson_compression** | **int** | Enable lossy compression of pixel values that preserves Poisson statistics. Requires to provide a numerical factor SQ. Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer. Compression is turned off if the value is missing or it is set to zero. | [optional] +**write_nxmx_hdf5_master** | **bool** | Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments and to turn off for other experiments. | [optional] [default to True] +**save_calibration** | **bool** | Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer. If parameter is not provided calibration will be saved only if more than 4 images are recorded. | [optional] +**polarization_factor** | **float** | Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization | [optional] +**ring_current_m_a** | **float** | Ring current at the beginning of the data collection | [optional] +**sample_temperature_k** | **float** | Sample temperature in Kelvin | [optional] +**poni_rot1_rad** | **float** | PONI angle rot1 (see PyFAI documentation for details) in radians | [optional] [default to 0.0] +**poni_rot2_rad** | **float** | PONI angle rot2 (see PyFAI documentation for details) in radians | [optional] [default to 0.0] +**poni_rot3_rad** | **float** | PONI angle rot3 (see PyFAI documentation for details) in radians | [optional] [default to 0.0] +**unit_cell** | [**UnitCell**](UnitCell.md) | | [optional] +**spot_finding** | **bool** | Enable spot finding and save spots | [optional] [default to True] +**max_spot_count** | **int** | Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected | [optional] [default to 250] +**detect_ice_rings** | **bool** | Flag spots as ice rings and reduce their effect on indexing | [optional] +**xray_fluorescence_spectrum** | [**DatasetSettingsXrayFluorescenceSpectrum**](DatasetSettingsXrayFluorescenceSpectrum.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.dataset_settings import DatasetSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of DatasetSettings from a JSON string +dataset_settings_instance = DatasetSettings.from_json(json) +# print the JSON string representation of the object +print(DatasetSettings.to_json()) + +# convert the object into a dict +dataset_settings_dict = dataset_settings_instance.to_dict() +# create an instance of DatasetSettings from a dict +dataset_settings_from_dict = DatasetSettings.from_dict(dataset_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DatasetSettingsUnitCell.md.txt b/_sources/python_client/docs/DatasetSettingsUnitCell.md.txt new file mode 100644 index 00000000..891252b1 --- /dev/null +++ b/_sources/python_client/docs/DatasetSettingsUnitCell.md.txt @@ -0,0 +1,35 @@ +# DatasetSettingsUnitCell + +Unit cell parameters. Necessary to run indexing. Units of angstrom and degree + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**a** | **float** | | +**b** | **float** | | +**c** | **float** | | +**alpha** | **float** | | +**beta** | **float** | | +**gamma** | **float** | | + +## Example + +```python +from jfjoch_client.models.dataset_settings_unit_cell import DatasetSettingsUnitCell + +# TODO update the JSON string below +json = "{}" +# create an instance of DatasetSettingsUnitCell from a JSON string +dataset_settings_unit_cell_instance = DatasetSettingsUnitCell.from_json(json) +# print the JSON string representation of the object +print(DatasetSettingsUnitCell.to_json()) + +# convert the object into a dict +dataset_settings_unit_cell_dict = dataset_settings_unit_cell_instance.to_dict() +# create an instance of DatasetSettingsUnitCell from a dict +dataset_settings_unit_cell_from_dict = DatasetSettingsUnitCell.from_dict(dataset_settings_unit_cell_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.md.txt b/_sources/python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.md.txt new file mode 100644 index 00000000..98802cfa --- /dev/null +++ b/_sources/python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.md.txt @@ -0,0 +1,30 @@ +# DatasetSettingsXrayFluorescenceSpectrum + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**energy_e_v** | **List[float]** | X-ray fluorescence scan energy for each measurement point | +**data** | **List[float]** | X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV | + +## Example + +```python +from jfjoch_client.models.dataset_settings_xray_fluorescence_spectrum import DatasetSettingsXrayFluorescenceSpectrum + +# TODO update the JSON string below +json = "{}" +# create an instance of DatasetSettingsXrayFluorescenceSpectrum from a JSON string +dataset_settings_xray_fluorescence_spectrum_instance = DatasetSettingsXrayFluorescenceSpectrum.from_json(json) +# print the JSON string representation of the object +print(DatasetSettingsXrayFluorescenceSpectrum.to_json()) + +# convert the object into a dict +dataset_settings_xray_fluorescence_spectrum_dict = dataset_settings_xray_fluorescence_spectrum_instance.to_dict() +# create an instance of DatasetSettingsXrayFluorescenceSpectrum from a dict +dataset_settings_xray_fluorescence_spectrum_from_dict = DatasetSettingsXrayFluorescenceSpectrum.from_dict(dataset_settings_xray_fluorescence_spectrum_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DefaultApi.md.txt b/_sources/python_client/docs/DefaultApi.md.txt new file mode 100644 index 00000000..fdcc7ef4 --- /dev/null +++ b/_sources/python_client/docs/DefaultApi.md.txt @@ -0,0 +1,4079 @@ +# jfjoch_client.DefaultApi + +All URIs are relative to *http://localhost:5232* + +Method | HTTP request | Description +------------- | ------------- | ------------- +[**cancel_post**](DefaultApi.md#cancel_post) | **POST** /cancel | Cancel running data collection +[**config_azim_int_get**](DefaultApi.md#config_azim_int_get) | **GET** /config/azim_int | Get azimuthal integration configuration +[**config_azim_int_put**](DefaultApi.md#config_azim_int_put) | **PUT** /config/azim_int | Configure azimuthal integration +[**config_dark_mask_get**](DefaultApi.md#config_dark_mask_get) | **GET** /config/dark_mask | Get settings for dark data collection to calculate mask +[**config_dark_mask_put**](DefaultApi.md#config_dark_mask_put) | **PUT** /config/dark_mask | Set configuration for dark data collection to calculate mask +[**config_detector_get**](DefaultApi.md#config_detector_get) | **GET** /config/detector | Get detector configuration +[**config_detector_put**](DefaultApi.md#config_detector_put) | **PUT** /config/detector | Change detector configuration +[**config_file_writer_get**](DefaultApi.md#config_file_writer_get) | **GET** /config/file_writer | Get file writer settings +[**config_file_writer_put**](DefaultApi.md#config_file_writer_put) | **PUT** /config/file_writer | Change file writer settings +[**config_image_format_conversion_post**](DefaultApi.md#config_image_format_conversion_post) | **POST** /config/image_format/conversion | Configure format for data collection with full conversion +[**config_image_format_get**](DefaultApi.md#config_image_format_get) | **GET** /config/image_format | Get image output format +[**config_image_format_put**](DefaultApi.md#config_image_format_put) | **PUT** /config/image_format | Change image output format +[**config_image_format_raw_post**](DefaultApi.md#config_image_format_raw_post) | **POST** /config/image_format/raw | Configure format for raw data collection +[**config_indexing_get**](DefaultApi.md#config_indexing_get) | **GET** /config/indexing | Get indexing configuration +[**config_indexing_put**](DefaultApi.md#config_indexing_put) | **PUT** /config/indexing | Change indexing algorithm settings +[**config_instrument_get**](DefaultApi.md#config_instrument_get) | **GET** /config/instrument | Get instrument metadata +[**config_instrument_put**](DefaultApi.md#config_instrument_put) | **PUT** /config/instrument | Change instrument metadata +[**config_internal_generator_image_put**](DefaultApi.md#config_internal_generator_image_put) | **PUT** /config/internal_generator_image | Load binary image for internal FPGA generator +[**config_internal_generator_image_tiff_put**](DefaultApi.md#config_internal_generator_image_tiff_put) | **PUT** /config/internal_generator_image.tiff | Load TIFF image for internal FPGA generator +[**config_mask_get**](DefaultApi.md#config_mask_get) | **GET** /config/mask | Get mask of the detector (binary) +[**config_mask_tiff_get**](DefaultApi.md#config_mask_tiff_get) | **GET** /config/mask.tiff | Get mask of the detector (TIFF) +[**config_roi_get**](DefaultApi.md#config_roi_get) | **GET** /config/roi | Get ROI definitions +[**config_roi_put**](DefaultApi.md#config_roi_put) | **PUT** /config/roi | Upload ROI definitions +[**config_select_detector_get**](DefaultApi.md#config_select_detector_get) | **GET** /config/select_detector | List available detectors +[**config_select_detector_put**](DefaultApi.md#config_select_detector_put) | **PUT** /config/select_detector | Select detector +[**config_spot_finding_get**](DefaultApi.md#config_spot_finding_get) | **GET** /config/spot_finding | Get data processing configuration +[**config_spot_finding_put**](DefaultApi.md#config_spot_finding_put) | **PUT** /config/spot_finding | Configure spot finding +[**config_user_mask_get**](DefaultApi.md#config_user_mask_get) | **GET** /config/user_mask | Detector must be Initialized. Get user mask of the detector (binary) +[**config_user_mask_put**](DefaultApi.md#config_user_mask_put) | **PUT** /config/user_mask | Upload user mask of the detector (binary) +[**config_user_mask_tiff_get**](DefaultApi.md#config_user_mask_tiff_get) | **GET** /config/user_mask.tiff | Detector must be Initialized. Get user mask of the detector (TIFF) +[**config_user_mask_tiff_put**](DefaultApi.md#config_user_mask_tiff_put) | **PUT** /config/user_mask.tiff | Upload user mask of the detector +[**config_zeromq_metadata_get**](DefaultApi.md#config_zeromq_metadata_get) | **GET** /config/zeromq_metadata | Get ZeroMQ metadata socket settings +[**config_zeromq_metadata_put**](DefaultApi.md#config_zeromq_metadata_put) | **PUT** /config/zeromq_metadata | Set ZeroMQ metadata settings +[**config_zeromq_preview_get**](DefaultApi.md#config_zeromq_preview_get) | **GET** /config/zeromq_preview | Get ZeroMQ preview settings +[**config_zeromq_preview_put**](DefaultApi.md#config_zeromq_preview_put) | **PUT** /config/zeromq_preview | Set ZeroMQ preview settings +[**deactivate_post**](DefaultApi.md#deactivate_post) | **POST** /deactivate | Prepare detector to turn off +[**detector_status_get**](DefaultApi.md#detector_status_get) | **GET** /detector/status | Get detector status +[**fpga_status_get**](DefaultApi.md#fpga_status_get) | **GET** /fpga_status | Get status of FPGA devices +[**image_buffer_clear_post**](DefaultApi.md#image_buffer_clear_post) | **POST** /image_buffer/clear | Clear image buffer +[**image_buffer_image_cbor_get**](DefaultApi.md#image_buffer_image_cbor_get) | **GET** /image_buffer/image.cbor | Get image message in CBOR format +[**image_buffer_image_jpeg_get**](DefaultApi.md#image_buffer_image_jpeg_get) | **GET** /image_buffer/image.jpeg | Get preview image in JPEG format using custom settings +[**image_buffer_image_tiff_get**](DefaultApi.md#image_buffer_image_tiff_get) | **GET** /image_buffer/image.tiff | Get preview image in TIFF format +[**image_buffer_start_cbor_get**](DefaultApi.md#image_buffer_start_cbor_get) | **GET** /image_buffer/start.cbor | Get Start message in CBOR format +[**image_buffer_status_get**](DefaultApi.md#image_buffer_status_get) | **GET** /image_buffer/status | Get status of the image buffers +[**initialize_post**](DefaultApi.md#initialize_post) | **POST** /initialize | Initialize detector and data acquisition +[**pedestal_post**](DefaultApi.md#pedestal_post) | **POST** /pedestal | Collect dark current for the detector +[**preview_pedestal_tiff_get**](DefaultApi.md#preview_pedestal_tiff_get) | **GET** /preview/pedestal.tiff | Get pedestal in TIFF format +[**preview_plot_bin_get**](DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. +[**preview_plot_get**](DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch +[**result_scan_get**](DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result +[**start_post**](DefaultApi.md#start_post) | **POST** /start | Start detector +[**statistics_calibration_get**](DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics +[**statistics_data_collection_get**](DefaultApi.md#statistics_data_collection_get) | **GET** /statistics/data_collection | Get data collection statistics +[**statistics_get**](DefaultApi.md#statistics_get) | **GET** /statistics | Get general statistics +[**status_get**](DefaultApi.md#status_get) | **GET** /status | Get Jungfraujoch status +[**trigger_post**](DefaultApi.md#trigger_post) | **POST** /trigger | Send soft trigger to the detector +[**version_get**](DefaultApi.md#version_get) | **GET** /version | Get Jungfraujoch version of jfjoch_broker +[**wait_till_done_post**](DefaultApi.md#wait_till_done_post) | **POST** /wait_till_done | Wait for acquisition done +[**xfel_event_code_get**](DefaultApi.md#xfel_event_code_get) | **GET** /xfel/event_code | Return XFEL event codes for the current data acquisition +[**xfel_pulse_id_get**](DefaultApi.md#xfel_pulse_id_get) | **GET** /xfel/pulse_id | Return XFEL pulse IDs for the current data acquisition + + +# **cancel_post** +> cancel_post() + +Cancel running data collection + +Command will inform FPGA network card to stop pedestal or data collection at the current stage. +Any frame that is currently being processed by CPU will be finished and sent to writer. +Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state. + +If data collection is not running, the command has no effect. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Cancel running data collection + api_instance.cancel_post() + except Exception as e: + print("Exception when calling DefaultApi->cancel_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: Not defined + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Cancel request sent to FPGAs (or ignored, as data collection is not running) | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_azim_int_get** +> AzimIntSettings config_azim_int_get() + +Get azimuthal integration configuration + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.azim_int_settings import AzimIntSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get azimuthal integration configuration + api_response = api_instance.config_azim_int_get() + print("The response of DefaultApi->config_azim_int_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_azim_int_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**AzimIntSettings**](AzimIntSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_azim_int_put** +> config_azim_int_put(azim_int_settings=azim_int_settings) + +Configure azimuthal integration + +Can be done when detector is Inactive or Idle + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.azim_int_settings import AzimIntSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + azim_int_settings = jfjoch_client.AzimIntSettings() # AzimIntSettings | (optional) + + try: + # Configure azimuthal integration + api_instance.config_azim_int_put(azim_int_settings=azim_int_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_azim_int_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **azim_int_settings** | [**AzimIntSettings**](AzimIntSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_dark_mask_get** +> DarkMaskSettings config_dark_mask_get() + +Get settings for dark data collection to calculate mask + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.dark_mask_settings import DarkMaskSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get settings for dark data collection to calculate mask + api_response = api_instance.config_dark_mask_get() + print("The response of DefaultApi->config_dark_mask_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_dark_mask_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**DarkMaskSettings**](DarkMaskSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_dark_mask_put** +> config_dark_mask_put(dark_mask_settings=dark_mask_settings) + +Set configuration for dark data collection to calculate mask + +This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point. +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.dark_mask_settings import DarkMaskSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + dark_mask_settings = jfjoch_client.DarkMaskSettings() # DarkMaskSettings | (optional) + + try: + # Set configuration for dark data collection to calculate mask + api_instance.config_dark_mask_put(dark_mask_settings=dark_mask_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_dark_mask_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **dark_mask_settings** | [**DarkMaskSettings**](DarkMaskSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_detector_get** +> DetectorSettings config_detector_get() + +Get detector configuration + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.detector_settings import DetectorSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get detector configuration + api_response = api_instance.config_detector_get() + print("The response of DefaultApi->config_detector_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_detector_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**DetectorSettings**](DetectorSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_detector_put** +> config_detector_put(detector_settings=detector_settings) + +Change detector configuration + +Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings. +This can only be done when detector is `Idle`, `Error` or `Inactive` states. +If detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation. +If detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.detector_settings import DetectorSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + detector_settings = jfjoch_client.DetectorSettings() # DetectorSettings | (optional) + + try: + # Change detector configuration + api_instance.config_detector_put(detector_settings=detector_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_detector_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **detector_settings** | [**DetectorSettings**](DetectorSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_file_writer_get** +> FileWriterSettings config_file_writer_get() + +Get file writer settings + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.file_writer_settings import FileWriterSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get file writer settings + api_response = api_instance.config_file_writer_get() + print("The response of DefaultApi->config_file_writer_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_file_writer_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**FileWriterSettings**](FileWriterSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_file_writer_put** +> config_file_writer_put(file_writer_settings=file_writer_settings) + +Change file writer settings + +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.file_writer_settings import FileWriterSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + file_writer_settings = jfjoch_client.FileWriterSettings() # FileWriterSettings | (optional) + + try: + # Change file writer settings + api_instance.config_file_writer_put(file_writer_settings=file_writer_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_file_writer_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **file_writer_settings** | [**FileWriterSettings**](FileWriterSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_image_format_conversion_post** +> config_image_format_conversion_post() + +Configure format for data collection with full conversion + +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Configure format for data collection with full conversion + api_instance.config_image_format_conversion_post() + except Exception as e: + print("Exception when calling DefaultApi->config_image_format_conversion_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_image_format_get** +> ImageFormatSettings config_image_format_get() + +Get image output format + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.image_format_settings import ImageFormatSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get image output format + api_response = api_instance.config_image_format_get() + print("The response of DefaultApi->config_image_format_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_image_format_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**ImageFormatSettings**](ImageFormatSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_image_format_put** +> config_image_format_put(image_format_settings=image_format_settings) + +Change image output format + +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.image_format_settings import ImageFormatSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + image_format_settings = jfjoch_client.ImageFormatSettings() # ImageFormatSettings | (optional) + + try: + # Change image output format + api_instance.config_image_format_put(image_format_settings=image_format_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_image_format_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **image_format_settings** | [**ImageFormatSettings**](ImageFormatSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_image_format_raw_post** +> config_image_format_raw_post() + +Configure format for raw data collection + +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Configure format for raw data collection + api_instance.config_image_format_raw_post() + except Exception as e: + print("Exception when calling DefaultApi->config_image_format_raw_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_indexing_get** +> IndexingSettings config_indexing_get() + +Get indexing configuration + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.indexing_settings import IndexingSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get indexing configuration + api_response = api_instance.config_indexing_get() + print("The response of DefaultApi->config_indexing_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_indexing_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**IndexingSettings**](IndexingSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_indexing_put** +> config_indexing_put(indexing_settings=indexing_settings) + +Change indexing algorithm settings + +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.indexing_settings import IndexingSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + indexing_settings = jfjoch_client.IndexingSettings() # IndexingSettings | (optional) + + try: + # Change indexing algorithm settings + api_instance.config_indexing_put(indexing_settings=indexing_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_indexing_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **indexing_settings** | [**IndexingSettings**](IndexingSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_instrument_get** +> InstrumentMetadata config_instrument_get() + +Get instrument metadata + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.instrument_metadata import InstrumentMetadata +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get instrument metadata + api_response = api_instance.config_instrument_get() + print("The response of DefaultApi->config_instrument_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_instrument_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**InstrumentMetadata**](InstrumentMetadata.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_instrument_put** +> config_instrument_put(instrument_metadata=instrument_metadata) + +Change instrument metadata + +This can only be done when detector is `Idle`, `Error` or `Inactive` states. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.instrument_metadata import InstrumentMetadata +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + instrument_metadata = jfjoch_client.InstrumentMetadata() # InstrumentMetadata | (optional) + + try: + # Change instrument metadata + api_instance.config_instrument_put(instrument_metadata=instrument_metadata) + except Exception as e: + print("Exception when calling DefaultApi->config_instrument_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **instrument_metadata** | [**InstrumentMetadata**](InstrumentMetadata.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_internal_generator_image_put** +> config_internal_generator_image_put(id=id, body=body) + +Load binary image for internal FPGA generator + +Load image for internal FPGA generator. This can only happen in Idle state of the detector. +Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates +(depending on detector settings). + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + id = 56 # int | Image id to upload (optional) + body = None # bytearray | (optional) + + try: + # Load binary image for internal FPGA generator + api_instance.config_internal_generator_image_put(id=id, body=body) + except Exception as e: + print("Exception when calling DefaultApi->config_internal_generator_image_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **id** | **int**| Image id to upload | [optional] + **body** | **bytearray**| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/octet-stream + - **Accept**: text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_internal_generator_image_tiff_put** +> config_internal_generator_image_tiff_put(id=id, body=body) + +Load TIFF image for internal FPGA generator + +Load image for internal FPGA generator. This can only happen in Idle state of the detector. +Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates +(depending on detector settings). + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + id = 56 # int | Image ID to upload (optional) + body = None # bytearray | (optional) + + try: + # Load TIFF image for internal FPGA generator + api_instance.config_internal_generator_image_tiff_put(id=id, body=body) + except Exception as e: + print("Exception when calling DefaultApi->config_internal_generator_image_tiff_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **id** | **int**| Image ID to upload | [optional] + **body** | **bytearray**| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: image/tiff + - **Accept**: text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_mask_get** +> bytearray config_mask_get() + +Get mask of the detector (binary) + +Detector must be Initialized. +Get full pixel mask of the detector. +See NXmx standard for meaning of pixel values. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get mask of the detector (binary) + api_response = api_instance.config_mask_get() + print("The response of DefaultApi->config_mask_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_mask_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/octet-stream + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Binary array (4 byte; unsigned) | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_mask_tiff_get** +> bytearray config_mask_tiff_get() + +Get mask of the detector (TIFF) + +Should be in `Idle` state. +Get full pixel mask of the detector +See NXmx standard for meaning of pixel values + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get mask of the detector (TIFF) + api_response = api_instance.config_mask_tiff_get() + print("The response of DefaultApi->config_mask_tiff_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_mask_tiff_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: image/tiff + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Pixel mask in TIFF format (4 byte; unsigned) | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_roi_get** +> RoiDefinitions config_roi_get() + +Get ROI definitions + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.roi_definitions import RoiDefinitions +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get ROI definitions + api_response = api_instance.config_roi_get() + print("The response of DefaultApi->config_roi_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_roi_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**RoiDefinitions**](RoiDefinitions.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_roi_put** +> config_roi_put(roi_definitions=roi_definitions) + +Upload ROI definitions + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.roi_definitions import RoiDefinitions +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + roi_definitions = jfjoch_client.RoiDefinitions() # RoiDefinitions | (optional) + + try: + # Upload ROI definitions + api_instance.config_roi_put(roi_definitions=roi_definitions) + except Exception as e: + print("Exception when calling DefaultApi->config_roi_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **roi_definitions** | [**RoiDefinitions**](RoiDefinitions.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_select_detector_get** +> DetectorList config_select_detector_get() + +List available detectors + +Configured detectors that can be selected by used + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.detector_list import DetectorList +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # List available detectors + api_response = api_instance.config_select_detector_get() + print("The response of DefaultApi->config_select_detector_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_select_detector_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**DetectorList**](DetectorList.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_select_detector_put** +> config_select_detector_put(detector_selection=detector_selection) + +Select detector + +Jungfraujoch allows to control multiple detectors and/or region-of-interests. +The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response). +Changing detector will set detector to `Inactive` state and will require reinitialization. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.detector_selection import DetectorSelection +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + detector_selection = jfjoch_client.DetectorSelection() # DetectorSelection | (optional) + + try: + # Select detector + api_instance.config_select_detector_put(detector_selection=detector_selection) + except Exception as e: + print("Exception when calling DefaultApi->config_select_detector_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **detector_selection** | [**DetectorSelection**](DetectorSelection.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_spot_finding_get** +> SpotFindingSettings config_spot_finding_get() + +Get data processing configuration + +Can be done anytime + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.spot_finding_settings import SpotFindingSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get data processing configuration + api_response = api_instance.config_spot_finding_get() + print("The response of DefaultApi->config_spot_finding_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_spot_finding_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**SpotFindingSettings**](SpotFindingSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_spot_finding_put** +> config_spot_finding_put(spot_finding_settings=spot_finding_settings) + +Configure spot finding + +Can be done anytime, also while data collection is running + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.spot_finding_settings import SpotFindingSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + spot_finding_settings = jfjoch_client.SpotFindingSettings() # SpotFindingSettings | (optional) + + try: + # Configure spot finding + api_instance.config_spot_finding_put(spot_finding_settings=spot_finding_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_spot_finding_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **spot_finding_settings** | [**SpotFindingSettings**](SpotFindingSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_user_mask_get** +> bytearray config_user_mask_get() + +Detector must be Initialized. Get user mask of the detector (binary) + +Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Detector must be Initialized. Get user mask of the detector (binary) + api_response = api_instance.config_user_mask_get() + print("The response of DefaultApi->config_user_mask_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_user_mask_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/octet-stream + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | User mask in binary format (4 byte; unsigned) | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_user_mask_put** +> config_user_mask_put(body=body) + +Upload user mask of the detector (binary) + +Should be in `Idle` state. +Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. +If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. +In the latter case - module gaps are ignored and don't need to be assigned value. +Mask is expected as binary array (4-byte; unsigned). +0 - good pixel, other value - masked +User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + body = None # bytearray | (optional) + + try: + # Upload user mask of the detector (binary) + api_instance.config_user_mask_put(body=body) + except Exception as e: + print("Exception when calling DefaultApi->config_user_mask_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **body** | **bytearray**| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/octet-stream + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | All good | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_user_mask_tiff_get** +> bytearray config_user_mask_tiff_get() + +Detector must be Initialized. Get user mask of the detector (TIFF) + +Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Detector must be Initialized. Get user mask of the detector (TIFF) + api_response = api_instance.config_user_mask_tiff_get() + print("The response of DefaultApi->config_user_mask_tiff_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_user_mask_tiff_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: image/tiff + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | User mask in TIFF format (4 byte; unsigned) | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_user_mask_tiff_put** +> config_user_mask_tiff_put(body=body) + +Upload user mask of the detector + +Should be in `Idle` state. +Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. +If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. +In the latter case - module gaps are ignored and don't need to be assigned value. +Mask is expected as TIFF (4-byte; unsigned). +0 - good pixel, other value - masked +User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. +User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + body = None # bytearray | (optional) + + try: + # Upload user mask of the detector + api_instance.config_user_mask_tiff_put(body=body) + except Exception as e: + print("Exception when calling DefaultApi->config_user_mask_tiff_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **body** | **bytearray**| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: image/tiff + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | All good | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_zeromq_metadata_get** +> ZeromqMetadataSettings config_zeromq_metadata_get() + +Get ZeroMQ metadata socket settings + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get ZeroMQ metadata socket settings + api_response = api_instance.config_zeromq_metadata_get() + print("The response of DefaultApi->config_zeromq_metadata_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_zeromq_metadata_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**ZeromqMetadataSettings**](ZeromqMetadataSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_zeromq_metadata_put** +> config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings) + +Set ZeroMQ metadata settings + +Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images. +Here settings of the socket can be adjusted. +While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + zeromq_metadata_settings = jfjoch_client.ZeromqMetadataSettings() # ZeromqMetadataSettings | (optional) + + try: + # Set ZeroMQ metadata settings + api_instance.config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_zeromq_metadata_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **zeromq_metadata_settings** | [**ZeromqMetadataSettings**](ZeromqMetadataSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_zeromq_preview_get** +> ZeromqPreviewSettings config_zeromq_preview_get() + +Get ZeroMQ preview settings + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.zeromq_preview_settings import ZeromqPreviewSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get ZeroMQ preview settings + api_response = api_instance.config_zeromq_preview_get() + print("The response of DefaultApi->config_zeromq_preview_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->config_zeromq_preview_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**ZeromqPreviewSettings**](ZeromqPreviewSettings.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **config_zeromq_preview_put** +> config_zeromq_preview_put(zeromq_preview_settings=zeromq_preview_settings) + +Set ZeroMQ preview settings + +Jungfraujoch can generate preview message stream on ZeroMQ SUB socket. +Here settings of the socket can be adjusted. +While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request. +Options set with this PUT request have no effect on HTTP based preview. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.zeromq_preview_settings import ZeromqPreviewSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + zeromq_preview_settings = jfjoch_client.ZeromqPreviewSettings() # ZeromqPreviewSettings | (optional) + + try: + # Set ZeroMQ preview settings + api_instance.config_zeromq_preview_put(zeromq_preview_settings=zeromq_preview_settings) + except Exception as e: + print("Exception when calling DefaultApi->config_zeromq_preview_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **zeromq_preview_settings** | [**ZeromqPreviewSettings**](ZeromqPreviewSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **deactivate_post** +> deactivate_post() + +Prepare detector to turn off + +Should be in `Idle` or `Error` state. +Command deactivates data acquisition and turns off detector high voltage and ASIC. +Should be used always before turning off power from the detector. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Prepare detector to turn off + api_instance.deactivate_post() + except Exception as e: + print("Exception when calling DefaultApi->deactivate_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Detector ready to turn off | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **detector_status_get** +> DetectorStatus detector_status_get() + +Get detector status + +Status of the JUNGFRAU detector + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.detector_status import DetectorStatus +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get detector status + api_response = api_instance.detector_status_get() + print("The response of DefaultApi->detector_status_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->detector_status_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**DetectorStatus**](DetectorStatus.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json, text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**404** | Running in \"simulator\" mode - no detector present | - | +**500** | Error encountered when trying to read status | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **fpga_status_get** +> List[FpgaStatusInner] fpga_status_get() + +Get status of FPGA devices + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.fpga_status_inner import FpgaStatusInner +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get status of FPGA devices + api_response = api_instance.fpga_status_get() + print("The response of DefaultApi->fpga_status_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->fpga_status_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**List[FpgaStatusInner]**](FpgaStatusInner.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **image_buffer_clear_post** +> image_buffer_clear_post() + +Clear image buffer + +Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data. + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Clear image buffer + api_instance.image_buffer_clear_post() + except Exception as e: + print("Exception when calling DefaultApi->image_buffer_clear_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Done | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **image_buffer_image_cbor_get** +> bytearray image_buffer_image_cbor_get(id=id) + +Get image message in CBOR format + +Contains full image data and metadata. The image must come from the latest data collection. + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + id = -1 # int | Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer (optional) (default to -1) + + try: + # Get image message in CBOR format + api_response = api_instance.image_buffer_image_cbor_get(id=id) + print("The response of DefaultApi->image_buffer_image_cbor_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->image_buffer_image_cbor_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **id** | **int**| Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer | [optional] [default to -1] + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/cbor, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Return image message | - | +**404** | Image not present in the buffer - either not yet measured or already replaced by a next image. | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **image_buffer_image_jpeg_get** +> bytearray image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est) + +Get preview image in JPEG format using custom settings + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + id = -1 # int | Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer (optional) (default to -1) + show_user_mask = False # bool | Show user mask (optional) (default to False) + show_roi = False # bool | Show ROI areas on the image (optional) (default to False) + show_spots = True # bool | Show spot finding results on the image (optional) (default to True) + show_beam_center = True # bool | Show beam center on the image (optional) (default to True) + saturation = 3.4 # float | Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used (optional) + jpeg_quality = 100 # int | Quality of JPEG image (100 - highest; 0 - lowest) (optional) (default to 100) + show_res_ring = 0.1 # float | Show resolution ring, provided in Angstrom (optional) (default to 0.1) + color = indigo # str | Color scale for preview image (optional) (default to indigo) + show_res_est = False # bool | Show resolution estimation as a ring (optional) (default to False) + + try: + # Get preview image in JPEG format using custom settings + api_response = api_instance.image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est) + print("The response of DefaultApi->image_buffer_image_jpeg_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->image_buffer_image_jpeg_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **id** | **int**| Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer | [optional] [default to -1] + **show_user_mask** | **bool**| Show user mask | [optional] [default to False] + **show_roi** | **bool**| Show ROI areas on the image | [optional] [default to False] + **show_spots** | **bool**| Show spot finding results on the image | [optional] [default to True] + **show_beam_center** | **bool**| Show beam center on the image | [optional] [default to True] + **saturation** | **float**| Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used | [optional] + **jpeg_quality** | **int**| Quality of JPEG image (100 - highest; 0 - lowest) | [optional] [default to 100] + **show_res_ring** | **float**| Show resolution ring, provided in Angstrom | [optional] [default to 0.1] + **color** | **str**| Color scale for preview image | [optional] [default to indigo] + **show_res_est** | **bool**| Show resolution estimation as a ring | [optional] [default to False] + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: image/jpeg, text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Preview image | - | +**404** | Image not present in the buffer - either not yet measured or already replaced by a next image. | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **image_buffer_image_tiff_get** +> bytearray image_buffer_image_tiff_get(id=id) + +Get preview image in TIFF format + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + id = -1 # int | Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer (optional) (default to -1) + + try: + # Get preview image in TIFF format + api_response = api_instance.image_buffer_image_tiff_get(id=id) + print("The response of DefaultApi->image_buffer_image_tiff_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->image_buffer_image_tiff_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **id** | **int**| Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer | [optional] [default to -1] + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: image/tiff + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Preview image | - | +**404** | No preview image recorded so far | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **image_buffer_start_cbor_get** +> bytearray image_buffer_start_cbor_get() + +Get Start message in CBOR format + +Contains metadata for a dataset (e.g., experimental geometry) + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get Start message in CBOR format + api_response = api_instance.image_buffer_start_cbor_get() + print("The response of DefaultApi->image_buffer_start_cbor_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->image_buffer_start_cbor_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/cbor, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Return start message | - | +**404** | No measurement so far | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **image_buffer_status_get** +> ImageBufferStatus image_buffer_status_get() + +Get status of the image buffers + +Can be run at any stage of Jungfraujoch operation, including during data collection. +The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots, +then image might be replaced in the buffer between calling /images and /image.cbor. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.image_buffer_status import ImageBufferStatus +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get status of the image buffers + api_response = api_instance.image_buffer_status_get() + print("The response of DefaultApi->image_buffer_status_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->image_buffer_status_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**ImageBufferStatus**](ImageBufferStatus.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Done | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **initialize_post** +> initialize_post() + +Initialize detector and data acquisition + +Should be used in two cases: + - Detector is in `Inactive` state + - Detector is in `Error` state +X-ray shutter must be closed. +This operation will reconfigure network interface of the detector. +During operation of the detector it is recommended to use the `POST /pedestal` operation instead. +If storage cells are used, the execution time might be few minutes. + +This is async function - one needs to use `POST /wait_till_done` to ensure operation is done. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Initialize detector and data acquisition + api_instance.initialize_post() + except Exception as e: + print("Exception when calling DefaultApi->initialize_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Initialization started | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **pedestal_post** +> pedestal_post() + +Collect dark current for the detector + +Updates calibration of the JUNGFRAU detector. Must be in `Idle` state. + +X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us). + +This is async function - one needs to use `POST /wait_till_done` to ensure operation is done. