leonarski_fandClaude Opus 5
61a7c91b90
The per-image ice score was read off the PLAIN azimuthal profile. That profile is a per-ring mean, so a few strong Bragg reflections landing in a ring's q bin lift it exactly as ice would. Measured over 37 rotation crystals, that did not merely add noise - it INVERTED the metric: the two highest-scoring crystals had no ice at all (4.23 and 4.06), while a clean control read 1.57. A decoy null - the identical statistic evaluated at q positions where hexagonal ice cannot be - reaches 1.51 at its 99th percentile and 2.70 at its maximum, so that metric cannot support any absolute threshold whatsoever. The adaptive spot finder already computes the right input for its own threshold: a sigma-clipped per-resolution-ring background, in the same bins. A powder ring is azimuthally smooth and survives the clip; Bragg peaks do not. On the clipped profile the clean population tightens to 1.00-1.22 and the crystals with confirmed ice sit at 2.08-2.37, against a decoy null that never exceeds 1.29. That channel is blind to one thing: ice in large crystallites diffracts as DISCRETE spots and leaves the radial profile flat. So a second channel counts found spots on the rings against the same q width of ice-free flanks beside them. The two barely overlap - the smooth-ice crystals read 2.1-2.4 / ~1.0 and the textured ones ~1.1 / 3.8-17.6, while a clean crystal reads 1.04 on both. Both are then used as a GATE (--ice-min-score 1.5, --ice-min-spot-ratio 2.0, both calibrated on the battery, 0 disables): the eleven fixed hexagonal bands cover 16-26 % of the unique reflections at typical resolutions whether or not the crystal has ice, so flagging, the exclusion from the scale fit and the merge-time CC1/2 ring mask are now all skipped when neither channel sees any. The gate is applied in the full pipeline and in --scale, which reads the stored per-image values back out of the _process.h5. Also fixes the merge-time mask's control: the shoulder now excludes reflections that are themselves on an ice ring. The rings are not evenly spaced - 1.947/1.916/1.882 A sit 0.05-0.06 apart in q - so for those three the [w,3w) shoulder landed squarely on the neighbours and the test compared ice against ice. Measured, that is the only thing this changes: it removes firings on those three rings and leaves every other firing's CC pair identical to three decimals. And the online ice half-width, which was 0.02 in the API against 0.03 offline, so the same data got a narrower band online than the measured ~0.06 ring FWHM justifies. Battery (37 rotation crystals, against the previous behaviour): space groups 34/37 in both and NO crystal's space group changes; 6 crystals gain unique reflections, 1 loses. Best of them gains 7082 unique reflections with R_meas 16.0 -> 14.3, CC1/2 95.9 -> 97.3 and ISa 13.7 -> 19.0; another goes R_meas 54.9 -> 42.9, CC1/2 84.0 -> 90.4, ISa 3.9 -> 5.5; a third reaches CC1/2 99.4 from 95.7 at an unchanged reflection count. The one crystal that loses reflections improves on both R_meas and CC1/2. Not done here: the ScanResult/API/plot-type/frontend/viewer layers for the new spot_count_ice_control (they need the OpenAPI regeneration). Message, CBOR, HDF5 write/read and the receiver plots are. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
3707 lines
124 KiB
YAML
3707 lines
124 KiB
YAML
openapi: 3.0.3
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info:
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title: Jungfraujoch
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description: |
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API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).
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Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.
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Jungfraujoch uses FPGA boards to acquire data at high data rates.
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# License Clarification
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While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**
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when this file is used solely to generate OpenAPI clients or when implementing applications that
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interact with the API. Generated client code and applications using this API definition are not
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subject to the GPL license requirements and may be distributed under terms of your choosing.
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This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and
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the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that
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user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not
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derivative works of the kernel and are not subject to the terms of the GPL.
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This exception is intended to allow wider use of this API specification without imposing GPL
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requirements on applications that merely interact with the API, regardless of whether they
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communicate through network calls or other mechanisms.
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version: 1.0.0-rc.161
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contact:
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name: Filip Leonarski (Paul Scherrer Institute)
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email: filip.leonarski@psi.ch
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license:
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name: GPL-3.0
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url: https://www.gnu.org/licenses/gpl-3.0.html
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servers:
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- url: http://localhost:5232
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description: Test Jungfraujoch system
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components:
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parameters:
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binning:
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in: query
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name: binning
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required: false
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schema:
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default: 1
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type: integer
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description: Binning of frames for the plot (0 = default binning)
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experimental_coord:
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in: query
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name: experimental_coord
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required: false
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schema:
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type: boolean
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default: false
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description: |
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If measurement has goniometer axis defined, plot X-axis will represent rotation angle
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If measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value
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For still measurement the number is ignored
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azint_unit:
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in: query
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name: azint_unit
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required: false
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schema:
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type: string
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enum:
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- "Q_recipA"
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- "d_A"
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- "two_theta_deg"
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default: "Q_recipA"
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description: |
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Unit used for azim int.