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Collect dark current for the detector + api_instance.pedestal_post() + except Exception as e: + print("Exception when calling DefaultApi->pedestal_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **preview_pedestal_tiff_get** +> bytearray preview_pedestal_tiff_get(gain_level, sc=sc) + +Get pedestal in TIFF format + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + gain_level = 56 # int | Gain level (0, 1, 2) + sc = 56 # int | Storage cell number (optional) + + try: + # Get pedestal in TIFF format + api_response = api_instance.preview_pedestal_tiff_get(gain_level, sc=sc) + print("The response of DefaultApi->preview_pedestal_tiff_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->preview_pedestal_tiff_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **gain_level** | **int**| Gain level (0, 1, 2) | + **sc** | **int**| Storage cell number | [optional] + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: image/tiff + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Calibration image | - | +**404** | No calibration recorded so far | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **preview_plot_bin_get** +> bytearray preview_plot_bin_get(type, roi=roi) + +Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + type = 'type_example' # str | Type of requested plot + roi = 'roi_example' # str | Name of ROI for which plot is requested (optional) + + try: + # Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. + api_response = api_instance.preview_plot_bin_get(type, roi=roi) + print("The response of DefaultApi->preview_plot_bin_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->preview_plot_bin_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **type** | **str**| Type of requested plot | + **roi** | **str**| Name of ROI for which plot is requested | [optional] + +### Return type + +**bytearray** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/octet-stream, text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK. | - | +**400** | Input parsing or validation error | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **preview_plot_get** +> Plots preview_plot_get(type, binning=binning, compression=compression, fill=fill, experimental_coord=experimental_coord, azint_unit=azint_unit) + +Generate 1D plot from Jungfraujoch + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.plots import Plots +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + type = 'type_example' # str | Type of requested plot + binning = 1 # int | Binning of frames for the plot (0 = default binning) (optional) (default to 1) + compression = False # bool | Enable DEFLATE compression of output data. (optional) (default to False) + fill = 3.4 # float | Fill value for elements that were missed during data collection (optional) + experimental_coord = False # bool | If measurement has goniometer axis defined, plot X-axis will represent rotation angle If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value For still measurement the number is ignored (optional) (default to False) + azint_unit = Q_recipA # str | Unit used for azim int. (optional) (default to Q_recipA) + + try: + # Generate 1D plot from Jungfraujoch + api_response = api_instance.preview_plot_get(type, binning=binning, compression=compression, fill=fill, experimental_coord=experimental_coord, azint_unit=azint_unit) + print("The response of DefaultApi->preview_plot_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->preview_plot_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **type** | **str**| Type of requested plot | + **binning** | **int**| Binning of frames for the plot (0 = default binning) | [optional] [default to 1] + **compression** | **bool**| Enable DEFLATE compression of output data. | [optional] [default to False] + **fill** | **float**| Fill value for elements that were missed during data collection | [optional] + **experimental_coord** | **bool**| If measurement has goniometer axis defined, plot X-axis will represent rotation angle If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value For still measurement the number is ignored | [optional] [default to False] + **azint_unit** | **str**| Unit used for azim int. | [optional] [default to Q_recipA] + +### Return type + +[**Plots**](Plots.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json, text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK. | - | +**400** | Input parsing or validation error | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **result_scan_get** +> ScanResult result_scan_get() + +Get full scan result + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.scan_result import ScanResult +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get full scan result + api_response = api_instance.result_scan_get() + print("The response of DefaultApi->result_scan_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->result_scan_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**ScanResult**](ScanResult.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK. | - | +**404** | No grid scan recorded | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **start_post** +> start_post(dataset_settings=dataset_settings) + +Start detector + +Start data acquisition. +Detector must be in `Idle` state. +Doesn't run calibration procedure. +When the function returns, detector is ready to accept soft/TTL triggers. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.dataset_settings import DatasetSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + dataset_settings = jfjoch_client.DatasetSettings() # DatasetSettings | (optional) + + try: + # Start detector + api_instance.start_post(dataset_settings=dataset_settings) + except Exception as e: + print("Exception when calling DefaultApi->start_post: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **dataset_settings** | [**DatasetSettings**](DatasetSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **statistics_calibration_get** +> List[CalibrationStatisticsInner] statistics_calibration_get() + +Get calibration statistics + +Statistics are provided for each module/storage cell separately + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.calibration_statistics_inner import CalibrationStatisticsInner +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get calibration statistics + api_response = api_instance.statistics_calibration_get() + print("The response of DefaultApi->statistics_calibration_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->statistics_calibration_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**List[CalibrationStatisticsInner]**](CalibrationStatisticsInner.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **statistics_data_collection_get** +> MeasurementStatistics statistics_data_collection_get() + +Get data collection statistics + +Results of the last data collection + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.measurement_statistics import MeasurementStatistics +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get data collection statistics + api_response = api_instance.statistics_data_collection_get() + print("The response of DefaultApi->statistics_data_collection_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->statistics_data_collection_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**MeasurementStatistics**](MeasurementStatistics.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**404** | No data collection performed so far | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **statistics_get** +> JfjochStatistics statistics_get(compression=compression) + +Get general statistics + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.jfjoch_statistics import JfjochStatistics +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + compression = False # bool | Enable DEFLATE compression of output data. (optional) (default to False) + + try: + # Get general statistics + api_response = api_instance.statistics_get(compression=compression) + print("The response of DefaultApi->statistics_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->statistics_get: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **compression** | **bool**| Enable DEFLATE compression of output data. | [optional] [default to False] + +### Return type + +[**JfjochStatistics**](JfjochStatistics.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **status_get** +> BrokerStatus status_get() + +Get Jungfraujoch status + +Status of the data acquisition + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.broker_status import BrokerStatus +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get Jungfraujoch status + api_response = api_instance.status_get() + print("The response of DefaultApi->status_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->status_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +[**BrokerStatus**](BrokerStatus.md) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **trigger_post** +> trigger_post() + +Send soft trigger to the detector + +Generate soft trigger + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Send soft trigger to the detector + api_instance.trigger_post() + except Exception as e: + print("Exception when calling DefaultApi->trigger_post: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: Not defined + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Trigger sent | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **version_get** +> str version_get() + +Get Jungfraujoch version of jfjoch_broker + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Get Jungfraujoch version of jfjoch_broker + api_response = api_instance.version_get() + print("The response of DefaultApi->version_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->version_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**str** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: text/plain + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Release number of Jungfraujoch | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **wait_till_done_post** +> wait_till_done_post(timeout=timeout) + +Wait for acquisition done + +Block execution of external script till initialization, data collection or pedestal is finished. +Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software. + +To not block web server for a indefinite period of time, the procedure is provided with a timeout. +Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection. + + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + timeout = 60 # int | Timeout in seconds (0 == immediate response) (optional) (default to 60) + + try: + # Wait for acquisition done + api_instance.wait_till_done_post(timeout=timeout) + except Exception as e: + print("Exception when calling DefaultApi->wait_till_done_post: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **timeout** | **int**| Timeout in seconds (0 == immediate response) | [optional] [default to 60] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Detector in `Idle` state, another data collection can start immediately | - | +**400** | Timeout parameter out of bounds | - | +**500** | Error within Jungfraujoch code - see output message. | - | +**502** | Detector is inactive mode | - | +**504** | Timeout reached, need to restart operation | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **xfel_event_code_get** +> List[int] xfel_event_code_get() + +Return XFEL event codes for the current data acquisition + +Return array of XFEL event codes + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Return XFEL event codes for the current data acquisition + api_response = api_instance.xfel_event_code_get() + print("The response of DefaultApi->xfel_event_code_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->xfel_event_code_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**List[int]** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Event codes collected | - | +**404** | Not in XFEL mode or no acquisition recorded | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **xfel_pulse_id_get** +> List[int] xfel_pulse_id_get() + +Return XFEL pulse IDs for the current data acquisition + +Return array of XFEL pulse IDs - (-1) if image not recorded + +### Example + + +```python +import jfjoch_client +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.DefaultApi(api_client) + + try: + # Return XFEL pulse IDs for the current data acquisition + api_response = api_instance.xfel_pulse_id_get() + print("The response of DefaultApi->xfel_pulse_id_get:\n") + pprint(api_response) + except Exception as e: + print("Exception when calling DefaultApi->xfel_pulse_id_get: %s\n" % e) +``` + + + +### Parameters + +This endpoint does not need any parameter. + +### Return type + +**List[int]** + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: Not defined + - **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Pulse ID collected | - | +**404** | Not in XFEL mode or no acquisition recorded | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + diff --git a/_sources/python_client/docs/Detector.md.txt b/_sources/python_client/docs/Detector.md.txt new file mode 100644 index 00000000..9aa1a608 --- /dev/null +++ b/_sources/python_client/docs/Detector.md.txt @@ -0,0 +1,49 @@ +# Detector + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**description** | **str** | | +**serial_number** | **str** | | [optional] [default to 'Unknown'] +**type** | [**DetectorType**](DetectorType.md) | | [optional] +**high_voltage_v** | **int** | | [optional] [default to 0] +**udp_interface_count** | **int** | | [optional] [default to 1] +**module_sync** | **bool** | Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER). | [optional] [default to True] +**sensor_thickness_um** | **float** | | [optional] [default to 320] +**readout_time_us** | **int** | Minimum difference between frame time and count time in microseconds Defaults are 3 us for EIGER and 20 us for JUNGFRAU | [optional] +**minimum_count_time_us** | **int** | Minimum count time available for the detector. | [optional] +**minimum_frame_time_us** | **int** | Minimum frame time available for the detector. | [optional] +**calibration_file** | **List[str]** | Can be empty for all detectors - default calibration used. For JUNGFRAU: list of gain files, one entry per module. For EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module. | [optional] +**hostname** | **List[str]** | Hostname for detector module. One entry per module One entry per module. Either empty or number of module entries. | [optional] +**sensor_material** | **str** | | [optional] [default to 'Si'] +**tx_delay** | **List[int]** | | [optional] +**base_data_ipv4_address** | **str** | | [optional] +**standard_geometry** | [**StandardDetectorGeometry**](StandardDetectorGeometry.md) | | [optional] +**custom_geometry** | [**List[DetectorModule]**](DetectorModule.md) | | [optional] +**roi_mode** | **str** | ROI setting for DECTRIS detectors | [optional] [default to ''] +**mirror_y** | **bool** | Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner | [optional] [default to True] +**temp_thresold_deg_c** | **int** | Temperature threshold for JUNGFRAU detector modules | [optional] [default to 55] +**default_settings** | [**DetectorSettings**](DetectorSettings.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.detector import Detector + +# TODO update the JSON string below +json = "{}" +# create an instance of Detector from a JSON string +detector_instance = Detector.from_json(json) +# print the JSON string representation of the object +print(Detector.to_json()) + +# convert the object into a dict +detector_dict = detector_instance.to_dict() +# create an instance of Detector from a dict +detector_from_dict = Detector.from_dict(detector_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorList.md.txt b/_sources/python_client/docs/DetectorList.md.txt new file mode 100644 index 00000000..c9928a2e --- /dev/null +++ b/_sources/python_client/docs/DetectorList.md.txt @@ -0,0 +1,30 @@ +# DetectorList + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**detectors** | [**List[DetectorListElement]**](DetectorListElement.md) | | +**current_id** | **int** | | + +## Example + +```python +from jfjoch_client.models.detector_list import DetectorList + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorList from a JSON string +detector_list_instance = DetectorList.from_json(json) +# print the JSON string representation of the object +print(DetectorList.to_json()) + +# convert the object into a dict +detector_list_dict = detector_list_instance.to_dict() +# create an instance of DetectorList from a dict +detector_list_from_dict = DetectorList.from_dict(detector_list_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorListDetectorsInner.md.txt b/_sources/python_client/docs/DetectorListDetectorsInner.md.txt new file mode 100644 index 00000000..99845c5b --- /dev/null +++ b/_sources/python_client/docs/DetectorListDetectorsInner.md.txt @@ -0,0 +1,36 @@ +# DetectorListDetectorsInner + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**id** | **int** | | +**description** | **str** | | +**serial_number** | **str** | | +**base_ipv4_addr** | **str** | | +**udp_interface_count** | **int** | Number of UDP interfaces per detector module | +**nmodules** | **int** | | +**width** | **int** | | +**height** | **int** | | + +## Example + +```python +from jfjoch_client.models.detector_list_detectors_inner import DetectorListDetectorsInner + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorListDetectorsInner from a JSON string +detector_list_detectors_inner_instance = DetectorListDetectorsInner.from_json(json) +# print the JSON string representation of the object +print(DetectorListDetectorsInner.to_json()) + +# convert the object into a dict +detector_list_detectors_inner_dict = detector_list_detectors_inner_instance.to_dict() +# create an instance of DetectorListDetectorsInner from a dict +detector_list_detectors_inner_from_dict = DetectorListDetectorsInner.from_dict(detector_list_detectors_inner_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorListElement.md.txt b/_sources/python_client/docs/DetectorListElement.md.txt new file mode 100644 index 00000000..c9f46183 --- /dev/null +++ b/_sources/python_client/docs/DetectorListElement.md.txt @@ -0,0 +1,41 @@ +# DetectorListElement + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**id** | **int** | | +**description** | **str** | | +**serial_number** | **str** | | +**base_ipv4_addr** | **str** | | +**udp_interface_count** | **int** | Number of UDP interfaces per detector module | +**nmodules** | **int** | | +**width** | **int** | | +**height** | **int** | | +**pixel_size_mm** | **float** | | [optional] +**readout_time_us** | **int** | | +**min_frame_time_us** | **int** | | +**min_count_time_us** | **int** | | +**type** | [**DetectorType**](DetectorType.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.detector_list_element import DetectorListElement + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorListElement from a JSON string +detector_list_element_instance = DetectorListElement.from_json(json) +# print the JSON string representation of the object +print(DetectorListElement.to_json()) + +# convert the object into a dict +detector_list_element_dict = detector_list_element_instance.to_dict() +# create an instance of DetectorListElement from a dict +detector_list_element_from_dict = DetectorListElement.from_dict(detector_list_element_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorModule.md.txt b/_sources/python_client/docs/DetectorModule.md.txt new file mode 100644 index 00000000..d5b6f2d7 --- /dev/null +++ b/_sources/python_client/docs/DetectorModule.md.txt @@ -0,0 +1,32 @@ +# DetectorModule + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**x0** | **float** | | +**y0** | **float** | | +**fast_axis** | [**DetectorModuleDirection**](DetectorModuleDirection.md) | | +**slow_axis** | [**DetectorModuleDirection**](DetectorModuleDirection.md) | | + +## Example + +```python +from jfjoch_client.models.detector_module import DetectorModule + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorModule from a JSON string +detector_module_instance = DetectorModule.from_json(json) +# print the JSON string representation of the object +print(DetectorModule.to_json()) + +# convert the object into a dict +detector_module_dict = detector_module_instance.to_dict() +# create an instance of DetectorModule from a dict +detector_module_from_dict = DetectorModule.from_dict(detector_module_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorModuleDirection.md.txt b/_sources/python_client/docs/DetectorModuleDirection.md.txt new file mode 100644 index 00000000..bbdac0cd --- /dev/null +++ b/_sources/python_client/docs/DetectorModuleDirection.md.txt @@ -0,0 +1,16 @@ +# DetectorModuleDirection + + +## Enum + +* `XP` (value: `'Xp'`) + +* `XN` (value: `'Xn'`) + +* `YP` (value: `'Yp'`) + +* `YN` (value: `'Yn'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorPowerState.md.txt b/_sources/python_client/docs/DetectorPowerState.md.txt new file mode 100644 index 00000000..21627663 --- /dev/null +++ b/_sources/python_client/docs/DetectorPowerState.md.txt @@ -0,0 +1,15 @@ +# DetectorPowerState + +Power on of ASICs + +## Enum + +* `POWERON` (value: `'PowerOn'`) + +* `POWEROFF` (value: `'PowerOff'`) + +* `PARTIAL` (value: `'Partial'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorSelection.md.txt b/_sources/python_client/docs/DetectorSelection.md.txt new file mode 100644 index 00000000..993fc33c --- /dev/null +++ b/_sources/python_client/docs/DetectorSelection.md.txt @@ -0,0 +1,29 @@ +# DetectorSelection + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**id** | **int** | | + +## Example + +```python +from jfjoch_client.models.detector_selection import DetectorSelection + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorSelection from a JSON string +detector_selection_instance = DetectorSelection.from_json(json) +# print the JSON string representation of the object +print(DetectorSelection.to_json()) + +# convert the object into a dict +detector_selection_dict = detector_selection_instance.to_dict() +# create an instance of DetectorSelection from a dict +detector_selection_from_dict = DetectorSelection.from_dict(detector_selection_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorSettings.md.txt b/_sources/python_client/docs/DetectorSettings.md.txt new file mode 100644 index 00000000..659508a7 --- /dev/null +++ b/_sources/python_client/docs/DetectorSettings.md.txt @@ -0,0 +1,44 @@ +# DetectorSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**frame_time_us** | **int** | Interval between consecutive frames. This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number. For EIGER detector this is default frame time, not used otherwise | +**count_time_us** | **int** | Integration time of the detector. If not provided count time will be set to maximum value for a given frame time. | [optional] +**internal_frame_generator** | **bool** | Use internal frame generator in FPGA instead of getting data from a real detector | [optional] [default to False] +**internal_frame_generator_images** | **int** | Number of images stored in the internal frame generator. | [optional] [default to 1] +**detector_trigger_delay_ns** | **int** | Delay between TTL trigger and acquisition start [ns] | [optional] [default to 0] +**timing** | [**DetectorTiming**](DetectorTiming.md) | | [optional] [default to DetectorTiming.TRIGGER] +**eiger_threshold_ke_v** | **float** | Threshold for the PSI EIGER detector and all DECTRIS detectors. If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy. If value is not provided, threshold will be determined on start of acquisition as half of incident energy. This might lead to increased start time. | [optional] +**eiger_bit_depth** | **int** | Bit depth of PSI EIGER read-out. This is If value is not provided, depth will be determined based on the image time: * Exposure time < 500 microseconds depth of 8 bit will be used, * 500 <= exposure time < 2622 microseconds depth of 16 bit will be used * Exposure time >= 2622 microseconds depth of 32 bit will be used. | [optional] +**jungfrau_pedestal_g0_frames** | **int** | | [optional] [default to 2000] +**jungfrau_pedestal_g1_frames** | **int** | | [optional] [default to 300] +**jungfrau_pedestal_g2_frames** | **int** | | [optional] [default to 300] +**jungfrau_pedestal_min_image_count** | **int** | Minimum number of collected images for pedestal to consider it viable | [optional] [default to 128] +**jungfrau_storage_cell_count** | **int** | | [optional] [default to 1] +**jungfrau_storage_cell_delay_ns** | **int** | Delay between two storage cells [ns] | [optional] [default to 5000] +**jungfrau_fixed_gain_g1** | **bool** | Fix gain to G1 (can be useful for storage cells) | [optional] [default to False] +**jungfrau_use_gain_hg0** | **bool** | Use high G0 (for low energy applications) | [optional] [default to False] + +## Example + +```python +from jfjoch_client.models.detector_settings import DetectorSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorSettings from a JSON string +detector_settings_instance = DetectorSettings.from_json(json) +# print the JSON string representation of the object +print(DetectorSettings.to_json()) + +# convert the object into a dict +detector_settings_dict = detector_settings_instance.to_dict() +# create an instance of DetectorSettings from a dict +detector_settings_from_dict = DetectorSettings.from_dict(detector_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorState.md.txt b/_sources/python_client/docs/DetectorState.md.txt new file mode 100644 index 00000000..cb7ab7a0 --- /dev/null +++ b/_sources/python_client/docs/DetectorState.md.txt @@ -0,0 +1,19 @@ +# DetectorState + +Current state of the detector + +## Enum + +* `IDLE` (value: `'Idle'`) + +* `WAITING` (value: `'Waiting'`) + +* `BUSY` (value: `'Busy'`) + +* `ERROR` (value: `'Error'`) + +* `NOT_CONNECTED` (value: `'Not connected'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorStatus.md.txt b/_sources/python_client/docs/DetectorStatus.md.txt new file mode 100644 index 00000000..a2b08e6d --- /dev/null +++ b/_sources/python_client/docs/DetectorStatus.md.txt @@ -0,0 +1,34 @@ +# DetectorStatus + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**state** | [**DetectorState**](DetectorState.md) | | +**powerchip** | [**DetectorPowerState**](DetectorPowerState.md) | | +**server_version** | **str** | Detector server (on read-out boards) version | +**number_of_triggers_left** | **int** | Remaining triggers to the detector (max of all modules) | +**fpga_temp_deg_c** | **List[int]** | Temperature of detector FPGAs | +**high_voltage_v** | **List[int]** | High voltage for detector modules | + +## Example + +```python +from jfjoch_client.models.detector_status import DetectorStatus + +# TODO update the JSON string below +json = "{}" +# create an instance of DetectorStatus from a JSON string +detector_status_instance = DetectorStatus.from_json(json) +# print the JSON string representation of the object +print(DetectorStatus.to_json()) + +# convert the object into a dict +detector_status_dict = detector_status_instance.to_dict() +# create an instance of DetectorStatus from a dict +detector_status_from_dict = DetectorStatus.from_dict(detector_status_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorTiming.md.txt b/_sources/python_client/docs/DetectorTiming.md.txt new file mode 100644 index 00000000..65eedbfd --- /dev/null +++ b/_sources/python_client/docs/DetectorTiming.md.txt @@ -0,0 +1,16 @@ +# DetectorTiming + + +## Enum + +* `AUTO` (value: `'auto'`) + +* `TRIGGER` (value: `'trigger'`) + +* `BURST` (value: `'burst'`) + +* `GATED` (value: `'gated'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/DetectorType.md.txt b/_sources/python_client/docs/DetectorType.md.txt new file mode 100644 index 00000000..223c249b --- /dev/null +++ b/_sources/python_client/docs/DetectorType.md.txt @@ -0,0 +1,14 @@ +# DetectorType + + +## Enum + +* `EIGER` (value: `'EIGER'`) + +* `JUNGFRAU` (value: `'JUNGFRAU'`) + +* `DECTRIS` (value: `'DECTRIS'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ErrorMessage.md.txt b/_sources/python_client/docs/ErrorMessage.md.txt new file mode 100644 index 00000000..89b25cc7 --- /dev/null +++ b/_sources/python_client/docs/ErrorMessage.md.txt @@ -0,0 +1,30 @@ +# ErrorMessage + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**msg** | **str** | Human readable message | +**reason** | **str** | Enumerate field for automated analysis | + +## Example + +```python +from jfjoch_client.models.error_message import ErrorMessage + +# TODO update the JSON string below +json = "{}" +# create an instance of ErrorMessage from a JSON string +error_message_instance = ErrorMessage.from_json(json) +# print the JSON string representation of the object +print(ErrorMessage.to_json()) + +# convert the object into a dict +error_message_dict = error_message_instance.to_dict() +# create an instance of ErrorMessage from a dict +error_message_from_dict = ErrorMessage.from_dict(error_message_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/FileWriterFormat.md.txt b/_sources/python_client/docs/FileWriterFormat.md.txt new file mode 100644 index 00000000..99f12a8f --- /dev/null +++ b/_sources/python_client/docs/FileWriterFormat.md.txt @@ -0,0 +1,21 @@ +# FileWriterFormat + +None - no master file written NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling + +## Enum + +* `NONE` (value: `'None'`) + +* `NXMXLEGACY` (value: `'NXmxLegacy'`) + +* `NXMXVDS` (value: `'NXmxVDS'`) + +* `CBF` (value: `'CBF'`) + +* `TIFF` (value: `'TIFF'`) + +* `NOFILEWRITTEN` (value: `'NoFileWritten'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/FileWriterSettings.md.txt b/_sources/python_client/docs/FileWriterSettings.md.txt new file mode 100644 index 00000000..3b041f79 --- /dev/null +++ b/_sources/python_client/docs/FileWriterSettings.md.txt @@ -0,0 +1,30 @@ +# FileWriterSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**overwrite** | **bool** | Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix. | [optional] [default to False] +**format** | [**FileWriterFormat**](FileWriterFormat.md) | | [optional] [default to FileWriterFormat.NXMXLEGACY] + +## Example + +```python +from jfjoch_client.models.file_writer_settings import FileWriterSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of FileWriterSettings from a JSON string +file_writer_settings_instance = FileWriterSettings.from_json(json) +# print the JSON string representation of the object +print(FileWriterSettings.to_json()) + +# convert the object into a dict +file_writer_settings_dict = file_writer_settings_instance.to_dict() +# create an instance of FileWriterSettings from a dict +file_writer_settings_from_dict = FileWriterSettings.from_dict(file_writer_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/FpgaStatusInner.md.txt b/_sources/python_client/docs/FpgaStatusInner.md.txt new file mode 100644 index 00000000..7461249f --- /dev/null +++ b/_sources/python_client/docs/FpgaStatusInner.md.txt @@ -0,0 +1,42 @@ +# FpgaStatusInner + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**pci_dev_id** | **str** | | +**serial_number** | **str** | | +**fw_version** | **str** | | +**base_mac_addr** | **str** | | +**eth_link_count** | **int** | | +**eth_link_status** | **int** | | +**power_usage_w** | **float** | | +**fpga_temp_c** | **float** | | +**hbm_temp_c** | **float** | | +**packets_udp** | **int** | | +**packets_sls** | **int** | | +**idle** | **bool** | | +**pcie_link_speed** | **int** | PCIe link speed measured by generation (expected value is 4 == PCIe Gen4) | +**pcie_link_width** | **int** | PCIe link width (expected value is 8 == x8) | + +## Example + +```python +from jfjoch_client.models.fpga_status_inner import FpgaStatusInner + +# TODO update the JSON string below +json = "{}" +# create an instance of FpgaStatusInner from a JSON string +fpga_status_inner_instance = FpgaStatusInner.from_json(json) +# print the JSON string representation of the object +print(FpgaStatusInner.to_json()) + +# convert the object into a dict +fpga_status_inner_dict = fpga_status_inner_instance.to_dict() +# create an instance of FpgaStatusInner from a dict +fpga_status_inner_from_dict = FpgaStatusInner.from_dict(fpga_status_inner_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/GeomRefinementAlgorithm.md.txt b/_sources/python_client/docs/GeomRefinementAlgorithm.md.txt new file mode 100644 index 00000000..cc250fe0 --- /dev/null +++ b/_sources/python_client/docs/GeomRefinementAlgorithm.md.txt @@ -0,0 +1,13 @@ +# GeomRefinementAlgorithm + +Selection of an post-indexing detector geometry refinement algorithm used by Jungfraujoch. This option is using non-linear least squares optimization to find unit cell and beam center. + +## Enum + +* `BEAMCENTER` (value: `'BeamCenter'`) + +* `NONE` (value: `'None'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/GridPlot.md.txt b/_sources/python_client/docs/GridPlot.md.txt new file mode 100644 index 00000000..4f16bdb9 --- /dev/null +++ b/_sources/python_client/docs/GridPlot.md.txt @@ -0,0 +1,30 @@ +# GridPlot + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**data** | **List[float]** | | +**width** | **int** | | + +## Example + +```python +from jfjoch_client.models.grid_plot import GridPlot + +# TODO update the JSON string below +json = "{}" +# create an instance of GridPlot from a JSON string +grid_plot_instance = GridPlot.from_json(json) +# print the JSON string representation of the object +print(GridPlot.to_json()) + +# convert the object into a dict +grid_plot_dict = grid_plot_instance.to_dict() +# create an instance of GridPlot from a dict +grid_plot_from_dict = GridPlot.from_dict(grid_plot_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/GridPlots.md.txt b/_sources/python_client/docs/GridPlots.md.txt new file mode 100644 index 00000000..309772c1 --- /dev/null +++ b/_sources/python_client/docs/GridPlots.md.txt @@ -0,0 +1,30 @@ +# GridPlots + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**plots** | [**List[GridPlot]**](GridPlot.md) | | +**width** | **int** | | + +## Example + +```python +from jfjoch_client.models.grid_plots import GridPlots + +# TODO update the JSON string below +json = "{}" +# create an instance of GridPlots from a JSON string +grid_plots_instance = GridPlots.from_json(json) +# print the JSON string representation of the object +print(GridPlots.to_json()) + +# convert the object into a dict +grid_plots_dict = grid_plots_instance.to_dict() +# create an instance of GridPlots from a dict +grid_plots_from_dict = GridPlots.from_dict(grid_plots_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/GridScan.md.txt b/_sources/python_client/docs/GridScan.md.txt new file mode 100644 index 00000000..81b36bf6 --- /dev/null +++ b/_sources/python_client/docs/GridScan.md.txt @@ -0,0 +1,34 @@ +# GridScan + +Definition of a grid scan (mutually exclusive with `rotation_axis`) + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**n_fast** | **int** | Number of elements in the fast direction | +**step_x_um** | **float** | Step in grid along the fast direction. Can be negative. Positive number: left to right Negative number: right to left | +**step_y_um** | **float** | Step in grid along the slow direction. Can be negative. Positive number: top to bottom Negative number: bottom to top | +**vertical** | **bool** | If disabled: fast direction = X, slow direction = Y If enabled: fast direction = Y, slow direction = X | [optional] [default to False] +**snake** | **bool** | Flip fast direction for every second row | [optional] [default to False] + +## Example + +```python +from jfjoch_client.models.grid_scan import GridScan + +# TODO update the JSON string below +json = "{}" +# create an instance of GridScan from a JSON string +grid_scan_instance = GridScan.from_json(json) +# print the JSON string representation of the object +print(GridScan.to_json()) + +# convert the object into a dict +grid_scan_dict = grid_scan_instance.to_dict() +# create an instance of GridScan from a dict +grid_scan_from_dict = GridScan.from_dict(grid_scan_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/GridScanResult.md.txt b/_sources/python_client/docs/GridScanResult.md.txt new file mode 100644 index 00000000..afc0caae --- /dev/null +++ b/_sources/python_client/docs/GridScanResult.md.txt @@ -0,0 +1,35 @@ +# GridScanResult + +Results of a grid scan + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**det_img** | **List[int]** | Detector image number for a given cell | +**bkg_estimate** | **List[float]** | | +**spot_count** | **List[int]** | | +**indexed_lattices** | **List[int]** | | +**mosaicity** | **List[float]** | | +**b_factor** | **List[float]** | | + +## Example + +```python +from jfjoch_client.models.grid_scan_result import GridScanResult + +# TODO update the JSON string below +json = "{}" +# create an instance of GridScanResult from a JSON string +grid_scan_result_instance = GridScanResult.from_json(json) +# print the JSON string representation of the object +print(GridScanResult.to_json()) + +# convert the object into a dict +grid_scan_result_dict = grid_scan_result_instance.to_dict() +# create an instance of GridScanResult from a dict +grid_scan_result_from_dict = GridScanResult.from_dict(grid_scan_result_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/GridScanResultImagesInner.md.txt b/_sources/python_client/docs/GridScanResultImagesInner.md.txt new file mode 100644 index 00000000..08c5fcfc --- /dev/null +++ b/_sources/python_client/docs/GridScanResultImagesInner.md.txt @@ -0,0 +1,36 @@ +# GridScanResultImagesInner + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**efficiency** | **float** | | +**number** | **int** | Detector image number for a given cell | +**bkg** | **float** | Background estimate | [optional] +**spots** | **int** | Spot count | [optional] +**index** | **int** | Indexing solution | [optional] +**mos** | **float** | Mosaicity estimate | [optional] +**b** | **float** | B-Factor estimate | [optional] +**uc** | [**UnitCell**](UnitCell.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.grid_scan_result_images_inner import GridScanResultImagesInner + +# TODO update the JSON string below +json = "{}" +# create an instance of GridScanResultImagesInner from a JSON string +grid_scan_result_images_inner_instance = GridScanResultImagesInner.from_json(json) +# print the JSON string representation of the object +print(GridScanResultImagesInner.to_json()) + +# convert the object into a dict +grid_scan_result_images_inner_dict = grid_scan_result_images_inner_instance.to_dict() +# create an instance of GridScanResultImagesInner from a dict +grid_scan_result_images_inner_from_dict = GridScanResultImagesInner.from_dict(grid_scan_result_images_inner_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ImageBufferStatus.md.txt b/_sources/python_client/docs/ImageBufferStatus.md.txt new file mode 100644 index 00000000..eb2e858f --- /dev/null +++ b/_sources/python_client/docs/ImageBufferStatus.md.txt @@ -0,0 +1,34 @@ +# ImageBufferStatus + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**min_image_number** | **int** | Smallest image number available in the buffer | +**max_image_number** | **int** | Largest image number available in the buffer | +**image_numbers** | **List[int]** | Image numbers currently present in the buffer. | +**total_slots** | **int** | Number of slots in the image buffer. This number, compared to number of images in data collection and frame rate will determine \"retention\" rate of the image buffer. | +**available_slots** | **int** | Slots available for the data collection | +**current_counter** | **int** | Counter of changes in the image buffer - either new start message or new image added. For optimization one can only load new images/datasets from the HTTP if this value changes. Counter is optional as it was not implemented in older versions to avoid breaking change | [optional] + +## Example + +```python +from jfjoch_client.models.image_buffer_status import ImageBufferStatus + +# TODO update the JSON string below +json = "{}" +# create an instance of ImageBufferStatus from a JSON string +image_buffer_status_instance = ImageBufferStatus.from_json(json) +# print the JSON string representation of the object +print(ImageBufferStatus.to_json()) + +# convert the object into a dict +image_buffer_status_dict = image_buffer_status_instance.to_dict() +# create an instance of ImageBufferStatus from a dict +image_buffer_status_from_dict = ImageBufferStatus.from_dict(image_buffer_status_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ImageFormatSettings.md.txt b/_sources/python_client/docs/ImageFormatSettings.md.txt new file mode 100644 index 00000000..5fc22d63 --- /dev/null +++ b/_sources/python_client/docs/ImageFormatSettings.md.txt @@ -0,0 +1,39 @@ +# ImageFormatSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**summation** | **bool** | Enable summation of images to a given image_time If disabled images are saved according to original detector speed, but image count is adjusted | +**geometry_transform** | **bool** | Place module read-out into their location on composed detector and extend multipixels | +**jungfrau_conversion** | **bool** | Convert pixel value in ADU to photon counts/energy Only affects JUNGFRAU detector | +**jungfrau_conversion_factor_ke_v** | **float** | Used to convert energy deposited into pixel to counts If not provided incident_energy_keV is used | [optional] +**bit_depth_image** | **int** | Bit depth of resulting image (it doesn't affect the detector read-out value) If not provided value is adjusted automatically | [optional] +**signed_output** | **bool** | Controls if pixels have signed output If not provided value is adjusted automatically | [optional] +**mask_module_edges** | **bool** | Mask 1 pixel on the module boundary | [default to True] +**mask_chip_edges** | **bool** | Mask multipixels on chip boundary | [default to True] +**jungfrau_mask_pixels_without_g0** | **bool** | JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1. This should be turned off for cases, where detector is operated at room temperature with long exposure time. | [optional] [default to True] +**apply_mask** | **bool** | Masked pixels are set to special value in the images produced by Jungfraujoch | [default to False] +**jungfrau_pedestal_g0_rms_limit** | **int** | Pixels with pedestal G0 RMS above the threshold are marked as masked pixels | [optional] [default to 100] + +## Example + +```python +from jfjoch_client.models.image_format_settings import ImageFormatSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of ImageFormatSettings from a JSON string +image_format_settings_instance = ImageFormatSettings.from_json(json) +# print the JSON string representation of the object +print(ImageFormatSettings.to_json()) + +# convert the object into a dict +image_format_settings_dict = image_format_settings_instance.to_dict() +# create an instance of ImageFormatSettings from a dict +image_format_settings_from_dict = ImageFormatSettings.from_dict(image_format_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ImagePusherType.md.txt b/_sources/python_client/docs/ImagePusherType.md.txt new file mode 100644 index 00000000..3706b1a8 --- /dev/null +++ b/_sources/python_client/docs/ImagePusherType.md.txt @@ -0,0 +1,16 @@ +# ImagePusherType + + +## Enum + +* `ZEROMQ` (value: `'ZeroMQ'`) + +* `HDF5` (value: `'HDF5'`) + +* `CBOR` (value: `'CBOR'`) + +* `NONE` (value: `'None'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/IndexingAlgorithm.md.txt b/_sources/python_client/docs/IndexingAlgorithm.md.txt new file mode 100644 index 00000000..67381323 --- /dev/null +++ b/_sources/python_client/docs/IndexingAlgorithm.md.txt @@ -0,0 +1,19 @@ +# IndexingAlgorithm + +Selection of an indexing algorithm used by Jungfraujoch + +## Enum + +* `FFBIDX` (value: `'FFBIDX'`) + +* `FFT` (value: `'FFT'`) + +* `FFTW` (value: `'FFTW'`) + +* `AUTO` (value: `'Auto'`) + +* `NONE` (value: `'None'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/IndexingSettings.md.txt b/_sources/python_client/docs/IndexingSettings.md.txt new file mode 100644 index 00000000..fdac9a17 --- /dev/null +++ b/_sources/python_client/docs/IndexingSettings.md.txt @@ -0,0 +1,43 @@ +# IndexingSettings + +Settings for crystallography indexing + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**algorithm** | [**IndexingAlgorithm**](IndexingAlgorithm.md) | | [default to IndexingAlgorithm.FFBIDX] +**fft_max_unit_cell_a** | **float** | Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT | [default to 250] +**fft_min_unit_cell_a** | **float** | Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT | [default to 10.0] +**fft_high_resolution_a** | **float** | Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT. There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems. | [default to 2.0] +**fft_num_vectors** | **int** | Number of search directions for the FFT algorithm; parameter value affects execution time of FFT. | [default to 16384] +**tolerance** | **float** | Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted | +**thread_count** | **int** | Thread count for indexing algorithm | +**geom_refinement_algorithm** | [**GeomRefinementAlgorithm**](GeomRefinementAlgorithm.md) | | +**unit_cell_dist_tolerance** | **float** | Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored | [default to 0.05] +**viable_cell_min_spots** | **int** | Minimum number of indexed spots required for a cell to be considered viable | [default to 10] +**index_ice_rings** | **bool** | Include spots marked as ice rings in the indexing run. If `dataset_settings` doesn't have `detect_ice_rings` on, this option will have no effect on processing. | [default to False] +**rotation_indexing** | **bool** | | [default to False] +**rotation_indexing_min_angular_range_deg** | **float** | | [default to 20.0] +**rotation_indexing_angular_stride_deg** | **float** | | [default to 0.5] + +## Example + +```python +from jfjoch_client.models.indexing_settings import IndexingSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of IndexingSettings from a JSON string +indexing_settings_instance = IndexingSettings.from_json(json) +# print the JSON string representation of the object +print(IndexingSettings.to_json()) + +# convert the object into a dict +indexing_settings_dict = indexing_settings_instance.to_dict() +# create an instance of IndexingSettings from a dict +indexing_settings_from_dict = IndexingSettings.from_dict(indexing_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/InstrumentMetadata.md.txt b/_sources/python_client/docs/InstrumentMetadata.md.txt new file mode 100644 index 00000000..7908c65c --- /dev/null +++ b/_sources/python_client/docs/InstrumentMetadata.md.txt @@ -0,0 +1,34 @@ +# InstrumentMetadata + +Metadata for a measurement instrument + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**source_name** | **str** | | +**source_type** | **str** | Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource NXsource allows the following: Spallation Neutron Source Pulsed Reactor Neutron Source Reactor Neutron Source Synchrotron X-ray Source Pulsed Muon Source Rotating Anode X-ray Fixed Tube X-ray UV Laser Free-Electron Laser Optical Laser Ion Source UV Plasma Source Metal Jet X-ray | [optional] [default to ''] +**instrument_name** | **str** | | +**pulsed_source** | **bool** | Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code) | [optional] [default to False] +**electron_source** | **bool** | Settings specific to electron source (e.g., wavelength definition) | [optional] [default to False] + +## Example + +```python +from jfjoch_client.models.instrument_metadata import InstrumentMetadata + +# TODO update the JSON string below +json = "{}" +# create an instance of InstrumentMetadata from a JSON string +instrument_metadata_instance = InstrumentMetadata.from_json(json) +# print the JSON string representation of the object +print(InstrumentMetadata.to_json()) + +# convert the object into a dict +instrument_metadata_dict = instrument_metadata_instance.to_dict() +# create an instance of InstrumentMetadata from a dict +instrument_metadata_from_dict = InstrumentMetadata.from_dict(instrument_metadata_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/JfjochBrokerApi.md.txt b/_sources/python_client/docs/JfjochBrokerApi.md.txt new file mode 100644 index 00000000..28cd069a --- /dev/null +++ b/_sources/python_client/docs/JfjochBrokerApi.md.txt @@ -0,0 +1,77 @@ +# jfjoch_client.JfjochBrokerApi + +All URIs are relative to *http://localhost:5232* + +Method | HTTP request | Description +------------- | ------------- | ------------- +[**config_zeromq_metadata_put**](JfjochBrokerApi.md#config_zeromq_metadata_put) | **PUT** /config/zeromq_metadata | Set ZeroMQ metadata settings + + +# **config_zeromq_metadata_put** +> config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings) + +Set ZeroMQ metadata settings + +Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images. Here settings of the socket can be adjusted. While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request. + +### Example + + +```python +import jfjoch_client +from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings +from jfjoch_client.rest import ApiException +from pprint import pprint + +# Defining the host is optional and defaults to http://localhost:5232 +# See configuration.py for a list of all supported configuration parameters. +configuration = jfjoch_client.Configuration( + host = "http://localhost:5232" +) + + +# Enter a context with an instance of the API client +with jfjoch_client.ApiClient(configuration) as api_client: + # Create an instance of the API class + api_instance = jfjoch_client.JfjochBrokerApi(api_client) + zeromq_metadata_settings = jfjoch_client.ZeromqMetadataSettings() # ZeromqMetadataSettings | (optional) + + try: + # Set ZeroMQ metadata settings + api_instance.config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings) + except Exception as e: + print("Exception when calling JfjochBrokerApi->config_zeromq_metadata_put: %s\n" % e) +``` + + + +### Parameters + + +Name | Type | Description | Notes +------------- | ------------- | ------------- | ------------- + **zeromq_metadata_settings** | [**ZeromqMetadataSettings**](ZeromqMetadataSettings.md)| | [optional] + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + + - **Content-Type**: application/json + - **Accept**: text/plain, application/json + +### HTTP response details + +| Status code | Description | Response headers | +|-------------|-------------|------------------| +**200** | Everything OK | - | +**400** | Input parsing or validation error | - | +**500** | Error within Jungfraujoch code - see output message. | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + diff --git a/_sources/python_client/docs/JfjochSettings.md.txt b/_sources/python_client/docs/JfjochSettings.md.txt new file mode 100644 index 00000000..c9875b45 --- /dev/null +++ b/_sources/python_client/docs/JfjochSettings.md.txt @@ -0,0 +1,49 @@ +# JfjochSettings + +Default settings for Jungfraujoch software. This structure is used to provide default settings using configuration JSON file and is not used in HTTP. + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**pcie** | [**List[PcieDevicesInner]**](PcieDevicesInner.md) | | [optional] +**zeromq** | [**ZeromqSettings**](ZeromqSettings.md) | | [optional] +**instrument** | [**InstrumentMetadata**](InstrumentMetadata.md) | | [optional] +**file_writer** | [**FileWriterSettings**](FileWriterSettings.md) | | [optional] +**detector** | [**List[Detector]**](Detector.md) | | +**indexing** | [**IndexingSettings**](IndexingSettings.md) | | [optional] +**detector_settings** | [**DetectorSettings**](DetectorSettings.md) | | [optional] +**azim_int** | [**AzimIntSettings**](AzimIntSettings.md) | | [optional] +**image_format** | [**ImageFormatSettings**](ImageFormatSettings.md) | | [optional] +**image_buffer_mi_b** | **int** | Size of internal buffer in MiB for images before they are sent to a stream | [optional] [default to 2048] +**verbose** | **bool** | Print extra debug information | [optional] [default to False] +**receiver_threads** | **int** | Number of threads used by the receiver | [optional] [default to 64] +**numa_policy** | **str** | NUMA policy to bind CPUs | [optional] +**frontend_directory** | **str** | Location of built JavaScript web frontend | +**ssl** | [**JfjochSettingsSsl**](JfjochSettingsSsl.md) | | [optional] +**spot_finding** | [**SpotFindingSettings**](SpotFindingSettings.md) | | [optional] +**image_pusher** | [**ImagePusherType**](ImagePusherType.md) | | [default to ImagePusherType.NONE] +**zeromq_preview** | [**ZeromqPreviewSettings**](ZeromqPreviewSettings.md) | | [optional] +**zeromq_metadata** | [**ZeromqMetadataSettings**](ZeromqMetadataSettings.md) | | [optional] +**dark_mask** | [**DarkMaskSettings**](DarkMaskSettings.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.jfjoch_settings import JfjochSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of JfjochSettings from a JSON string +jfjoch_settings_instance = JfjochSettings.from_json(json) +# print the JSON string representation of the object +print(JfjochSettings.to_json()) + +# convert the object into a dict +jfjoch_settings_dict = jfjoch_settings_instance.to_dict() +# create an instance of JfjochSettings from a dict +jfjoch_settings_from_dict = JfjochSettings.from_dict(jfjoch_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/JfjochSettingsSsl.md.txt b/_sources/python_client/docs/JfjochSettingsSsl.md.txt new file mode 100644 index 00000000..058fb06a --- /dev/null +++ b/_sources/python_client/docs/JfjochSettingsSsl.md.txt @@ -0,0 +1,30 @@ +# JfjochSettingsSsl + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**certificate** | **str** | | +**key** | **str** | | + +## Example + +```python +from jfjoch_client.models.jfjoch_settings_ssl import JfjochSettingsSsl + +# TODO update the JSON string below +json = "{}" +# create an instance of JfjochSettingsSsl from a JSON string +jfjoch_settings_ssl_instance = JfjochSettingsSsl.from_json(json) +# print the JSON string representation of the object +print(JfjochSettingsSsl.to_json()) + +# convert the object into a dict +jfjoch_settings_ssl_dict = jfjoch_settings_ssl_instance.to_dict() +# create an instance of JfjochSettingsSsl from a dict +jfjoch_settings_ssl_from_dict = JfjochSettingsSsl.from_dict(jfjoch_settings_ssl_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/JfjochStatistics.md.txt b/_sources/python_client/docs/JfjochStatistics.md.txt new file mode 100644 index 00000000..43c15895 --- /dev/null +++ b/_sources/python_client/docs/JfjochStatistics.md.txt @@ -0,0 +1,48 @@ +# JfjochStatistics + +Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**detector** | [**DetectorStatus**](DetectorStatus.md) | | [optional] +**detector_list** | [**DetectorList**](DetectorList.md) | | [optional] +**detector_settings** | [**DetectorSettings**](DetectorSettings.md) | | [optional] +**image_format_settings** | [**ImageFormatSettings**](ImageFormatSettings.md) | | [optional] +**instrument_metadata** | [**InstrumentMetadata**](InstrumentMetadata.md) | | [optional] +**file_writer_settings** | [**FileWriterSettings**](FileWriterSettings.md) | | [optional] +**data_processing_settings** | [**SpotFindingSettings**](SpotFindingSettings.md) | | [optional] +**measurement** | [**MeasurementStatistics**](MeasurementStatistics.md) | | [optional] +**broker** | [**BrokerStatus**](BrokerStatus.md) | | [optional] +**fpga** | [**List[FpgaStatusInner]**](FpgaStatusInner.md) | | [optional] +**calibration** | [**List[CalibrationStatisticsInner]**](CalibrationStatisticsInner.md) | | [optional] +**zeromq_preview** | [**ZeromqPreviewSettings**](ZeromqPreviewSettings.md) | | [optional] +**zeromq_metadata** | [**ZeromqMetadataSettings**](ZeromqMetadataSettings.md) | | [optional] +**dark_mask** | [**DarkMaskSettings**](DarkMaskSettings.md) | | [optional] +**pixel_mask** | [**PixelMaskStatistics**](PixelMaskStatistics.md) | | [optional] +**roi** | [**RoiDefinitions**](RoiDefinitions.md) | | [optional] +**az_int** | [**AzimIntSettings**](AzimIntSettings.md) | | [optional] +**buffer** | [**ImageBufferStatus**](ImageBufferStatus.md) | | [optional] +**indexing** | [**IndexingSettings**](IndexingSettings.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.jfjoch_statistics import JfjochStatistics + +# TODO update the JSON string below +json = "{}" +# create an instance of JfjochStatistics from a JSON string +jfjoch_statistics_instance = JfjochStatistics.from_json(json) +# print the JSON string representation of the object +print(JfjochStatistics.to_json()) + +# convert the object into a dict +jfjoch_statistics_dict = jfjoch_statistics_instance.to_dict() +# create an instance of JfjochStatistics from a dict +jfjoch_statistics_from_dict = JfjochStatistics.from_dict(jfjoch_statistics_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/MeasurementStatistics.md.txt b/_sources/python_client/docs/MeasurementStatistics.md.txt new file mode 100644 index 00000000..582577e3 --- /dev/null +++ b/_sources/python_client/docs/MeasurementStatistics.md.txt @@ -0,0 +1,50 @@ +# MeasurementStatistics + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**file_prefix** | **str** | | [optional] +**run_number** | **int** | Number of data collection run. This can be either automatically incremented or provided externally for each data collection. | [optional] +**experiment_group** | **str** | Name of group owning the data (e.g. p-group or proposal number). | [optional] +**images_expected** | **int** | | [optional] +**images_collected** | **int** | Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance. | [optional] +**images_sent** | **int** | Images sent to the writer. The value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue. | [optional] +**images_discarded_lossy_compression** | **int** | Images discarded by the lossy compression filter | [optional] +**max_image_number_sent** | **int** | | [optional] +**collection_efficiency** | **float** | | [optional] +**compression_ratio** | **float** | | [optional] +**cancelled** | **bool** | | [optional] +**max_receiver_delay** | **int** | | [optional] +**indexing_rate** | **float** | | [optional] +**detector_width** | **int** | | [optional] +**detector_height** | **int** | | [optional] +**detector_pixel_depth** | **int** | | [optional] +**bkg_estimate** | **float** | | [optional] +**unit_cell** | **str** | | [optional] +**error_pixels** | **float** | Moving average of 1000 images counting number of error pixels on the detector | [optional] +**saturated_pixels** | **float** | Moving average of 1000 images counting number of saturated pixels on the detector | [optional] +**roi_beam_pixels** | **float** | If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images for number of valid pixels within this ROI | [optional] +**roi_beam_sum** | **float** | If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images for sum of valid pixels within this ROI | [optional] + +## Example + +```python +from jfjoch_client.models.measurement_statistics import MeasurementStatistics + +# TODO update the JSON string below +json = "{}" +# create an instance of MeasurementStatistics from a JSON string +measurement_statistics_instance = MeasurementStatistics.from_json(json) +# print the JSON string representation of the object +print(MeasurementStatistics.to_json()) + +# convert the object into a dict +measurement_statistics_dict = measurement_statistics_instance.to_dict() +# create an instance of MeasurementStatistics from a dict +measurement_statistics_from_dict = MeasurementStatistics.from_dict(measurement_statistics_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/PcieDevicesInner.md.txt b/_sources/python_client/docs/PcieDevicesInner.md.txt new file mode 100644 index 00000000..26bf9cc1 --- /dev/null +++ b/_sources/python_client/docs/PcieDevicesInner.md.txt @@ -0,0 +1,30 @@ +# PcieDevicesInner + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**blk** | **str** | Block device name | [optional] +**ipv4** | **str** | IPv4 address of the block device | [optional] + +## Example + +```python +from jfjoch_client.models.pcie_devices_inner import PcieDevicesInner + +# TODO update the JSON string below +json = "{}" +# create an instance of PcieDevicesInner from a JSON string +pcie_devices_inner_instance = PcieDevicesInner.from_json(json) +# print the JSON string representation of the object +print(PcieDevicesInner.to_json()) + +# convert the object into a dict +pcie_devices_inner_dict = pcie_devices_inner_instance.to_dict() +# create an instance of PcieDevicesInner from a dict +pcie_devices_inner_from_dict = PcieDevicesInner.from_dict(pcie_devices_inner_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/PixelMaskStatistics.md.txt b/_sources/python_client/docs/PixelMaskStatistics.md.txt new file mode 100644 index 00000000..5b707d19 --- /dev/null +++ b/_sources/python_client/docs/PixelMaskStatistics.md.txt @@ -0,0 +1,31 @@ +# PixelMaskStatistics + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**user_mask** | **int** | Number of pixels masked using the user mask | [optional] +**too_high_pedestal_rms** | **int** | Number of pixels with G0 pedestal RMS higher than provided threshold | [optional] +**wrong_gain** | **int** | Number of pixels that show wrong gain level during the pedestal procedure | [optional] + +## Example + +```python +from jfjoch_client.models.pixel_mask_statistics import PixelMaskStatistics + +# TODO update the JSON string below +json = "{}" +# create an instance of PixelMaskStatistics from a JSON string +pixel_mask_statistics_instance = PixelMaskStatistics.from_json(json) +# print the JSON string representation of the object +print(PixelMaskStatistics.to_json()) + +# convert the object into a dict +pixel_mask_statistics_dict = pixel_mask_statistics_instance.to_dict() +# create an instance of PixelMaskStatistics from a dict +pixel_mask_statistics_from_dict = PixelMaskStatistics.from_dict(pixel_mask_statistics_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/Plot.md.txt b/_sources/python_client/docs/Plot.md.txt new file mode 100644 index 00000000..24ddb47c --- /dev/null +++ b/_sources/python_client/docs/Plot.md.txt @@ -0,0 +1,33 @@ +# Plot + +x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**title** | **str** | | [default to ''] +**x** | **List[float]** | | +**y** | **List[Optional[float]]** | | +**z** | **List[Optional[float]]** | | [optional] + +## Example + +```python +from jfjoch_client.models.plot import Plot + +# TODO update the JSON string below +json = "{}" +# create an instance of Plot from a JSON string +plot_instance = Plot.from_json(json) +# print the JSON string representation of the object +print(Plot.to_json()) + +# convert the object into a dict +plot_dict = plot_instance.to_dict() +# create an instance of Plot from a dict +plot_from_dict = Plot.from_dict(plot_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/PlotTypeEnum.md.txt b/_sources/python_client/docs/PlotTypeEnum.md.txt new file mode 100644 index 00000000..272e8743 --- /dev/null +++ b/_sources/python_client/docs/PlotTypeEnum.md.txt @@ -0,0 +1,48 @@ +# PlotTypeEnum + + +## Enum + +* `BKG_ESTIMATE` (value: `'bkg_estimate'`) + +* `AZINT` (value: `'azint'`) + +* `SPOT_COUNT` (value: `'spot_count'`) + +* `INDEXING_RATE` (value: `'indexing_rate'`) + +* `INDEXING_UNIT_CELL_LENGTH` (value: `'indexing_unit_cell_length'`) + +* `INDEXING_UNIT_CELL_ANGLE` (value: `'indexing_unit_cell_angle'`) + +* `ERROR_PIXELS` (value: `'error_pixels'`) + +* `IMAGE_COLLECTION_EFFICIENCY` (value: `'image_collection_efficiency'`) + +* `RECEIVER_DELAY` (value: `'receiver_delay'`) + +* `RECEIVER_FREE_SEND_BUF` (value: `'receiver_free_send_buf'`) + +* `STRONG_PIXELS` (value: `'strong_pixels'`) + +* `ROI_SUM` (value: `'roi_sum'`) + +* `ROI_MEAN` (value: `'roi_mean'`) + +* `ROI_MAX_COUNT` (value: `'roi_max_count'`) + +* `ROI_PIXELS` (value: `'roi_pixels'`) + +* `ROI_WEIGHTED_X` (value: `'roi_weighted_x'`) + +* `ROI_WEIGHTED_Y` (value: `'roi_weighted_y'`) + +* `PACKETS_RECEIVED` (value: `'packets_received'`) + +* `MAX_PIXEL_VALUE` (value: `'max_pixel_value'`) + +* `RESOLUTION_ESTIMATE` (value: `'resolution_estimate'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/PlotUnitX.md.txt b/_sources/python_client/docs/PlotUnitX.md.txt new file mode 100644 index 00000000..2b0f2e93 --- /dev/null +++ b/_sources/python_client/docs/PlotUnitX.md.txt @@ -0,0 +1,20 @@ +# PlotUnitX + + +## Enum + +* `IMAGE_NUMBER` (value: `'image_number'`) + +* `Q_RECIP_A` (value: `'q_recipA'`) + +* `D_A` (value: `'d_A'`) + +* `ANGLE_DEG` (value: `'angle_deg'`) + +* `ADU` (value: `'ADU'`) + +* `GRID_UM` (value: `'grid_um'`) + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/Plots.md.txt b/_sources/python_client/docs/Plots.md.txt new file mode 100644 index 00000000..2efd9e2a --- /dev/null +++ b/_sources/python_client/docs/Plots.md.txt @@ -0,0 +1,33 @@ +# Plots + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**title** | **str** | | [optional] +**unit_x** | [**PlotUnitX**](PlotUnitX.md) | | [default to PlotUnitX.IMAGE_NUMBER] +**size_x** | **float** | Max X range of the plot | [optional] +**size_y** | **float** | Max Y range of the plot | [optional] +**plot** | [**List[Plot]**](Plot.md) | | + +## Example + +```python +from jfjoch_client.models.plots import Plots + +# TODO update the JSON string below +json = "{}" +# create an instance of Plots from a JSON string +plots_instance = Plots.from_json(json) +# print the JSON string representation of the object +print(Plots.to_json()) + +# convert the object into a dict +plots_dict = plots_instance.to_dict() +# create an instance of Plots from a dict +plots_from_dict = Plots.from_dict(plots_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/PreviewSettings.md.txt b/_sources/python_client/docs/PreviewSettings.md.txt new file mode 100644 index 00000000..0ffb0f04 --- /dev/null +++ b/_sources/python_client/docs/PreviewSettings.md.txt @@ -0,0 +1,36 @@ +# PreviewSettings + +Settings for JPEG rendering of preview images + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**saturation** | **int** | Saturation value to set contrast in the preview image | +**show_spots** | **bool** | Show spot finding results on the image | [optional] [default to True] +**show_roi** | **bool** | Show ROI areas on the image | [optional] [default to False] +**jpeg_quality** | **int** | Quality of JPEG image (100 - highest; 0 - lowest) | [optional] [default to 100] +**show_indexed** | **bool** | Preview indexed images only | [optional] [default to False] +**show_user_mask** | **bool** | Show user mask | [optional] [default to False] +**resolution_ring** | **float** | | [optional] [default to 0.1] + +## Example + +```python +from jfjoch_client.models.preview_settings import PreviewSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of PreviewSettings from a JSON string +preview_settings_instance = PreviewSettings.from_json(json) +# print the JSON string representation of the object +print(PreviewSettings.to_json()) + +# convert the object into a dict +preview_settings_dict = preview_settings_instance.to_dict() +# create an instance of PreviewSettings from a dict +preview_settings_from_dict = PreviewSettings.from_dict(preview_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiAzimList.md.txt b/_sources/python_client/docs/RoiAzimList.md.txt new file mode 100644 index 00000000..fe7b3fe9 --- /dev/null +++ b/_sources/python_client/docs/RoiAzimList.md.txt @@ -0,0 +1,30 @@ +# RoiAzimList + +List of azimuthal ROIs + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**rois** | [**List[RoiAzimuthal]**](RoiAzimuthal.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.roi_azim_list import RoiAzimList + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiAzimList from a JSON string +roi_azim_list_instance = RoiAzimList.from_json(json) +# print the JSON string representation of the object +print(RoiAzimList.to_json()) + +# convert the object into a dict +roi_azim_list_dict = roi_azim_list_instance.to_dict() +# create an instance of RoiAzimList from a dict +roi_azim_list_from_dict = RoiAzimList.from_dict(roi_azim_list_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiAzimuthal.md.txt b/_sources/python_client/docs/RoiAzimuthal.md.txt new file mode 100644 index 00000000..b736ad68 --- /dev/null +++ b/_sources/python_client/docs/RoiAzimuthal.md.txt @@ -0,0 +1,32 @@ +# RoiAzimuthal + +ROI as Q-range (or resolution range) + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**name** | **str** | Name for the ROI; used in the plots | +**q_min_recip_a** | **float** | Minimum Q-range for the ROI | +**q_max_recip_a** | **float** | Maximum Q-range for the ROI | + +## Example + +```python +from jfjoch_client.models.roi_azimuthal import RoiAzimuthal + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiAzimuthal from a JSON string +roi_azimuthal_instance = RoiAzimuthal.from_json(json) +# print the JSON string representation of the object +print(RoiAzimuthal.to_json()) + +# convert the object into a dict +roi_azimuthal_dict = roi_azimuthal_instance.to_dict() +# create an instance of RoiAzimuthal from a dict +roi_azimuthal_from_dict = RoiAzimuthal.from_dict(roi_azimuthal_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiBox.md.txt b/_sources/python_client/docs/RoiBox.md.txt new file mode 100644 index 00000000..f485d133 --- /dev/null +++ b/_sources/python_client/docs/RoiBox.md.txt @@ -0,0 +1,34 @@ +# RoiBox + +Box ROI + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**name** | **str** | Name for the ROI; used in the plots | +**min_x_pxl** | **int** | Lower bound (inclusive) in X coordinate for the box | +**max_x_pxl** | **int** | Upper bound (inclusive) in X coordinate for the box | +**min_y_pxl** | **int** | Lower bound (inclusive) in Y coordinate for the box | +**max_y_pxl** | **int** | Upper bound (inclusive) in Y coordinate for the box | + +## Example + +```python +from jfjoch_client.models.roi_box import RoiBox + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiBox from a JSON string +roi_box_instance = RoiBox.from_json(json) +# print the JSON string representation of the object +print(RoiBox.to_json()) + +# convert the object into a dict +roi_box_dict = roi_box_instance.to_dict() +# create an instance of RoiBox from a dict +roi_box_from_dict = RoiBox.from_dict(roi_box_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiBoxList.md.txt b/_sources/python_client/docs/RoiBoxList.md.txt new file mode 100644 index 00000000..7cd200d0 --- /dev/null +++ b/_sources/python_client/docs/RoiBoxList.md.txt @@ -0,0 +1,30 @@ +# RoiBoxList + +List of box ROIs + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**rois** | [**List[RoiBox]**](RoiBox.md) | | [optional] + +## Example + +```python +from jfjoch_client.models.roi_box_list import RoiBoxList + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiBoxList from a JSON string +roi_box_list_instance = RoiBoxList.from_json(json) +# print the JSON string representation of the object +print(RoiBoxList.to_json()) + +# convert the object into a dict +roi_box_list_dict = roi_box_list_instance.to_dict() +# create an instance of RoiBoxList from a dict +roi_box_list_from_dict = RoiBoxList.from_dict(roi_box_list_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiCircle.md.txt b/_sources/python_client/docs/RoiCircle.md.txt new file mode 100644 index 00000000..b2dabb67 --- /dev/null +++ b/_sources/python_client/docs/RoiCircle.md.txt @@ -0,0 +1,33 @@ +# RoiCircle + +Circular ROI + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**name** | **str** | Name for the ROI; used in the plots | +**center_x_pxl** | **float** | X coordinate of center of the circle [pixels] | +**center_y_pxl** | **float** | Y coordinate of center of the circle [pixels] | +**radius_pxl** | **float** | Radius of the circle [pixels] | + +## Example + +```python +from jfjoch_client.models.roi_circle import RoiCircle + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiCircle from a JSON string +roi_circle_instance = RoiCircle.from_json(json) +# print the JSON string representation of the object +print(RoiCircle.to_json()) + +# convert the object into a dict +roi_circle_dict = roi_circle_instance.to_dict() +# create an instance of RoiCircle from a dict +roi_circle_from_dict = RoiCircle.from_dict(roi_circle_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiCircleList.md.txt b/_sources/python_client/docs/RoiCircleList.md.txt new file mode 100644 index 00000000..5873af15 --- /dev/null +++ b/_sources/python_client/docs/RoiCircleList.md.txt @@ -0,0 +1,30 @@ +# RoiCircleList + +List of circular ROIs + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**rois** | [**List[RoiCircle]**](RoiCircle.md) | | + +## Example + +```python +from jfjoch_client.models.roi_circle_list import RoiCircleList + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiCircleList from a JSON string +roi_circle_list_instance = RoiCircleList.from_json(json) +# print the JSON string representation of the object +print(RoiCircleList.to_json()) + +# convert the object into a dict +roi_circle_list_dict = roi_circle_list_instance.to_dict() +# create an instance of RoiCircleList from a dict +roi_circle_list_from_dict = RoiCircleList.from_dict(roi_circle_list_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RoiDefinitions.md.txt b/_sources/python_client/docs/RoiDefinitions.md.txt new file mode 100644 index 00000000..f47c4c10 --- /dev/null +++ b/_sources/python_client/docs/RoiDefinitions.md.txt @@ -0,0 +1,32 @@ +# RoiDefinitions + +ROI defintions + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**box** | [**RoiBoxList**](RoiBoxList.md) | | +**circle** | [**RoiCircleList**](RoiCircleList.md) | | +**azim** | [**RoiAzimList**](RoiAzimList.md) | | + +## Example + +```python +from jfjoch_client.models.roi_definitions import RoiDefinitions + +# TODO update the JSON string below +json = "{}" +# create an instance of RoiDefinitions from a JSON string +roi_definitions_instance = RoiDefinitions.from_json(json) +# print the JSON string representation of the object +print(RoiDefinitions.to_json()) + +# convert the object into a dict +roi_definitions_dict = roi_definitions_instance.to_dict() +# create an instance of RoiDefinitions from a dict +roi_definitions_from_dict = RoiDefinitions.from_dict(roi_definitions_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/RotationAxis.md.txt b/_sources/python_client/docs/RotationAxis.md.txt new file mode 100644 index 00000000..a78b26ba --- /dev/null +++ b/_sources/python_client/docs/RotationAxis.md.txt @@ -0,0 +1,35 @@ +# RotationAxis + +Definition of a crystal rotation axis + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**name** | **str** | Name of rotation axis (e.g., omega, phi) | [optional] [default to 'omega'] +**step** | **float** | Angle step (per image) in degrees | +**start** | **float** | Start angle in degrees | [optional] [default to 0] +**vector** | **List[float]** | Rotation axis | +**helical_step_um** | **List[float]** | Translation (per image) for helical scan | [optional] +**screening_wedge_deg** | **float** | Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening) | [optional] + +## Example + +```python +from jfjoch_client.models.rotation_axis import RotationAxis + +# TODO update the JSON string below +json = "{}" +# create an instance of RotationAxis from a JSON string +rotation_axis_instance = RotationAxis.from_json(json) +# print the JSON string representation of the object +print(RotationAxis.to_json()) + +# convert the object into a dict +rotation_axis_dict = rotation_axis_instance.to_dict() +# create an instance of RotationAxis from a dict +rotation_axis_from_dict = RotationAxis.from_dict(rotation_axis_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ScanResult.md.txt b/_sources/python_client/docs/ScanResult.md.txt new file mode 100644 index 00000000..73857ff6 --- /dev/null +++ b/_sources/python_client/docs/ScanResult.md.txt @@ -0,0 +1,33 @@ +# ScanResult + +Results of a scan + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**file_prefix** | **str** | | [optional] +**rotation_unit_cell** | [**UnitCell**](UnitCell.md) | | [optional] +**rotation_crystal_lattice** | **List[float]** | Real-space crystal lattice 3D vectors in Angstrom. Order is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z) | [optional] +**images** | [**List[ScanResultImagesInner]**](ScanResultImagesInner.md) | | + +## Example + +```python +from jfjoch_client.models.scan_result import ScanResult + +# TODO update the JSON string below +json = "{}" +# create an instance of ScanResult from a JSON string +scan_result_instance = ScanResult.from_json(json) +# print the JSON string representation of the object +print(ScanResult.to_json()) + +# convert the object into a dict +scan_result_dict = scan_result_instance.to_dict() +# create an instance of ScanResult from a dict +scan_result_from_dict = ScanResult.from_dict(scan_result_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ScanResultImagesInner.md.txt b/_sources/python_client/docs/ScanResultImagesInner.md.txt new file mode 100644 index 00000000..129b827d --- /dev/null +++ b/_sources/python_client/docs/ScanResultImagesInner.md.txt @@ -0,0 +1,48 @@ +# ScanResultImagesInner + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**efficiency** | **float** | | +**number** | **int** | Detector image number for a given cell | +**nx** | **int** | Cell position in X for grid scan | [optional] +**ny** | **int** | Cell position in Y for grid scan | [optional] +**angle** | **float** | Rotation angle associated with the image | [optional] +**bkg** | **float** | Background estimate | [optional] +**spots** | **int** | Spot count | [optional] +**spots_low_res** | **int** | Spot count in low resolution range | [optional] +**spots_indexed** | **int** | Spot count within indexing tolerance | [optional] +**spots_ice** | **int** | Spot count within common ice ring resolutions | [optional] +**index** | **int** | Indexing solution | [optional] +**pr** | **float** | Profile radius, i.e. how far reflections are from the Ewald sphere | [optional] +**b** | **float** | B-Factor estimate | [optional] +**uc** | [**UnitCell**](UnitCell.md) | | [optional] +**xfel_pulseid** | **int** | XFEL pulse ID | [optional] +**pixel_sum** | **int** | Total sum of all pixels | [optional] +**max** | **int** | Max viable pixel | [optional] +**sat** | **int** | Number of saturated pixels | [optional] +**err** | **int** | Number of error pixels | [optional] +**res** | **float** | Diffraction resolution estimate | [optional] + +## Example + +```python +from jfjoch_client.models.scan_result_images_inner import ScanResultImagesInner + +# TODO update the JSON string below +json = "{}" +# create an instance of ScanResultImagesInner from a JSON string +scan_result_images_inner_instance = ScanResultImagesInner.from_json(json) +# print the JSON string representation of the object +print(ScanResultImagesInner.to_json()) + +# convert the object into a dict +scan_result_images_inner_dict = scan_result_images_inner_instance.to_dict() +# create an instance of ScanResultImagesInner from a dict +scan_result_images_inner_from_dict = ScanResultImagesInner.from_dict(scan_result_images_inner_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/SpotFindingSettings.md.txt b/_sources/python_client/docs/SpotFindingSettings.md.txt new file mode 100644 index 00000000..a15baaac --- /dev/null +++ b/_sources/python_client/docs/SpotFindingSettings.md.txt @@ -0,0 +1,40 @@ +# SpotFindingSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**enable** | **bool** | Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. Even if disabled spot finding information will still be send and written, though always with zero spots. | [default to True] +**indexing** | **bool** | Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection. | [default to True] +**signal_to_noise_threshold** | **float** | | +**photon_count_threshold** | **int** | | +**min_pix_per_spot** | **int** | | +**max_pix_per_spot** | **int** | | +**high_resolution_limit** | **float** | High resolution limit for spot finding [Angstrom] | +**low_resolution_limit** | **float** | Low resolution limit for spot finding [Angstrom] | +**high_resolution_limit_for_spot_count_low_res** | **float** | High resolution threshold to consider spot \"low resolution\" [Angstrom] | +**quick_integration** | **bool** | Quick integration of Bragg spots in diffraction images. If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate. (experimental feature) | [default to False] +**ice_ring_width_q_recip_a** | **float** | Width of ice ring in q-space in reciprocal space | [default to 0.02] +**high_res_gap_q_recip_a** | **float** | This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector. If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter. This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case. | [optional] [default to 1.5] + +## Example + +```python +from jfjoch_client.models.spot_finding_settings import SpotFindingSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of SpotFindingSettings from a JSON string +spot_finding_settings_instance = SpotFindingSettings.from_json(json) +# print the JSON string representation of the object +print(SpotFindingSettings.to_json()) + +# convert the object into a dict +spot_finding_settings_dict = spot_finding_settings_instance.to_dict() +# create an instance of SpotFindingSettings from a dict +spot_finding_settings_from_dict = SpotFindingSettings.from_dict(spot_finding_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/StandardDetectorGeometry.md.txt b/_sources/python_client/docs/StandardDetectorGeometry.md.txt new file mode 100644 index 00000000..cf66170f --- /dev/null +++ b/_sources/python_client/docs/StandardDetectorGeometry.md.txt @@ -0,0 +1,33 @@ +# StandardDetectorGeometry + +Regular rectangular geometry, first module is in the bottom left corner of the detector + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**nmodules** | **int** | Number of modules in the detector | +**gap_x** | **int** | Gap size in X direction [pixels] | [optional] [default to 8] +**gap_y** | **int** | Gap size in Y direction [pixels] | [optional] [default to 36] +**modules_in_row** | **int** | Number of modules in one row | [optional] [default to 1] + +## Example + +```python +from jfjoch_client.models.standard_detector_geometry import StandardDetectorGeometry + +# TODO update the JSON string below +json = "{}" +# create an instance of StandardDetectorGeometry from a JSON string +standard_detector_geometry_instance = StandardDetectorGeometry.from_json(json) +# print the JSON string representation of the object +print(StandardDetectorGeometry.to_json()) + +# convert the object into a dict +standard_detector_geometry_dict = standard_detector_geometry_instance.to_dict() +# create an instance of StandardDetectorGeometry from a dict +standard_detector_geometry_from_dict = StandardDetectorGeometry.from_dict(standard_detector_geometry_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/UnitCell.md.txt b/_sources/python_client/docs/UnitCell.md.txt new file mode 100644 index 00000000..80e2f4e7 --- /dev/null +++ b/_sources/python_client/docs/UnitCell.md.txt @@ -0,0 +1,35 @@ +# UnitCell + +Unit cell parameters. Necessary to run indexing. Units of angstrom and degree + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**a** | **float** | | +**b** | **float** | | +**c** | **float** | | +**alpha** | **float** | | +**beta** | **float** | | +**gamma** | **float** | | + +## Example + +```python +from jfjoch_client.models.unit_cell import UnitCell + +# TODO update the JSON string below +json = "{}" +# create an instance of UnitCell from a JSON string +unit_cell_instance = UnitCell.from_json(json) +# print the JSON string representation of the object +print(UnitCell.to_json()) + +# convert the object into a dict +unit_cell_dict = unit_cell_instance.to_dict() +# create an instance of UnitCell from a dict +unit_cell_from_dict = UnitCell.from_dict(unit_cell_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ZeromqMetadataSettings.md.txt b/_sources/python_client/docs/ZeromqMetadataSettings.md.txt new file mode 100644 index 00000000..e584ac88 --- /dev/null +++ b/_sources/python_client/docs/ZeromqMetadataSettings.md.txt @@ -0,0 +1,31 @@ +# ZeromqMetadataSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**enabled** | **bool** | ZeroMQ metadata socket is enabled. | [default to True] +**period_ms** | **int** | Period for generating metadata package sent to the ZeroMQ interface in milliseconds. | [default to 1000] +**socket_address** | **str** | PUB ZeroMQ socket for image metadata information. Image metadata are serialized using CBOR. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces. | [optional] + +## Example + +```python +from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of ZeromqMetadataSettings from a JSON string +zeromq_metadata_settings_instance = ZeromqMetadataSettings.from_json(json) +# print the JSON string representation of the object +print(ZeromqMetadataSettings.to_json()) + +# convert the object into a dict +zeromq_metadata_settings_dict = zeromq_metadata_settings_instance.to_dict() +# create an instance of ZeromqMetadataSettings from a dict +zeromq_metadata_settings_from_dict = ZeromqMetadataSettings.from_dict(zeromq_metadata_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ZeromqPreviewSettings.md.txt b/_sources/python_client/docs/ZeromqPreviewSettings.md.txt new file mode 100644 index 00000000..2198076a --- /dev/null +++ b/_sources/python_client/docs/ZeromqPreviewSettings.md.txt @@ -0,0 +1,31 @@ +# ZeromqPreviewSettings + + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**enabled** | **bool** | ZeroMQ preview socket is enabled. | [default to True] +**period_ms** | **int** | Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection). This has no effect on HTTP based preview, which updates always at rate of 1 second. | [default to 1000] +**socket_address** | **str** | PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate. Images are serialized using CBOR. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces. | [optional] + +## Example + +```python +from jfjoch_client.models.zeromq_preview_settings import ZeromqPreviewSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of ZeromqPreviewSettings from a JSON string +zeromq_preview_settings_instance = ZeromqPreviewSettings.from_json(json) +# print the JSON string representation of the object +print(ZeromqPreviewSettings.to_json()) + +# convert the object into a dict +zeromq_preview_settings_dict = zeromq_preview_settings_instance.to_dict() +# create an instance of ZeromqPreviewSettings from a dict +zeromq_preview_settings_from_dict = ZeromqPreviewSettings.from_dict(zeromq_preview_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_sources/python_client/docs/ZeromqSettings.md.txt b/_sources/python_client/docs/ZeromqSettings.md.txt new file mode 100644 index 00000000..ededb477 --- /dev/null +++ b/_sources/python_client/docs/ZeromqSettings.md.txt @@ -0,0 +1,33 @@ +# ZeromqSettings + +ZeroMQ configuration for Jungfraujoch software. This structure is used to provide default settings using configuration JSON file and is not used in HTTP. + +## Properties + +Name | Type | Description | Notes +------------ | ------------- | ------------- | ------------- +**send_watermark** | **int** | Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue) | [optional] [default to 100] +**send_buffer_size** | **int** | Send buffer size for ZeroMQ socket | [optional] +**image_socket** | **List[str]** | PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets. Images are serialized using CBOR. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces. | [optional] +**writer_notification_socket** | **str** | PULL ZeroMQ socket for notifications from writer that it finished operation. This allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous. Using * (star) instead of port number is allowed and it means a random free port number. | [optional] + +## Example + +```python +from jfjoch_client.models.zeromq_settings import ZeromqSettings + +# TODO update the JSON string below +json = "{}" +# create an instance of ZeromqSettings from a JSON string +zeromq_settings_instance = ZeromqSettings.from_json(json) +# print the JSON string representation of the object +print(ZeromqSettings.to_json()) + +# convert the object into a dict +zeromq_settings_dict = zeromq_settings_instance.to_dict() +# create an instance of ZeromqSettings from a dict +zeromq_settings_from_dict = ZeromqSettings.from_dict(zeromq_settings_dict) +``` +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) + + diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 00000000..95140fbf --- /dev/null +++ b/_static/basic.css @@ -0,0 +1 @@ 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(o = u.documentElement, function(e) { + var t = u.createElement("script"); + t.onreadystatechange = function() { + h(e), t.onreadystatechange = null, o.removeChild(t), t = null + }, o.appendChild(t) + }) : function(e) { + setTimeout(h, 0, e) + }, f.setImmediate = function(e) { + "function" != typeof e && (e = new Function("" + e)); + for (var t = new Array(arguments.length - 1), n = 0; n < t.length; n++) t[n] = arguments[n + 1]; + var r = { + callback: e, + args: t + }; + return c[s] = r, i(s), s++ + }, f.clearImmediate = d + } + + function d(e) { + delete c[e] + } + + function h(e) { + if (l) setTimeout(h, 0, e); + else { + var t = c[e]; + if (t) { + l = !0; + try { + ! function(e) { + var t = e.callback, + n = e.args; + switch (n.length) { + case 0: + t(); + break; + case 1: + t(n[0]); + break; + case 2: + t(n[0], n[1]); + break; + case 3: + t(n[0], n[1], n[2]); + break; + default: + t.apply(r, n) + } + }(t) + } finally { + d(e), l = !1 + } + } + } + } + }("undefined" == typeof self ? void 0 === e ? this : e : self) + }).call(this, n(4), n(23)) +}, function(e, t) { + var n, r, i = e.exports = {}; + + function o() { + throw new Error("setTimeout has not been defined") + } + + function a() { + throw new Error("clearTimeout has not been defined") + } + + function s(t) { + if (n === setTimeout) return setTimeout(t, 0); + if ((n === o || !n) && setTimeout) return n = setTimeout, setTimeout(t, 0); + try { + return n(t, 0) + } catch (e) { + try { + return n.call(null, t, 0) + } catch (e) { + return n.call(this, t, 0) + } + } + }! function() { + try { + n = "function" == typeof setTimeout ? setTimeout : o + } catch (e) { + n = o + } + try { + r = "function" == typeof clearTimeout ? clearTimeout : a + } catch (e) { + r = a + } + }(); + var c, l = [], + u = !1, + f = -1; + + function d() { + u && c && (u = !1, c.length ? l = c.concat(l) : f = -1, l.length && h()) + } + + function h() { + if (!u) { + var e = s(d); + u = !0; + for (var t = l.length; t;) { + for (c = l, l = []; ++f < t;) c && c[f].run(); + f = -1, t = l.length + } + c = null, u = !1, + function(t) { + if (r === clearTimeout) return clearTimeout(t); + if ((r === a || !r) && clearTimeout) return r = clearTimeout, clearTimeout(t); + try { + r(t) + } catch (e) { + try { + return r.call(null, t) + } catch (e) { + return r.call(this, t) + } + } + }(e) + } + } + + function p(e, t) { + this.fun = e, this.array = t + } + + function m() {} + i.nextTick = function(e) { + var t = new Array(arguments.length - 1); + if (1 < arguments.length) + for (var n = 1; n < arguments.length; n++) t[n - 1] = arguments[n]; + l.push(new p(e, t)), 1 !== l.length || u || s(h) + }, p.prototype.run = function() { + this.fun.apply(null, this.array) + }, i.title = "browser", i.browser = !0, i.env = {}, i.argv = [], i.version = "", i.versions = {}, i.on = m, i.addListener = m, i.once = m, i.off = m, i.removeListener = m, i.removeAllListeners = m, i.emit = m, i.prependListener = m, i.prependOnceListener = m, i.listeners = function(e) { + return [] + }, i.binding = function(e) { + throw new Error("process.binding is not supported") + }, i.cwd = function() { + return "/" + }, i.chdir = function(e) { + throw new Error("process.chdir is not supported") + }, i.umask = function() { + return 0 + } +}, function(i, o, a) { + var s, c; + /** + * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.6 + * Copyright (C) 2019 Oliver Nightingale + * @license MIT + */ + ! function() { + var t, l, u, e, n, f, d, h, p, m, y, v, g, w, _, E, x, b, k, S, T, L, R, O, C, r, D = function(e) { + var t = new D.Builder; + return t.pipeline.add(D.trimmer, D.stopWordFilter, D.stemmer), t.searchPipeline.add(D.stemmer), e.call(t, t), t.build() + }; + D.version = "2.3.6", D.utils = {}, D.utils.warn = (t = this, function(e) { + t.console && console.warn && console.warn(e) + }), D.utils.asString = function(e) { + return null == e ? "" : e.toString() + }, D.utils.clone = function(e) { + if (null == e) return e; + for (var t = Object.create(null), n = Object.keys(e), r = 0; r < n.length; r++) { + var i = n[r], + o = e[i]; + if (Array.isArray(o)) t[i] = o.slice(); + else { + if ("string" != typeof o && "number" != typeof o && "boolean" != typeof o) throw new TypeError("clone is not deep and does not support nested objects"); + t[i] = o + } + } + return t + }, D.FieldRef = function(e, t, n) { + this.docRef = e, this.fieldName = t, this._stringValue = n + }, D.FieldRef.joiner = "/", D.FieldRef.fromString = function(e) { + var t = e.indexOf(D.FieldRef.joiner); + if (-1 === t) throw "malformed field ref string"; + var n = e.slice(0, t), + r = e.slice(t + 1); + return new D.FieldRef(r, n, e) + }, D.FieldRef.prototype.toString = function() { + return null == this._stringValue && (this._stringValue = this.fieldName + D.FieldRef.joiner + this.docRef), this._stringValue + }, D.Set = function(e) { + if (this.elements = Object.create(null), e) { + this.length = e.length; + for (var t = 0; t < this.length; t++) this.elements[e[t]] = !0 + } else this.length = 0 + }, D.Set.complete = { + intersect: function(e) { + return e + }, + union: function(e) { + return e + }, + contains: function() { + return !0 + } + }, D.Set.empty = { + intersect: function() { + return this + }, + union: function(e) { + return e + }, + contains: function() { + return !1 + } + }, D.Set.prototype.contains = function(e) { + return !!this.elements[e] + }, D.Set.prototype.intersect = function(e) { + var t, n, r, i = []; + if (e === D.Set.complete) return this; + if (e === D.Set.empty) return e; + n = this.length < e.length ? (t = this, e) : (t = e, this), r = Object.keys(t.elements); + for (var o = 0; o < r.length; o++) { + var a = r[o]; + a in n.elements && i.push(a) + } + return new D.Set(i) + }, D.Set.prototype.union = function(e) { + return e === D.Set.complete ? D.Set.complete : e === D.Set.empty ? this : new D.Set(Object.keys(this.elements).concat(Object.keys(e.elements))) + }, D.idf = function(e, t) { + var n = 0; + for (var r in e) "_index" != r && (n += Object.keys(e[r]).length); + var i = (t - n + .5) / (n + .5); + return Math.log(1 + Math.abs(i)) + }, D.Token = function(e, t) { + this.str = e || "", this.metadata = t || {} + }, D.Token.prototype.toString = function() { + return this.str + }, D.Token.prototype.update = function(e) { + return this.str = e(this.str, this.metadata), this + }, D.Token.prototype.clone = function(e) { + return e = e || function(e) { + return e + }, new D.Token(e(this.str, this.metadata), this.metadata) + }, D.tokenizer = function(e, t) { + if (null == e || null == e) return []; + if (Array.isArray(e)) return e.map(function(e) { + return new D.Token(D.utils.asString(e).toLowerCase(), D.utils.clone(t)) + }); + for (var n = e.toString().trim().toLowerCase(), r = n.length, i = [], o = 0, a = 0; o <= r; o++) { + var s = o - a; + if (n.charAt(o).match(D.tokenizer.separator) || o == r) { + if (0 < s) { + var c = D.utils.clone(t) || {}; + c.position = [a, s], c.index = i.length, i.push(new D.Token(n.slice(a, o), c)) + } + a = o + 1 + } + } + return i + }, D.tokenizer.separator = /[\s\-]+/, D.Pipeline = function() { + this._stack = [] + }, D.Pipeline.registeredFunctions = Object.create(null), D.Pipeline.registerFunction = function(e, t) { + t in this.registeredFunctions && D.utils.warn("Overwriting existing registered function: " + t), e.label = t, D.Pipeline.registeredFunctions[e.label] = e + }, D.Pipeline.warnIfFunctionNotRegistered = function(e) { + e.label && e.label in this.registeredFunctions || D.utils.warn("Function is not registered with pipeline. This may cause problems when serialising the index.\n", e) + }, D.Pipeline.load = function(e) { + var n = new D.Pipeline; + return e.forEach(function(e) { + var t = D.Pipeline.registeredFunctions[e]; + if (!t) throw new Error("Cannot load unregistered function: " + e); + n.add(t) + }), n + }, D.Pipeline.prototype.add = function() { + Array.prototype.slice.call(arguments).forEach(function(e) { + D.Pipeline.warnIfFunctionNotRegistered(e), this._stack.push(e) + }, this) + }, D.Pipeline.prototype.after = function(e, t) { + D.Pipeline.warnIfFunctionNotRegistered(t); + var n = this._stack.indexOf(e); + if (-1 == n) throw new Error("Cannot find existingFn"); + n += 1, this._stack.splice(n, 0, t) + }, D.Pipeline.prototype.before = function(e, t) { + D.Pipeline.warnIfFunctionNotRegistered(t); + var n = this._stack.indexOf(e); + if (-1 == n) throw new Error("Cannot find existingFn"); + this._stack.splice(n, 0, t) + }, D.Pipeline.prototype.remove = function(e) { + var t = this._stack.indexOf(e); - 1 != t && this._stack.splice(t, 1) + }, D.Pipeline.prototype.run = function(e) { + for (var t = this._stack.length, n = 0; n < t; n++) { + for (var r = this._stack[n], i = [], o = 0; o < e.length; o++) { + var a = r(e[o], o, e); + if (void 0 !== a && "" !== a) + if (Array.isArray(a)) + for (var s = 0; s < a.length; s++) i.push(a[s]); + else i.push(a) + } + e = i + } + return e + }, D.Pipeline.prototype.runString = function(e, t) { + var n = new D.Token(e, t); + return this.run([n]).map(function(e) { + return e.toString() + }) + }, D.Pipeline.prototype.reset = function() { + this._stack = [] + }, D.Pipeline.prototype.toJSON = function() { + return this._stack.map(function(e) { + return D.Pipeline.warnIfFunctionNotRegistered(e), e.label + }) + }, D.Vector = function(e) { + this._magnitude = 0, this.elements = e || [] + }, D.Vector.prototype.positionForIndex = function(e) { + if (0 == this.elements.length) return 0; + for (var t = 0, n = this.elements.length / 2, r = n - t, i = Math.floor(r / 2), o = this.elements[2 * i]; 1 < r && (o < e && (t = i), e < o && (n = i), o != e);) r = n - t, i = t + Math.floor(r / 2), o = this.elements[2 * i]; + return o == e ? 2 * i : e < o ? 2 * i : o < e ? 2 * (i + 1) : void 0 + }, D.Vector.prototype.insert = function(e, t) { + this.upsert(e, t, function() { + throw "duplicate index" + }) + }, D.Vector.prototype.upsert = function(e, t, n) { + this._magnitude = 0; + var r = this.positionForIndex(e); + this.elements[r] == e ? this.elements[r + 1] = n(this.elements[r + 1], t) : this.elements.splice(r, 0, e, t) + }, D.Vector.prototype.magnitude = function() { + if (this._magnitude) return this._magnitude; + for (var e = 0, t = this.elements.length, n = 1; n < t; n += 2) { + var r = this.elements[n]; + e += r * r + } + return this._magnitude = Math.sqrt(e) + }, D.Vector.prototype.dot = function(e) { + for (var t = 0, n = this.elements, r = e.elements, i = n.length, o = r.length, a = 0, s = 0, c = 0, l = 0; c < i && l < o;)(a = n[c]) < (s = r[l]) ? c += 2 : s < a ? l += 2 : a == s && (t += n[c + 1] * r[l + 1], c += 2, l += 2); + return t + }, D.Vector.prototype.similarity = function(e) { + return this.dot(e) / this.magnitude() || 0 + }, D.Vector.prototype.toArray = function() { + for (var e = new Array(this.elements.length / 2), t = 1, n = 0; t < this.elements.length; t += 2, n++) e[n] = this.elements[t]; + return e + }, D.Vector.prototype.toJSON = function() { + return this.elements + }, D.stemmer = (l = { + ational: "ate", + tional: "tion", + enci: "ence", + anci: "ance", + izer: "ize", + bli: "ble", + alli: "al", + entli: "ent", + eli: "e", + ousli: "ous", + ization: "ize", + ation: "ate", + ator: "ate", + alism: "al", + iveness: "ive", + fulness: "ful", + ousness: "ous", + aliti: "al", + iviti: "ive", + biliti: "ble", + logi: "log" + }, u = { + icate: "ic", + ative: "", + alize: "al", + iciti: "ic", + ical: "ic", + ful: "", + ness: "" + }, e = "[aeiouy]", n = "[^aeiou][^aeiouy]*", f = new RegExp("^([^aeiou][^aeiouy]*)?[aeiouy][aeiou]*[^aeiou][^aeiouy]*"), d = new RegExp("^([^aeiou][^aeiouy]*)?[aeiouy][aeiou]*[^aeiou][^aeiouy]*[aeiouy][aeiou]*[^aeiou][^aeiouy]*"), h = new RegExp("^([^aeiou][^aeiouy]*)?[aeiouy][aeiou]*[^aeiou][^aeiouy]*([aeiouy][aeiou]*)?$"), p = new RegExp("^([^aeiou][^aeiouy]*)?[aeiouy]"), m = /^(.+?)(ss|i)es$/, y = /^(.+?)([^s])s$/, v = /^(.+?)eed$/, g = /^(.+?)(ed|ing)$/, w = /.$/, _ = /(at|bl|iz)$/, E = new RegExp("([^aeiouylsz])\\1$"), x = new RegExp("^" + n + e + "[^aeiouwxy]$"), b = /^(.+?[^aeiou])y$/, k = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/, S = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/, T = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/, L = /^(.+?)(s|t)(ion)$/, R = /^(.+?)e$/, O = /ll$/, C = new RegExp("^" + n + e + "[^aeiouwxy]$"), r = function(e) { + var t, n, r, i, o, a, s; + if (e.length < 3) return e; + if ("y" == (r = e.substr(0, 1)) && (e = r.toUpperCase() + e.substr(1)), o = y, (i = m).test(e) ? e = e.replace(i, "$1$2") : o.test(e) && (e = e.replace(o, "$1$2")), o = g, (i = v).test(e)) { + var c = i.exec(e); + (i = f).test(c[1]) && (i = w, e = e.replace(i, "")) + } else if (o.test(e)) { + t = (c = o.exec(e))[1], (o = p).test(t) && (a = E, s = x, (o = _).test(e = t) ? e += "e" : a.test(e) ? (i = w, e = e.replace(i, "")) : s.test(e) && (e += "e")) + }(i = b).test(e) && (e = (t = (c = i.exec(e))[1]) + "i"); + (i = k).test(e) && (t = (c = i.exec(e))[1], n = c[2], (i = f).test(t) && (e = t + l[n])); + (i = S).test(e) && (t = (c = i.exec(e))[1], n = c[2], (i = f).test(t) && (e = t + u[n])); + if (o = L, (i = T).test(e)) t = (c = i.exec(e))[1], (i = d).test(t) && (e = t); + else if (o.test(e)) { + t = (c = o.exec(e))[1] + c[2], (o = d).test(t) && (e = t) + }(i = R).test(e) && (t = (c = i.exec(e))[1], o = h, a = C, ((i = d).test(t) || o.test(t) && !a.test(t)) && (e = t)); + return o = d, (i = O).test(e) && o.test(e) && (i = w, e = e.replace(i, "")), "y" == r && (e = r.toLowerCase() + e.substr(1)), e + }, function(e) { + return e.update(r) + }), D.Pipeline.registerFunction(D.stemmer, "stemmer"), D.generateStopWordFilter = function(e) { + var t = e.reduce(function(e, t) { + return e[t] = t, e + }, {}); + return function(e) { + if (e && t[e.toString()] !== e.toString()) return e + } + }, D.stopWordFilter = D.generateStopWordFilter(["a", "able", "about", "across", "after", "all", "almost", "also", "am", "among", "an", "and", "any", "are", "as", "at", "be", "because", "been", "but", "by", "can", "cannot", "could", "dear", "did", "do", "does", "either", "else", "ever", "every", "for", "from", "get", "got", "had", "has", "have", "he", "her", "hers", "him", "his", "how", "however", "i", "if", "in", "into", "is", "it", "its", "just", "least", "let", "like", "likely", "may", "me", "might", "most", "must", "my", "neither", "no", "nor", "not", "of", "off", "often", "on", "only", "or", "other", "our", "own", "rather", "said", "say", "says", "she", "should", "since", "so", "some", "than", "that", "the", "their", "them", "then", "there", "these", "they", "this", "tis", "to", "too", "twas", "us", "wants", "was", "we", "were", "what", "when", "where", "which", "while", "who", "whom", "why", "will", "with", "would", "yet", "you", "your"]), D.Pipeline.registerFunction(D.stopWordFilter, "stopWordFilter"), D.trimmer = function(e) { + return e.update(function(e) { + return e.replace(/^\W+/, "").replace(/\W+$/, "") + }) + }, D.Pipeline.registerFunction(D.trimmer, "trimmer"), D.TokenSet = function() { + this.final = !1, this.edges = {}, this.id = D.TokenSet._nextId, D.TokenSet._nextId += 1 + }, D.TokenSet._nextId = 1, D.TokenSet.fromArray = function(e) { + for (var t = new D.TokenSet.Builder, n = 0, r = e.length; n < r; n++) t.insert(e[n]); + return t.finish(), t.root + }, D.TokenSet.fromClause = function(e) { + return "editDistance" in e ? D.TokenSet.fromFuzzyString(e.term, e.editDistance) : D.TokenSet.fromString(e.term) + }, D.TokenSet.fromFuzzyString = function(e, t) { + for (var n = new D.TokenSet, r = [{ + node: n, + editsRemaining: t, + str: e + }]; r.length;) { + var i = r.pop(); + if (0 < i.str.length) { + var o, a = i.str.charAt(0); + a in i.node.edges ? o = i.node.edges[a] : (o = new D.TokenSet, i.node.edges[a] = o), 1 == i.str.length && (o.final = !0), r.push({ + node: o, + editsRemaining: i.editsRemaining, + str: i.str.slice(1) + }) + } + if (0 != i.editsRemaining) { + if ("*" in i.node.edges) var s = i.node.edges["*"]; + else { + s = new D.TokenSet; + i.node.edges["*"] = s + } + if (0 == i.str.length && (s.final = !0), r.push({ + node: s, + editsRemaining: i.editsRemaining - 1, + str: i.str + }), 1 < i.str.length && r.push({ + node: i.node, + editsRemaining: i.editsRemaining - 1, + str: i.str.slice(1) + }), 1 == i.str.length && (i.node.final = !0), 1 <= i.str.length) { + if ("*" in i.node.edges) var c = i.node.edges["*"]; + else { + c = new D.TokenSet; + i.node.edges["*"] = c + } + 1 == i.str.length && (c.final = !0), r.push({ + node: c, + editsRemaining: i.editsRemaining - 1, + str: i.str.slice(1) + }) + } + if (1 < i.str.length) { + var l, u = i.str.charAt(0), + f = i.str.charAt(1); + f in i.node.edges ? l = i.node.edges[f] : (l = new D.TokenSet, i.node.edges[f] = l), 1 == i.str.length && (l.final = !0), r.push({ + node: l, + editsRemaining: i.editsRemaining - 1, + str: u + i.str.slice(2) + }) + } + } + } + return n + }, D.TokenSet.fromString = function(e) { + for (var t = new D.TokenSet, n = t, r = 0, i = e.length; r < i; r++) { + var o = e[r], + a = r == i - 1; + if ("*" == o)(t.edges[o] = t).final = a; + else { + var s = new D.TokenSet; + s.final = a, t.edges[o] = s, t = s + } + } + return n + }, D.TokenSet.prototype.toArray = function() { + for (var e = [], t = [{ + prefix: "", + node: this + }]; t.length;) { + var n = t.pop(), + r = Object.keys(n.node.edges), + i = r.length; + n.node.final && (n.prefix.charAt(0), e.push(n.prefix)); + for (var o = 0; o < i; o++) { + var a = r[o]; + t.push({ + prefix: n.prefix.concat(a), + node: n.node.edges[a] + }) + } + } + return e + }, D.TokenSet.prototype.toString = function() { + if (this._str) return this._str; + for (var e = this.final ? "1" : "0", t = Object.keys(this.edges).sort(), n = t.length, r = 0; r < n; r++) { + var i = t[r]; + e = e + i + this.edges[i].id + } + return e + }, D.TokenSet.prototype.intersect = function(e) { + for (var t = new D.TokenSet, n = void 0, r = [{ + qNode: e, + output: t, + node: this + }]; r.length;) { + n = r.pop(); + for (var i = Object.keys(n.qNode.edges), o = i.length, a = Object.keys(n.node.edges), s = a.length, c = 0; c < o; c++) + for (var l = i[c], u = 0; u < s; u++) { + var f = a[u]; + if (f == l || "*" == l) { + var d = n.node.edges[f], + h = n.qNode.edges[l], + p = d.final && h.final, + m = void 0; + f in n.output.edges ? (m = n.output.edges[f]).final = m.final || p : ((m = new D.TokenSet).final = p, n.output.edges[f] = m), r.push({ + qNode: h, + output: m, + node: d + }) + } + } + } + return t + }, D.TokenSet.Builder = function() { + this.previousWord = "", this.root = new D.TokenSet, this.uncheckedNodes = [], this.minimizedNodes = {} + }, D.TokenSet.Builder.prototype.insert = function(e) { + var t, n = 0; + if (e < this.previousWord) throw new Error("Out of order word insertion"); + for (var r = 0; r < e.length && r < this.previousWord.length && e[r] == this.previousWord[r]; r++) n++; + this.minimize(n), t = 0 == this.uncheckedNodes.length ? this.root : this.uncheckedNodes[this.uncheckedNodes.length - 1].child; + for (r = n; r < e.length; r++) { + var i = new D.TokenSet, + o = e[r]; + t.edges[o] = i, this.uncheckedNodes.push({ + parent: t, + char: o, + child: i + }), t = i + } + t.final = !0, this.previousWord = e + }, D.TokenSet.Builder.prototype.finish = function() { + this.minimize(0) + }, D.TokenSet.Builder.prototype.minimize = function(e) { + for (var t = this.uncheckedNodes.length - 1; e <= t; t--) { + var n = this.uncheckedNodes[t], + r = n.child.toString(); + r in this.minimizedNodes ? n.parent.edges[n.char] = this.minimizedNodes[r] : (n.child._str = r, this.minimizedNodes[r] = n.child), this.uncheckedNodes.pop() + } + }, D.Index = function(e) { + this.invertedIndex = e.invertedIndex, this.fieldVectors = e.fieldVectors, this.tokenSet = e.tokenSet, this.fields = e.fields, this.pipeline = e.pipeline + }, D.Index.prototype.search = function(t) { + return this.query(function(e) { + new D.QueryParser(t, e).parse() + }) + }, D.Index.prototype.query = function(e) { + for (var t = new D.Query(this.fields), n = Object.create(null), r = Object.create(null), i = Object.create(null), o = Object.create(null), a = Object.create(null), s = 0; s < this.fields.length; s++) r[this.fields[s]] = new D.Vector; + e.call(t, t); + for (s = 0; s < t.clauses.length; s++) { + var c = t.clauses[s], + l = null, + u = D.Set.complete; + l = c.usePipeline ? this.pipeline.runString(c.term, { + fields: c.fields + }) : [c.term]; + for (var f = 0; f < l.length; f++) { + var d = l[f]; + c.term = d; + var h = D.TokenSet.fromClause(c), + p = this.tokenSet.intersect(h).toArray(); + if (0 === p.length && c.presence === D.Query.presence.REQUIRED) { + for (var m = 0; m < c.fields.length; m++) { + o[Q = c.fields[m]] = D.Set.empty + } + break + } + for (var y = 0; y < p.length; y++) { + var v = p[y], + g = this.invertedIndex[v], + w = g._index; + for (m = 0; m < c.fields.length; m++) { + var _ = g[Q = c.fields[m]], + E = Object.keys(_), + x = v + "/" + Q, + b = new D.Set(E); + if (c.presence == D.Query.presence.REQUIRED && (u = u.union(b), void 0 === o[Q] && (o[Q] = D.Set.complete)), c.presence != D.Query.presence.PROHIBITED) { + if (r[Q].upsert(w, c.boost, function(e, t) { + return e + t + }), !i[x]) { + for (var k = 0; k < E.length; k++) { + var S, T = E[k], + L = new D.FieldRef(T, Q), + R = _[T]; + void 0 === (S = n[L]) ? n[L] = new D.MatchData(v, Q, R) : S.add(v, Q, R) + } + i[x] = !0 + } + } else void 0 === a[Q] && (a[Q] = D.Set.empty), a[Q] = a[Q].union(b) + } + } + } + if (c.presence === D.Query.presence.REQUIRED) + for (m = 0; m < c.fields.length; m++) { + o[Q = c.fields[m]] = o[Q].intersect(u) + } + } + var O = D.Set.complete, + C = D.Set.empty; + for (s = 0; s < this.fields.length; s++) { + var Q; + o[Q = this.fields[s]] && (O = O.intersect(o[Q])), a[Q] && (C = C.union(a[Q])) + } + var P = Object.keys(n), + A = [], + I = Object.create(null); + if (t.isNegated()) { + P = Object.keys(this.fieldVectors); + for (s = 0; s < P.length; s++) { + L = P[s]; + var M = D.FieldRef.fromString(L); + n[L] = new D.MatchData + } + } + for (s = 0; s < P.length; s++) { + var N = (M = D.FieldRef.fromString(P[s])).docRef; + if (O.contains(N) && !C.contains(N)) { + var j, F = this.fieldVectors[M], + H = r[M.fieldName].similarity(F); + if (void 0 !== (j = I[N])) j.score += H, j.matchData.combine(n[M]); + else { + var q = { + ref: N, + score: H, + matchData: n[M] + }; + I[N] = q, A.push(q) + } + } + } + return A.sort(function(e, t) { + return t.score - e.score + }) + }, D.Index.prototype.toJSON = function() { + var e = Object.keys(this.invertedIndex).sort().map(function(e) { + return [e, this.invertedIndex[e]] + }, this), + t = Object.keys(this.fieldVectors).map(function(e) { + return [e, this.fieldVectors[e].toJSON()] + }, this); + return { + version: D.version, + fields: this.fields, + fieldVectors: t, + invertedIndex: e, + pipeline: this.pipeline.toJSON() + } + }, D.Index.load = function(e) { + var t = {}, + n = {}, + r = e.fieldVectors, + i = Object.create(null), + o = e.invertedIndex, + a = new D.TokenSet.Builder, + s = D.Pipeline.load(e.pipeline); + e.version != D.version && D.utils.warn("Version mismatch when loading serialised index. Current version of lunr '" + D.version + "' does not match serialized index '" + e.version + "'"); + for (var c = 0; c < r.length; c++) { + var l = (f = r[c])[0], + u = f[1]; + n[l] = new D.Vector(u) + } + for (c = 0; c < o.length; c++) { + var f, d = (f = o[c])[0], + h = f[1]; + a.insert(d), i[d] = h + } + return a.finish(), t.fields = e.fields, t.fieldVectors = n, t.invertedIndex = i, t.tokenSet = a.root, t.pipeline = s, new D.Index(t) + }, D.Builder = function() { + this._ref = "id", this._fields = Object.create(null), this._documents = Object.create(null), this.invertedIndex = Object.create(null), this.fieldTermFrequencies = {}, this.fieldLengths = {}, this.tokenizer = D.tokenizer, this.pipeline = new D.Pipeline, this.searchPipeline = new D.Pipeline, this.documentCount = 0, this._b = .75, this._k1 = 1.2, this.termIndex = 0, this.metadataWhitelist = [] + }, D.Builder.prototype.ref = function(e) { + this._ref = e + }, D.Builder.prototype.field = function(e, t) { + if (/\//.test(e)) throw new RangeError("Field '" + e + "' contains illegal character '/'"); + this._fields[e] = t || {} + }, D.Builder.prototype.b = function(e) { + this._b = e < 0 ? 0 : 1 < e ? 1 : e + }, D.Builder.prototype.k1 = function(e) { + this._k1 = e + }, D.Builder.prototype.add = function(e, t) { + var n = e[this._ref], + r = Object.keys(this._fields); + this._documents[n] = t || {}, this.documentCount += 1; + for (var i = 0; i < r.length; i++) { + var o = r[i], + a = this._fields[o].extractor, + s = a ? a(e) : e[o], + c = this.tokenizer(s, { + fields: [o] + }), + l = this.pipeline.run(c), + u = new D.FieldRef(n, o), + f = Object.create(null); + this.fieldTermFrequencies[u] = f, this.fieldLengths[u] = 0, this.fieldLengths[u] += l.length; + for (var d = 0; d < l.length; d++) { + var h = l[d]; + if (null == f[h] && (f[h] = 0), f[h] += 1, null == this.invertedIndex[h]) { + var p = Object.create(null); + p._index = this.termIndex, this.termIndex += 1; + for (var m = 0; m < r.length; m++) p[r[m]] = Object.create(null); + this.invertedIndex[h] = p + } + null == this.invertedIndex[h][o][n] && (this.invertedIndex[h][o][n] = Object.create(null)); + for (var y = 0; y < this.metadataWhitelist.length; y++) { + var v = this.metadataWhitelist[y], + g = h.metadata[v]; + null == this.invertedIndex[h][o][n][v] && (this.invertedIndex[h][o][n][v] = []), this.invertedIndex[h][o][n][v].push(g) + } + } + } + }, D.Builder.prototype.calculateAverageFieldLengths = function() { + for (var e = Object.keys(this.fieldLengths), t = e.length, n = {}, r = {}, i = 0; i < t; i++) { + var o = D.FieldRef.fromString(e[i]), + a = o.fieldName; + r[a] || (r[a] = 0), r[a] += 1, n[a] || (n[a] = 0), n[a] += this.fieldLengths[o] + } + var s = Object.keys(this._fields); + for (i = 0; i < s.length; i++) { + var c = s[i]; + n[c] = n[c] / r[c] + } + this.averageFieldLength = n + }, D.Builder.prototype.createFieldVectors = function() { + for (var e = {}, t = Object.keys(this.fieldTermFrequencies), n = t.length, r = Object.create(null), i = 0; i < n; i++) { + for (var o = D.FieldRef.fromString(t[i]), a = o.fieldName, s = this.fieldLengths[o], c = new D.Vector, l = this.fieldTermFrequencies[o], u = Object.keys(l), f = u.length, d = this._fields[a].boost || 1, h = this._documents[o.docRef].boost || 1, p = 0; p < f; p++) { + var m, y, v, g = u[p], + w = l[g], + _ = this.invertedIndex[g]._index; + void 0 === r[g] ? (m = D.idf(this.invertedIndex[g], this.documentCount), r[g] = m) : m = r[g], y = m * ((this._k1 + 1) * w) / (this._k1 * (1 - this._b + this._b * (s / this.averageFieldLength[a])) + w), y *= d, y *= h, v = Math.round(1e3 * y) / 1e3, c.insert(_, v) + } + e[o] = c + } + this.fieldVectors = e + }, D.Builder.prototype.createTokenSet = function() { + this.tokenSet = D.TokenSet.fromArray(Object.keys(this.invertedIndex).sort()) + }, D.Builder.prototype.build = function() { + return this.calculateAverageFieldLengths(), this.createFieldVectors(), this.createTokenSet(), new D.Index({ + invertedIndex: this.invertedIndex, + fieldVectors: this.fieldVectors, + tokenSet: this.tokenSet, + fields: Object.keys(this._fields), + pipeline: this.searchPipeline + }) + }, D.Builder.prototype.use = function(e) { + var t = Array.prototype.slice.call(arguments, 1); + t.unshift(this), e.apply(this, t) + }, D.MatchData = function(e, t, n) { + for (var r = Object.create(null), i = Object.keys(n || {}), o = 0; o < i.length; o++) { + var a = i[o]; + r[a] = n[a].slice() + } + this.metadata = Object.create(null), void 0 !== e && (this.metadata[e] = Object.create(null), this.metadata[e][t] = r) + }, D.MatchData.prototype.combine = function(e) { + for (var t = Object.keys(e.metadata), n = 0; n < t.length; n++) { + var r = t[n], + i = Object.keys(e.metadata[r]); + null == this.metadata[r] && (this.metadata[r] = Object.create(null)); + for (var o = 0; o < i.length; o++) { + var a = i[o], + s = Object.keys(e.metadata[r][a]); + null == this.metadata[r][a] && (this.metadata[r][a] = Object.create(null)); + for (var c = 0; c < s.length; c++) { + var l = s[c]; + null == this.metadata[r][a][l] ? this.metadata[r][a][l] = e.metadata[r][a][l] : this.metadata[r][a][l] = this.metadata[r][a][l].concat(e.metadata[r][a][l]) + } + } + } + }, D.MatchData.prototype.add = function(e, t, n) { + if (!(e in this.metadata)) return this.metadata[e] = Object.create(null), void(this.metadata[e][t] = n); + if (t in this.metadata[e]) + for (var r = Object.keys(n), i = 0; i < r.length; i++) { + var o = r[i]; + o in this.metadata[e][t] ? this.metadata[e][t][o] = this.metadata[e][t][o].concat(n[o]) : this.metadata[e][t][o] = n[o] + } else this.metadata[e][t] = n + }, D.Query = function(e) { + this.clauses = [], this.allFields = e + }, D.Query.wildcard = new String("*"), D.Query.wildcard.NONE = 0, D.Query.wildcard.LEADING = 1, D.Query.wildcard.TRAILING = 2, D.Query.presence = { + OPTIONAL: 1, + REQUIRED: 2, + PROHIBITED: 3 + }, D.Query.prototype.clause = function(e) { + return "fields" in e || (e.fields = this.allFields), "boost" in e || (e.boost = 1), "usePipeline" in e || (e.usePipeline = !0), "wildcard" in e || (e.wildcard = D.Query.wildcard.NONE), e.wildcard & D.Query.wildcard.LEADING && e.term.charAt(0) != D.Query.wildcard && (e.term = "*" + e.term), e.wildcard & D.Query.wildcard.TRAILING && e.term.slice(-1) != D.Query.wildcard && (e.term = e.term + "*"), "presence" in e || (e.presence = D.Query.presence.OPTIONAL), this.clauses.push(e), this + }, D.Query.prototype.isNegated = function() { + for (var e = 0; e < this.clauses.length; e++) + if (this.clauses[e].presence != D.Query.presence.PROHIBITED) return !1; + return !0 + }, D.Query.prototype.term = function(e, t) { + if (Array.isArray(e)) return e.forEach(function(e) { + this.term(e, D.utils.clone(t)) + }, this), this; + var n = t || {}; + return n.term = e.toString(), this.clause(n), this + }, D.QueryParseError = function(e, t, n) { + this.name = "QueryParseError", this.message = e, this.start = t, this.end = n + }, D.QueryParseError.prototype = new Error, D.QueryLexer = function(e) { + this.lexemes = [], this.str = e, this.length = e.length, this.pos = 0, this.start = 0, this.escapeCharPositions = [] + }, D.QueryLexer.prototype.run = function() { + for (var e = D.QueryLexer.lexText; e;) e = e(this) + }, D.QueryLexer.prototype.sliceString = function() { + for (var e = [], t = this.start, n = this.pos, r = 0; r < this.escapeCharPositions.length; r++) n = this.escapeCharPositions[r], e.push(this.str.slice(t, n)), t = n + 1; + return e.push(this.str.slice(t, this.pos)), this.escapeCharPositions.length = 0, e.join("") + }, D.QueryLexer.prototype.emit = function(e) { + this.lexemes.push({ + type: e, + str: this.sliceString(), + start: this.start, + end: this.pos + }), this.start = this.pos + }, D.QueryLexer.prototype.escapeCharacter = function() { + this.escapeCharPositions.push(this.pos - 1), this.pos += 1 + }, D.QueryLexer.prototype.next = function() { + if (this.pos >= this.length) return D.QueryLexer.EOS; + var e = this.str.charAt(this.pos); + return this.pos += 1, e + }, D.QueryLexer.prototype.width = function() { + return this.pos - this.start + }, D.QueryLexer.prototype.ignore = function() { + this.start == this.pos && (this.pos += 1), this.start = this.pos + }, D.QueryLexer.prototype.backup = function() { + this.pos -= 1 + }, D.QueryLexer.prototype.acceptDigitRun = function() { + for (var e, t; 47 < (t = (e = this.next()).charCodeAt(0)) && t < 58;); + e != D.QueryLexer.EOS && this.backup() + }, D.QueryLexer.prototype.more = function() { + return this.pos < this.length + }, D.QueryLexer.EOS = "EOS", D.QueryLexer.FIELD = "FIELD", D.QueryLexer.TERM = "TERM", D.QueryLexer.EDIT_DISTANCE = "EDIT_DISTANCE", D.QueryLexer.BOOST = "BOOST", D.QueryLexer.PRESENCE = "PRESENCE", D.QueryLexer.lexField = function(e) { + return e.backup(), e.emit(D.QueryLexer.FIELD), e.ignore(), D.QueryLexer.lexText + }, D.QueryLexer.lexTerm = function(e) { + if (1 < e.width() && (e.backup(), e.emit(D.QueryLexer.TERM)), e.ignore(), e.more()) return D.QueryLexer.lexText + }, D.QueryLexer.lexEditDistance = function(e) { + return e.ignore(), e.acceptDigitRun(), e.emit(D.QueryLexer.EDIT_DISTANCE), D.QueryLexer.lexText + }, D.QueryLexer.lexBoost = function(e) { + return e.ignore(), e.acceptDigitRun(), e.emit(D.QueryLexer.BOOST), D.QueryLexer.lexText + }, D.QueryLexer.lexEOS = function(e) { + 0 < e.width() && e.emit(D.QueryLexer.TERM) + }, D.QueryLexer.termSeparator = D.tokenizer.separator, D.QueryLexer.lexText = function(e) { + for (;;) { + var t = e.next(); + if (t == D.QueryLexer.EOS) return D.QueryLexer.lexEOS; + if (92 != t.charCodeAt(0)) { + if (":" == t) return D.QueryLexer.lexField; + if ("~" == t) return e.backup(), 0 < e.width() && e.emit(D.QueryLexer.TERM), D.QueryLexer.lexEditDistance; + if ("^" == t) return e.backup(), 0 < e.width() && e.emit(D.QueryLexer.TERM), D.QueryLexer.lexBoost; + if ("+" == t && 1 === e.width()) return e.emit(D.QueryLexer.PRESENCE), D.QueryLexer.lexText; + if ("-" == t && 1 === e.width()) return e.emit(D.QueryLexer.PRESENCE), D.QueryLexer.lexText; + if (t.match(D.QueryLexer.termSeparator)) return D.QueryLexer.lexTerm + } else e.escapeCharacter() + } + }, D.QueryParser = function(e, t) { + this.lexer = new D.QueryLexer(e), this.query = t, this.currentClause = {}, this.lexemeIdx = 0 + }, D.QueryParser.prototype.parse = function() { + this.lexer.run(), this.lexemes = this.lexer.lexemes; + for (var e = D.QueryParser.parseClause; e;) e = e(this); + return this.query + }, D.QueryParser.prototype.peekLexeme = function() { + return this.lexemes[this.lexemeIdx] + }, D.QueryParser.prototype.consumeLexeme = function() { + var e = this.peekLexeme(); + return this.lexemeIdx += 1, e + }, D.QueryParser.prototype.nextClause = function() { + var e = this.currentClause; + this.query.clause(e), this.currentClause = {} + }, D.QueryParser.parseClause = function(e) { + var t = e.peekLexeme(); + if (null != t) switch (t.type) { + case D.QueryLexer.PRESENCE: + return D.QueryParser.parsePresence; + case D.QueryLexer.FIELD: + return D.QueryParser.parseField; + case D.QueryLexer.TERM: + return D.QueryParser.parseTerm; + default: + var n = "expected either a field or a term, found " + t.type; + throw 1 <= t.str.length && (n += " with value '" + t.str + "'"), new D.QueryParseError(n, t.start, t.end) + } + }, D.QueryParser.parsePresence = function(e) { + var t = e.consumeLexeme(); + if (null != t) { + switch (t.str) { + case "-": + e.currentClause.presence = D.Query.presence.PROHIBITED; + break; + case "+": + e.currentClause.presence = D.Query.presence.REQUIRED; + break; + default: + var n = "unrecognised presence operator'" + t.str + "'"; + throw new D.QueryParseError(n, t.start, t.end) + } + var r = e.peekLexeme(); + if (null == r) { + n = "expecting term or field, found nothing"; + throw new D.QueryParseError(n, t.start, t.end) + } + switch (r.type) { + case D.QueryLexer.FIELD: + return D.QueryParser.parseField; + case D.QueryLexer.TERM: + return D.QueryParser.parseTerm; + default: + n = "expecting term or field, found '" + r.type + "'"; + throw new D.QueryParseError(n, r.start, r.end) + } + } + }, D.QueryParser.parseField = function(e) { + var t = e.consumeLexeme(); + if (null != t) { + if (-1 == e.query.allFields.indexOf(t.str)) { + var n = e.query.allFields.map(function(e) { + return "'" + e + "'" + }).join(", "), + r = "unrecognised field '" + t.str + "', possible fields: " + n; + throw new D.QueryParseError(r, t.start, t.end) + } + e.currentClause.fields = [t.str]; + var i = e.peekLexeme(); + if (null == i) { + r = "expecting term, found nothing"; + throw new D.QueryParseError(r, t.start, t.end) + } + switch (i.type) { + case D.QueryLexer.TERM: + return D.QueryParser.parseTerm; + default: + r = "expecting term, found '" + i.type + "'"; + throw new D.QueryParseError(r, i.start, i.end) + } + } + }, D.QueryParser.parseTerm = function(e) { + var t = e.consumeLexeme(); + if (null != t) { + e.currentClause.term = t.str.toLowerCase(), -1 != t.str.indexOf("*") && (e.currentClause.usePipeline = !1); + var n = e.peekLexeme(); + if (null != n) switch (n.type) { + case D.QueryLexer.TERM: + return e.nextClause(), D.QueryParser.parseTerm; + case D.QueryLexer.FIELD: + return e.nextClause(), D.QueryParser.parseField; + case D.QueryLexer.EDIT_DISTANCE: + return D.QueryParser.parseEditDistance; + case D.QueryLexer.BOOST: + return D.QueryParser.parseBoost; + case D.QueryLexer.PRESENCE: + return e.nextClause(), D.QueryParser.parsePresence; + default: + var r = "Unexpected lexeme type '" + n.type + "'"; + throw new D.QueryParseError(r, n.start, n.end) + } else e.nextClause() + } + }, D.QueryParser.parseEditDistance = function(e) { + var t = e.consumeLexeme(); + if (null != t) { + var n = parseInt(t.str, 10); + if (isNaN(n)) { + var r = "edit distance must be numeric"; + throw new D.QueryParseError(r, t.start, t.end) + } + e.currentClause.editDistance = n; + var i = e.peekLexeme(); + if (null != i) switch (i.type) { + case D.QueryLexer.TERM: + return e.nextClause(), D.QueryParser.parseTerm; + case D.QueryLexer.FIELD: + return e.nextClause(), D.QueryParser.parseField; + case D.QueryLexer.EDIT_DISTANCE: + return D.QueryParser.parseEditDistance; + case D.QueryLexer.BOOST: + return D.QueryParser.parseBoost; + case D.QueryLexer.PRESENCE: + return e.nextClause(), D.QueryParser.parsePresence; + default: + r = "Unexpected lexeme type '" + i.type + "'"; + throw new D.QueryParseError(r, i.start, i.end) + } else e.nextClause() + } + }, D.QueryParser.parseBoost = function(e) { + var t = e.consumeLexeme(); + if (null != t) { + var n = parseInt(t.str, 10); + if (isNaN(n)) { + var r = "boost must be numeric"; + throw new D.QueryParseError(r, t.start, t.end) + } + e.currentClause.boost = n; + var i = e.peekLexeme(); + if (null != i) switch (i.type) { + case D.QueryLexer.TERM: + return e.nextClause(), D.QueryParser.parseTerm; + case D.QueryLexer.FIELD: + return e.nextClause(), D.QueryParser.parseField; + case D.QueryLexer.EDIT_DISTANCE: + return D.QueryParser.parseEditDistance; + case D.QueryLexer.BOOST: + return D.QueryParser.parseBoost; + case D.QueryLexer.PRESENCE: + return e.nextClause(), D.QueryParser.parsePresence; + default: + r = "Unexpected lexeme type '" + i.type + "'"; + throw new D.QueryParseError(r, i.start, i.end) + } else e.nextClause() + } + }, void 0 === (c = "function" == typeof(s = function() { + return D + }) ? s.call(o, a, o, i) : s) || (i.exports = c) + }() +}])); \ No newline at end of file diff --git a/_static/javascripts/lunr/lunr.da.js b/_static/javascripts/lunr/lunr.da.js new file mode 100644 index 00000000..34910dfe --- /dev/null +++ b/_static/javascripts/lunr/lunr.da.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r,m,i;e.da=function(){this.pipeline.reset(),this.pipeline.add(e.da.trimmer,e.da.stopWordFilter,e.da.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.da.stemmer))},e.da.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.da.trimmer=e.trimmerSupport.generateTrimmer(e.da.wordCharacters),e.Pipeline.registerFunction(e.da.trimmer,"trimmer-da"),e.da.stemmer=(r=e.stemmerSupport.Among,m=e.stemmerSupport.SnowballProgram,i=new function(){var i,t,n,s=[new r("hed",-1,1),new r("ethed",0,1),new r("ered",-1,1),new r("e",-1,1),new r("erede",3,1),new r("ende",3,1),new r("erende",5,1),new r("ene",3,1),new r("erne",3,1),new r("ere",3,1),new r("en",-1,1),new r("heden",10,1),new r("eren",10,1),new r("er",-1,1),new r("heder",13,1),new r("erer",13,1),new r("s",-1,2),new r("heds",16,1),new r("es",16,1),new r("endes",18,1),new r("erendes",19,1),new r("enes",18,1),new r("ernes",18,1),new r("eres",18,1),new r("ens",16,1),new r("hedens",24,1),new r("erens",24,1),new r("ers",16,1),new r("ets",16,1),new r("erets",28,1),new r("et",-1,1),new r("eret",30,1)],o=[new r("gd",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1)],a=[new r("ig",-1,1),new r("lig",0,1),new r("elig",1,1),new r("els",-1,1),new r("løst",-1,2)],d=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],u=[239,254,42,3,0,0,0,0,0,0,0,0,0,0,0,0,16],c=new m;function l(){var e,r=c.limit-c.cursor;c.cursor>=t&&(e=c.limit_backward,c.limit_backward=t,c.ket=c.cursor,c.find_among_b(o,4)?(c.bra=c.cursor,c.limit_backward=e,c.cursor=c.limit-r,c.cursor>c.limit_backward&&(c.cursor--,c.bra=c.cursor,c.slice_del())):c.limit_backward=e)}this.setCurrent=function(e){c.setCurrent(e)},this.getCurrent=function(){return c.getCurrent()},this.stem=function(){var e,r=c.cursor;return function(){var e,r=c.cursor+3;if(t=c.limit,0<=r&&r<=c.limit){for(i=r;;){if(e=c.cursor,c.in_grouping(d,97,248)){c.cursor=e;break}if((c.cursor=e)>=c.limit)return;c.cursor++}for(;!c.out_grouping(d,97,248);){if(c.cursor>=c.limit)return;c.cursor++}(t=c.cursor)=t&&(r=c.limit_backward,c.limit_backward=t,c.ket=c.cursor,e=c.find_among_b(s,32),c.limit_backward=r,e))switch(c.bra=c.cursor,e){case 1:c.slice_del();break;case 2:c.in_grouping_b(u,97,229)&&c.slice_del()}}(),c.cursor=c.limit,l(),c.cursor=c.limit,function(){var e,r,i,n=c.limit-c.cursor;if(c.ket=c.cursor,c.eq_s_b(2,"st")&&(c.bra=c.cursor,c.eq_s_b(2,"ig")&&c.slice_del()),c.cursor=c.limit-n,c.cursor>=t&&(r=c.limit_backward,c.limit_backward=t,c.ket=c.cursor,e=c.find_among_b(a,5),c.limit_backward=r,e))switch(c.bra=c.cursor,e){case 1:c.slice_del(),i=c.limit-c.cursor,l(),c.cursor=c.limit-i;break;case 2:c.slice_from("løs")}}(),c.cursor=c.limit,c.cursor>=t&&(e=c.limit_backward,c.limit_backward=t,c.ket=c.cursor,c.out_grouping_b(d,97,248)?(c.bra=c.cursor,n=c.slice_to(n),c.limit_backward=e,c.eq_v_b(n)&&c.slice_del()):c.limit_backward=e),!0}},function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}),e.Pipeline.registerFunction(e.da.stemmer,"stemmer-da"),e.da.stopWordFilter=e.generateStopWordFilter("ad af alle alt anden at blev blive bliver da de dem den denne der deres det dette dig din disse dog du efter eller en end er et for fra ham han hans har havde have hende hendes her hos hun hvad hvis hvor i ikke ind jeg jer jo kunne man mange med meget men mig min mine mit mod ned noget nogle nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}}); \ No newline at end of file diff --git a/_static/javascripts/lunr/lunr.de.js b/_static/javascripts/lunr/lunr.de.js new file mode 100644 index 00000000..1529892c --- /dev/null +++ b/_static/javascripts/lunr/lunr.de.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var _,p,r;e.de=function(){this.pipeline.reset(),this.pipeline.add(e.de.trimmer,e.de.stopWordFilter,e.de.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.de.stemmer))},e.de.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.de.trimmer=e.trimmerSupport.generateTrimmer(e.de.wordCharacters),e.Pipeline.registerFunction(e.de.trimmer,"trimmer-de"),e.de.stemmer=(_=e.stemmerSupport.Among,p=e.stemmerSupport.SnowballProgram,r=new function(){var r,n,i,s=[new _("",-1,6),new _("U",0,2),new _("Y",0,1),new _("ä",0,3),new _("ö",0,4),new _("ü",0,5)],o=[new _("e",-1,2),new _("em",-1,1),new _("en",-1,2),new _("ern",-1,1),new _("er",-1,1),new _("s",-1,3),new _("es",5,2)],c=[new _("en",-1,1),new _("er",-1,1),new _("st",-1,2),new _("est",2,1)],u=[new _("ig",-1,1),new _("lich",-1,1)],a=[new _("end",-1,1),new _("ig",-1,2),new _("ung",-1,1),new _("lich",-1,3),new _("isch",-1,2),new _("ik",-1,2),new _("heit",-1,3),new _("keit",-1,4)],t=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,8,0,32,8],d=[117,30,5],l=[117,30,4],m=new p;function h(e,r,n){return!(!m.eq_s(1,e)||(m.ket=m.cursor,!m.in_grouping(t,97,252)))&&(m.slice_from(r),m.cursor=n,!0)}function w(){for(;!m.in_grouping(t,97,252);){if(m.cursor>=m.limit)return!0;m.cursor++}for(;!m.out_grouping(t,97,252);){if(m.cursor>=m.limit)return!0;m.cursor++}return!1}function f(){return i<=m.cursor}function b(){return n<=m.cursor}this.setCurrent=function(e){m.setCurrent(e)},this.getCurrent=function(){return m.getCurrent()},this.stem=function(){var e=m.cursor;return function(){for(var e,r,n,i,s=m.cursor;;)if(e=m.cursor,m.bra=e,m.eq_s(1,"ß"))m.ket=m.cursor,m.slice_from("ss");else{if(e>=m.limit)break;m.cursor=e+1}for(m.cursor=s;;)for(r=m.cursor;;){if(n=m.cursor,m.in_grouping(t,97,252)){if(i=m.cursor,m.bra=i,h("u","U",n))break;if(m.cursor=i,h("y","Y",n))break}if(n>=m.limit)return m.cursor=r;m.cursor=n+1}}(),m.cursor=e,function(){i=m.limit,n=i;var e=m.cursor+3;0<=e&&e<=m.limit&&(r=e,w()||((i=m.cursor)=m.limit)return;m.cursor++}}}(),!0}},function(e){return"function"==typeof e.update?e.update(function(e){return r.setCurrent(e),r.stem(),r.getCurrent()}):(r.setCurrent(e),r.stem(),r.getCurrent())}),e.Pipeline.registerFunction(e.de.stemmer,"stemmer-de"),e.de.stopWordFilter=e.generateStopWordFilter("aber alle allem allen aller alles als also am an ander andere anderem anderen anderer anderes anderm andern anderr anders auch auf aus bei bin bis bist da damit dann das dasselbe dazu daß dein deine deinem deinen deiner deines dem demselben den denn denselben der derer derselbe derselben des desselben dessen dich die dies diese dieselbe dieselben diesem diesen dieser dieses dir doch dort du durch ein eine einem einen einer eines einig einige einigem einigen einiger einiges einmal er es etwas euch euer eure eurem euren eurer eures für gegen gewesen hab habe haben hat hatte hatten hier hin hinter ich ihm ihn ihnen ihr ihre ihrem ihren ihrer ihres im in indem ins ist jede jedem jeden jeder jedes jene jenem jenen jener jenes jetzt kann kein keine keinem keinen keiner keines können könnte machen man manche manchem manchen mancher manches mein meine meinem meinen meiner meines mich mir mit muss musste nach nicht nichts noch nun nur ob oder ohne sehr sein seine seinem seinen seiner seines selbst sich sie sind so solche solchem solchen solcher solches soll sollte sondern sonst um und uns unse unsem unsen unser unses unter viel vom von vor war waren warst was weg weil weiter welche welchem welchen welcher welches wenn werde werden wie wieder will wir wird wirst wo wollen wollte während würde würden zu zum zur zwar zwischen über".split(" ")),e.Pipeline.registerFunction(e.de.stopWordFilter,"stopWordFilter-de")}}); \ No newline at end of file diff --git a/_static/javascripts/lunr/lunr.du.js b/_static/javascripts/lunr/lunr.du.js new file mode 100644 index 00000000..52632004 --- /dev/null +++ b/_static/javascripts/lunr/lunr.du.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var v,q,r;console.warn('[Lunr Languages] Please use the "nl" instead of the "du". The "nl" code is the standard code for Dutch language, and "du" will be removed in the next major versions.'),e.du=function(){this.pipeline.reset(),this.pipeline.add(e.du.trimmer,e.du.stopWordFilter,e.du.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.du.stemmer))},e.du.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.du.trimmer=e.trimmerSupport.generateTrimmer(e.du.wordCharacters),e.Pipeline.registerFunction(e.du.trimmer,"trimmer-du"),e.du.stemmer=(v=e.stemmerSupport.Among,q=e.stemmerSupport.SnowballProgram,r=new function(){var r,i,u,o=[new v("",-1,6),new v("á",0,1),new v("ä",0,1),new v("é",0,2),new v("ë",0,2),new v("í",0,3),new v("ï",0,3),new v("ó",0,4),new v("ö",0,4),new v("ú",0,5),new v("ü",0,5)],n=[new v("",-1,3),new v("I",0,2),new v("Y",0,1)],t=[new v("dd",-1,-1),new v("kk",-1,-1),new v("tt",-1,-1)],c=[new v("ene",-1,2),new v("se",-1,3),new v("en",-1,2),new v("heden",2,1),new v("s",-1,3)],a=[new v("end",-1,1),new v("ig",-1,2),new v("ing",-1,1),new v("lijk",-1,3),new v("baar",-1,4),new v("bar",-1,5)],l=[new v("aa",-1,-1),new v("ee",-1,-1),new v("oo",-1,-1),new v("uu",-1,-1)],m=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],d=[1,0,0,17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],f=[17,67,16,1,0,0,0,0,0,0,0,0,0,0,0,0,128],_=new q;function s(e){return(_.cursor=e)>=_.limit||(_.cursor++,!1)}function w(){for(;!_.in_grouping(m,97,232);){if(_.cursor>=_.limit)return!0;_.cursor++}for(;!_.out_grouping(m,97,232);){if(_.cursor>=_.limit)return!0;_.cursor++}return!1}function b(){return i<=_.cursor}function p(){return r<=_.cursor}function g(){var e=_.limit-_.cursor;_.find_among_b(t,3)&&(_.cursor=_.limit-e,_.ket=_.cursor,_.cursor>_.limit_backward&&(_.cursor--,_.bra=_.cursor,_.slice_del()))}function h(){var e;u=!1,_.ket=_.cursor,_.eq_s_b(1,"e")&&(_.bra=_.cursor,b()&&(e=_.limit-_.cursor,_.out_grouping_b(m,97,232)&&(_.cursor=_.limit-e,_.slice_del(),u=!0,g())))}function k(){var e;b()&&(e=_.limit-_.cursor,_.out_grouping_b(m,97,232)&&(_.cursor=_.limit-e,_.eq_s_b(3,"gem")||(_.cursor=_.limit-e,_.slice_del(),g())))}this.setCurrent=function(e){_.setCurrent(e)},this.getCurrent=function(){return _.getCurrent()},this.stem=function(){var e=_.cursor;return function(){for(var e,r,i,n=_.cursor;;){if(_.bra=_.cursor,e=_.find_among(o,11))switch(_.ket=_.cursor,e){case 1:_.slice_from("a");continue;case 2:_.slice_from("e");continue;case 3:_.slice_from("i");continue;case 4:_.slice_from("o");continue;case 5:_.slice_from("u");continue;case 6:if(_.cursor>=_.limit)break;_.cursor++;continue}break}for(_.cursor=n,_.bra=n,_.eq_s(1,"y")?(_.ket=_.cursor,_.slice_from("Y")):_.cursor=n;;)if(r=_.cursor,_.in_grouping(m,97,232)){if(i=_.cursor,_.bra=i,_.eq_s(1,"i"))_.ket=_.cursor,_.in_grouping(m,97,232)&&(_.slice_from("I"),_.cursor=r);else if(_.cursor=i,_.eq_s(1,"y"))_.ket=_.cursor,_.slice_from("Y"),_.cursor=r;else if(s(r))break}else 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\ No newline at end of file diff --git a/_static/javascripts/lunr/lunr.no.js b/_static/javascripts/lunr/lunr.no.js new file mode 100644 index 00000000..3d156b9c --- /dev/null +++ b/_static/javascripts/lunr/lunr.no.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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pelas pelo pelos por qual quando que quem se seja sejam sejamos sem serei seremos seria seriam será serão seríamos seu seus somos sou sua suas são só também te tem temos tenha tenham tenhamos tenho terei teremos teria teriam terá terão teríamos teu teus teve tinha tinham tive tivemos tiver tivera tiveram tiverem tivermos tivesse tivessem tivéramos tivéssemos tu tua tuas tém tínhamos um uma você vocês vos à às éramos".split(" ")),e.Pipeline.registerFunction(e.pt.stopWordFilter,"stopWordFilter-pt")}}); \ No newline at end of file diff --git a/_static/javascripts/lunr/lunr.ro.js b/_static/javascripts/lunr/lunr.ro.js new file mode 100644 index 00000000..b19627e1 --- /dev/null +++ b/_static/javascripts/lunr/lunr.ro.js @@ -0,0 +1 @@ +!function(e,i){"function"==typeof define&&define.amd?define(i):"object"==typeof exports?module.exports=i():i()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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către da dacă dar datorită dată dau de deci deja deoarece departe deşi din dinaintea dintr- dintre doi doilea două drept după dă ea ei el ele eram este eu eşti face fata fi fie fiecare fii fim fiu fiţi frumos fără graţie halbă iar ieri la le li lor lui lângă lîngă mai mea mei mele mereu meu mi mie mine mult multă mulţi mulţumesc mâine mîine mă ne nevoie nici nicăieri nimeni nimeri nimic nişte noastre noastră noi noroc nostru nouă noştri nu opt ori oricare orice oricine oricum oricând oricât oricînd oricît oriunde patra patru patrulea pe pentru peste pic poate pot prea prima primul prin puţin puţina puţină până pînă rog sa sale sau se spate spre sub sunt suntem sunteţi sută sînt sîntem sînteţi să săi său ta tale te timp tine toate toată tot totuşi toţi trei treia treilea tu tăi tău un una unde undeva unei uneia unele uneori unii unor unora unu unui unuia unul vi voastre voastră voi vostru vouă voştri vreme vreo vreun vă zece zero zi zice îi îl îmi împotriva în înainte înaintea încotro 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\ No newline at end of file diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 00000000..c7fe6c6f --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + diff --git a/_static/material.css b/_static/material.css new file mode 100644 index 00000000..a3d9b27d --- /dev/null +++ b/_static/material.css @@ -0,0 +1 @@ +@charset "utf-8";.dropdown{width:125px;vertical-align:middle}.dropdownbutton{color:inherit;font-weight:700;font-size:.65rem}.dropdown-content{display:none;position:absolute;z-index:1;background-color:inherit}.dropdown-content a{display:block;width:125px;margin:8px;font-size:.65rem;font-weight:200}.dropdown-content a:hover{}.dropdown:hover .dropdown-content{display:block}.dropdown:hover .dropbtn{} \ No newline at end of file diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 00000000..d96755fd Binary files /dev/null and b/_static/minus.png differ diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 00000000..7107cec9 Binary files /dev/null and b/_static/plus.png differ diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 00000000..53526e7a --- /dev/null +++ b/_static/pygments.css @@ -0,0 +1 @@ +@charset "utf-8";pre{line-height:125%}td.linenos .normal{color:inherit;background-color:transparent;padding-left:5px;padding-right:5px}span.linenos{color:inherit;background-color:transparent;padding-left:5px;padding-right:5px}td.linenos .special{color:#000;background-color:#ffffc0;padding-left:5px;padding-right:5px}span.linenos.special{color:#000;background-color:#ffffc0;padding-left:5px;padding-right:5px}.highlight .hll{background-color:#ffc}.highlight{background:#f8f8f8}.highlight .c{color:#080;font-style:italic}.highlight .err{border:1px solid #F00}.highlight .k{color:#A2F;font-weight:bold}.highlight .o{color:#666}.highlight 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.vc{color:#B8860B}.highlight .vg{color:#B8860B}.highlight .vi{color:#B8860B}.highlight .vm{color:#B8860B}.highlight .il{color:#666} \ No newline at end of file diff --git a/_static/redoc-static.html b/_static/redoc-static.html new file mode 100644 index 00000000..f66e2520 --- /dev/null +++ b/_static/redoc-static.html @@ -0,0 +1,921 @@ + + + + + + Jungfraujoch + + + + + + + + + +
API docs by Redocly

Jungfraujoch (1.0.0-rc.126)

Download OpenAPI specification:

Filip Leonarski (Paul Scherrer Institute): filip.leonarski@psi.ch License: GPL-3.0

API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). +Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. +Jungfraujoch uses FPGA boards to acquire data at high data rates.

+

License Clarification

While this API definition is licensed under GPL-3.0, the GPL copyleft provisions do not apply +when this file is used solely to generate OpenAPI clients or when implementing applications that +interact with the API. Generated client code and applications using this API definition are not +subject to the GPL license requirements and may be distributed under terms of your choosing.

+

This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and +the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that +user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not +derivative works of the kernel and are not subject to the terms of the GPL.

+

This exception is intended to allow wider use of this API specification without imposing GPL +requirements on applications that merely interact with the API, regardless of whether they +communicate through network calls or other mechanisms.

+

Initialize detector and data acquisition

Should be used in two cases:

+
    +
  • Detector is in Inactive state
    • +
  • Detector is in Error state +X-ray shutter must be closed. +This operation will reconfigure network interface of the detector. +During operation of the detector it is recommended to use the POST /pedestal operation instead. +If storage cells are used, the execution time might be few minutes.
    • +
+

This is async function - one needs to use POST /wait_till_done to ensure operation is done.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Collect dark current for the detector

Updates calibration of the JUNGFRAU detector. Must be in Idle state.

+

X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).

+

This is async function - one needs to use POST /wait_till_done to ensure operation is done.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Start detector

Start data acquisition. +Detector must be in Idle state. +Doesn't run calibration procedure. +When the function returns, detector is ready to accept soft/TTL triggers.

+
Request Body schema: application/json
images_per_trigger
integer <int64> >= 1
Default: 1

For standard synchrotron data collection - this is number of images collected per one TTL trigger +For XFEL (pulsed source) - this number is ignored and set to 1 +For storage cell mode - this number is ignored and set to number of storage cells

+
ntrigger
integer <int64> >= 1
Default: 1

Number of TTL trigger that the detector is expected to receive during data collection

+
image_time_us
integer <int64> >= 0

Image time. +If not provided (or zero value) the frame time is assumed as default. +For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.
In XFEL mode: summation happens for frames collected with multiple triggers. +Ignored for storage cells and if raw data are saved.

+
beam_x_pxl
required
number <float>

/entry/detector/beam_center_x in NXmx +Beam center in X direction [pixels]

+
beam_y_pxl
required
number <float>

/entry/detector/beam_center_y in NXmx +Beam center in X direction [pixels]

+
detector_distance_mm
required
number <float> >= 0

/entry/detector/distance in NXmx Detector distance [mm]

+
incident_energy_keV
required
number <float> [ 0.001 .. 500 ]

Used to calculate /entry/beam/incident_wavelength in NXmx +Incident particle (photon, electron) energy in keV

+
file_prefix
string
Default: ""

Prefix for filenames. If left empty, no file will be saved.

+
images_per_file
integer <int64> >= 0
Default: 1000

Number of files in a single HDF5 data file (0 = write all images to a single data file).

+
space_group_number
integer <int64> [ 1 .. 194 ]

Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.

+
sample_name
string
Default: ""

/entry/sample/name in NXmx +Sample name

+
compression
string
Default: "bslz4"
Enum: "bslz4" "bszstd" "bszstd_rle" "none"

Compression type for the images transferred over ZeroMQ and saved to HDF5 file.

+
total_flux
number <float>

/entry/beam/total_flux in NXmx +Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]

+
transmission
number <float> [ 0 .. 1 ]

/entry/instrument/attenuator/attenuator_transmission +Transmission of attenuator (filter) [no units]

+
object (rotation_axis)

Definition of a crystal rotation axis

+
object (grid_scan)

Definition of a grid scan (mutually exclusive with rotation_axis)

+
header_appendix
any

Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) +In general, it is not saved in HDF5 file.

+

However, if values are placed in "hdf5" object, jfjoch_writer will write them in /entry/data of the HDF5 file. +This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. +For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.

+
image_appendix
any

Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) +Not saved in HDF5 file

+
data_reduction_factor_serialmx
number <float> [ 0 .. 1 ]
Default: 1

Rate at which non-indexed images are accepted to be forwarded to writer. +Value of 1.0 (default) means that all images are written. +Values below zero mean that non-indexed images will be accepted with a given probability.

+
pixel_value_low_threshold
integer <int64> >= 0

Set all counts lower than the value to zero. +When the value is set, negative numbers other than error pixel value are always set to zero. +Setting to zero is equivalent to turning the option off.

+
run_number
integer <int64> >= 0

Number of run within an experimental session. +Transferred over CBOR stream as "series ID", though not saved in HDF5 file. +It is highly recommended to keep this number unique for each data collection during experimental series. +If not provided, the number will be automatically incremented.

+
run_name
string

Unique ID of run. +Transferred over CBOR stream as "unique series ID", though not saved in HDF5 file. +It is highly recommended to keep this name unique for each data collection during experimental series. +If not provided, the name will be automatically generated as number + colon + file_prefix.

+
experiment_group
string

Name of group owning the data (e.g. p-group or proposal number). +Transferred over CBOR stream, though not saved in HDF5 file.

+
poisson_compression
integer <int64> [ 0 .. 16 ]

Enable lossy compression of pixel values that preserves Poisson statistics. +Requires to provide a numerical factor SQ. +Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer. +Compression is turned off if the value is missing or it is set to zero.

+
write_nxmx_hdf5_master
boolean
Default: true

Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments +and to turn off for other experiments.

+
save_calibration
boolean

Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer. +If parameter is not provided calibration will be saved only if more than 4 images are recorded.

+
polarization_factor
number <float> [ -1 .. 1 ]

Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization

+
ring_current_mA
number <float> >= 0

Ring current at the beginning of the data collection

+
sample_temperature_K
number <float> >= 0

Sample temperature in Kelvin

+
poni_rot1_rad
number <float> [ -6.28318530718 .. 6.28318530718 ]
Default: 0

PONI angle rot1 (see PyFAI documentation for details) in radians

+
poni_rot2_rad
number <float> [ -6.28318530718 .. 6.28318530718 ]
Default: 0

PONI angle rot2 (see PyFAI documentation for details) in radians

+
poni_rot3_rad
number <float> [ -6.28318530718 .. 6.28318530718 ]
Default: 0

PONI angle rot3 (see PyFAI documentation for details) in radians

+
object (unit_cell)

Unit cell parameters. Necessary to run indexing. Units of angstrom and degree

+
spot_finding
boolean
Default: true

Enable spot finding and save spots

+
max_spot_count
integer [ 10 .. 2000 ]
Default: 250

Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected

+
detect_ice_rings
boolean

Flag spots as ice rings and reduce their effect on indexing

+
object

Responses

Request samples

Content type
application/json
{
  • "images_per_trigger": 1,
  • "ntrigger": 1,
  • "image_time_us": 0,
  • "beam_x_pxl": 0.1,
  • "beam_y_pxl": 0.1,
  • "detector_distance_mm": 0.1,
  • "incident_energy_keV": 0.001,
  • "file_prefix": "",
  • "images_per_file": 1000,
  • "space_group_number": 1,
  • "sample_name": "",
  • "compression": "bslz4",
  • "total_flux": 0.1,
  • "transmission": 1,
  • "goniometer": {
    },
  • "grid_scan": {
    },
  • "header_appendix": null,
  • "image_appendix": null,
  • "data_reduction_factor_serialmx": 1,
  • "pixel_value_low_threshold": 0,
  • "run_number": 0,
  • "run_name": "string",
  • "experiment_group": "string",
  • "poisson_compression": 16,
  • "write_nxmx_hdf5_master": true,
  • "save_calibration": true,
  • "polarization_factor": -1,
  • "ring_current_mA": 0.1,
  • "sample_temperature_K": 0.1,
  • "poni_rot1_rad": 0,
  • "poni_rot2_rad": 0,
  • "poni_rot3_rad": 0,
  • "unit_cell": {
    },
  • "spot_finding": true,
  • "max_spot_count": 250,
  • "detect_ice_rings": true,
  • "xray_fluorescence_spectrum": {
    }
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Wait for acquisition done

Block execution of external script till initialization, data collection or pedestal is finished. +Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.

+

To not block web server for a indefinite period of time, the procedure is provided with a timeout. +Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.

+
query Parameters
timeout
integer [ 0 .. 3600 ]
Default: 60

Timeout in seconds (0 == immediate response)

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Send soft trigger to the detector

Generate soft trigger

+

Responses

Cancel running data collection

Command will inform FPGA network card to stop pedestal or data collection at the current stage. +Any frame that is currently being processed by CPU will be finished and sent to writer. +Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to Idle state.

+

If data collection is not running, the command has no effect.

+

Responses

Prepare detector to turn off

Should be in Idle or Error state. +Command deactivates data acquisition and turns off detector high voltage and ASIC. +Should be used always before turning off power from the detector.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Change detector configuration

Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings. +This can only be done when detector is Idle, Error or Inactive states. +If detector is in Idle state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation. +If detector is in Inactive or Error states, new settings will be saved, but no calibration will be executed.

+
Request Body schema: application/json
frame_time_us
required
integer <int64> >= 1

Interval between consecutive frames. +This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number. +For EIGER detector this is default frame time, not used otherwise

+
count_time_us
integer <int64>

Integration time of the detector. +If not provided count time will be set to maximum value for a given frame time.

+
internal_frame_generator
boolean
Default: false

Use internal frame generator in FPGA instead of getting data from a real detector

+
internal_frame_generator_images
integer <int64> [ 1 .. 64 ]
Default: 1

Number of images stored in the internal frame generator.

+
detector_trigger_delay_ns
integer <int64> >= 0
Default: 0

Delay between TTL trigger and acquisition start [ns]

+
timing
string (detector_timing)
Default: "trigger"
Enum: "auto" "trigger" "burst" "gated"
eiger_threshold_keV
number <float> [ 1 .. 100 ]

Threshold for the PSI EIGER detector and all DECTRIS detectors. +If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy. +If value is not provided, threshold will be determined on start of acquisition as half of incident energy. +This might lead to increased start time.

+
eiger_bit_depth
integer <int64>
Enum: 8 16 32

Bit depth of PSI EIGER read-out. This is
If value is not provided, depth will be determined based on the image time:

+
    +
  • Exposure time < 500 microseconds depth of 8 bit will be used,
    • +
  • 500 <= exposure time < 2622 microseconds depth of 16 bit will be used
    • +
  • Exposure time >= 2622 microseconds depth of 32 bit will be used.
    • +
+
jungfrau_pedestal_g0_frames
integer <int64> >= 0
Default: 2000
jungfrau_pedestal_g1_frames
integer <int64> >= 0
Default: 300
jungfrau_pedestal_g2_frames
integer <int64> >= 0
Default: 300
jungfrau_pedestal_min_image_count
integer <int64> >= 32
Default: 128

Minimum number of collected images for pedestal to consider it viable

+
jungfrau_storage_cell_count
integer <int64> [ 1 .. 16 ]
Default: 1
jungfrau_storage_cell_delay_ns
integer <int64> >= 2100
Default: 5000

Delay between two storage cells [ns]

+
jungfrau_fixed_gain_g1
boolean
Default: false

Fix gain to G1 (can be useful for storage cells)

+
jungfrau_use_gain_hg0
boolean
Default: false

Use high G0 (for low energy applications)

+

Responses

Request samples

Content type
application/json
{
  • "frame_time_us": 1,
  • "count_time_us": 0,
  • "internal_frame_generator": false,
  • "internal_frame_generator_images": 1,
  • "detector_trigger_delay_ns": 0,
  • "timing": "auto",
  • "eiger_threshold_keV": 1,
  • "eiger_bit_depth": 8,
  • "jungfrau_pedestal_g0_frames": 2000,
  • "jungfrau_pedestal_g1_frames": 300,
  • "jungfrau_pedestal_g2_frames": 300,
  • "jungfrau_pedestal_min_image_count": 128,
  • "jungfrau_storage_cell_count": 1,
  • "jungfrau_storage_cell_delay_ns": 5000,
  • "jungfrau_fixed_gain_g1": false,
  • "jungfrau_use_gain_hg0": false
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get detector configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "frame_time_us": 1,
  • "count_time_us": 0,
  • "internal_frame_generator": false,
  • "internal_frame_generator_images": 1,
  • "detector_trigger_delay_ns": 0,
  • "timing": "auto",
  • "eiger_threshold_keV": 1,
  • "eiger_bit_depth": 8,
  • "jungfrau_pedestal_g0_frames": 2000,
  • "jungfrau_pedestal_g1_frames": 300,
  • "jungfrau_pedestal_g2_frames": 300,
  • "jungfrau_pedestal_min_image_count": 128,
  • "jungfrau_storage_cell_count": 1,
  • "jungfrau_storage_cell_delay_ns": 5000,
  • "jungfrau_fixed_gain_g1": false,
  • "jungfrau_use_gain_hg0": false
}

Change indexing algorithm settings

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
algorithm
required
string (indexing_algorithm)
Default: "FFBIDX"
Enum: "FFBIDX" "FFT" "FFTW" "Auto" "None"

Selection of an indexing algorithm used by Jungfraujoch

+
fft_max_unit_cell_A
required
number <float> [ 50 .. 500 ]
Default: 250

Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT

+
fft_min_unit_cell_A
required
number <float> [ 5 .. 40 ]
Default: 10

Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT

+
fft_high_resolution_A
required
number <float> [ 0.5 .. 6 ]
Default: 2

Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT. +There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.

+
fft_num_vectors
required
integer <int64> >= 128
Default: 16384

Number of search directions for the FFT algorithm; parameter value affects execution time of FFT.

+
tolerance
required
number <float> [ 0 .. 0.5 ]

Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted

+
thread_count
required
integer <int64> [ 1 .. 64 ]

Thread count for indexing algorithm

+
geom_refinement_algorithm
required
string (geom_refinement_algorithm)
Enum: "BeamCenter" "None"

Selection of an post-indexing detector geometry refinement algorithm used by Jungfraujoch. +This option is using non-linear least squares optimization to find unit cell and beam center.

+
unit_cell_dist_tolerance
required
number <float> [ 0.0001 .. 0.2001 ]
Default: 0.05

Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored

+
viable_cell_min_spots
required
integer <int64> >= 5
Default: 10

Minimum number of indexed spots required for a cell to be considered viable

+
index_ice_rings
required
boolean
Default: false

Include spots marked as ice rings in the indexing run. +If dataset_settings doesn't have detect_ice_rings on, this option will have no effect on processing.

+
rotation_indexing
required
boolean
Default: false
rotation_indexing_min_angular_range_deg
required
number <float> >= 1
Default: 20
rotation_indexing_angular_stride_deg
required
number <float> >= 0
Default: 0.5

Responses

Request samples

Content type
application/json
{
  • "algorithm": "FFBIDX",
  • "fft_max_unit_cell_A": 250,
  • "fft_min_unit_cell_A": 10,
  • "fft_high_resolution_A": 2,
  • "fft_num_vectors": 16384,
  • "tolerance": 0.5,
  • "thread_count": 1,
  • "geom_refinement_algorithm": "BeamCenter",
  • "unit_cell_dist_tolerance": 0.05,
  • "viable_cell_min_spots": 10,
  • "index_ice_rings": false,
  • "rotation_indexing": false,
  • "rotation_indexing_min_angular_range_deg": 20,
  • "rotation_indexing_angular_stride_deg": 0.5
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get indexing configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "algorithm": "FFBIDX",
  • "fft_max_unit_cell_A": 250,
  • "fft_min_unit_cell_A": 10,
  • "fft_high_resolution_A": 2,
  • "fft_num_vectors": 16384,
  • "tolerance": 0.5,
  • "thread_count": 1,
  • "geom_refinement_algorithm": "BeamCenter",
  • "unit_cell_dist_tolerance": 0.05,
  • "viable_cell_min_spots": 10,
  • "index_ice_rings": false,
  • "rotation_indexing": false,
  • "rotation_indexing_min_angular_range_deg": 20,
  • "rotation_indexing_angular_stride_deg": 0.5
}

Change file writer settings

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
overwrite
boolean
Default: false

Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.

+
format
string (file_writer_format)
Default: "NXmxLegacy"
Enum: "None" "NXmxLegacy" "NXmxVDS" "CBF" "TIFF" "NoFileWritten"

None - no master file written +NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling

+

Responses

Request samples

Content type
application/json
{
  • "overwrite": false,
  • "format": "None"
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get file writer settings

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "overwrite": false,
  • "format": "None"
}

Change instrument metadata

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
source_name
required
string
source_type
string
Default: ""

Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. +https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource +NXsource allows the following:

+

Spallation Neutron Source +Pulsed Reactor Neutron Source +Reactor Neutron Source +Synchrotron X-ray Source +Pulsed Muon Source +Rotating Anode X-ray +Fixed Tube X-ray +UV Laser +Free-Electron Laser +Optical Laser +Ion Source +UV Plasma Source +Metal Jet X-ray

+
instrument_name
required
string
pulsed_source
boolean
Default: false

Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)

+
electron_source
boolean
Default: false

Settings specific to electron source (e.g., wavelength definition)

+

Responses

Request samples

Content type
application/json
{
  • "source_name": "Swiss Light Source",
  • "source_type": "Synchrotron X-ray Source",
  • "instrument_name": "CristallinaMX",
  • "pulsed_source": false,
  • "electron_source": false
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get instrument metadata

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "source_name": "Swiss Light Source",
  • "source_type": "Synchrotron X-ray Source",
  • "instrument_name": "CristallinaMX",
  • "pulsed_source": false,
  • "electron_source": false
}

Change image output format

This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
summation
required
boolean

Enable summation of images to a given image_time +If disabled images are saved according to original detector speed, but image count is adjusted

+
geometry_transform
required
boolean

Place module read-out into their location on composed detector and extend multipixels

+
jungfrau_conversion
required
boolean

Convert pixel value in ADU to photon counts/energy +Only affects JUNGFRAU detector

+
jungfrau_conversion_factor_keV
number <float> [ 0.001 .. 500 ]

Used to convert energy deposited into pixel to counts +If not provided incident_energy_keV is used

+
bit_depth_image
integer <int64>
Enum: 8 16 32

Bit depth of resulting image (it doesn't affect the detector read-out value) +If not provided value is adjusted automatically

+
signed_output
boolean

Controls if pixels have signed output +If not provided value is adjusted automatically

+
mask_module_edges
required
boolean
Default: true

Mask 1 pixel on the module boundary

+
mask_chip_edges
required
boolean
Default: true

Mask multipixels on chip boundary

+
jungfrau_mask_pixels_without_g0
boolean
Default: true

JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1. +This should be turned off for cases, where detector is operated at room temperature with long exposure time.

+
apply_mask
required
boolean
Default: false

Masked pixels are set to special value in the images produced by Jungfraujoch

+
jungfrau_pedestal_g0_rms_limit
integer <int64> >= 0
Default: 100

Pixels with pedestal G0 RMS above the threshold are marked as masked pixels

+

Responses

Request samples

Content type
application/json
{
  • "summation": true,
  • "geometry_transform": true,
  • "jungfrau_conversion": true,
  • "jungfrau_conversion_factor_keV": 0.001,
  • "bit_depth_image": 8,
  • "signed_output": true,
  • "mask_module_edges": true,
  • "mask_chip_edges": true,
  • "jungfrau_mask_pixels_without_g0": true,
  • "apply_mask": false,
  • "jungfrau_pedestal_g0_rms_limit": 100
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get image output format

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "summation": true,
  • "geometry_transform": true,
  • "jungfrau_conversion": true,
  • "jungfrau_conversion_factor_keV": 0.001,
  • "bit_depth_image": 8,
  • "signed_output": true,
  • "mask_module_edges": true,
  • "mask_chip_edges": true,
  • "jungfrau_mask_pixels_without_g0": true,
  • "apply_mask": false,
  • "jungfrau_pedestal_g0_rms_limit": 100
}

Configure format for raw data collection

This can only be done when detector is Idle, Error or Inactive states.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Configure format for data collection with full conversion

This can only be done when detector is Idle, Error or Inactive states.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Configure spot finding

Can be done anytime, also while data collection is running

+
Request Body schema: application/json
enable
required
boolean
Default: true

Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. +Even if disabled spot finding information will still be send and written, though always with zero spots.

+
indexing
required
boolean
Default: true

Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.

+
signal_to_noise_threshold
required
number <float> >= 0
photon_count_threshold
required
integer <int64> >= 0
min_pix_per_spot
required
integer <int64> >= 1
max_pix_per_spot
required
integer <int64> >= 1
high_resolution_limit
required
number <float>

High resolution limit for spot finding [Angstrom]

+
low_resolution_limit
required
number <float>

Low resolution limit for spot finding [Angstrom]

+
high_resolution_limit_for_spot_count_low_res
required
number <float> [ 2 .. 8 ]

High resolution threshold to consider spot "low resolution" [Angstrom]

+
quick_integration
required
boolean
Default: false

Quick integration of Bragg spots in diffraction images. +If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate. +(experimental feature)

+
ice_ring_width_q_recipA
required
number <float> [ 0 .. 1 ]
Default: 0.02

Width of ice ring in q-space in reciprocal space

+
high_res_gap_Q_recipA
number <float> [ 0.1 .. 5 ]
Default: 1.5

This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector. +If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter. +This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.

+

Responses

Request samples

Content type
application/json
{
  • "enable": true,
  • "indexing": true,
  • "signal_to_noise_threshold": 0.1,
  • "photon_count_threshold": 0,
  • "min_pix_per_spot": 1,
  • "max_pix_per_spot": 1,
  • "high_resolution_limit": 0.1,
  • "low_resolution_limit": 0.1,
  • "high_resolution_limit_for_spot_count_low_res": 2,
  • "quick_integration": false,
  • "ice_ring_width_q_recipA": 0.02,
  • "high_res_gap_Q_recipA": 1.5
}

Get data processing configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "enable": true,
  • "indexing": true,
  • "signal_to_noise_threshold": 0.1,
  • "photon_count_threshold": 0,
  • "min_pix_per_spot": 1,
  • "max_pix_per_spot": 1,
  • "high_resolution_limit": 0.1,
  • "low_resolution_limit": 0.1,
  • "high_resolution_limit_for_spot_count_low_res": 2,
  • "quick_integration": false,
  • "ice_ring_width_q_recipA": 0.02,
  • "high_res_gap_Q_recipA": 1.5
}

Configure azimuthal integration

Can be done when detector is Inactive or Idle

+
Request Body schema: application/json
polarization_corr
required
boolean
Default: true

Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)

+
solid_angle_corr
required
boolean
Default: true

Apply solid angle correction for azimuthal integration

+
high_q_recipA
required
number <float>
low_q_recipA
required
number <float>
q_spacing
required
number <float>
azimuthal_bins
integer <int64> [ 1 .. 256 ]
Default: 1

Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration

+

Responses

Request samples

Content type
application/json
{
  • "polarization_corr": true,
  • "solid_angle_corr": true,
  • "high_q_recipA": 0.1,
  • "low_q_recipA": 0.1,
  • "q_spacing": 0.1,
  • "azimuthal_bins": 1
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get azimuthal integration configuration

Can be done anytime

+

Responses

Response samples

Content type
application/json
{
  • "polarization_corr": true,
  • "solid_angle_corr": true,
  • "high_q_recipA": 0.1,
  • "low_q_recipA": 0.1,
  • "q_spacing": 0.1,
  • "azimuthal_bins": 1
}

Load binary image for internal FPGA generator

Load image for internal FPGA generator. This can only happen in Idle state of the detector. +Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates +(depending on detector settings).

+
query Parameters
id
integer <int64> [ 0 .. 127 ]

Image id to upload

+
Request Body schema: application/octet-stream
string <binary>

Responses

Load TIFF image for internal FPGA generator

Load image for internal FPGA generator. This can only happen in Idle state of the detector. +Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates +(depending on detector settings).

+
query Parameters
id
integer [ 0 .. 127 ]

Image ID to upload

+
Request Body schema: image/tiff
string <binary>

Responses

Select detector

Jungfraujoch allows to control multiple detectors and/or region-of-interests. +The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response). +Changing detector will set detector to Inactive state and will require reinitialization.

+
Request Body schema: application/json
id
required
integer <int64>

Responses

Request samples

Content type
application/json
{
  • "id": 1
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

List available detectors

Configured detectors that can be selected by used

+

Responses

Response samples

Content type
application/json
{
  • "detectors": [
    ],
  • "current_id": 0
}

Set ZeroMQ preview settings

Jungfraujoch can generate preview message stream on ZeroMQ SUB socket. +Here settings of the socket can be adjusted. +While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request. +Options set with this PUT request have no effect on HTTP based preview.

+
Request Body schema: application/json
enabled
required
boolean
Default: true

ZeroMQ preview socket is enabled.

+
period_ms
required
integer <int64>
Default: 1000

Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. +If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection). +This has no effect on HTTP based preview, which updates always at rate of 1 second.

+
socket_address
string

PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate. +Images are serialized using CBOR. +Address follows ZeroMQ convention for sockets - in practice ipc:// and tcp://: sockets are OK. +0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

+

Responses

Request samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get ZeroMQ preview settings

Responses

Response samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Set ZeroMQ metadata settings

Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images. +Here settings of the socket can be adjusted. +While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.

+
Request Body schema: application/json
enabled
required
boolean
Default: true

ZeroMQ metadata socket is enabled.

+
period_ms
required
integer <int64> >= 1
Default: 1000

Period for generating metadata package sent to the ZeroMQ interface in milliseconds.

+
socket_address
string

PUB ZeroMQ socket for image metadata information. +Image metadata are serialized using CBOR. +Address follows ZeroMQ convention for sockets - in practice ipc:// and tcp://: sockets are OK. +0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

+

Responses

Request samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get ZeroMQ metadata socket settings

Responses

Response samples

Content type
application/json
{
  • "enabled": true,
  • "period_ms": 1000,
  • "socket_address": "string"
}

Set configuration for dark data collection to calculate mask

This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point. +This can only be done when detector is Idle, Error or Inactive states.

+
Request Body schema: application/json
detector_threshold_keV
required
number <float> [ 2.5 .. 100 ]
Default: 3.5

Energy threshold for dark image collection

+
frame_time_us
required
integer <int64> [ 500 .. 100000 ]
Default: 10000

Time between frames for dark image collection

+
number_of_frames
required
integer <int64> >= 0
Default: 1000

Number of frames for dark image collection; zero means no dark collection

+
max_allowed_pixel_count
required
integer <int64> >= 0
Default: 1

Maximum count in a pixel considered normal (not-masked)

+
max_frames_with_signal
required
integer <int64> >= 0
Default: 10

Maximum number of frames with signal in a pixel considered normal (not-masked)

+

Responses

Request samples

Content type
application/json
{
  • "detector_threshold_keV": 3.5,
  • "frame_time_us": 10000,
  • "number_of_frames": 1000,
  • "max_allowed_pixel_count": 1,
  • "max_frames_with_signal": 10
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get settings for dark data collection to calculate mask

Responses

Response samples

Content type
application/json
{
  • "detector_threshold_keV": 3.5,
  • "frame_time_us": 10000,
  • "number_of_frames": 1000,
  • "max_allowed_pixel_count": 1,
  • "max_frames_with_signal": 10
}

Get Jungfraujoch status

Status of the data acquisition

+

Responses

Response samples

Content type
application/json
{
  • "state": "Inactive",
  • "progress": 1,
  • "message": "string",
  • "message_severity": "success",
  • "gpu_count": 0
}

Get status of FPGA devices

Responses

Response samples

Content type
application/json
[
  • {
    }
]

Return XFEL pulse IDs for the current data acquisition

Return array of XFEL pulse IDs - (-1) if image not recorded

+

Responses

Response samples

Content type
application/json
[
  • 0
]

Return XFEL event codes for the current data acquisition

Return array of XFEL event codes

+

Responses

Response samples

Content type
application/json
[
  • 0
]

Get detector status

Status of the JUNGFRAU detector

+

Responses

Response samples

Content type
application/json
{
  • "state": "Idle",
  • "powerchip": "PowerOn",
  • "server_version": "string",
  • "number_of_triggers_left": 0,
  • "fpga_temp_degC": [
    ],
  • "high_voltage_V": [
    ]
}

Get ROI definitions

Responses

Response samples

Content type
application/json
{
  • "box": {
    },
  • "circle": {
    },
  • "azim": {
    }
}

Upload ROI definitions

Request Body schema: application/json
required
object (roi_box_list)

List of box ROIs

+
required
object (roi_circle_list)

List of circular ROIs

+
required
object (roi_azim_list)

List of azimuthal ROIs

+

Responses

Request samples

Content type
application/json
{
  • "box": {
    },
  • "circle": {
    },
  • "azim": {
    }
}

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get general statistics

query Parameters
compression
boolean
Default: false

Enable DEFLATE compression of output data.

+

Responses

Response samples

Content type
application/json
{
  • "detector": {
    },
  • "detector_list": {
    },
  • "detector_settings": {
    },
  • "image_format_settings": {
    },
  • "instrument_metadata": {
    },
  • "file_writer_settings": {
    },
  • "data_processing_settings": {
    },
  • "measurement": {
    },
  • "broker": {
    },
  • "fpga": [
    ],
  • "calibration": [
    ],
  • "zeromq_preview": {
    },
  • "zeromq_metadata": {
    },
  • "dark_mask": {
    },
  • "pixel_mask": {
    },
  • "roi": {
    },
  • "az_int": {
    },
  • "buffer": {
    },
  • "indexing": {
    }
}

Get data collection statistics

Results of the last data collection

+

Responses

Response samples

Content type
application/json
{
  • "file_prefix": "string",
  • "run_number": 0,
  • "experiment_group": "string",
  • "images_expected": 0,
  • "images_collected": 0,
  • "images_sent": 0,
  • "images_discarded_lossy_compression": 0,
  • "max_image_number_sent": 0,
  • "collection_efficiency": 1,
  • "compression_ratio": 5.3,
  • "cancelled": true,
  • "max_receiver_delay": 0,
  • "indexing_rate": 0.1,
  • "detector_width": 0,
  • "detector_height": 0,
  • "detector_pixel_depth": 2,
  • "bkg_estimate": 0.1,
  • "unit_cell": "string",
  • "error_pixels": 0.1,
  • "saturated_pixels": 0.1,
  • "roi_beam_pixels": 0.1,
  • "roi_beam_sum": 0.1
}

Get calibration statistics

Statistics are provided for each module/storage cell separately

+

Responses

Response samples

Content type
application/json
[
  • {
    }
]

Get mask of the detector (binary)

Detector must be Initialized. +Get full pixel mask of the detector. +See NXmx standard for meaning of pixel values.

+

Responses

Detector must be Initialized. +Get user mask of the detector (binary) +

Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked

+

Responses

Upload user mask of the detector (binary)

Should be in Idle state. +Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. +If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. +In the latter case - module gaps are ignored and don't need to be assigned value. +Mask is expected as binary array (4-byte; unsigned). +0 - good pixel, other value - masked +User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.

+
Request Body schema: application/octet-stream
string <binary>

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get mask of the detector (TIFF)

Should be in Idle state. +Get full pixel mask of the detector +See NXmx standard for meaning of pixel values

+

Responses

Detector must be Initialized. +Get user mask of the detector (TIFF) +

Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked

+

Responses

Upload user mask of the detector

Should be in Idle state. +Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. +If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. +In the latter case - module gaps are ignored and don't need to be assigned value. +Mask is expected as TIFF (4-byte; unsigned). +0 - good pixel, other value - masked +User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. +User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.

+
Request Body schema: image/tiff
string <binary>

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get pedestal in TIFF format

query Parameters
gain_level
required
integer

Gain level (0, 1, 2)

+
sc
integer

Storage cell number

+

Responses

Generate 1D plot from Jungfraujoch

query Parameters
binning
integer
Default: 1

Binning of frames for the plot (0 = default binning)

+
compression
boolean
Default: false

Enable DEFLATE compression of output data.

+
type
required
string
Enum: "bkg_estimate" "azint" "azint_1d" "spot_count" "spot_count_low_res" "spot_count_indexed" "spot_count_ice" "indexing_rate" "indexing_time" "indexing_unit_cell_length" "indexing_unit_cell_angle" "profile_radius" "mosaicity" "b_factor" "error_pixels" "saturated_pixels" "image_collection_efficiency" "receiver_delay" "receiver_free_send_buf" "strong_pixels" "roi_sum" "roi_mean" "roi_max_count" "roi_pixels" "roi_weighted_x" "roi_weighted_y" "packets_received" "max_pixel_value" "resolution_estimate" "pixel_sum" "processing_time" "beam_center_x" "beam_center_y"

Type of requested plot

+
fill
number <float>

Fill value for elements that were missed during data collection

+
experimental_coord
boolean
Default: false

If measurement has goniometer axis defined, plot X-axis will represent rotation angle +If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value +For still measurement the number is ignored

+
azint_unit
string
Default: "Q_recipA"
Enum: "Q_recipA" "d_A" "two_theta_deg"

Unit used for azim int.

+

Responses

Response samples

Content type
application/json
{
  • "title": "string",
  • "unit_x": "image_number",
  • "size_x": 0.1,
  • "size_y": 0.1,
  • "plot": [
    ]
}

Generate 1D plot from Jungfraujoch and send in raw binary format. +Data are provided as (32-bit) float binary array. +This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. +

query Parameters
type
required
string
Enum: "bkg_estimate" "azint" "azint_1d" "spot_count" "spot_count_low_res" "spot_count_indexed" "spot_count_ice" "indexing_rate" "indexing_time" "indexing_unit_cell_length" "indexing_unit_cell_angle" "profile_radius" "mosaicity" "b_factor" "error_pixels" "saturated_pixels" "image_collection_efficiency" "receiver_delay" "receiver_free_send_buf" "strong_pixels" "roi_sum" "roi_mean" "roi_max_count" "roi_pixels" "roi_weighted_x" "roi_weighted_y" "packets_received" "max_pixel_value" "resolution_estimate" "pixel_sum" "processing_time" "beam_center_x" "beam_center_y"

Type of requested plot

+
roi
string non-empty

Name of ROI for which plot is requested

+

Responses

Get full scan result

Responses

Response samples

Content type
application/json
{
  • "file_prefix": "string",
  • "rotation_unit_cell": {
    },
  • "rotation_crystal_lattice": [
    ],
  • "images": [
    ]
}

Get Start message in CBOR format

Contains metadata for a dataset (e.g., experimental geometry)

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get image message in CBOR format

Contains full image data and metadata. The image must come from the latest data collection.

+
query Parameters
id
integer <int64> >= -2
Default: -1

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get preview image in JPEG format using custom settings

query Parameters
id
integer <int64> >= -2
Default: -1

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

+
show_user_mask
boolean
Default: false

Show user mask

+
show_roi
boolean
Default: false

Show ROI areas on the image

+
show_spots
boolean
Default: true

Show spot finding results on the image

+
show_beam_center
boolean
Default: true

Show beam center on the image

+
saturation
number <float> [ -32767 .. 32767 ]

Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used

+
jpeg_quality
integer <int64> [ 0 .. 100 ]
Default: 100

Quality of JPEG image (100 - highest; 0 - lowest)

+
show_res_ring
number <float> [ 0.1 .. 100 ]
Default: 0.1

Show resolution ring, provided in Angstrom

+
color
string
Default: "indigo"
Enum: "indigo" "viridis" "bw" "wb" "green" "heat" "magma" "inferno"

Color scale for preview image

+
show_res_est
boolean
Default: false

Show resolution estimation as a ring

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get preview image in TIFF format

query Parameters
id
integer <int64> >= -2
Default: -1

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

+

Responses

Clear image buffer

Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.

+

Responses

Response samples

Content type
application/json
{
  • "msg": "Detector in wrong state",
  • "reason": "WrongDAQState"
}

Get status of the image buffers

Can be run at any stage of Jungfraujoch operation, including during data collection. +The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots, +then image might be replaced in the buffer between calling /images and /image.cbor.

+

Responses

Response samples

Content type
application/json
{
  • "min_image_number": 0,
  • "max_image_number": 0,
  • "image_numbers": [
    ],
  • "total_slots": 0,
  • "available_slots": 0,
  • "current_counter": 0
}

Get Jungfraujoch version of jfjoch_broker

Responses

+ + + + diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 00000000..2c774d17 --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,632 @@ +/* + * Sphinx JavaScript utilities for the full-text search. + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 00000000..8a96c69a --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/stylesheets/application-fixes.css b/_static/stylesheets/application-fixes.css new file mode 100644 index 00000000..bbe6ad0e --- /dev/null +++ b/_static/stylesheets/application-fixes.css @@ -0,0 +1 @@ +@charset "utf-8";.md-nav--primary ul,.md-nav--primary ul li ul,.md-nav--secondary ul,.md-nav--secondary ul li ul{margin:0;padding:0;list-style:none}.md-nav--primary ul li,.md-nav--primary ul li ul li,.md-nav--secondary ul li,.md-nav--secondary ul li ul li{padding:0 .6rem}.md-nav--primary a.reference,.md-nav--secondary a.reference{display:block;margin-top:.625em;transition:color .125s;text-overflow:ellipsis;cursor:pointer;overflow:hidden}.md-typeset td p,.md-typeset th p{margin:0}.md-typeset .admonition,.md-typeset 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a{color:#7cb342}[data-md-color-primary=light-green] .md-header,[data-md-color-primary=light-green] .md-hero{background-color:#7cb342}[data-md-color-primary=light-green] .md-nav__link--active,[data-md-color-primary=light-green] .md-nav__link:active{color:#7cb342}[data-md-color-primary=light-green] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=lime]{background-color:#c0ca33}[data-md-color-primary=lime] .md-typeset a{color:#c0ca33}[data-md-color-primary=lime] .md-header,[data-md-color-primary=lime] .md-hero{background-color:#c0ca33}[data-md-color-primary=lime] .md-nav__link--active,[data-md-color-primary=lime] .md-nav__link:active{color:#c0ca33}[data-md-color-primary=lime] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=yellow]{background-color:#f9a825}[data-md-color-primary=yellow] .md-typeset a{color:#f9a825}[data-md-color-primary=yellow] .md-header,[data-md-color-primary=yellow] .md-hero{background-color:#f9a825}[data-md-color-primary=yellow] .md-nav__link--active,[data-md-color-primary=yellow] .md-nav__link:active{color:#f9a825}[data-md-color-primary=yellow] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=amber]{background-color:#ffa000}[data-md-color-primary=amber] .md-typeset a{color:#ffa000}[data-md-color-primary=amber] .md-header,[data-md-color-primary=amber] .md-hero{background-color:#ffa000}[data-md-color-primary=amber] .md-nav__link--active,[data-md-color-primary=amber] .md-nav__link:active{color:#ffa000}[data-md-color-primary=amber] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=orange]{background-color:#fb8c00}[data-md-color-primary=orange] .md-typeset a{color:#fb8c00}[data-md-color-primary=orange] .md-header,[data-md-color-primary=orange] .md-hero{background-color:#fb8c00}[data-md-color-primary=orange] .md-nav__link--active,[data-md-color-primary=orange] .md-nav__link:active{color:#fb8c00}[data-md-color-primary=orange] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=deep-orange]{background-color:#ff7043}[data-md-color-primary=deep-orange] .md-typeset a{color:#ff7043}[data-md-color-primary=deep-orange] .md-header,[data-md-color-primary=deep-orange] .md-hero{background-color:#ff7043}[data-md-color-primary=deep-orange] .md-nav__link--active,[data-md-color-primary=deep-orange] .md-nav__link:active{color:#ff7043}[data-md-color-primary=deep-orange] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=brown]{background-color:#795548}[data-md-color-primary=brown] .md-typeset a{color:#795548}[data-md-color-primary=brown] .md-header,[data-md-color-primary=brown] .md-hero{background-color:#795548}[data-md-color-primary=brown] .md-nav__link--active,[data-md-color-primary=brown] .md-nav__link:active{color:#795548}[data-md-color-primary=brown] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=grey]{background-color:#757575}[data-md-color-primary=grey] .md-typeset a{color:#757575}[data-md-color-primary=grey] .md-header,[data-md-color-primary=grey] .md-hero{background-color:#757575}[data-md-color-primary=grey] .md-nav__link--active,[data-md-color-primary=grey] .md-nav__link:active{color:#757575}[data-md-color-primary=grey] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=blue-grey]{background-color:#546e7a}[data-md-color-primary=blue-grey] .md-typeset a{color:#546e7a}[data-md-color-primary=blue-grey] .md-header,[data-md-color-primary=blue-grey] .md-hero{background-color:#546e7a}[data-md-color-primary=blue-grey] .md-nav__link--active,[data-md-color-primary=blue-grey] .md-nav__link:active{color:#546e7a}[data-md-color-primary=blue-grey] .md-nav__item--nested>.md-nav__link{color:inherit}button[data-md-color-primary=white]{box-shadow:inset 0 0 .05rem rgba(0,0,0,.54)}[data-md-color-primary=white] .md-header,[data-md-color-primary=white] .md-hero,button[data-md-color-primary=white]{background-color:#fff;color:rgba(0,0,0,.87)}[data-md-color-primary=white] .md-hero--expand{border-bottom:.05rem solid rgba(0,0,0,.07)}button[data-md-color-accent=red]{background-color:#ff1744}[data-md-color-accent=red] .md-typeset a:active,[data-md-color-accent=red] .md-typeset a:hover{color:#ff1744}[data-md-color-accent=red] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=red] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#ff1744}[data-md-color-accent=red] .md-nav__link:focus,[data-md-color-accent=red] .md-nav__link:hover,[data-md-color-accent=red] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=red] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=red] .md-typeset .md-clipboard:active:before,[data-md-color-accent=red] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=red] .md-typeset [id] .headerlink:focus,[data-md-color-accent=red] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=red] .md-typeset [id]:target .headerlink{color:#ff1744}[data-md-color-accent=red] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#ff1744}[data-md-color-accent=red] .md-search-result__link:hover,[data-md-color-accent=red] .md-search-result__link[data-md-state=active]{background-color:rgba(255,23,68,.1)}[data-md-color-accent=red] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#ff1744}[data-md-color-accent=red] .md-source-file:hover:before{background-color:#ff1744}button[data-md-color-accent=pink]{background-color:#f50057}[data-md-color-accent=pink] .md-typeset a:active,[data-md-color-accent=pink] .md-typeset a:hover{color:#f50057}[data-md-color-accent=pink] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=pink] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#f50057}[data-md-color-accent=pink] .md-nav__link:focus,[data-md-color-accent=pink] .md-nav__link:hover,[data-md-color-accent=pink] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=pink] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=pink] .md-typeset .md-clipboard:active:before,[data-md-color-accent=pink] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=pink] .md-typeset [id] .headerlink:focus,[data-md-color-accent=pink] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=pink] .md-typeset [id]:target .headerlink{color:#f50057}[data-md-color-accent=pink] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#f50057}[data-md-color-accent=pink] .md-search-result__link:hover,[data-md-color-accent=pink] .md-search-result__link[data-md-state=active]{background-color:rgba(245,0,87,.1)}[data-md-color-accent=pink] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#f50057}[data-md-color-accent=pink] .md-source-file:hover:before{background-color:#f50057}button[data-md-color-accent=purple]{background-color:#e040fb}[data-md-color-accent=purple] .md-typeset a:active,[data-md-color-accent=purple] .md-typeset a:hover{color:#e040fb}[data-md-color-accent=purple] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=purple] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#e040fb}[data-md-color-accent=purple] .md-nav__link:focus,[data-md-color-accent=purple] .md-nav__link:hover,[data-md-color-accent=purple] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=purple] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=purple] .md-typeset .md-clipboard:active:before,[data-md-color-accent=purple] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=purple] .md-typeset [id] .headerlink:focus,[data-md-color-accent=purple] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=purple] .md-typeset [id]:target .headerlink{color:#e040fb}[data-md-color-accent=purple] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#e040fb}[data-md-color-accent=purple] .md-search-result__link:hover,[data-md-color-accent=purple] .md-search-result__link[data-md-state=active]{background-color:rgba(224,64,251,.1)}[data-md-color-accent=purple] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#e040fb}[data-md-color-accent=purple] .md-source-file:hover:before{background-color:#e040fb}button[data-md-color-accent=deep-purple]{background-color:#7c4dff}[data-md-color-accent=deep-purple] .md-typeset a:active,[data-md-color-accent=deep-purple] .md-typeset a:hover{color:#7c4dff}[data-md-color-accent=deep-purple] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=deep-purple] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#7c4dff}[data-md-color-accent=deep-purple] .md-nav__link:focus,[data-md-color-accent=deep-purple] .md-nav__link:hover,[data-md-color-accent=deep-purple] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=deep-purple] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=deep-purple] .md-typeset .md-clipboard:active:before,[data-md-color-accent=deep-purple] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=deep-purple] .md-typeset [id] .headerlink:focus,[data-md-color-accent=deep-purple] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=deep-purple] .md-typeset [id]:target .headerlink{color:#7c4dff}[data-md-color-accent=deep-purple] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#7c4dff}[data-md-color-accent=deep-purple] .md-search-result__link:hover,[data-md-color-accent=deep-purple] .md-search-result__link[data-md-state=active]{background-color:rgba(124,77,255,.1)}[data-md-color-accent=deep-purple] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#7c4dff}[data-md-color-accent=deep-purple] .md-source-file:hover:before{background-color:#7c4dff}button[data-md-color-accent=indigo]{background-color:#536dfe}[data-md-color-accent=indigo] .md-typeset a:active,[data-md-color-accent=indigo] .md-typeset a:hover{color:#536dfe}[data-md-color-accent=indigo] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=indigo] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#536dfe}[data-md-color-accent=indigo] .md-nav__link:focus,[data-md-color-accent=indigo] .md-nav__link:hover,[data-md-color-accent=indigo] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=indigo] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=indigo] .md-typeset .md-clipboard:active:before,[data-md-color-accent=indigo] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=indigo] .md-typeset [id] .headerlink:focus,[data-md-color-accent=indigo] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=indigo] .md-typeset [id]:target .headerlink{color:#536dfe}[data-md-color-accent=indigo] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#536dfe}[data-md-color-accent=indigo] .md-search-result__link:hover,[data-md-color-accent=indigo] .md-search-result__link[data-md-state=active]{background-color:rgba(83,109,254,.1)}[data-md-color-accent=indigo] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#536dfe}[data-md-color-accent=indigo] .md-source-file:hover:before{background-color:#536dfe}button[data-md-color-accent=blue]{background-color:#448aff}[data-md-color-accent=blue] .md-typeset a:active,[data-md-color-accent=blue] .md-typeset a:hover{color:#448aff}[data-md-color-accent=blue] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=blue] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#448aff}[data-md-color-accent=blue] .md-nav__link:focus,[data-md-color-accent=blue] .md-nav__link:hover,[data-md-color-accent=blue] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=blue] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=blue] .md-typeset .md-clipboard:active:before,[data-md-color-accent=blue] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=blue] .md-typeset [id] .headerlink:focus,[data-md-color-accent=blue] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=blue] .md-typeset [id]:target .headerlink{color:#448aff}[data-md-color-accent=blue] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#448aff}[data-md-color-accent=blue] .md-search-result__link:hover,[data-md-color-accent=blue] .md-search-result__link[data-md-state=active]{background-color:rgba(68,138,255,.1)}[data-md-color-accent=blue] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#448aff}[data-md-color-accent=blue] .md-source-file:hover:before{background-color:#448aff}button[data-md-color-accent=light-blue]{background-color:#0091ea}[data-md-color-accent=light-blue] .md-typeset a:active,[data-md-color-accent=light-blue] .md-typeset a:hover{color:#0091ea}[data-md-color-accent=light-blue] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=light-blue] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#0091ea}[data-md-color-accent=light-blue] .md-nav__link:focus,[data-md-color-accent=light-blue] .md-nav__link:hover,[data-md-color-accent=light-blue] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=light-blue] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=light-blue] .md-typeset .md-clipboard:active:before,[data-md-color-accent=light-blue] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=light-blue] .md-typeset [id] .headerlink:focus,[data-md-color-accent=light-blue] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=light-blue] .md-typeset [id]:target .headerlink{color:#0091ea}[data-md-color-accent=light-blue] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#0091ea}[data-md-color-accent=light-blue] .md-search-result__link:hover,[data-md-color-accent=light-blue] .md-search-result__link[data-md-state=active]{background-color:rgba(0,145,234,.1)}[data-md-color-accent=light-blue] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#0091ea}[data-md-color-accent=light-blue] .md-source-file:hover:before{background-color:#0091ea}button[data-md-color-accent=cyan]{background-color:#00b8d4}[data-md-color-accent=cyan] .md-typeset a:active,[data-md-color-accent=cyan] .md-typeset a:hover{color:#00b8d4}[data-md-color-accent=cyan] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=cyan] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#00b8d4}[data-md-color-accent=cyan] .md-nav__link:focus,[data-md-color-accent=cyan] .md-nav__link:hover,[data-md-color-accent=cyan] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=cyan] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=cyan] .md-typeset .md-clipboard:active:before,[data-md-color-accent=cyan] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=cyan] .md-typeset [id] .headerlink:focus,[data-md-color-accent=cyan] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=cyan] .md-typeset [id]:target .headerlink{color:#00b8d4}[data-md-color-accent=cyan] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#00b8d4}[data-md-color-accent=cyan] .md-search-result__link:hover,[data-md-color-accent=cyan] .md-search-result__link[data-md-state=active]{background-color:rgba(0,184,212,.1)}[data-md-color-accent=cyan] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#00b8d4}[data-md-color-accent=cyan] .md-source-file:hover:before{background-color:#00b8d4}button[data-md-color-accent=teal]{background-color:#00bfa5}[data-md-color-accent=teal] .md-typeset a:active,[data-md-color-accent=teal] .md-typeset a:hover{color:#00bfa5}[data-md-color-accent=teal] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=teal] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#00bfa5}[data-md-color-accent=teal] .md-nav__link:focus,[data-md-color-accent=teal] .md-nav__link:hover,[data-md-color-accent=teal] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=teal] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=teal] .md-typeset .md-clipboard:active:before,[data-md-color-accent=teal] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=teal] .md-typeset [id] .headerlink:focus,[data-md-color-accent=teal] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=teal] .md-typeset [id]:target .headerlink{color:#00bfa5}[data-md-color-accent=teal] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#00bfa5}[data-md-color-accent=teal] .md-search-result__link:hover,[data-md-color-accent=teal] .md-search-result__link[data-md-state=active]{background-color:rgba(0,191,165,.1)}[data-md-color-accent=teal] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#00bfa5}[data-md-color-accent=teal] .md-source-file:hover:before{background-color:#00bfa5}button[data-md-color-accent=green]{background-color:#00c853}[data-md-color-accent=green] .md-typeset a:active,[data-md-color-accent=green] .md-typeset a:hover{color:#00c853}[data-md-color-accent=green] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=green] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#00c853}[data-md-color-accent=green] .md-nav__link:focus,[data-md-color-accent=green] .md-nav__link:hover,[data-md-color-accent=green] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=green] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=green] .md-typeset .md-clipboard:active:before,[data-md-color-accent=green] .md-typeset .md-clipboard:hover:before,[data-md-color-accent=green] .md-typeset [id] .headerlink:focus,[data-md-color-accent=green] .md-typeset [id]:hover .headerlink:hover,[data-md-color-accent=green] .md-typeset [id]:target .headerlink{color:#00c853}[data-md-color-accent=green] .md-search__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#00c853}[data-md-color-accent=green] .md-search-result__link:hover,[data-md-color-accent=green] .md-search-result__link[data-md-state=active]{background-color:rgba(0,200,83,.1)}[data-md-color-accent=green] .md-sidebar__scrollwrap::-webkit-scrollbar-thumb:hover{background-color:#00c853}[data-md-color-accent=green] .md-source-file:hover:before{background-color:#00c853}button[data-md-color-accent=light-green]{background-color:#64dd17}[data-md-color-accent=light-green] .md-typeset a:active,[data-md-color-accent=light-green] .md-typeset a:hover{color:#64dd17}[data-md-color-accent=light-green] .md-typeset .codehilite pre::-webkit-scrollbar-thumb:hover,[data-md-color-accent=light-green] .md-typeset pre code::-webkit-scrollbar-thumb:hover{background-color:#64dd17}[data-md-color-accent=light-green] .md-nav__link:focus,[data-md-color-accent=light-green] .md-nav__link:hover,[data-md-color-accent=light-green] .md-typeset .footnote li:hover .footnote-backref:hover,[data-md-color-accent=light-green] .md-typeset .footnote li:target .footnote-backref,[data-md-color-accent=light-green] 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screen and (min-width:30em) and (max-width:44.9375em){[data-md-toggle=search]:checked~.md-header .md-search__overlay{-webkit-transform:scale(60);transform:scale(60)}}@media only screen and (min-width:45em) and (max-width:59.9375em){[data-md-toggle=search]:checked~.md-header .md-search__overlay{-webkit-transform:scale(75);transform:scale(75)}}@media only screen and (min-width:60em) and (max-width:76.1875em){.md-search__scrollwrap,[data-md-toggle=search]:checked~.md-header .md-search__inner{width:23.4rem}.md-search-result__teaser{max-height:2.5rem;-webkit-line-clamp:3}} \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 00000000..9898d0c7 --- /dev/null +++ b/genindex.html @@ -0,0 +1 @@ + Index — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

Index

\ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 00000000..4ccfa33f --- /dev/null +++ b/index.html @@ -0,0 +1 @@ + PSI Jungfraujoch — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
_images/jfjoch.png

PSI Jungfraujoch

Jungfraujoch is data acquisition and on-the-fly analysis system developed by the Paul Scherrer Institut.

It can be currently used with PSI and DECTRIS detectors.

Jungfraujoch is distributed under the GPLv3 license.

General

Software

FPGA

Reference

OpenAPI Python client

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jfjoch-client

API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.

License Clarification

While this API definition is licensed under GPL-3.0, the GPL copyleft provisions do not apply when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.

This exception is similar in spirit to the Linux Kernel’s approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.

This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms.

This Python package is automatically generated by the OpenAPI Generator project:

  • API version: 1.0.0-rc.126

  • Package version: 1.0.0-rc.126

  • Generator version: 7.20.0

  • Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.9+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://git.psi.ch/jungfraujoch/jungfraujoch.git
+

(you may need to run pip with root permission: sudo pip install git+https://git.psi.ch/jungfraujoch/jungfraujoch.git)

Then import the package:

import jfjoch_client
+

Setuptools

Install via Setuptools.

python setup.py install --user
+

(or sudo python setup.py install to install the package for all users)

Then import the package:

import jfjoch_client
+

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:


+import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Cancel running data collection
+        api_instance.cancel_post()
+    except ApiException as e:
+        print("Exception when calling DefaultApi->cancel_post: %s\n" % e)
+
+

Documentation for API Endpoints

All URIs are relative to http://localhost:5232

Class

Method

HTTP request

Description

DefaultApi

cancel_post

POST /cancel

Cancel running data collection

DefaultApi

config_azim_int_get

GET /config/azim_int

Get azimuthal integration configuration

DefaultApi

config_azim_int_put

PUT /config/azim_int

Configure azimuthal integration

DefaultApi

config_dark_mask_get

GET /config/dark_mask

Get settings for dark data collection to calculate mask

DefaultApi

config_dark_mask_put

PUT /config/dark_mask

Set configuration for dark data collection to calculate mask

DefaultApi

config_detector_get

GET /config/detector

Get detector configuration

DefaultApi

config_detector_put

PUT /config/detector

Change detector configuration

DefaultApi

config_file_writer_get

GET /config/file_writer

Get file writer settings

DefaultApi

config_file_writer_put

PUT /config/file_writer

Change file writer settings

DefaultApi

config_image_format_conversion_post

POST /config/image_format/conversion

Configure format for data collection with full conversion

DefaultApi

config_image_format_get

GET /config/image_format

Get image output format

DefaultApi

config_image_format_put

PUT /config/image_format

Change image output format

DefaultApi

config_image_format_raw_post

POST /config/image_format/raw

Configure format for raw data collection

DefaultApi

config_indexing_get

GET /config/indexing

Get indexing configuration

DefaultApi

config_indexing_put

PUT /config/indexing

Change indexing algorithm settings

DefaultApi

config_instrument_get

GET /config/instrument

Get instrument metadata

DefaultApi

config_instrument_put

PUT /config/instrument

Change instrument metadata

DefaultApi

config_internal_generator_image_put

PUT /config/internal_generator_image

Load binary image for internal FPGA generator

DefaultApi

config_internal_generator_image_tiff_put

PUT /config/internal_generator_image.tiff

Load TIFF image for internal FPGA generator

DefaultApi

config_mask_get

GET /config/mask

Get mask of the detector (binary)

DefaultApi

config_mask_tiff_get

GET /config/mask.tiff

Get mask of the detector (TIFF)

DefaultApi

config_roi_get

GET /config/roi

Get ROI definitions

DefaultApi

config_roi_put

PUT /config/roi

Upload ROI definitions

DefaultApi

config_select_detector_get

GET /config/select_detector

List available detectors

DefaultApi

config_select_detector_put

PUT /config/select_detector

Select detector

DefaultApi

config_spot_finding_get

GET /config/spot_finding

Get data processing configuration

DefaultApi

config_spot_finding_put

PUT /config/spot_finding

Configure spot finding

DefaultApi

config_user_mask_get

GET /config/user_mask

Detector must be Initialized. Get user mask of the detector (binary)

DefaultApi

config_user_mask_put

PUT /config/user_mask

Upload user mask of the detector (binary)

DefaultApi

config_user_mask_tiff_get

GET /config/user_mask.tiff

Detector must be Initialized. Get user mask of the detector (TIFF)

DefaultApi

config_user_mask_tiff_put

PUT /config/user_mask.tiff

Upload user mask of the detector

DefaultApi

config_zeromq_metadata_get

GET /config/zeromq_metadata

Get ZeroMQ metadata socket settings

DefaultApi

config_zeromq_metadata_put

PUT /config/zeromq_metadata

Set ZeroMQ metadata settings

DefaultApi

config_zeromq_preview_get

GET /config/zeromq_preview

Get ZeroMQ preview settings

DefaultApi

config_zeromq_preview_put

PUT /config/zeromq_preview

Set ZeroMQ preview settings

DefaultApi

deactivate_post

POST /deactivate

Prepare detector to turn off

DefaultApi

detector_status_get

GET /detector/status

Get detector status

DefaultApi

fpga_status_get

GET /fpga_status

Get status of FPGA devices

DefaultApi

image_buffer_clear_post

POST /image_buffer/clear

Clear image buffer

DefaultApi

image_buffer_image_cbor_get

GET /image_buffer/image.cbor

Get image message in CBOR format

DefaultApi

image_buffer_image_jpeg_get

GET /image_buffer/image.jpeg

Get preview image in JPEG format using custom settings

DefaultApi

image_buffer_image_tiff_get

GET /image_buffer/image.tiff

Get preview image in TIFF format

DefaultApi

image_buffer_start_cbor_get

GET /image_buffer/start.cbor

Get Start message in CBOR format

DefaultApi

image_buffer_status_get

GET /image_buffer/status

Get status of the image buffers

DefaultApi

initialize_post

POST /initialize

Initialize detector and data acquisition

DefaultApi

pedestal_post

POST /pedestal

Collect dark current for the detector

DefaultApi

preview_pedestal_tiff_get

GET /preview/pedestal.tiff

Get pedestal in TIFF format

DefaultApi

preview_plot_bin_get

GET /preview/plot.bin

Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn’t transmit information about X-axis, only values, so it is of limited use for azimuthal integration.

DefaultApi

preview_plot_get

GET /preview/plot

Generate 1D plot from Jungfraujoch

DefaultApi

result_scan_get

GET /result/scan

Get full scan result

DefaultApi

start_post

POST /start

Start detector

DefaultApi

statistics_calibration_get

GET /statistics/calibration

Get calibration statistics

DefaultApi

statistics_data_collection_get

GET /statistics/data_collection

Get data collection statistics

DefaultApi

statistics_get

GET /statistics

Get general statistics

DefaultApi

status_get

GET /status

Get Jungfraujoch status

DefaultApi

trigger_post

POST /trigger

Send soft trigger to the detector

DefaultApi

version_get

GET /version

Get Jungfraujoch version of jfjoch_broker

DefaultApi

wait_till_done_post

POST /wait_till_done

Wait for acquisition done

DefaultApi

xfel_event_code_get

GET /xfel/event_code

Return XFEL event codes for the current data acquisition

DefaultApi

xfel_pulse_id_get

GET /xfel/pulse_id

Return XFEL pulse IDs for the current data acquisition

Documentation For Models

Documentation For Authorization

Endpoints do not require authorization.

Author

filip.leonarski@psi.ch

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AzimIntSettings

Properties

Name

Type

Description

Notes

polarization_corr

bool

Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)

[default to True]

solid_angle_corr

bool

Apply solid angle correction for azimuthal integration

[default to True]

high_q_recip_a

float

low_q_recip_a

float

q_spacing

float

azimuthal_bins

int

Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration

[optional] [default to 1]

Example

from jfjoch_client.models.azim_int_settings import AzimIntSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of AzimIntSettings from a JSON string
+azim_int_settings_instance = AzimIntSettings.from_json(json)
+# print the JSON string representation of the object
+print(AzimIntSettings.to_json())
+
+# convert the object into a dict
+azim_int_settings_dict = azim_int_settings_instance.to_dict()
+# create an instance of AzimIntSettings from a dict
+azim_int_settings_from_dict = AzimIntSettings.from_dict(azim_int_settings_dict)
+

[Back to Model list] [Back to API list] [Back to README]

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BrokerStatus

Properties

Name

Type

Description

Notes

state

str

progress

float

Progress of data collection (only available if receiving is running)

[optional]

message

str

Message to display besides state of the jfjoch_broker; mostly used for errors and warnings This matters especially for async functions (start/initialize), where API won’t return reason for the error during async operation.

[optional]

message_severity

str

Level of the message to display

[optional] [default to ‘error’]

gpu_count

int

Number of installed GPUs

[optional]

Example

from jfjoch_client.models.broker_status import BrokerStatus
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of BrokerStatus from a JSON string
+broker_status_instance = BrokerStatus.from_json(json)
+# print the JSON string representation of the object
+print(BrokerStatus.to_json())
+
+# convert the object into a dict
+broker_status_dict = broker_status_instance.to_dict()
+# create an instance of BrokerStatus from a dict
+broker_status_from_dict = BrokerStatus.from_dict(broker_status_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/CalibrationStatisticsInner.html b/python_client/docs/CalibrationStatisticsInner.html new file mode 100644 index 00000000..183ff104 --- /dev/null +++ b/python_client/docs/CalibrationStatisticsInner.html @@ -0,0 +1,14 @@ + CalibrationStatisticsInner — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

CalibrationStatisticsInner

Properties

Name

Type

Description

Notes

module_number

int

storage_cell_number

int

pedestal_g0_mean

float

pedestal_g1_mean

float

pedestal_g2_mean

float

gain_g0_mean

float

gain_g1_mean

float

gain_g2_mean

float

masked_pixels

int

Example

from jfjoch_client.models.calibration_statistics_inner import CalibrationStatisticsInner
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of CalibrationStatisticsInner from a JSON string
+calibration_statistics_inner_instance = CalibrationStatisticsInner.from_json(json)
+# print the JSON string representation of the object
+print(CalibrationStatisticsInner.to_json())
+
+# convert the object into a dict
+calibration_statistics_inner_dict = calibration_statistics_inner_instance.to_dict()
+# create an instance of CalibrationStatisticsInner from a dict
+calibration_statistics_inner_from_dict = CalibrationStatisticsInner.from_dict(calibration_statistics_inner_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ColorScale.html b/python_client/docs/ColorScale.html new file mode 100644 index 00000000..9b28dd50 --- /dev/null +++ b/python_client/docs/ColorScale.html @@ -0,0 +1 @@ + ColorScale — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
\ No newline at end of file diff --git a/python_client/docs/DarkMaskSettings.html b/python_client/docs/DarkMaskSettings.html new file mode 100644 index 00000000..adea257d --- /dev/null +++ b/python_client/docs/DarkMaskSettings.html @@ -0,0 +1,14 @@ + DarkMaskSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DarkMaskSettings

Settings for collection of dark images to be used for mask calculation

Properties

Name

Type

Description

Notes

detector_threshold_ke_v

float

Energy threshold for dark image collection

[default to 3.5]

frame_time_us

int

Time between frames for dark image collection

[default to 10000]

number_of_frames

int

Number of frames for dark image collection; zero means no dark collection

[default to 1000]

max_allowed_pixel_count

int

Maximum count in a pixel considered normal (not-masked)

[default to 1]

max_frames_with_signal

int

Maximum number of frames with signal in a pixel considered normal (not-masked)

[default to 10]

Example

from jfjoch_client.models.dark_mask_settings import DarkMaskSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DarkMaskSettings from a JSON string
+dark_mask_settings_instance = DarkMaskSettings.from_json(json)
+# print the JSON string representation of the object
+print(DarkMaskSettings.to_json())
+
+# convert the object into a dict
+dark_mask_settings_dict = dark_mask_settings_instance.to_dict()
+# create an instance of DarkMaskSettings from a dict
+dark_mask_settings_from_dict = DarkMaskSettings.from_dict(dark_mask_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DatasetSettings.html b/python_client/docs/DatasetSettings.html new file mode 100644 index 00000000..f7e5c371 --- /dev/null +++ b/python_client/docs/DatasetSettings.html @@ -0,0 +1,14 @@ + DatasetSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DatasetSettings

Properties

Name

Type

Description

Notes

images_per_trigger

int

For standard synchrotron data collection - this is number of images collected per one TTL trigger For XFEL (pulsed source) - this number is ignored and set to 1 For storage cell mode - this number is ignored and set to number of storage cells

[optional] [default to 1]

ntrigger

int

Number of TTL trigger that the detector is expected to receive during data collection

[optional] [default to 1]

image_time_us

int

Image time. If not provided (or zero value) the frame time is assumed as default. For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time. In XFEL mode: summation happens for frames collected with multiple triggers. Ignored for storage cells and if raw data are saved.

[optional]

beam_x_pxl

float

/entry/detector/beam_center_x in NXmx Beam center in X direction [pixels]

beam_y_pxl

float

/entry/detector/beam_center_y in NXmx Beam center in X direction [pixels]

detector_distance_mm

float

/entry/detector/distance in NXmx Detector distance [mm]

incident_energy_ke_v

float

Used to calculate /entry/beam/incident_wavelength in NXmx Incident particle (photon, electron) energy in keV

file_prefix

str

Prefix for filenames. If left empty, no file will be saved.

[optional] [default to ‘’]

images_per_file

int

Number of files in a single HDF5 data file (0 = write all images to a single data file).

[optional] [default to 1000]

space_group_number

int

Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.

[optional]

sample_name

str

/entry/sample/name in NXmx Sample name

[optional] [default to ‘’]

compression

str

Compression type for the images transferred over ZeroMQ and saved to HDF5 file.

[optional] [default to ‘bslz4’]

total_flux

float

/entry/beam/total_flux in NXmx Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]

[optional]

transmission

float

/entry/instrument/attenuator/attenuator_transmission Transmission of attenuator (filter) [no units]

[optional]

goniometer

RotationAxis

[optional]

grid_scan

GridScan

[optional]

header_appendix

object

Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file. However, if values are placed in &quot;hdf5&quot; object, `jfjoch_writer` will write them in /entry/data of the HDF5 file. This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {&quot;hdf5&quot;: {&quot;val1&quot;:1, &quot;val2&quot;:&quot;xyz&quot;}}, will write /entry/user/val1 and /entry/user/val2.

[optional]

image_appendix

object

Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) Not saved in HDF5 file

[optional]

data_reduction_factor_serialmx

float

Rate at which non-indexed images are accepted to be forwarded to writer. Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability.

[optional] [default to 1.0]

pixel_value_low_threshold

int

Set all counts lower than the value to zero. When the value is set, negative numbers other than error pixel value are always set to zero. Setting to zero is equivalent to turning the option off.

[optional]

run_number

int

Number of run within an experimental session. Transferred over CBOR stream as &quot;series ID&quot;, though not saved in HDF5 file. It is highly recommended to keep this number unique for each data collection during experimental series. If not provided, the number will be automatically incremented.

[optional]

run_name

str

Unique ID of run. Transferred over CBOR stream as &quot;unique series ID&quot;, though not saved in HDF5 file. It is highly recommended to keep this name unique for each data collection during experimental series. If not provided, the name will be automatically generated as number + colon + file_prefix.

[optional]

experiment_group

str

Name of group owning the data (e.g. p-group or proposal number). Transferred over CBOR stream, though not saved in HDF5 file.

[optional]

poisson_compression

int

Enable lossy compression of pixel values that preserves Poisson statistics. Requires to provide a numerical factor SQ. Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer. Compression is turned off if the value is missing or it is set to zero.

[optional]

write_nxmx_hdf5_master

bool

Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments and to turn off for other experiments.

[optional] [default to True]

save_calibration

bool

Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer. If parameter is not provided calibration will be saved only if more than 4 images are recorded.

[optional]

polarization_factor

float

Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization

[optional]

ring_current_m_a

float

Ring current at the beginning of the data collection

[optional]

sample_temperature_k

float

Sample temperature in Kelvin

[optional]

poni_rot1_rad

float

PONI angle rot1 (see PyFAI documentation for details) in radians

[optional] [default to 0.0]

poni_rot2_rad

float

PONI angle rot2 (see PyFAI documentation for details) in radians

[optional] [default to 0.0]

poni_rot3_rad

float

PONI angle rot3 (see PyFAI documentation for details) in radians

[optional] [default to 0.0]

unit_cell

UnitCell

[optional]

spot_finding

bool

Enable spot finding and save spots

[optional] [default to True]

max_spot_count

int

Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected

[optional] [default to 250]

detect_ice_rings

bool

Flag spots as ice rings and reduce their effect on indexing

[optional]

xray_fluorescence_spectrum

DatasetSettingsXrayFluorescenceSpectrum

[optional]

Example

from jfjoch_client.models.dataset_settings import DatasetSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DatasetSettings from a JSON string
+dataset_settings_instance = DatasetSettings.from_json(json)
+# print the JSON string representation of the object
+print(DatasetSettings.to_json())
+
+# convert the object into a dict
+dataset_settings_dict = dataset_settings_instance.to_dict()
+# create an instance of DatasetSettings from a dict
+dataset_settings_from_dict = DatasetSettings.from_dict(dataset_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DatasetSettingsUnitCell.html b/python_client/docs/DatasetSettingsUnitCell.html new file mode 100644 index 00000000..18ca6fbc --- /dev/null +++ b/python_client/docs/DatasetSettingsUnitCell.html @@ -0,0 +1,14 @@ + DatasetSettingsUnitCell — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DatasetSettingsUnitCell

Unit cell parameters. Necessary to run indexing. Units of angstrom and degree

Properties

Name

Type

Description

Notes

a

float

b

float

c

float

alpha

float

beta

float

gamma

float

Example

from jfjoch_client.models.dataset_settings_unit_cell import DatasetSettingsUnitCell
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DatasetSettingsUnitCell from a JSON string
+dataset_settings_unit_cell_instance = DatasetSettingsUnitCell.from_json(json)
+# print the JSON string representation of the object
+print(DatasetSettingsUnitCell.to_json())
+
+# convert the object into a dict
+dataset_settings_unit_cell_dict = dataset_settings_unit_cell_instance.to_dict()
+# create an instance of DatasetSettingsUnitCell from a dict
+dataset_settings_unit_cell_from_dict = DatasetSettingsUnitCell.from_dict(dataset_settings_unit_cell_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.html b/python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.html new file mode 100644 index 00000000..d8acec99 --- /dev/null +++ b/python_client/docs/DatasetSettingsXrayFluorescenceSpectrum.html @@ -0,0 +1,14 @@ + DatasetSettingsXrayFluorescenceSpectrum — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DatasetSettingsXrayFluorescenceSpectrum

Properties

Name

Type

Description

Notes

energy_e_v

List[float]

X-ray fluorescence scan energy for each measurement point

data

List[float]

X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV

Example

from jfjoch_client.models.dataset_settings_xray_fluorescence_spectrum import DatasetSettingsXrayFluorescenceSpectrum
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DatasetSettingsXrayFluorescenceSpectrum from a JSON string
+dataset_settings_xray_fluorescence_spectrum_instance = DatasetSettingsXrayFluorescenceSpectrum.from_json(json)
+# print the JSON string representation of the object
+print(DatasetSettingsXrayFluorescenceSpectrum.to_json())
+
+# convert the object into a dict
+dataset_settings_xray_fluorescence_spectrum_dict = dataset_settings_xray_fluorescence_spectrum_instance.to_dict()
+# create an instance of DatasetSettingsXrayFluorescenceSpectrum from a dict
+dataset_settings_xray_fluorescence_spectrum_from_dict = DatasetSettingsXrayFluorescenceSpectrum.from_dict(dataset_settings_xray_fluorescence_spectrum_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DefaultApi.html b/python_client/docs/DefaultApi.html new file mode 100644 index 00000000..ca59b1be --- /dev/null +++ b/python_client/docs/DefaultApi.html @@ -0,0 +1,1406 @@ + jfjoch_client.DefaultApi — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

jfjoch_client.DefaultApi

All URIs are relative to http://localhost:5232

Method

HTTP request

Description

cancel_post

POST /cancel

Cancel running data collection

config_azim_int_get

GET /config/azim_int

Get azimuthal integration configuration

config_azim_int_put

PUT /config/azim_int

Configure azimuthal integration

config_dark_mask_get

GET /config/dark_mask

Get settings for dark data collection to calculate mask

config_dark_mask_put

PUT /config/dark_mask

Set configuration for dark data collection to calculate mask

config_detector_get

GET /config/detector

Get detector configuration

config_detector_put

PUT /config/detector

Change detector configuration

config_file_writer_get

GET /config/file_writer

Get file writer settings

config_file_writer_put

PUT /config/file_writer

Change file writer settings

config_image_format_conversion_post

POST /config/image_format/conversion

Configure format for data collection with full conversion

config_image_format_get

GET /config/image_format

Get image output format

config_image_format_put

PUT /config/image_format

Change image output format

config_image_format_raw_post

POST /config/image_format/raw

Configure format for raw data collection

config_indexing_get

GET /config/indexing

Get indexing configuration

config_indexing_put

PUT /config/indexing

Change indexing algorithm settings

config_instrument_get

GET /config/instrument

Get instrument metadata

config_instrument_put

PUT /config/instrument

Change instrument metadata

config_internal_generator_image_put

PUT /config/internal_generator_image

Load binary image for internal FPGA generator

config_internal_generator_image_tiff_put

PUT /config/internal_generator_image.tiff

Load TIFF image for internal FPGA generator

config_mask_get

GET /config/mask

Get mask of the detector (binary)

config_mask_tiff_get

GET /config/mask.tiff

Get mask of the detector (TIFF)

config_roi_get

GET /config/roi

Get ROI definitions

config_roi_put

PUT /config/roi

Upload ROI definitions

config_select_detector_get

GET /config/select_detector

List available detectors

config_select_detector_put

PUT /config/select_detector

Select detector

config_spot_finding_get

GET /config/spot_finding

Get data processing configuration

config_spot_finding_put

PUT /config/spot_finding

Configure spot finding

config_user_mask_get

GET /config/user_mask

Detector must be Initialized. Get user mask of the detector (binary)

config_user_mask_put

PUT /config/user_mask

Upload user mask of the detector (binary)

config_user_mask_tiff_get

GET /config/user_mask.tiff

Detector must be Initialized. Get user mask of the detector (TIFF)

config_user_mask_tiff_put

PUT /config/user_mask.tiff

Upload user mask of the detector

config_zeromq_metadata_get

GET /config/zeromq_metadata

Get ZeroMQ metadata socket settings

config_zeromq_metadata_put

PUT /config/zeromq_metadata

Set ZeroMQ metadata settings

config_zeromq_preview_get

GET /config/zeromq_preview

Get ZeroMQ preview settings

config_zeromq_preview_put

PUT /config/zeromq_preview

Set ZeroMQ preview settings

deactivate_post

POST /deactivate

Prepare detector to turn off

detector_status_get

GET /detector/status

Get detector status

fpga_status_get

GET /fpga_status

Get status of FPGA devices

image_buffer_clear_post

POST /image_buffer/clear

Clear image buffer

image_buffer_image_cbor_get

GET /image_buffer/image.cbor

Get image message in CBOR format

image_buffer_image_jpeg_get

GET /image_buffer/image.jpeg

Get preview image in JPEG format using custom settings

image_buffer_image_tiff_get

GET /image_buffer/image.tiff

Get preview image in TIFF format

image_buffer_start_cbor_get

GET /image_buffer/start.cbor

Get Start message in CBOR format

image_buffer_status_get

GET /image_buffer/status

Get status of the image buffers

initialize_post

POST /initialize

Initialize detector and data acquisition

pedestal_post

POST /pedestal

Collect dark current for the detector

preview_pedestal_tiff_get

GET /preview/pedestal.tiff

Get pedestal in TIFF format

preview_plot_bin_get

GET /preview/plot.bin

Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn’t transmit information about X-axis, only values, so it is of limited use for azimuthal integration.

preview_plot_get

GET /preview/plot

Generate 1D plot from Jungfraujoch

result_scan_get

GET /result/scan

Get full scan result

start_post

POST /start

Start detector

statistics_calibration_get

GET /statistics/calibration

Get calibration statistics

statistics_data_collection_get

GET /statistics/data_collection

Get data collection statistics

statistics_get

GET /statistics

Get general statistics

status_get

GET /status

Get Jungfraujoch status

trigger_post

POST /trigger

Send soft trigger to the detector

version_get

GET /version

Get Jungfraujoch version of jfjoch_broker

wait_till_done_post

POST /wait_till_done

Wait for acquisition done

xfel_event_code_get

GET /xfel/event_code

Return XFEL event codes for the current data acquisition

xfel_pulse_id_get

GET /xfel/pulse_id

Return XFEL pulse IDs for the current data acquisition

cancel_post

cancel_post()

Cancel running data collection

Command will inform FPGA network card to stop pedestal or data collection at the current stage. Any frame that is currently being processed by CPU will be finished and sent to writer. Given the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to Idle state.

If data collection is not running, the command has no effect.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Cancel running data collection
+        api_instance.cancel_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->cancel_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: Not defined

HTTP response details

Status code

Description

Response headers

200

Cancel request sent to FPGAs (or ignored, as data collection is not running)

-

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config_azim_int_get

AzimIntSettings config_azim_int_get()

Get azimuthal integration configuration

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.azim_int_settings import AzimIntSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get azimuthal integration configuration
+        api_response = api_instance.config_azim_int_get()
+        print("The response of DefaultApi->config_azim_int_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_azim_int_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

AzimIntSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_azim_int_put

config_azim_int_put(azim_int_settings=azim_int_settings)

Configure azimuthal integration

Can be done when detector is Inactive or Idle

Example

import jfjoch_client
+from jfjoch_client.models.azim_int_settings import AzimIntSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    azim_int_settings = jfjoch_client.AzimIntSettings() # AzimIntSettings |  (optional)
+
+    try:
+        # Configure azimuthal integration
+        api_instance.config_azim_int_put(azim_int_settings=azim_int_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_azim_int_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

azim_int_settings

AzimIntSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_dark_mask_get

DarkMaskSettings config_dark_mask_get()

Get settings for dark data collection to calculate mask

Example

import jfjoch_client
+from jfjoch_client.models.dark_mask_settings import DarkMaskSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get settings for dark data collection to calculate mask
+        api_response = api_instance.config_dark_mask_get()
+        print("The response of DefaultApi->config_dark_mask_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_dark_mask_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

DarkMaskSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_dark_mask_put

config_dark_mask_put(dark_mask_settings=dark_mask_settings)

Set configuration for dark data collection to calculate mask

This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point. This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.models.dark_mask_settings import DarkMaskSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    dark_mask_settings = jfjoch_client.DarkMaskSettings() # DarkMaskSettings |  (optional)
+
+    try:
+        # Set configuration for dark data collection to calculate mask
+        api_instance.config_dark_mask_put(dark_mask_settings=dark_mask_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_dark_mask_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

dark_mask_settings

DarkMaskSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_detector_get

DetectorSettings config_detector_get()

Get detector configuration

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.detector_settings import DetectorSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get detector configuration
+        api_response = api_instance.config_detector_get()
+        print("The response of DefaultApi->config_detector_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_detector_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

DetectorSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_detector_put

config_detector_put(detector_settings=detector_settings)

Change detector configuration

Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings. This can only be done when detector is Idle, Error or Inactive states. If detector is in Idle state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation. If detector is in Inactive or Error states, new settings will be saved, but no calibration will be executed.

Example

import jfjoch_client
+from jfjoch_client.models.detector_settings import DetectorSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    detector_settings = jfjoch_client.DetectorSettings() # DetectorSettings |  (optional)
+
+    try:
+        # Change detector configuration
+        api_instance.config_detector_put(detector_settings=detector_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_detector_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

detector_settings

DetectorSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_file_writer_get

FileWriterSettings config_file_writer_get()

Get file writer settings

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.file_writer_settings import FileWriterSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get file writer settings
+        api_response = api_instance.config_file_writer_get()
+        print("The response of DefaultApi->config_file_writer_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_file_writer_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

FileWriterSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_file_writer_put

config_file_writer_put(file_writer_settings=file_writer_settings)

Change file writer settings

This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.models.file_writer_settings import FileWriterSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    file_writer_settings = jfjoch_client.FileWriterSettings() # FileWriterSettings |  (optional)
+
+    try:
+        # Change file writer settings
+        api_instance.config_file_writer_put(file_writer_settings=file_writer_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_file_writer_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

file_writer_settings

FileWriterSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_image_format_conversion_post

config_image_format_conversion_post()

Configure format for data collection with full conversion

This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Configure format for data collection with full conversion
+        api_instance.config_image_format_conversion_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_image_format_conversion_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

500

Error within Jungfraujoch code - see output message.

-

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config_image_format_get

ImageFormatSettings config_image_format_get()

Get image output format

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.image_format_settings import ImageFormatSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get image output format
+        api_response = api_instance.config_image_format_get()
+        print("The response of DefaultApi->config_image_format_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_image_format_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

ImageFormatSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_image_format_put

config_image_format_put(image_format_settings=image_format_settings)

Change image output format

This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.models.image_format_settings import ImageFormatSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    image_format_settings = jfjoch_client.ImageFormatSettings() # ImageFormatSettings |  (optional)
+
+    try:
+        # Change image output format
+        api_instance.config_image_format_put(image_format_settings=image_format_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_image_format_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

image_format_settings

ImageFormatSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_image_format_raw_post

config_image_format_raw_post()

Configure format for raw data collection

This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Configure format for raw data collection
+        api_instance.config_image_format_raw_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_image_format_raw_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

500

Error within Jungfraujoch code - see output message.

-

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config_indexing_get

IndexingSettings config_indexing_get()

Get indexing configuration

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.indexing_settings import IndexingSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get indexing configuration
+        api_response = api_instance.config_indexing_get()
+        print("The response of DefaultApi->config_indexing_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_indexing_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

IndexingSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_indexing_put

config_indexing_put(indexing_settings=indexing_settings)

Change indexing algorithm settings

This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.models.indexing_settings import IndexingSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    indexing_settings = jfjoch_client.IndexingSettings() # IndexingSettings |  (optional)
+
+    try:
+        # Change indexing algorithm settings
+        api_instance.config_indexing_put(indexing_settings=indexing_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_indexing_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

indexing_settings

IndexingSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_instrument_get

InstrumentMetadata config_instrument_get()

Get instrument metadata

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.instrument_metadata import InstrumentMetadata
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get instrument metadata
+        api_response = api_instance.config_instrument_get()
+        print("The response of DefaultApi->config_instrument_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_instrument_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

InstrumentMetadata

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_instrument_put

config_instrument_put(instrument_metadata=instrument_metadata)

Change instrument metadata

This can only be done when detector is Idle, Error or Inactive states.

Example

import jfjoch_client
+from jfjoch_client.models.instrument_metadata import InstrumentMetadata
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    instrument_metadata = jfjoch_client.InstrumentMetadata() # InstrumentMetadata |  (optional)
+
+    try:
+        # Change instrument metadata
+        api_instance.config_instrument_put(instrument_metadata=instrument_metadata)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_instrument_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

instrument_metadata

InstrumentMetadata

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_internal_generator_image_put

config_internal_generator_image_put(id=id, body=body)

Load binary image for internal FPGA generator

Load image for internal FPGA generator. This can only happen in Idle state of the detector. Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates (depending on detector settings).

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    id = 56 # int | Image id to upload (optional)
+    body = None # bytearray |  (optional)
+
+    try:
+        # Load binary image for internal FPGA generator
+        api_instance.config_internal_generator_image_put(id=id, body=body)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_internal_generator_image_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

id

int

Image id to upload

[optional]

body

bytearray

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/octet-stream

  • Accept: text/plain

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

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config_internal_generator_image_tiff_put

config_internal_generator_image_tiff_put(id=id, body=body)

Load TIFF image for internal FPGA generator

Load image for internal FPGA generator. This can only happen in Idle state of the detector. Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates (depending on detector settings).

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    id = 56 # int | Image ID to upload (optional)
+    body = None # bytearray |  (optional)
+
+    try:
+        # Load TIFF image for internal FPGA generator
+        api_instance.config_internal_generator_image_tiff_put(id=id, body=body)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_internal_generator_image_tiff_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

id

int

Image ID to upload

[optional]

body

bytearray

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: image/tiff

  • Accept: text/plain

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

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config_mask_get

bytearray config_mask_get()

Get mask of the detector (binary)

Detector must be Initialized. Get full pixel mask of the detector. See NXmx standard for meaning of pixel values.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get mask of the detector (binary)
+        api_response = api_instance.config_mask_get()
+        print("The response of DefaultApi->config_mask_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_mask_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/octet-stream

HTTP response details

Status code

Description

Response headers

200

Binary array (4 byte; unsigned)

-

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config_mask_tiff_get

bytearray config_mask_tiff_get()

Get mask of the detector (TIFF)

Should be in Idle state. Get full pixel mask of the detector See NXmx standard for meaning of pixel values

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get mask of the detector (TIFF)
+        api_response = api_instance.config_mask_tiff_get()
+        print("The response of DefaultApi->config_mask_tiff_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_mask_tiff_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: image/tiff

HTTP response details

Status code

Description

Response headers

200

Pixel mask in TIFF format (4 byte; unsigned)

-

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config_roi_get

RoiDefinitions config_roi_get()

Get ROI definitions

Example

import jfjoch_client
+from jfjoch_client.models.roi_definitions import RoiDefinitions
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get ROI definitions
+        api_response = api_instance.config_roi_get()
+        print("The response of DefaultApi->config_roi_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_roi_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

RoiDefinitions

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

OK

-

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config_roi_put

config_roi_put(roi_definitions=roi_definitions)

Upload ROI definitions

Example

import jfjoch_client
+from jfjoch_client.models.roi_definitions import RoiDefinitions
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    roi_definitions = jfjoch_client.RoiDefinitions() # RoiDefinitions |  (optional)
+
+    try:
+        # Upload ROI definitions
+        api_instance.config_roi_put(roi_definitions=roi_definitions)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_roi_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

roi_definitions

RoiDefinitions

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_select_detector_get

DetectorList config_select_detector_get()

List available detectors

Configured detectors that can be selected by used

Example

import jfjoch_client
+from jfjoch_client.models.detector_list import DetectorList
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # List available detectors
+        api_response = api_instance.config_select_detector_get()
+        print("The response of DefaultApi->config_select_detector_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_select_detector_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

DetectorList

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_select_detector_put

config_select_detector_put(detector_selection=detector_selection)

Select detector

Jungfraujoch allows to control multiple detectors and/or region-of-interests. The command allows to choose one detector from the list (ID has to be consistent with one provided by GET response). Changing detector will set detector to Inactive state and will require reinitialization.

Example

import jfjoch_client
+from jfjoch_client.models.detector_selection import DetectorSelection
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    detector_selection = jfjoch_client.DetectorSelection() # DetectorSelection |  (optional)
+
+    try:
+        # Select detector
+        api_instance.config_select_detector_put(detector_selection=detector_selection)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_select_detector_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

detector_selection

DetectorSelection

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_spot_finding_get

SpotFindingSettings config_spot_finding_get()

Get data processing configuration

Can be done anytime

Example

import jfjoch_client
+from jfjoch_client.models.spot_finding_settings import SpotFindingSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get data processing configuration
+        api_response = api_instance.config_spot_finding_get()
+        print("The response of DefaultApi->config_spot_finding_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_spot_finding_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

SpotFindingSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_spot_finding_put

config_spot_finding_put(spot_finding_settings=spot_finding_settings)

Configure spot finding

Can be done anytime, also while data collection is running

Example

import jfjoch_client
+from jfjoch_client.models.spot_finding_settings import SpotFindingSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    spot_finding_settings = jfjoch_client.SpotFindingSettings() # SpotFindingSettings |  (optional)
+
+    try:
+        # Configure spot finding
+        api_instance.config_spot_finding_put(spot_finding_settings=spot_finding_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_spot_finding_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

spot_finding_settings

SpotFindingSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

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config_user_mask_get

bytearray config_user_mask_get()

Detector must be Initialized. Get user mask of the detector (binary)

Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Detector must be Initialized. Get user mask of the detector (binary) 
+        api_response = api_instance.config_user_mask_get()
+        print("The response of DefaultApi->config_user_mask_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_user_mask_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/octet-stream

HTTP response details

Status code

Description

Response headers

200

User mask in binary format (4 byte; unsigned)

-

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config_user_mask_put

config_user_mask_put(body=body)

Upload user mask of the detector (binary)

Should be in Idle state. Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. In the latter case - module gaps are ignored and don’t need to be assigned value. Mask is expected as binary array (4-byte; unsigned). 0 - good pixel, other value - masked User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    body = None # bytearray |  (optional)
+
+    try:
+        # Upload user mask of the detector (binary)
+        api_instance.config_user_mask_put(body=body)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_user_mask_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

body

bytearray

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/octet-stream

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

All good

-

500

Error within Jungfraujoch code - see output message.

-

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config_user_mask_tiff_get

bytearray config_user_mask_tiff_get()

Detector must be Initialized. Get user mask of the detector (TIFF)

Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Detector must be Initialized. Get user mask of the detector (TIFF) 
+        api_response = api_instance.config_user_mask_tiff_get()
+        print("The response of DefaultApi->config_user_mask_tiff_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_user_mask_tiff_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: image/tiff

HTTP response details

Status code

Description

Response headers

200

User mask in TIFF format (4 byte; unsigned)

-

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config_user_mask_tiff_put

config_user_mask_tiff_put(body=body)

Upload user mask of the detector

Should be in Idle state. Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. In the latter case - module gaps are ignored and don’t need to be assigned value. Mask is expected as TIFF (4-byte; unsigned). 0 - good pixel, other value - masked User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    body = None # bytearray |  (optional)
+
+    try:
+        # Upload user mask of the detector
+        api_instance.config_user_mask_tiff_put(body=body)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_user_mask_tiff_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

body

bytearray

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: image/tiff

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

All good

-

500

Error within Jungfraujoch code - see output message.

-

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config_zeromq_metadata_get

ZeromqMetadataSettings config_zeromq_metadata_get()

Get ZeroMQ metadata socket settings

Example

import jfjoch_client
+from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get ZeroMQ metadata socket settings
+        api_response = api_instance.config_zeromq_metadata_get()
+        print("The response of DefaultApi->config_zeromq_metadata_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_zeromq_metadata_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

ZeromqMetadataSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_zeromq_metadata_put

config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings)

Set ZeroMQ metadata settings

Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images. Here settings of the socket can be adjusted. While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.

Example

import jfjoch_client
+from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    zeromq_metadata_settings = jfjoch_client.ZeromqMetadataSettings() # ZeromqMetadataSettings |  (optional)
+
+    try:
+        # Set ZeroMQ metadata settings
+        api_instance.config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_zeromq_metadata_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

zeromq_metadata_settings

ZeromqMetadataSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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config_zeromq_preview_get

ZeromqPreviewSettings config_zeromq_preview_get()

Get ZeroMQ preview settings

Example

import jfjoch_client
+from jfjoch_client.models.zeromq_preview_settings import ZeromqPreviewSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get ZeroMQ preview settings
+        api_response = api_instance.config_zeromq_preview_get()
+        print("The response of DefaultApi->config_zeromq_preview_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_zeromq_preview_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

ZeromqPreviewSettings

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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config_zeromq_preview_put

config_zeromq_preview_put(zeromq_preview_settings=zeromq_preview_settings)

Set ZeroMQ preview settings

Jungfraujoch can generate preview message stream on ZeroMQ SUB socket. Here settings of the socket can be adjusted. While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request. Options set with this PUT request have no effect on HTTP based preview.

Example

import jfjoch_client
+from jfjoch_client.models.zeromq_preview_settings import ZeromqPreviewSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    zeromq_preview_settings = jfjoch_client.ZeromqPreviewSettings() # ZeromqPreviewSettings |  (optional)
+
+    try:
+        # Set ZeroMQ preview settings
+        api_instance.config_zeromq_preview_put(zeromq_preview_settings=zeromq_preview_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_zeromq_preview_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

zeromq_preview_settings

ZeromqPreviewSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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deactivate_post

deactivate_post()

Prepare detector to turn off

Should be in Idle or Error state. Command deactivates data acquisition and turns off detector high voltage and ASIC. Should be used always before turning off power from the detector.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Prepare detector to turn off
+        api_instance.deactivate_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->deactivate_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Detector ready to turn off

-

500

Error within Jungfraujoch code - see output message.

-

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detector_status_get

DetectorStatus detector_status_get()

Get detector status

Status of the JUNGFRAU detector

Example

import jfjoch_client
+from jfjoch_client.models.detector_status import DetectorStatus
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get detector status
+        api_response = api_instance.detector_status_get()
+        print("The response of DefaultApi->detector_status_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->detector_status_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

DetectorStatus

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json, text/plain

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

404

Running in &quot;simulator&quot; mode - no detector present

-

500

Error encountered when trying to read status

-

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fpga_status_get

List[FpgaStatusInner] fpga_status_get()

Get status of FPGA devices

Example

import jfjoch_client
+from jfjoch_client.models.fpga_status_inner import FpgaStatusInner
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get status of FPGA devices
+        api_response = api_instance.fpga_status_get()
+        print("The response of DefaultApi->fpga_status_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->fpga_status_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

List[FpgaStatusInner]

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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image_buffer_clear_post

image_buffer_clear_post()

Clear image buffer

Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Clear image buffer
+        api_instance.image_buffer_clear_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->image_buffer_clear_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Done

-

500

Error within Jungfraujoch code - see output message.

-

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image_buffer_image_cbor_get

bytearray image_buffer_image_cbor_get(id=id)

Get image message in CBOR format

Contains full image data and metadata. The image must come from the latest data collection.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    id = -1 # int | Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer (optional) (default to -1)
+
+    try:
+        # Get image message in CBOR format
+        api_response = api_instance.image_buffer_image_cbor_get(id=id)
+        print("The response of DefaultApi->image_buffer_image_cbor_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->image_buffer_image_cbor_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

id

int

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

[optional] [default to -1]

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/cbor, application/json

HTTP response details

Status code

Description

Response headers

200

Return image message

-

404

Image not present in the buffer - either not yet measured or already replaced by a next image.

-

500

Error within Jungfraujoch code - see output message.

-

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image_buffer_image_jpeg_get

bytearray image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)

Get preview image in JPEG format using custom settings

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    id = -1 # int | Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer (optional) (default to -1)
+    show_user_mask = False # bool | Show user mask (optional) (default to False)
+    show_roi = False # bool | Show ROI areas on the image (optional) (default to False)
+    show_spots = True # bool | Show spot finding results on the image (optional) (default to True)
+    show_beam_center = True # bool | Show beam center on the image (optional) (default to True)
+    saturation = 3.4 # float | Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used (optional)
+    jpeg_quality = 100 # int | Quality of JPEG image (100 - highest; 0 - lowest) (optional) (default to 100)
+    show_res_ring = 0.1 # float | Show resolution ring, provided in Angstrom (optional) (default to 0.1)
+    color = indigo # str | Color scale for preview image (optional) (default to indigo)
+    show_res_est = False # bool | Show resolution estimation as a ring (optional) (default to False)
+
+    try:
+        # Get preview image in JPEG format using custom settings
+        api_response = api_instance.image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
+        print("The response of DefaultApi->image_buffer_image_jpeg_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->image_buffer_image_jpeg_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

id

int

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

[optional] [default to -1]

show_user_mask

bool

Show user mask

[optional] [default to False]

show_roi

bool

Show ROI areas on the image

[optional] [default to False]

show_spots

bool

Show spot finding results on the image

[optional] [default to True]

show_beam_center

bool

Show beam center on the image

[optional] [default to True]

saturation

float

Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used

[optional]

jpeg_quality

int

Quality of JPEG image (100 - highest; 0 - lowest)

[optional] [default to 100]

show_res_ring

float

Show resolution ring, provided in Angstrom

[optional] [default to 0.1]

color

str

Color scale for preview image

[optional] [default to indigo]

show_res_est

bool

Show resolution estimation as a ring

[optional] [default to False]

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: image/jpeg, text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Preview image

-

404

Image not present in the buffer - either not yet measured or already replaced by a next image.

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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image_buffer_image_tiff_get

bytearray image_buffer_image_tiff_get(id=id)

Get preview image in TIFF format

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    id = -1 # int | Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer (optional) (default to -1)
+
+    try:
+        # Get preview image in TIFF format
+        api_response = api_instance.image_buffer_image_tiff_get(id=id)
+        print("The response of DefaultApi->image_buffer_image_tiff_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->image_buffer_image_tiff_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

id

int

Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer

[optional] [default to -1]

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: image/tiff

HTTP response details

Status code

Description

Response headers

200

Preview image

-

404

No preview image recorded so far

-

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image_buffer_start_cbor_get

bytearray image_buffer_start_cbor_get()

Get Start message in CBOR format

Contains metadata for a dataset (e.g., experimental geometry)

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get Start message in CBOR format
+        api_response = api_instance.image_buffer_start_cbor_get()
+        print("The response of DefaultApi->image_buffer_start_cbor_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->image_buffer_start_cbor_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/cbor, application/json

HTTP response details

Status code

Description

Response headers

200

Return start message

-

404

No measurement so far

-

500

Error within Jungfraujoch code - see output message.

-

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image_buffer_status_get

ImageBufferStatus image_buffer_status_get()

Get status of the image buffers

Can be run at any stage of Jungfraujoch operation, including during data collection. The status of the image buffer is volatile during data collection - if data collection goes for more images than available buffer slots, then image might be replaced in the buffer between calling /images and /image.cbor.

Example

import jfjoch_client
+from jfjoch_client.models.image_buffer_status import ImageBufferStatus
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get status of the image buffers
+        api_response = api_instance.image_buffer_status_get()
+        print("The response of DefaultApi->image_buffer_status_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->image_buffer_status_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

ImageBufferStatus

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Done

-

500

Error within Jungfraujoch code - see output message.

-

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initialize_post

initialize_post()

Initialize detector and data acquisition

Should be used in two cases:

  • Detector is in Inactive state

  • Detector is in Error state X-ray shutter must be closed. This operation will reconfigure network interface of the detector. During operation of the detector it is recommended to use the POST /pedestal operation instead. If storage cells are used, the execution time might be few minutes.

This is async function - one needs to use POST /wait_till_done to ensure operation is done.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Initialize detector and data acquisition
+        api_instance.initialize_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->initialize_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Initialization started

-

500

Error within Jungfraujoch code - see output message.

-

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pedestal_post

pedestal_post()

Collect dark current for the detector

Updates calibration of the JUNGFRAU detector. Must be in Idle state.

X-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).

This is async function - one needs to use POST /wait_till_done to ensure operation is done.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Collect dark current for the detector
+        api_instance.pedestal_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->pedestal_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

500

Error within Jungfraujoch code - see output message.

-

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preview_pedestal_tiff_get

bytearray preview_pedestal_tiff_get(gain_level, sc=sc)

Get pedestal in TIFF format

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    gain_level = 56 # int | Gain level (0, 1, 2)
+    sc = 56 # int | Storage cell number (optional)
+
+    try:
+        # Get pedestal in TIFF format
+        api_response = api_instance.preview_pedestal_tiff_get(gain_level, sc=sc)
+        print("The response of DefaultApi->preview_pedestal_tiff_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->preview_pedestal_tiff_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

gain_level

int

Gain level (0, 1, 2)

sc

int

Storage cell number

[optional]

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: image/tiff

HTTP response details

Status code

Description

Response headers

200

Calibration image

-

404

No calibration recorded so far

-

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preview_plot_bin_get

bytearray preview_plot_bin_get(type, roi=roi)

Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn’t transmit information about X-axis, only values, so it is of limited use for azimuthal integration.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    type = 'type_example' # str | Type of requested plot
+    roi = 'roi_example' # str | Name of ROI for which plot is requested (optional)
+
+    try:
+        # Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. 
+        api_response = api_instance.preview_plot_bin_get(type, roi=roi)
+        print("The response of DefaultApi->preview_plot_bin_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->preview_plot_bin_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

type

str

Type of requested plot

roi

str

Name of ROI for which plot is requested

[optional]

Return type

bytearray

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/octet-stream, text/plain

HTTP response details

Status code

Description

Response headers

200

Everything OK.

-

400

Input parsing or validation error

-

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preview_plot_get

Plots preview_plot_get(type, binning=binning, compression=compression, fill=fill, experimental_coord=experimental_coord, azint_unit=azint_unit)

Generate 1D plot from Jungfraujoch

Example

import jfjoch_client
+from jfjoch_client.models.plots import Plots
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    type = 'type_example' # str | Type of requested plot
+    binning = 1 # int | Binning of frames for the plot (0 = default binning) (optional) (default to 1)
+    compression = False # bool | Enable DEFLATE compression of output data. (optional) (default to False)
+    fill = 3.4 # float | Fill value for elements that were missed during data collection  (optional)
+    experimental_coord = False # bool | If measurement has goniometer axis defined, plot X-axis will represent rotation angle If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value For still measurement the number is ignored  (optional) (default to False)
+    azint_unit = Q_recipA # str | Unit used for azim int.  (optional) (default to Q_recipA)
+
+    try:
+        # Generate 1D plot from Jungfraujoch
+        api_response = api_instance.preview_plot_get(type, binning=binning, compression=compression, fill=fill, experimental_coord=experimental_coord, azint_unit=azint_unit)
+        print("The response of DefaultApi->preview_plot_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->preview_plot_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

type

str

Type of requested plot

binning

int

Binning of frames for the plot (0 = default binning)

[optional] [default to 1]

compression

bool

Enable DEFLATE compression of output data.

[optional] [default to False]

fill

float

Fill value for elements that were missed during data collection

[optional]

experimental_coord

bool

If measurement has goniometer axis defined, plot X-axis will represent rotation angle If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value For still measurement the number is ignored

[optional] [default to False]

azint_unit

str

Unit used for azim int.

[optional] [default to Q_recipA]

Return type

Plots

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json, text/plain

HTTP response details

Status code

Description

Response headers

200

Everything OK.

-

400

Input parsing or validation error

-

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result_scan_get

ScanResult result_scan_get()

Get full scan result

Example

import jfjoch_client
+from jfjoch_client.models.scan_result import ScanResult
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get full scan result
+        api_response = api_instance.result_scan_get()
+        print("The response of DefaultApi->result_scan_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->result_scan_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

ScanResult

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK.

-

404

No grid scan recorded

-

500

Error within Jungfraujoch code - see output message.

-

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start_post

start_post(dataset_settings=dataset_settings)

Start detector

Start data acquisition. Detector must be in Idle state. Doesn’t run calibration procedure. When the function returns, detector is ready to accept soft/TTL triggers.

Example

import jfjoch_client
+from jfjoch_client.models.dataset_settings import DatasetSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    dataset_settings = jfjoch_client.DatasetSettings() # DatasetSettings |  (optional)
+
+    try:
+        # Start detector
+        api_instance.start_post(dataset_settings=dataset_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->start_post: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

dataset_settings

DatasetSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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statistics_calibration_get

List[CalibrationStatisticsInner] statistics_calibration_get()

Get calibration statistics

Statistics are provided for each module/storage cell separately

Example

import jfjoch_client
+from jfjoch_client.models.calibration_statistics_inner import CalibrationStatisticsInner
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get calibration statistics
+        api_response = api_instance.statistics_calibration_get()
+        print("The response of DefaultApi->statistics_calibration_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->statistics_calibration_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

List[CalibrationStatisticsInner]

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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statistics_data_collection_get

MeasurementStatistics statistics_data_collection_get()

Get data collection statistics

Results of the last data collection

Example

import jfjoch_client
+from jfjoch_client.models.measurement_statistics import MeasurementStatistics
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get data collection statistics
+        api_response = api_instance.statistics_data_collection_get()
+        print("The response of DefaultApi->statistics_data_collection_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->statistics_data_collection_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

MeasurementStatistics

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

404

No data collection performed so far

-

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statistics_get

JfjochStatistics statistics_get(compression=compression)

Get general statistics

Example

import jfjoch_client
+from jfjoch_client.models.jfjoch_statistics import JfjochStatistics
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    compression = False # bool | Enable DEFLATE compression of output data. (optional) (default to False)
+
+    try:
+        # Get general statistics
+        api_response = api_instance.statistics_get(compression=compression)
+        print("The response of DefaultApi->statistics_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->statistics_get: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

compression

bool

Enable DEFLATE compression of output data.

[optional] [default to False]

Return type

JfjochStatistics

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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status_get

BrokerStatus status_get()

Get Jungfraujoch status

Status of the data acquisition

Example

import jfjoch_client
+from jfjoch_client.models.broker_status import BrokerStatus
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get Jungfraujoch status
+        api_response = api_instance.status_get()
+        print("The response of DefaultApi->status_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->status_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

BrokerStatus

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

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trigger_post

trigger_post()

Send soft trigger to the detector

Generate soft trigger

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Send soft trigger to the detector
+        api_instance.trigger_post()
+    except Exception as e:
+        print("Exception when calling DefaultApi->trigger_post: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: Not defined

HTTP response details

Status code

Description

Response headers

200

Trigger sent

-

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version_get

str version_get()

Get Jungfraujoch version of jfjoch_broker

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get Jungfraujoch version of jfjoch_broker
+        api_response = api_instance.version_get()
+        print("The response of DefaultApi->version_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->version_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

str

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: text/plain

HTTP response details

Status code

Description

Response headers

200

Release number of Jungfraujoch

-

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wait_till_done_post

wait_till_done_post(timeout=timeout)

Wait for acquisition done

Block execution of external script till initialization, data collection or pedestal is finished. Running this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.

To not block web server for a indefinite period of time, the procedure is provided with a timeout. Extending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    timeout = 60 # int | Timeout in seconds (0 == immediate response) (optional) (default to 60)
+
+    try:
+        # Wait for acquisition done
+        api_instance.wait_till_done_post(timeout=timeout)
+    except Exception as e:
+        print("Exception when calling DefaultApi->wait_till_done_post: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

timeout

int

Timeout in seconds (0 == immediate response)

[optional] [default to 60]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Detector in `Idle` state, another data collection can start immediately

-

400

Timeout parameter out of bounds

-

500

Error within Jungfraujoch code - see output message.

-

502

Detector is inactive mode

-

504

Timeout reached, need to restart operation

-

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xfel_event_code_get

List[int] xfel_event_code_get()

Return XFEL event codes for the current data acquisition

Return array of XFEL event codes

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Return XFEL event codes for the current data acquisition
+        api_response = api_instance.xfel_event_code_get()
+        print("The response of DefaultApi->xfel_event_code_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->xfel_event_code_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

List[int]

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Event codes collected

-

404

Not in XFEL mode or no acquisition recorded

-

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xfel_pulse_id_get

List[int] xfel_pulse_id_get()

Return XFEL pulse IDs for the current data acquisition

Return array of XFEL pulse IDs - (-1) if image not recorded

Example

import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Return XFEL pulse IDs for the current data acquisition
+        api_response = api_instance.xfel_pulse_id_get()
+        print("The response of DefaultApi->xfel_pulse_id_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->xfel_pulse_id_get: %s\n" % e)
+

Parameters

This endpoint does not need any parameter.

Return type

List[int]

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined

  • Accept: application/json

HTTP response details

Status code

Description

Response headers

200

Pulse ID collected

-

404

Not in XFEL mode or no acquisition recorded

-

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\ No newline at end of file diff --git a/python_client/docs/Detector.html b/python_client/docs/Detector.html new file mode 100644 index 00000000..88c00766 --- /dev/null +++ b/python_client/docs/Detector.html @@ -0,0 +1,14 @@ + Detector — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

Detector

Properties

Name

Type

Description

Notes

description

str

serial_number

str

[optional] [default to ‘Unknown’]

type

DetectorType

[optional]

high_voltage_v

int

[optional] [default to 0]

udp_interface_count

int

[optional] [default to 1]

module_sync

bool

Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER).

[optional] [default to True]

sensor_thickness_um

float

[optional] [default to 320]

readout_time_us

int

Minimum difference between frame time and count time in microseconds Defaults are 3 us for EIGER and 20 us for JUNGFRAU

[optional]

minimum_count_time_us

int

Minimum count time available for the detector.

[optional]

minimum_frame_time_us

int

Minimum frame time available for the detector.

[optional]

calibration_file

List[str]

Can be empty for all detectors - default calibration used. For JUNGFRAU: list of gain files, one entry per module. For EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.

[optional]

hostname

List[str]

Hostname for detector module. One entry per module One entry per module. Either empty or number of module entries.

[optional]

sensor_material

str

[optional] [default to ‘Si’]

tx_delay

List[int]

[optional]

base_data_ipv4_address

str

[optional]

standard_geometry

StandardDetectorGeometry

[optional]

custom_geometry

List[DetectorModule]

[optional]

roi_mode

str

ROI setting for DECTRIS detectors

[optional] [default to ‘’]

mirror_y

bool

Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner

[optional] [default to True]

temp_thresold_deg_c

int

Temperature threshold for JUNGFRAU detector modules

[optional] [default to 55]

default_settings

DetectorSettings

[optional]

Example

from jfjoch_client.models.detector import Detector
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of Detector from a JSON string
+detector_instance = Detector.from_json(json)
+# print the JSON string representation of the object
+print(Detector.to_json())
+
+# convert the object into a dict
+detector_dict = detector_instance.to_dict()
+# create an instance of Detector from a dict
+detector_from_dict = Detector.from_dict(detector_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorList.html b/python_client/docs/DetectorList.html new file mode 100644 index 00000000..9a07cd9d --- /dev/null +++ b/python_client/docs/DetectorList.html @@ -0,0 +1,14 @@ + DetectorList — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DetectorList

Properties

Name

Type

Description

Notes

detectors

List[DetectorListElement]

current_id

int

Example

from jfjoch_client.models.detector_list import DetectorList
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorList from a JSON string
+detector_list_instance = DetectorList.from_json(json)
+# print the JSON string representation of the object
+print(DetectorList.to_json())
+
+# convert the object into a dict
+detector_list_dict = detector_list_instance.to_dict()
+# create an instance of DetectorList from a dict
+detector_list_from_dict = DetectorList.from_dict(detector_list_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorListDetectorsInner.html b/python_client/docs/DetectorListDetectorsInner.html new file mode 100644 index 00000000..8c0a7001 --- /dev/null +++ b/python_client/docs/DetectorListDetectorsInner.html @@ -0,0 +1,14 @@ + DetectorListDetectorsInner — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DetectorListDetectorsInner

Properties

Name

Type

Description

Notes

id

int

description

str

serial_number

str

base_ipv4_addr

str

udp_interface_count

int

Number of UDP interfaces per detector module

nmodules

int

width

int

height

int

Example

from jfjoch_client.models.detector_list_detectors_inner import DetectorListDetectorsInner
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorListDetectorsInner from a JSON string
+detector_list_detectors_inner_instance = DetectorListDetectorsInner.from_json(json)
+# print the JSON string representation of the object
+print(DetectorListDetectorsInner.to_json())
+
+# convert the object into a dict
+detector_list_detectors_inner_dict = detector_list_detectors_inner_instance.to_dict()
+# create an instance of DetectorListDetectorsInner from a dict
+detector_list_detectors_inner_from_dict = DetectorListDetectorsInner.from_dict(detector_list_detectors_inner_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorListElement.html b/python_client/docs/DetectorListElement.html new file mode 100644 index 00000000..a233b68d --- /dev/null +++ b/python_client/docs/DetectorListElement.html @@ -0,0 +1,14 @@ + DetectorListElement — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DetectorListElement

Properties

Name

Type

Description

Notes

id

int

description

str

serial_number

str

base_ipv4_addr

str

udp_interface_count

int

Number of UDP interfaces per detector module

nmodules

int

width

int

height

int

pixel_size_mm

float

[optional]

readout_time_us

int

min_frame_time_us

int

min_count_time_us

int

type

DetectorType

[optional]

Example

from jfjoch_client.models.detector_list_element import DetectorListElement
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorListElement from a JSON string
+detector_list_element_instance = DetectorListElement.from_json(json)
+# print the JSON string representation of the object
+print(DetectorListElement.to_json())
+
+# convert the object into a dict
+detector_list_element_dict = detector_list_element_instance.to_dict()
+# create an instance of DetectorListElement from a dict
+detector_list_element_from_dict = DetectorListElement.from_dict(detector_list_element_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorModule.html b/python_client/docs/DetectorModule.html new file mode 100644 index 00000000..52d10c12 --- /dev/null +++ b/python_client/docs/DetectorModule.html @@ -0,0 +1,14 @@ + DetectorModule — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DetectorModule

Properties

Name

Type

Description

Notes

x0

float

y0

float

fast_axis

DetectorModuleDirection

slow_axis

DetectorModuleDirection

Example

from jfjoch_client.models.detector_module import DetectorModule
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorModule from a JSON string
+detector_module_instance = DetectorModule.from_json(json)
+# print the JSON string representation of the object
+print(DetectorModule.to_json())
+
+# convert the object into a dict
+detector_module_dict = detector_module_instance.to_dict()
+# create an instance of DetectorModule from a dict
+detector_module_from_dict = DetectorModule.from_dict(detector_module_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorModuleDirection.html b/python_client/docs/DetectorModuleDirection.html new file mode 100644 index 00000000..54429842 --- /dev/null +++ b/python_client/docs/DetectorModuleDirection.html @@ -0,0 +1 @@ + DetectorModuleDirection — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
\ No newline at end of file diff --git a/python_client/docs/DetectorPowerState.html b/python_client/docs/DetectorPowerState.html new file mode 100644 index 00000000..9be80d0e --- /dev/null +++ b/python_client/docs/DetectorPowerState.html @@ -0,0 +1 @@ + DetectorPowerState — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
\ No newline at end of file diff --git a/python_client/docs/DetectorSelection.html b/python_client/docs/DetectorSelection.html new file mode 100644 index 00000000..3b974671 --- /dev/null +++ b/python_client/docs/DetectorSelection.html @@ -0,0 +1,14 @@ + DetectorSelection — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DetectorSelection

Properties

Name

Type

Description

Notes

id

int

Example

from jfjoch_client.models.detector_selection import DetectorSelection
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorSelection from a JSON string
+detector_selection_instance = DetectorSelection.from_json(json)
+# print the JSON string representation of the object
+print(DetectorSelection.to_json())
+
+# convert the object into a dict
+detector_selection_dict = detector_selection_instance.to_dict()
+# create an instance of DetectorSelection from a dict
+detector_selection_from_dict = DetectorSelection.from_dict(detector_selection_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorSettings.html b/python_client/docs/DetectorSettings.html new file mode 100644 index 00000000..1ac29cb0 --- /dev/null +++ b/python_client/docs/DetectorSettings.html @@ -0,0 +1,14 @@ + DetectorSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

DetectorSettings

Properties

Name

Type

Description

Notes

frame_time_us

int

Interval between consecutive frames. This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number. For EIGER detector this is default frame time, not used otherwise

count_time_us

int

Integration time of the detector. If not provided count time will be set to maximum value for a given frame time.

[optional]

internal_frame_generator

bool

Use internal frame generator in FPGA instead of getting data from a real detector

[optional] [default to False]

internal_frame_generator_images

int

Number of images stored in the internal frame generator.

[optional] [default to 1]

detector_trigger_delay_ns

int

Delay between TTL trigger and acquisition start [ns]

[optional] [default to 0]

timing

DetectorTiming

[optional] [default to DetectorTiming.TRIGGER]

eiger_threshold_ke_v

float

Threshold for the PSI EIGER detector and all DECTRIS detectors. If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy. If value is not provided, threshold will be determined on start of acquisition as half of incident energy. This might lead to increased start time.

[optional]

eiger_bit_depth

int

Bit depth of PSI EIGER read-out. This is If value is not provided, depth will be determined based on the image time: * Exposure time < 500 microseconds depth of 8 bit will be used, * 500 <= exposure time < 2622 microseconds depth of 16 bit will be used * Exposure time >= 2622 microseconds depth of 32 bit will be used.

[optional]

jungfrau_pedestal_g0_frames

int

[optional] [default to 2000]

jungfrau_pedestal_g1_frames

int

[optional] [default to 300]

jungfrau_pedestal_g2_frames

int

[optional] [default to 300]

jungfrau_pedestal_min_image_count

int

Minimum number of collected images for pedestal to consider it viable

[optional] [default to 128]

jungfrau_storage_cell_count

int

[optional] [default to 1]

jungfrau_storage_cell_delay_ns

int

Delay between two storage cells [ns]

[optional] [default to 5000]

jungfrau_fixed_gain_g1

bool

Fix gain to G1 (can be useful for storage cells)

[optional] [default to False]

jungfrau_use_gain_hg0

bool

Use high G0 (for low energy applications)

[optional] [default to False]

Example

from jfjoch_client.models.detector_settings import DetectorSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorSettings from a JSON string
+detector_settings_instance = DetectorSettings.from_json(json)
+# print the JSON string representation of the object
+print(DetectorSettings.to_json())
+
+# convert the object into a dict
+detector_settings_dict = detector_settings_instance.to_dict()
+# create an instance of DetectorSettings from a dict
+detector_settings_from_dict = DetectorSettings.from_dict(detector_settings_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/DetectorState.html b/python_client/docs/DetectorState.html new file mode 100644 index 00000000..8efe2de6 --- /dev/null +++ b/python_client/docs/DetectorState.html @@ -0,0 +1 @@ + DetectorState — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
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DetectorStatus

Properties

Name

Type

Description

Notes

state

DetectorState

powerchip

DetectorPowerState

server_version

str

Detector server (on read-out boards) version

number_of_triggers_left

int

Remaining triggers to the detector (max of all modules)

fpga_temp_deg_c

List[int]

Temperature of detector FPGAs

high_voltage_v

List[int]

High voltage for detector modules

Example

from jfjoch_client.models.detector_status import DetectorStatus
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of DetectorStatus from a JSON string
+detector_status_instance = DetectorStatus.from_json(json)
+# print the JSON string representation of the object
+print(DetectorStatus.to_json())
+
+# convert the object into a dict
+detector_status_dict = detector_status_instance.to_dict()
+# create an instance of DetectorStatus from a dict
+detector_status_from_dict = DetectorStatus.from_dict(detector_status_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/DetectorTiming.html b/python_client/docs/DetectorTiming.html new file mode 100644 index 00000000..bda97098 --- /dev/null +++ b/python_client/docs/DetectorTiming.html @@ -0,0 +1 @@ + DetectorTiming — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
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ErrorMessage

Properties

Name

Type

Description

Notes

msg

str

Human readable message

reason

str

Enumerate field for automated analysis

Example

from jfjoch_client.models.error_message import ErrorMessage
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ErrorMessage from a JSON string
+error_message_instance = ErrorMessage.from_json(json)
+# print the JSON string representation of the object
+print(ErrorMessage.to_json())
+
+# convert the object into a dict
+error_message_dict = error_message_instance.to_dict()
+# create an instance of ErrorMessage from a dict
+error_message_from_dict = ErrorMessage.from_dict(error_message_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/FileWriterFormat.html b/python_client/docs/FileWriterFormat.html new file mode 100644 index 00000000..46867e5b --- /dev/null +++ b/python_client/docs/FileWriterFormat.html @@ -0,0 +1 @@ + FileWriterFormat — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

FileWriterFormat

None - no master file written NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling

Enum

  • NONE (value: 'None')

  • NXMXLEGACY (value: 'NXmxLegacy')

  • NXMXVDS (value: 'NXmxVDS')

  • CBF (value: 'CBF')

  • TIFF (value: 'TIFF')

  • NOFILEWRITTEN (value: 'NoFileWritten')

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\ No newline at end of file diff --git a/python_client/docs/FileWriterSettings.html b/python_client/docs/FileWriterSettings.html new file mode 100644 index 00000000..d1c03180 --- /dev/null +++ b/python_client/docs/FileWriterSettings.html @@ -0,0 +1,14 @@ + FileWriterSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

FileWriterSettings

Properties

Name

Type

Description

Notes

overwrite

bool

Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.

[optional] [default to False]

format

FileWriterFormat

[optional] [default to FileWriterFormat.NXMXLEGACY]

Example

from jfjoch_client.models.file_writer_settings import FileWriterSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of FileWriterSettings from a JSON string
+file_writer_settings_instance = FileWriterSettings.from_json(json)
+# print the JSON string representation of the object
+print(FileWriterSettings.to_json())
+
+# convert the object into a dict
+file_writer_settings_dict = file_writer_settings_instance.to_dict()
+# create an instance of FileWriterSettings from a dict
+file_writer_settings_from_dict = FileWriterSettings.from_dict(file_writer_settings_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/FpgaStatusInner.html b/python_client/docs/FpgaStatusInner.html new file mode 100644 index 00000000..6f3bc48c --- /dev/null +++ b/python_client/docs/FpgaStatusInner.html @@ -0,0 +1,14 @@ + FpgaStatusInner — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

FpgaStatusInner

Properties

Name

Type

Description

Notes

pci_dev_id

str

serial_number

str

fw_version

str

base_mac_addr

str

eth_link_count

int

eth_link_status

int

power_usage_w

float

fpga_temp_c

float

hbm_temp_c

float

packets_udp

int

packets_sls

int

idle

bool

pcie_link_speed

int

PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)

pcie_link_width

int

PCIe link width (expected value is 8 == x8)

Example

from jfjoch_client.models.fpga_status_inner import FpgaStatusInner
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of FpgaStatusInner from a JSON string
+fpga_status_inner_instance = FpgaStatusInner.from_json(json)
+# print the JSON string representation of the object
+print(FpgaStatusInner.to_json())
+
+# convert the object into a dict
+fpga_status_inner_dict = fpga_status_inner_instance.to_dict()
+# create an instance of FpgaStatusInner from a dict
+fpga_status_inner_from_dict = FpgaStatusInner.from_dict(fpga_status_inner_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/GeomRefinementAlgorithm.html b/python_client/docs/GeomRefinementAlgorithm.html new file mode 100644 index 00000000..9d4fd72d --- /dev/null +++ b/python_client/docs/GeomRefinementAlgorithm.html @@ -0,0 +1 @@ + GeomRefinementAlgorithm — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

GeomRefinementAlgorithm

Selection of an post-indexing detector geometry refinement algorithm used by Jungfraujoch. This option is using non-linear least squares optimization to find unit cell and beam center.

Enum

  • BEAMCENTER (value: 'BeamCenter')

  • NONE (value: 'None')

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\ No newline at end of file diff --git a/python_client/docs/GridPlot.html b/python_client/docs/GridPlot.html new file mode 100644 index 00000000..6f932316 --- /dev/null +++ b/python_client/docs/GridPlot.html @@ -0,0 +1,14 @@ + GridPlot — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

GridPlot

Properties

Name

Type

Description

Notes

data

List[float]

width

int

Example

from jfjoch_client.models.grid_plot import GridPlot
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of GridPlot from a JSON string
+grid_plot_instance = GridPlot.from_json(json)
+# print the JSON string representation of the object
+print(GridPlot.to_json())
+
+# convert the object into a dict
+grid_plot_dict = grid_plot_instance.to_dict()
+# create an instance of GridPlot from a dict
+grid_plot_from_dict = GridPlot.from_dict(grid_plot_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/GridPlots.html b/python_client/docs/GridPlots.html new file mode 100644 index 00000000..e52affbe --- /dev/null +++ b/python_client/docs/GridPlots.html @@ -0,0 +1,14 @@ + GridPlots — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

GridPlots

Properties

Name

Type

Description

Notes

plots

List[GridPlot]

width

int

Example

from jfjoch_client.models.grid_plots import GridPlots
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of GridPlots from a JSON string
+grid_plots_instance = GridPlots.from_json(json)
+# print the JSON string representation of the object
+print(GridPlots.to_json())
+
+# convert the object into a dict
+grid_plots_dict = grid_plots_instance.to_dict()
+# create an instance of GridPlots from a dict
+grid_plots_from_dict = GridPlots.from_dict(grid_plots_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/GridScan.html b/python_client/docs/GridScan.html new file mode 100644 index 00000000..ae411634 --- /dev/null +++ b/python_client/docs/GridScan.html @@ -0,0 +1,14 @@ + GridScan — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

GridScan

Definition of a grid scan (mutually exclusive with rotation_axis)

Properties

Name

Type

Description

Notes

n_fast

int

Number of elements in the fast direction

step_x_um

float

Step in grid along the fast direction. Can be negative. Positive number: left to right Negative number: right to left

step_y_um

float

Step in grid along the slow direction. Can be negative. Positive number: top to bottom Negative number: bottom to top

vertical

bool

If disabled: fast direction = X, slow direction = Y If enabled: fast direction = Y, slow direction = X

[optional] [default to False]

snake

bool

Flip fast direction for every second row

[optional] [default to False]

Example

from jfjoch_client.models.grid_scan import GridScan
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of GridScan from a JSON string
+grid_scan_instance = GridScan.from_json(json)
+# print the JSON string representation of the object
+print(GridScan.to_json())
+
+# convert the object into a dict
+grid_scan_dict = grid_scan_instance.to_dict()
+# create an instance of GridScan from a dict
+grid_scan_from_dict = GridScan.from_dict(grid_scan_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/GridScanResult.html b/python_client/docs/GridScanResult.html new file mode 100644 index 00000000..09488d40 --- /dev/null +++ b/python_client/docs/GridScanResult.html @@ -0,0 +1,14 @@ + GridScanResult — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

GridScanResult

Results of a grid scan

Properties

Name

Type

Description

Notes

det_img

List[int]

Detector image number for a given cell

bkg_estimate

List[float]

spot_count

List[int]

indexed_lattices

List[int]

mosaicity

List[float]

b_factor

List[float]

Example

from jfjoch_client.models.grid_scan_result import GridScanResult
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of GridScanResult from a JSON string
+grid_scan_result_instance = GridScanResult.from_json(json)
+# print the JSON string representation of the object
+print(GridScanResult.to_json())
+
+# convert the object into a dict
+grid_scan_result_dict = grid_scan_result_instance.to_dict()
+# create an instance of GridScanResult from a dict
+grid_scan_result_from_dict = GridScanResult.from_dict(grid_scan_result_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/GridScanResultImagesInner.html b/python_client/docs/GridScanResultImagesInner.html new file mode 100644 index 00000000..2e31519c --- /dev/null +++ b/python_client/docs/GridScanResultImagesInner.html @@ -0,0 +1,14 @@ + GridScanResultImagesInner — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

GridScanResultImagesInner

Properties

Name

Type

Description

Notes

efficiency

float

number

int

Detector image number for a given cell

bkg

float

Background estimate

[optional]

spots

int

Spot count

[optional]

index

int

Indexing solution

[optional]

mos

float

Mosaicity estimate

[optional]

b

float

B-Factor estimate

[optional]

uc

UnitCell

[optional]

Example

from jfjoch_client.models.grid_scan_result_images_inner import GridScanResultImagesInner
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of GridScanResultImagesInner from a JSON string
+grid_scan_result_images_inner_instance = GridScanResultImagesInner.from_json(json)
+# print the JSON string representation of the object
+print(GridScanResultImagesInner.to_json())
+
+# convert the object into a dict
+grid_scan_result_images_inner_dict = grid_scan_result_images_inner_instance.to_dict()
+# create an instance of GridScanResultImagesInner from a dict
+grid_scan_result_images_inner_from_dict = GridScanResultImagesInner.from_dict(grid_scan_result_images_inner_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ImageBufferStatus.html b/python_client/docs/ImageBufferStatus.html new file mode 100644 index 00000000..b9b0f0e9 --- /dev/null +++ b/python_client/docs/ImageBufferStatus.html @@ -0,0 +1,14 @@ + ImageBufferStatus — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ImageBufferStatus

Properties

Name

Type

Description

Notes

min_image_number

int

Smallest image number available in the buffer

max_image_number

int

Largest image number available in the buffer

image_numbers

List[int]

Image numbers currently present in the buffer.

total_slots

int

Number of slots in the image buffer. This number, compared to number of images in data collection and frame rate will determine &quot;retention&quot; rate of the image buffer.

available_slots

int

Slots available for the data collection

current_counter

int

Counter of changes in the image buffer - either new start message or new image added. For optimization one can only load new images/datasets from the HTTP if this value changes. Counter is optional as it was not implemented in older versions to avoid breaking change

[optional]

Example

from jfjoch_client.models.image_buffer_status import ImageBufferStatus
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ImageBufferStatus from a JSON string
+image_buffer_status_instance = ImageBufferStatus.from_json(json)
+# print the JSON string representation of the object
+print(ImageBufferStatus.to_json())
+
+# convert the object into a dict
+image_buffer_status_dict = image_buffer_status_instance.to_dict()
+# create an instance of ImageBufferStatus from a dict
+image_buffer_status_from_dict = ImageBufferStatus.from_dict(image_buffer_status_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ImageFormatSettings.html b/python_client/docs/ImageFormatSettings.html new file mode 100644 index 00000000..9bca4efa --- /dev/null +++ b/python_client/docs/ImageFormatSettings.html @@ -0,0 +1,14 @@ + ImageFormatSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ImageFormatSettings

Properties

Name

Type

Description

Notes

summation

bool

Enable summation of images to a given image_time If disabled images are saved according to original detector speed, but image count is adjusted

geometry_transform

bool

Place module read-out into their location on composed detector and extend multipixels

jungfrau_conversion

bool

Convert pixel value in ADU to photon counts/energy Only affects JUNGFRAU detector

jungfrau_conversion_factor_ke_v

float

Used to convert energy deposited into pixel to counts If not provided incident_energy_keV is used

[optional]

bit_depth_image

int

Bit depth of resulting image (it doesn’t affect the detector read-out value) If not provided value is adjusted automatically

[optional]

signed_output

bool

Controls if pixels have signed output If not provided value is adjusted automatically

[optional]

mask_module_edges

bool

Mask 1 pixel on the module boundary

[default to True]

mask_chip_edges

bool

Mask multipixels on chip boundary

[default to True]

jungfrau_mask_pixels_without_g0

bool

JUNGFRAU: mask pixels that don’t operate in G0, but do operate in G1 and G1. This should be turned off for cases, where detector is operated at room temperature with long exposure time.

[optional] [default to True]

apply_mask

bool

Masked pixels are set to special value in the images produced by Jungfraujoch

[default to False]

jungfrau_pedestal_g0_rms_limit

int

Pixels with pedestal G0 RMS above the threshold are marked as masked pixels

[optional] [default to 100]

Example

from jfjoch_client.models.image_format_settings import ImageFormatSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ImageFormatSettings from a JSON string
+image_format_settings_instance = ImageFormatSettings.from_json(json)
+# print the JSON string representation of the object
+print(ImageFormatSettings.to_json())
+
+# convert the object into a dict
+image_format_settings_dict = image_format_settings_instance.to_dict()
+# create an instance of ImageFormatSettings from a dict
+image_format_settings_from_dict = ImageFormatSettings.from_dict(image_format_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ImagePusherType.html b/python_client/docs/ImagePusherType.html new file mode 100644 index 00000000..ee379335 --- /dev/null +++ b/python_client/docs/ImagePusherType.html @@ -0,0 +1 @@ + ImagePusherType — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
\ No newline at end of file diff --git a/python_client/docs/IndexingAlgorithm.html b/python_client/docs/IndexingAlgorithm.html new file mode 100644 index 00000000..c497d70d --- /dev/null +++ b/python_client/docs/IndexingAlgorithm.html @@ -0,0 +1 @@ + IndexingAlgorithm — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
\ No newline at end of file diff --git a/python_client/docs/IndexingSettings.html b/python_client/docs/IndexingSettings.html new file mode 100644 index 00000000..ccc09515 --- /dev/null +++ b/python_client/docs/IndexingSettings.html @@ -0,0 +1,14 @@ + IndexingSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

IndexingSettings

Settings for crystallography indexing

Properties

Name

Type

Description

Notes

algorithm

IndexingAlgorithm

[default to IndexingAlgorithm.FFBIDX]

fft_max_unit_cell_a

float

Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT

[default to 250]

fft_min_unit_cell_a

float

Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT

[default to 10.0]

fft_high_resolution_a

float

Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT. There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems.

[default to 2.0]

fft_num_vectors

int

Number of search directions for the FFT algorithm; parameter value affects execution time of FFT.

[default to 16384]

tolerance

float

Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted

thread_count

int

Thread count for indexing algorithm

geom_refinement_algorithm

GeomRefinementAlgorithm

unit_cell_dist_tolerance

float

Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored

[default to 0.05]

viable_cell_min_spots

int

Minimum number of indexed spots required for a cell to be considered viable

[default to 10]

index_ice_rings

bool

Include spots marked as ice rings in the indexing run. If `dataset_settings` doesn’t have `detect_ice_rings` on, this option will have no effect on processing.

[default to False]

rotation_indexing

bool

[default to False]

rotation_indexing_min_angular_range_deg

float

[default to 20.0]

rotation_indexing_angular_stride_deg

float

[default to 0.5]

Example

from jfjoch_client.models.indexing_settings import IndexingSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of IndexingSettings from a JSON string
+indexing_settings_instance = IndexingSettings.from_json(json)
+# print the JSON string representation of the object
+print(IndexingSettings.to_json())
+
+# convert the object into a dict
+indexing_settings_dict = indexing_settings_instance.to_dict()
+# create an instance of IndexingSettings from a dict
+indexing_settings_from_dict = IndexingSettings.from_dict(indexing_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/InstrumentMetadata.html b/python_client/docs/InstrumentMetadata.html new file mode 100644 index 00000000..e8b68053 --- /dev/null +++ b/python_client/docs/InstrumentMetadata.html @@ -0,0 +1,14 @@ + InstrumentMetadata — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

InstrumentMetadata

Metadata for a measurement instrument

Properties

Name

Type

Description

Notes

source_name

str

source_type

str

Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource NXsource allows the following: Spallation Neutron Source Pulsed Reactor Neutron Source Reactor Neutron Source Synchrotron X-ray Source Pulsed Muon Source Rotating Anode X-ray Fixed Tube X-ray UV Laser Free-Electron Laser Optical Laser Ion Source UV Plasma Source Metal Jet X-ray

[optional] [default to ‘’]

instrument_name

str

pulsed_source

bool

Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)

[optional] [default to False]

electron_source

bool

Settings specific to electron source (e.g., wavelength definition)

[optional] [default to False]

Example

from jfjoch_client.models.instrument_metadata import InstrumentMetadata
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of InstrumentMetadata from a JSON string
+instrument_metadata_instance = InstrumentMetadata.from_json(json)
+# print the JSON string representation of the object
+print(InstrumentMetadata.to_json())
+
+# convert the object into a dict
+instrument_metadata_dict = instrument_metadata_instance.to_dict()
+# create an instance of InstrumentMetadata from a dict
+instrument_metadata_from_dict = InstrumentMetadata.from_dict(instrument_metadata_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/JfjochBrokerApi.html b/python_client/docs/JfjochBrokerApi.html new file mode 100644 index 00000000..961f9942 --- /dev/null +++ b/python_client/docs/JfjochBrokerApi.html @@ -0,0 +1,24 @@ + jfjoch_client.JfjochBrokerApi — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

jfjoch_client.JfjochBrokerApi

All URIs are relative to http://localhost:5232

Method

HTTP request

Description

config_zeromq_metadata_put

PUT /config/zeromq_metadata

Set ZeroMQ metadata settings

config_zeromq_metadata_put

config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings)

Set ZeroMQ metadata settings

Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images. Here settings of the socket can be adjusted. While the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.

Example

import jfjoch_client
+from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.JfjochBrokerApi(api_client)
+    zeromq_metadata_settings = jfjoch_client.ZeromqMetadataSettings() # ZeromqMetadataSettings |  (optional)
+
+    try:
+        # Set ZeroMQ metadata settings
+        api_instance.config_zeromq_metadata_put(zeromq_metadata_settings=zeromq_metadata_settings)
+    except Exception as e:
+        print("Exception when calling JfjochBrokerApi->config_zeromq_metadata_put: %s\n" % e)
+

Parameters

Name

Type

Description

Notes

zeromq_metadata_settings

ZeromqMetadataSettings

[optional]

Return type

void (empty response body)

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json

  • Accept: text/plain, application/json

HTTP response details

Status code

Description

Response headers

200

Everything OK

-

400

Input parsing or validation error

-

500

Error within Jungfraujoch code - see output message.

-

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\ No newline at end of file diff --git a/python_client/docs/JfjochSettings.html b/python_client/docs/JfjochSettings.html new file mode 100644 index 00000000..1857ad82 --- /dev/null +++ b/python_client/docs/JfjochSettings.html @@ -0,0 +1,14 @@ + JfjochSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

JfjochSettings

Default settings for Jungfraujoch software. This structure is used to provide default settings using configuration JSON file and is not used in HTTP.

Properties

Name

Type

Description

Notes

pcie

List[PcieDevicesInner]

[optional]

zeromq

ZeromqSettings

[optional]

instrument

InstrumentMetadata

[optional]

file_writer

FileWriterSettings

[optional]

detector

List[Detector]

indexing

IndexingSettings

[optional]

detector_settings

DetectorSettings

[optional]

azim_int

AzimIntSettings

[optional]

image_format

ImageFormatSettings

[optional]

image_buffer_mi_b

int

Size of internal buffer in MiB for images before they are sent to a stream

[optional] [default to 2048]

verbose

bool

Print extra debug information

[optional] [default to False]

receiver_threads

int

Number of threads used by the receiver

[optional] [default to 64]

numa_policy

str

NUMA policy to bind CPUs

[optional]

frontend_directory

str

Location of built JavaScript web frontend

ssl

JfjochSettingsSsl

[optional]

spot_finding

SpotFindingSettings

[optional]

image_pusher

ImagePusherType

[default to ImagePusherType.NONE]

zeromq_preview

ZeromqPreviewSettings

[optional]

zeromq_metadata

ZeromqMetadataSettings

[optional]

dark_mask

DarkMaskSettings

[optional]

Example

from jfjoch_client.models.jfjoch_settings import JfjochSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of JfjochSettings from a JSON string
+jfjoch_settings_instance = JfjochSettings.from_json(json)
+# print the JSON string representation of the object
+print(JfjochSettings.to_json())
+
+# convert the object into a dict
+jfjoch_settings_dict = jfjoch_settings_instance.to_dict()
+# create an instance of JfjochSettings from a dict
+jfjoch_settings_from_dict = JfjochSettings.from_dict(jfjoch_settings_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/JfjochSettingsSsl.html b/python_client/docs/JfjochSettingsSsl.html new file mode 100644 index 00000000..32172ec1 --- /dev/null +++ b/python_client/docs/JfjochSettingsSsl.html @@ -0,0 +1,14 @@ + JfjochSettingsSsl — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

JfjochSettingsSsl

Properties

Name

Type

Description

Notes

certificate

str

key

str

Example

from jfjoch_client.models.jfjoch_settings_ssl import JfjochSettingsSsl
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of JfjochSettingsSsl from a JSON string
+jfjoch_settings_ssl_instance = JfjochSettingsSsl.from_json(json)
+# print the JSON string representation of the object
+print(JfjochSettingsSsl.to_json())
+
+# convert the object into a dict
+jfjoch_settings_ssl_dict = jfjoch_settings_ssl_instance.to_dict()
+# create an instance of JfjochSettingsSsl from a dict
+jfjoch_settings_ssl_from_dict = JfjochSettingsSsl.from_dict(jfjoch_settings_ssl_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/JfjochStatistics.html b/python_client/docs/JfjochStatistics.html new file mode 100644 index 00000000..b96b4f08 --- /dev/null +++ b/python_client/docs/JfjochStatistics.html @@ -0,0 +1,14 @@ + JfjochStatistics — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

JfjochStatistics

Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker

Properties

Name

Type

Description

Notes

detector

DetectorStatus

[optional]

detector_list

DetectorList

[optional]

detector_settings

DetectorSettings

[optional]

image_format_settings

ImageFormatSettings

[optional]

instrument_metadata

InstrumentMetadata

[optional]

file_writer_settings

FileWriterSettings

[optional]

data_processing_settings

SpotFindingSettings

[optional]

measurement

MeasurementStatistics

[optional]

broker

BrokerStatus

[optional]

fpga

List[FpgaStatusInner]

[optional]

calibration

List[CalibrationStatisticsInner]

[optional]

zeromq_preview

ZeromqPreviewSettings

[optional]

zeromq_metadata

ZeromqMetadataSettings

[optional]

dark_mask

DarkMaskSettings

[optional]

pixel_mask

PixelMaskStatistics

[optional]

roi

RoiDefinitions

[optional]

az_int

AzimIntSettings

[optional]

buffer

ImageBufferStatus

[optional]

indexing

IndexingSettings

[optional]

Example

from jfjoch_client.models.jfjoch_statistics import JfjochStatistics
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of JfjochStatistics from a JSON string
+jfjoch_statistics_instance = JfjochStatistics.from_json(json)
+# print the JSON string representation of the object
+print(JfjochStatistics.to_json())
+
+# convert the object into a dict
+jfjoch_statistics_dict = jfjoch_statistics_instance.to_dict()
+# create an instance of JfjochStatistics from a dict
+jfjoch_statistics_from_dict = JfjochStatistics.from_dict(jfjoch_statistics_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/MeasurementStatistics.html b/python_client/docs/MeasurementStatistics.html new file mode 100644 index 00000000..886ad0c3 --- /dev/null +++ b/python_client/docs/MeasurementStatistics.html @@ -0,0 +1,14 @@ + MeasurementStatistics — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

MeasurementStatistics

Properties

Name

Type

Description

Notes

file_prefix

str

[optional]

run_number

int

Number of data collection run. This can be either automatically incremented or provided externally for each data collection.

[optional]

experiment_group

str

Name of group owning the data (e.g. p-group or proposal number).

[optional]

images_expected

int

[optional]

images_collected

int

Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.

[optional]

images_sent

int

Images sent to the writer. The value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.

[optional]

images_discarded_lossy_compression

int

Images discarded by the lossy compression filter

[optional]

max_image_number_sent

int

[optional]

collection_efficiency

float

[optional]

compression_ratio

float

[optional]

cancelled

bool

[optional]

max_receiver_delay

int

[optional]

indexing_rate

float

[optional]

detector_width

int

[optional]

detector_height

int

[optional]

detector_pixel_depth

int

[optional]

bkg_estimate

float

[optional]

unit_cell

str

[optional]

error_pixels

float

Moving average of 1000 images counting number of error pixels on the detector

[optional]

saturated_pixels

float

Moving average of 1000 images counting number of saturated pixels on the detector

[optional]

roi_beam_pixels

float

If there is an ROI defined with name &quot;beam&quot;, this number will hold moving average of 1000 images for number of valid pixels within this ROI

[optional]

roi_beam_sum

float

If there is an ROI defined with name &quot;beam&quot;, this number will hold moving average of 1000 images for sum of valid pixels within this ROI

[optional]

Example

from jfjoch_client.models.measurement_statistics import MeasurementStatistics
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of MeasurementStatistics from a JSON string
+measurement_statistics_instance = MeasurementStatistics.from_json(json)
+# print the JSON string representation of the object
+print(MeasurementStatistics.to_json())
+
+# convert the object into a dict
+measurement_statistics_dict = measurement_statistics_instance.to_dict()
+# create an instance of MeasurementStatistics from a dict
+measurement_statistics_from_dict = MeasurementStatistics.from_dict(measurement_statistics_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/PcieDevicesInner.html b/python_client/docs/PcieDevicesInner.html new file mode 100644 index 00000000..74396108 --- /dev/null +++ b/python_client/docs/PcieDevicesInner.html @@ -0,0 +1,14 @@ + PcieDevicesInner — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

PcieDevicesInner

Properties

Name

Type

Description

Notes

blk

str

Block device name

[optional]

ipv4

str

IPv4 address of the block device

[optional]

Example

from jfjoch_client.models.pcie_devices_inner import PcieDevicesInner
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of PcieDevicesInner from a JSON string
+pcie_devices_inner_instance = PcieDevicesInner.from_json(json)
+# print the JSON string representation of the object
+print(PcieDevicesInner.to_json())
+
+# convert the object into a dict
+pcie_devices_inner_dict = pcie_devices_inner_instance.to_dict()
+# create an instance of PcieDevicesInner from a dict
+pcie_devices_inner_from_dict = PcieDevicesInner.from_dict(pcie_devices_inner_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/PixelMaskStatistics.html b/python_client/docs/PixelMaskStatistics.html new file mode 100644 index 00000000..be5dca4c --- /dev/null +++ b/python_client/docs/PixelMaskStatistics.html @@ -0,0 +1,14 @@ + PixelMaskStatistics — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

PixelMaskStatistics

Properties

Name

Type

Description

Notes

user_mask

int

Number of pixels masked using the user mask

[optional]

too_high_pedestal_rms

int

Number of pixels with G0 pedestal RMS higher than provided threshold

[optional]

wrong_gain

int

Number of pixels that show wrong gain level during the pedestal procedure

[optional]

Example

from jfjoch_client.models.pixel_mask_statistics import PixelMaskStatistics
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of PixelMaskStatistics from a JSON string
+pixel_mask_statistics_instance = PixelMaskStatistics.from_json(json)
+# print the JSON string representation of the object
+print(PixelMaskStatistics.to_json())
+
+# convert the object into a dict
+pixel_mask_statistics_dict = pixel_mask_statistics_instance.to_dict()
+# create an instance of PixelMaskStatistics from a dict
+pixel_mask_statistics_from_dict = PixelMaskStatistics.from_dict(pixel_mask_statistics_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/Plot.html b/python_client/docs/Plot.html new file mode 100644 index 00000000..bc5326ae --- /dev/null +++ b/python_client/docs/Plot.html @@ -0,0 +1,14 @@ + Plot — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

Plot

x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly

Properties

Name

Type

Description

Notes

title

str

[default to ‘’]

x

List[float]

y

List[Optional[float]]

z

List[Optional[float]]

[optional]

Example

from jfjoch_client.models.plot import Plot
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of Plot from a JSON string
+plot_instance = Plot.from_json(json)
+# print the JSON string representation of the object
+print(Plot.to_json())
+
+# convert the object into a dict
+plot_dict = plot_instance.to_dict()
+# create an instance of Plot from a dict
+plot_from_dict = Plot.from_dict(plot_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/PlotTypeEnum.html b/python_client/docs/PlotTypeEnum.html new file mode 100644 index 00000000..5d0f3bca --- /dev/null +++ b/python_client/docs/PlotTypeEnum.html @@ -0,0 +1 @@ + PlotTypeEnum — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

PlotTypeEnum

Enum

  • BKG_ESTIMATE (value: 'bkg_estimate')

  • AZINT (value: 'azint')

  • SPOT_COUNT (value: 'spot_count')

  • INDEXING_RATE (value: 'indexing_rate')

  • INDEXING_UNIT_CELL_LENGTH (value: 'indexing_unit_cell_length')

  • INDEXING_UNIT_CELL_ANGLE (value: 'indexing_unit_cell_angle')

  • ERROR_PIXELS (value: 'error_pixels')

  • IMAGE_COLLECTION_EFFICIENCY (value: 'image_collection_efficiency')

  • RECEIVER_DELAY (value: 'receiver_delay')

  • RECEIVER_FREE_SEND_BUF (value: 'receiver_free_send_buf')

  • STRONG_PIXELS (value: 'strong_pixels')

  • ROI_SUM (value: 'roi_sum')

  • ROI_MEAN (value: 'roi_mean')

  • ROI_MAX_COUNT (value: 'roi_max_count')

  • ROI_PIXELS (value: 'roi_pixels')

  • ROI_WEIGHTED_X (value: 'roi_weighted_x')

  • ROI_WEIGHTED_Y (value: 'roi_weighted_y')

  • PACKETS_RECEIVED (value: 'packets_received')

  • MAX_PIXEL_VALUE (value: 'max_pixel_value')

  • RESOLUTION_ESTIMATE (value: 'resolution_estimate')

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/PlotUnitX.html b/python_client/docs/PlotUnitX.html new file mode 100644 index 00000000..5845b1c4 --- /dev/null +++ b/python_client/docs/PlotUnitX.html @@ -0,0 +1 @@ + PlotUnitX — Jungfraujoch 1.0.0-rc.126 documentation Skip to content
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Plots

Properties

Name

Type

Description

Notes

title

str

[optional]

unit_x

PlotUnitX

[default to PlotUnitX.IMAGE_NUMBER]

size_x

float

Max X range of the plot

[optional]

size_y

float

Max Y range of the plot

[optional]

plot

List[Plot]

Example

from jfjoch_client.models.plots import Plots
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of Plots from a JSON string
+plots_instance = Plots.from_json(json)
+# print the JSON string representation of the object
+print(Plots.to_json())
+
+# convert the object into a dict
+plots_dict = plots_instance.to_dict()
+# create an instance of Plots from a dict
+plots_from_dict = Plots.from_dict(plots_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/PreviewSettings.html b/python_client/docs/PreviewSettings.html new file mode 100644 index 00000000..74177bba --- /dev/null +++ b/python_client/docs/PreviewSettings.html @@ -0,0 +1,14 @@ + PreviewSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

PreviewSettings

Settings for JPEG rendering of preview images

Properties

Name

Type

Description

Notes

saturation

int

Saturation value to set contrast in the preview image

show_spots

bool

Show spot finding results on the image

[optional] [default to True]

show_roi

bool

Show ROI areas on the image

[optional] [default to False]

jpeg_quality

int

Quality of JPEG image (100 - highest; 0 - lowest)

[optional] [default to 100]

show_indexed

bool

Preview indexed images only

[optional] [default to False]

show_user_mask

bool

Show user mask

[optional] [default to False]

resolution_ring

float

[optional] [default to 0.1]

Example

from jfjoch_client.models.preview_settings import PreviewSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of PreviewSettings from a JSON string
+preview_settings_instance = PreviewSettings.from_json(json)
+# print the JSON string representation of the object
+print(PreviewSettings.to_json())
+
+# convert the object into a dict
+preview_settings_dict = preview_settings_instance.to_dict()
+# create an instance of PreviewSettings from a dict
+preview_settings_from_dict = PreviewSettings.from_dict(preview_settings_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/RoiAzimList.html b/python_client/docs/RoiAzimList.html new file mode 100644 index 00000000..cc913ab5 --- /dev/null +++ b/python_client/docs/RoiAzimList.html @@ -0,0 +1,14 @@ + RoiAzimList — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiAzimList

List of azimuthal ROIs

Properties

Name

Type

Description

Notes

rois

List[RoiAzimuthal]

[optional]

Example

from jfjoch_client.models.roi_azim_list import RoiAzimList
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiAzimList from a JSON string
+roi_azim_list_instance = RoiAzimList.from_json(json)
+# print the JSON string representation of the object
+print(RoiAzimList.to_json())
+
+# convert the object into a dict
+roi_azim_list_dict = roi_azim_list_instance.to_dict()
+# create an instance of RoiAzimList from a dict
+roi_azim_list_from_dict = RoiAzimList.from_dict(roi_azim_list_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/RoiAzimuthal.html b/python_client/docs/RoiAzimuthal.html new file mode 100644 index 00000000..8d2e1621 --- /dev/null +++ b/python_client/docs/RoiAzimuthal.html @@ -0,0 +1,14 @@ + RoiAzimuthal — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiAzimuthal

ROI as Q-range (or resolution range)

Properties

Name

Type

Description

Notes

name

str

Name for the ROI; used in the plots

q_min_recip_a

float

Minimum Q-range for the ROI

q_max_recip_a

float

Maximum Q-range for the ROI

Example

from jfjoch_client.models.roi_azimuthal import RoiAzimuthal
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiAzimuthal from a JSON string
+roi_azimuthal_instance = RoiAzimuthal.from_json(json)
+# print the JSON string representation of the object
+print(RoiAzimuthal.to_json())
+
+# convert the object into a dict
+roi_azimuthal_dict = roi_azimuthal_instance.to_dict()
+# create an instance of RoiAzimuthal from a dict
+roi_azimuthal_from_dict = RoiAzimuthal.from_dict(roi_azimuthal_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/RoiBox.html b/python_client/docs/RoiBox.html new file mode 100644 index 00000000..bfdd6a7a --- /dev/null +++ b/python_client/docs/RoiBox.html @@ -0,0 +1,14 @@ + RoiBox — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiBox

Box ROI

Properties

Name

Type

Description

Notes

name

str

Name for the ROI; used in the plots

min_x_pxl

int

Lower bound (inclusive) in X coordinate for the box

max_x_pxl

int

Upper bound (inclusive) in X coordinate for the box

min_y_pxl

int

Lower bound (inclusive) in Y coordinate for the box

max_y_pxl

int

Upper bound (inclusive) in Y coordinate for the box

Example

from jfjoch_client.models.roi_box import RoiBox
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiBox from a JSON string
+roi_box_instance = RoiBox.from_json(json)
+# print the JSON string representation of the object
+print(RoiBox.to_json())
+
+# convert the object into a dict
+roi_box_dict = roi_box_instance.to_dict()
+# create an instance of RoiBox from a dict
+roi_box_from_dict = RoiBox.from_dict(roi_box_dict)
+

[Back to Model list] [Back to API list] [Back to README]

\ No newline at end of file diff --git a/python_client/docs/RoiBoxList.html b/python_client/docs/RoiBoxList.html new file mode 100644 index 00000000..3b22833d --- /dev/null +++ b/python_client/docs/RoiBoxList.html @@ -0,0 +1,14 @@ + RoiBoxList — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiBoxList

List of box ROIs

Properties

Name

Type

Description

Notes

rois

List[RoiBox]

[optional]

Example

from jfjoch_client.models.roi_box_list import RoiBoxList
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiBoxList from a JSON string
+roi_box_list_instance = RoiBoxList.from_json(json)
+# print the JSON string representation of the object
+print(RoiBoxList.to_json())
+
+# convert the object into a dict
+roi_box_list_dict = roi_box_list_instance.to_dict()
+# create an instance of RoiBoxList from a dict
+roi_box_list_from_dict = RoiBoxList.from_dict(roi_box_list_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/RoiCircle.html b/python_client/docs/RoiCircle.html new file mode 100644 index 00000000..372525a8 --- /dev/null +++ b/python_client/docs/RoiCircle.html @@ -0,0 +1,14 @@ + RoiCircle — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiCircle

Circular ROI

Properties

Name

Type

Description

Notes

name

str

Name for the ROI; used in the plots

center_x_pxl

float

X coordinate of center of the circle [pixels]

center_y_pxl

float

Y coordinate of center of the circle [pixels]

radius_pxl

float

Radius of the circle [pixels]

Example

from jfjoch_client.models.roi_circle import RoiCircle
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiCircle from a JSON string
+roi_circle_instance = RoiCircle.from_json(json)
+# print the JSON string representation of the object
+print(RoiCircle.to_json())
+
+# convert the object into a dict
+roi_circle_dict = roi_circle_instance.to_dict()
+# create an instance of RoiCircle from a dict
+roi_circle_from_dict = RoiCircle.from_dict(roi_circle_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/RoiCircleList.html b/python_client/docs/RoiCircleList.html new file mode 100644 index 00000000..19db291f --- /dev/null +++ b/python_client/docs/RoiCircleList.html @@ -0,0 +1,14 @@ + RoiCircleList — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiCircleList

List of circular ROIs

Properties

Name

Type

Description

Notes

rois

List[RoiCircle]

Example

from jfjoch_client.models.roi_circle_list import RoiCircleList
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiCircleList from a JSON string
+roi_circle_list_instance = RoiCircleList.from_json(json)
+# print the JSON string representation of the object
+print(RoiCircleList.to_json())
+
+# convert the object into a dict
+roi_circle_list_dict = roi_circle_list_instance.to_dict()
+# create an instance of RoiCircleList from a dict
+roi_circle_list_from_dict = RoiCircleList.from_dict(roi_circle_list_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/RoiDefinitions.html b/python_client/docs/RoiDefinitions.html new file mode 100644 index 00000000..a7762dab --- /dev/null +++ b/python_client/docs/RoiDefinitions.html @@ -0,0 +1,14 @@ + RoiDefinitions — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RoiDefinitions

ROI defintions

Properties

Name

Type

Description

Notes

box

RoiBoxList

circle

RoiCircleList

azim

RoiAzimList

Example

from jfjoch_client.models.roi_definitions import RoiDefinitions
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RoiDefinitions from a JSON string
+roi_definitions_instance = RoiDefinitions.from_json(json)
+# print the JSON string representation of the object
+print(RoiDefinitions.to_json())
+
+# convert the object into a dict
+roi_definitions_dict = roi_definitions_instance.to_dict()
+# create an instance of RoiDefinitions from a dict
+roi_definitions_from_dict = RoiDefinitions.from_dict(roi_definitions_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/RotationAxis.html b/python_client/docs/RotationAxis.html new file mode 100644 index 00000000..75dc241d --- /dev/null +++ b/python_client/docs/RotationAxis.html @@ -0,0 +1,14 @@ + RotationAxis — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

RotationAxis

Definition of a crystal rotation axis

Properties

Name

Type

Description

Notes

name

str

Name of rotation axis (e.g., omega, phi)

[optional] [default to ‘omega’]

step

float

Angle step (per image) in degrees

start

float

Start angle in degrees

[optional] [default to 0]

vector

List[float]

Rotation axis

helical_step_um

List[float]

Translation (per image) for helical scan

[optional]

screening_wedge_deg

float

Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)

[optional]

Example

from jfjoch_client.models.rotation_axis import RotationAxis
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RotationAxis from a JSON string
+rotation_axis_instance = RotationAxis.from_json(json)
+# print the JSON string representation of the object
+print(RotationAxis.to_json())
+
+# convert the object into a dict
+rotation_axis_dict = rotation_axis_instance.to_dict()
+# create an instance of RotationAxis from a dict
+rotation_axis_from_dict = RotationAxis.from_dict(rotation_axis_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ScanResult.html b/python_client/docs/ScanResult.html new file mode 100644 index 00000000..18e554ce --- /dev/null +++ b/python_client/docs/ScanResult.html @@ -0,0 +1,14 @@ + ScanResult — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ScanResult

Results of a scan

Properties

Name

Type

Description

Notes

file_prefix

str

[optional]

rotation_unit_cell

UnitCell

[optional]

rotation_crystal_lattice

List[float]

Real-space crystal lattice 3D vectors in Angstrom. Order is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)

[optional]

images

List[ScanResultImagesInner]

Example

from jfjoch_client.models.scan_result import ScanResult
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ScanResult from a JSON string
+scan_result_instance = ScanResult.from_json(json)
+# print the JSON string representation of the object
+print(ScanResult.to_json())
+
+# convert the object into a dict
+scan_result_dict = scan_result_instance.to_dict()
+# create an instance of ScanResult from a dict
+scan_result_from_dict = ScanResult.from_dict(scan_result_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ScanResultImagesInner.html b/python_client/docs/ScanResultImagesInner.html new file mode 100644 index 00000000..56b9ee7c --- /dev/null +++ b/python_client/docs/ScanResultImagesInner.html @@ -0,0 +1,14 @@ + ScanResultImagesInner — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ScanResultImagesInner

Properties

Name

Type

Description

Notes

efficiency

float

number

int

Detector image number for a given cell

nx

int

Cell position in X for grid scan

[optional]

ny

int

Cell position in Y for grid scan

[optional]

angle

float

Rotation angle associated with the image

[optional]

bkg

float

Background estimate

[optional]

spots

int

Spot count

[optional]

spots_low_res

int

Spot count in low resolution range

[optional]

spots_indexed

int

Spot count within indexing tolerance

[optional]

spots_ice

int

Spot count within common ice ring resolutions

[optional]

index

int

Indexing solution

[optional]

pr

float

Profile radius, i.e. how far reflections are from the Ewald sphere

[optional]

b

float

B-Factor estimate

[optional]

uc

UnitCell

[optional]

xfel_pulseid

int

XFEL pulse ID

[optional]

pixel_sum

int

Total sum of all pixels

[optional]

max

int

Max viable pixel

[optional]

sat

int

Number of saturated pixels

[optional]

err

int

Number of error pixels

[optional]

res

float

Diffraction resolution estimate

[optional]

Example

from jfjoch_client.models.scan_result_images_inner import ScanResultImagesInner
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ScanResultImagesInner from a JSON string
+scan_result_images_inner_instance = ScanResultImagesInner.from_json(json)
+# print the JSON string representation of the object
+print(ScanResultImagesInner.to_json())
+
+# convert the object into a dict
+scan_result_images_inner_dict = scan_result_images_inner_instance.to_dict()
+# create an instance of ScanResultImagesInner from a dict
+scan_result_images_inner_from_dict = ScanResultImagesInner.from_dict(scan_result_images_inner_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/SpotFindingSettings.html b/python_client/docs/SpotFindingSettings.html new file mode 100644 index 00000000..e81f14d0 --- /dev/null +++ b/python_client/docs/SpotFindingSettings.html @@ -0,0 +1,14 @@ + SpotFindingSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

SpotFindingSettings

Properties

Name

Type

Description

Notes

enable

bool

Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. Even if disabled spot finding information will still be send and written, though always with zero spots.

[default to True]

indexing

bool

Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.

[default to True]

signal_to_noise_threshold

float

photon_count_threshold

int

min_pix_per_spot

int

max_pix_per_spot

int

high_resolution_limit

float

High resolution limit for spot finding [Angstrom]

low_resolution_limit

float

Low resolution limit for spot finding [Angstrom]

high_resolution_limit_for_spot_count_low_res

float

High resolution threshold to consider spot &quot;low resolution&quot; [Angstrom]

quick_integration

bool

Quick integration of Bragg spots in diffraction images. If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate. (experimental feature)

[default to False]

ice_ring_width_q_recip_a

float

Width of ice ring in q-space in reciprocal space

[default to 0.02]

high_res_gap_q_recip_a

float

This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector. If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter. This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.

[optional] [default to 1.5]

Example

from jfjoch_client.models.spot_finding_settings import SpotFindingSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of SpotFindingSettings from a JSON string
+spot_finding_settings_instance = SpotFindingSettings.from_json(json)
+# print the JSON string representation of the object
+print(SpotFindingSettings.to_json())
+
+# convert the object into a dict
+spot_finding_settings_dict = spot_finding_settings_instance.to_dict()
+# create an instance of SpotFindingSettings from a dict
+spot_finding_settings_from_dict = SpotFindingSettings.from_dict(spot_finding_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/StandardDetectorGeometry.html b/python_client/docs/StandardDetectorGeometry.html new file mode 100644 index 00000000..4e9f8ba2 --- /dev/null +++ b/python_client/docs/StandardDetectorGeometry.html @@ -0,0 +1,14 @@ + StandardDetectorGeometry — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

StandardDetectorGeometry

Regular rectangular geometry, first module is in the bottom left corner of the detector

Properties

Name

Type

Description

Notes

nmodules

int

Number of modules in the detector

gap_x

int

Gap size in X direction [pixels]

[optional] [default to 8]

gap_y

int

Gap size in Y direction [pixels]

[optional] [default to 36]

modules_in_row

int

Number of modules in one row

[optional] [default to 1]

Example

from jfjoch_client.models.standard_detector_geometry import StandardDetectorGeometry
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of StandardDetectorGeometry from a JSON string
+standard_detector_geometry_instance = StandardDetectorGeometry.from_json(json)
+# print the JSON string representation of the object
+print(StandardDetectorGeometry.to_json())
+
+# convert the object into a dict
+standard_detector_geometry_dict = standard_detector_geometry_instance.to_dict()
+# create an instance of StandardDetectorGeometry from a dict
+standard_detector_geometry_from_dict = StandardDetectorGeometry.from_dict(standard_detector_geometry_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/UnitCell.html b/python_client/docs/UnitCell.html new file mode 100644 index 00000000..da92e4a6 --- /dev/null +++ b/python_client/docs/UnitCell.html @@ -0,0 +1,14 @@ + UnitCell — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

UnitCell

Unit cell parameters. Necessary to run indexing. Units of angstrom and degree

Properties

Name

Type

Description

Notes

a

float

b

float

c

float

alpha

float

beta

float

gamma

float

Example

from jfjoch_client.models.unit_cell import UnitCell
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of UnitCell from a JSON string
+unit_cell_instance = UnitCell.from_json(json)
+# print the JSON string representation of the object
+print(UnitCell.to_json())
+
+# convert the object into a dict
+unit_cell_dict = unit_cell_instance.to_dict()
+# create an instance of UnitCell from a dict
+unit_cell_from_dict = UnitCell.from_dict(unit_cell_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ZeromqMetadataSettings.html b/python_client/docs/ZeromqMetadataSettings.html new file mode 100644 index 00000000..c419646e --- /dev/null +++ b/python_client/docs/ZeromqMetadataSettings.html @@ -0,0 +1,14 @@ + ZeromqMetadataSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ZeromqMetadataSettings

Properties

Name

Type

Description

Notes

enabled

bool

ZeroMQ metadata socket is enabled.

[default to True]

period_ms

int

Period for generating metadata package sent to the ZeroMQ interface in milliseconds.

[default to 1000]

socket_address

str

PUB ZeroMQ socket for image metadata information. Image metadata are serialized using CBOR. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

[optional]

Example

from jfjoch_client.models.zeromq_metadata_settings import ZeromqMetadataSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ZeromqMetadataSettings from a JSON string
+zeromq_metadata_settings_instance = ZeromqMetadataSettings.from_json(json)
+# print the JSON string representation of the object
+print(ZeromqMetadataSettings.to_json())
+
+# convert the object into a dict
+zeromq_metadata_settings_dict = zeromq_metadata_settings_instance.to_dict()
+# create an instance of ZeromqMetadataSettings from a dict
+zeromq_metadata_settings_from_dict = ZeromqMetadataSettings.from_dict(zeromq_metadata_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ZeromqPreviewSettings.html b/python_client/docs/ZeromqPreviewSettings.html new file mode 100644 index 00000000..08eaaba8 --- /dev/null +++ b/python_client/docs/ZeromqPreviewSettings.html @@ -0,0 +1,14 @@ + ZeromqPreviewSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ZeromqPreviewSettings

Properties

Name

Type

Description

Notes

enabled

bool

ZeroMQ preview socket is enabled.

[default to True]

period_ms

int

Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection). This has no effect on HTTP based preview, which updates always at rate of 1 second.

[default to 1000]

socket_address

str

PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate. Images are serialized using CBOR. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

[optional]

Example

from jfjoch_client.models.zeromq_preview_settings import ZeromqPreviewSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ZeromqPreviewSettings from a JSON string
+zeromq_preview_settings_instance = ZeromqPreviewSettings.from_json(json)
+# print the JSON string representation of the object
+print(ZeromqPreviewSettings.to_json())
+
+# convert the object into a dict
+zeromq_preview_settings_dict = zeromq_preview_settings_instance.to_dict()
+# create an instance of ZeromqPreviewSettings from a dict
+zeromq_preview_settings_from_dict = ZeromqPreviewSettings.from_dict(zeromq_preview_settings_dict)
+

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\ No newline at end of file diff --git a/python_client/docs/ZeromqSettings.html b/python_client/docs/ZeromqSettings.html new file mode 100644 index 00000000..75381b8f --- /dev/null +++ b/python_client/docs/ZeromqSettings.html @@ -0,0 +1,14 @@ + ZeromqSettings — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

ZeromqSettings

ZeroMQ configuration for Jungfraujoch software. This structure is used to provide default settings using configuration JSON file and is not used in HTTP.

Properties

Name

Type

Description

Notes

send_watermark

int

Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)

[optional] [default to 100]

send_buffer_size

int

Send buffer size for ZeroMQ socket

[optional]

image_socket

List[str]

PUSH ZeroMQ socket for images. In case multiple sockets are provided, images are streamed over multiple sockets. Images are serialized using CBOR. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.

[optional]

writer_notification_socket

str

PULL ZeroMQ socket for notifications from writer that it finished operation. This allows Jungfraujoch to operate in a synchronous manner, with end of acquisition being also end of writing. Address follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tpc://<IP address>:<port> sockets are OK. 0.0.0.0 instead of IP address should be avoided, as this socket address is forwarded to the writer process via START ZerOMQ message and in case of multiple ineterfaces the address might be ambigous. Using * (star) instead of port number is allowed and it means a random free port number.

[optional]

Example

from jfjoch_client.models.zeromq_settings import ZeromqSettings
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of ZeromqSettings from a JSON string
+zeromq_settings_instance = ZeromqSettings.from_json(json)
+# print the JSON string representation of the object
+print(ZeromqSettings.to_json())
+
+# convert the object into a dict
+zeromq_settings_dict = zeromq_settings_instance.to_dict()
+# create an instance of ZeromqSettings from a dict
+zeromq_settings_from_dict = ZeromqSettings.from_dict(zeromq_settings_dict)
+

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\ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 00000000..17264478 --- /dev/null +++ b/search.html @@ -0,0 +1 @@ + Search — Jungfraujoch 1.0.0-rc.126 documentation Skip to content

Search

Please activate JavaScript to enable the search functionality.

\ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 00000000..4255514b --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"1.0.0": [[2, "id1"]], "1.0.0-rc.100": [[2, "rc-100"]], "1.0.0-rc.101": [[2, "rc-101"]], "1.0.0-rc.102": [[2, "rc-102"]], "1.0.0-rc.103": [[2, "rc-103"]], "1.0.0-rc.104": [[2, "rc-104"]], "1.0.0-rc.105": [[2, "rc-105"]], "1.0.0-rc.106": [[2, "rc-106"]], "1.0.0-rc.107": [[2, "rc-107"]], "1.0.0-rc.108": [[2, "rc-108"]], "1.0.0-rc.109": [[2, "rc-109"]], "1.0.0-rc.110": [[2, "rc-110"]], "1.0.0-rc.111": [[2, "rc-111"]], "1.0.0-rc.112": [[2, "rc-112"]], "1.0.0-rc.113": [[2, "rc-113"]], "1.0.0-rc.114": [[2, "rc-114"]], "1.0.0-rc.115": [[2, "rc-115"]], "1.0.0-rc.116": [[2, "rc-116"]], "1.0.0-rc.117": [[2, "rc-117"]], "1.0.0-rc.118": [[2, "rc-118"]], "1.0.0-rc.119": [[2, "rc-119"]], "1.0.0-rc.120": [[2, "rc-120"]], "1.0.0-rc.121": [[2, "rc-121"]], "1.0.0-rc.122": [[2, "rc-122"]], "1.0.0-rc.123": 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