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fill_value:
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in: query
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name: fill
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required: false
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schema:
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type: number
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format: float
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description: |
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Fill value for elements that were missed during data collection
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plot_type:
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in: query
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name: type
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required: true
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description: Type of requested plot
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schema:
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type: string
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enum:
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- bkg_estimate
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- azint
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- azint_1d
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- spot_count
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- spot_count_low_res
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- spot_count_indexed
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- spot_count_ice
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- indexing_rate
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- indexing_lattice_count
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- indexing_unit_cell_length
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- indexing_unit_cell_angle
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- profile_radius
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- mosaicity
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- b_factor
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- error_pixels
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- saturated_pixels
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- image_collection_efficiency
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- receiver_delay
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- receiver_free_send_buf
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- strong_pixels
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- roi_sum
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- roi_mean
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- roi_max_count
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- roi_pixels
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- roi_weighted_x
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- roi_weighted_y
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- packets_received
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- max_pixel_value
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- resolution_estimate
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- pixel_sum
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- processing_time
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- beam_center_x
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- beam_center_y
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- integrated_reflections
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- image_scale_factor
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- image_scale_cc
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- compression_ratio
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- ice_ring_score
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roi:
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in: query
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name: roi
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required: false
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schema:
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type: string
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minLength: 1
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description: Name of ROI for which plot is requested
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image_id:
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in: query
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name: id
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required: false
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schema:
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type: integer
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format: int64
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default: -1
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minimum: -2
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description: "Image ID in the image buffer. Special values: -1 - last image in the buffer, -2: last indexed image in the buffer"
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saturation:
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in: query
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name: saturation
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required: false
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schema:
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type: number
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format: float
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minimum: -32767
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maximum: 32767
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description: "Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used"
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background:
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in: query
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name: background
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required: false
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schema:
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type: number
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format: float
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default: 0
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minimum: -32767
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maximum: 32767
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description: "Background value to set contrast in the preview image"
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show_spots:
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in: query
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name: show_spots
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schema:
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type: boolean
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default: true
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description: "Show spot finding results on the image"
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show_predictions:
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in: query
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name: show_predictions
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schema:
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type: boolean
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default: false
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description: "Show Bragg spot predictions on the image (if available for the image)"
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show_beam_center:
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in: query
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name: show_beam_center
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schema:
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type: boolean
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default: true
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description: "Show beam center on the image"
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show_roi:
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in: query
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name: show_roi
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schema:
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type: boolean
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default: false
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description: "Show ROI areas on the image"
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jpeg_quality:
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in: query
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name: jpeg_quality
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description: "Quality of JPEG image (100 - highest; 0 - lowest)"
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schema:
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type: integer
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format: int64
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default: 100
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minimum: 0
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maximum: 100
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show_user_mask:
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in: query
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name: show_user_mask
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schema:
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type: boolean
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default: false
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description: "Show user mask"
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resolution_ring:
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in: query
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name: show_res_ring
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description: "Show resolution ring, provided in Angstrom"
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schema:
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type: number
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format: float
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default: 0.1
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minimum: 0.1
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maximum: 100.0
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resolution_estimate:
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in: query
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name: show_res_est
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description: "Show resolution estimation as a ring"
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schema:
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type: boolean
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default: false
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color_scale:
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in: query
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name: color
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description: "Color scale for preview image"
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schema:
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type: string
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enum:
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- "indigo"
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- "viridis"
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- "bw"
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- "wb"
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- "green"
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- "heat"
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- "magma"
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- "inferno"
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default: "indigo"
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schemas:
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grid_scan:
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description: Definition of a grid scan (mutually exclusive with `rotation_axis`)
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type: object
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required:
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- n_fast
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- step_x_um
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- step_y_um
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properties:
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n_fast:
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type: integer
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format: int64
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minimum: 1
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example: 20
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description: Number of elements in the fast direction
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step_x_um:
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type: number
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format: float
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example: 5.0
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description: |
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Step in grid along the fast direction. Can be negative.
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Positive number: left to right
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Negative number: right to left
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step_y_um:
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type: number
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format: float
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example: -3.0
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description: |
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Step in grid along the slow direction. Can be negative.
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Positive number: top to bottom
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Negative number: bottom to top
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vertical:
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type: boolean
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default: false
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description: |
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If disabled: fast direction = X, slow direction = Y
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If enabled: fast direction = Y, slow direction = X
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snake:
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type: boolean
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default: false
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description: |
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Flip fast direction for every second row
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rotation_axis:
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description: Definition of a crystal rotation axis
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type: object
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required:
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- step
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- vector
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properties:
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name:
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type: string
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default: omega
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minLength: 1
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description: Name of rotation axis (e.g., omega, phi)
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step:
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type: number
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format: float
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example: 0.1
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description: Angle step (per image) in degrees
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start:
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type: number
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format: float
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example: 50
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description: Start angle in degrees
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default: 0
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vector:
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type: array
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description: Rotation axis
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example: [ 1, 0, 0 ]
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items:
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type: number
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format: float
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minItems: 3
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maxItems: 3
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helical_step_um:
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type: array
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description: Translation (per image) for helical scan
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example: [ -5, -2, 0 ]
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items:
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type: number
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format: float
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minItems: 3
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maxItems: 3
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screening_wedge_deg:
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type: number
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format: float
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description: Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)
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indexing_algorithm:
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type: string
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description: |
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Selection of an indexing algorithm used by Jungfraujoch
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enum:
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- "FFBIDX"
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- "FFT"
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- "FFTW"
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- "Auto"
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- "None"
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default: "FFBIDX"
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geom_refinement_algorithm:
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type: string
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description: |
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Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
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BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
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OrientationOnly - This option is refining only orientation of the lattice.
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Flex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).
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enum:
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- "BeamCenter"
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- "OrientationOnly"
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- "Flex"
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- "None"
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integration_model:
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type: string
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description: |
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Bragg spot integration model.
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ProfileGaussian - profile fit with a measured-width Gaussian (Kabsch-style), the default; more
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accurate intensities than box summation.
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ProfileEmpirical - profile fit with a per-resolution-shell empirical profile learned from strong spots.
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BoxSum - classical uniform box summation minus a ring-mean background; the simpler, faster fallback.
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enum:
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- "ProfileGaussian"
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- "ProfileEmpirical"
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- "BoxSum"
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default: "ProfileGaussian"
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dataset_settings:
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type: object
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required:
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- beam_x_pxl
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- beam_y_pxl
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- detector_distance_mm
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- incident_energy_keV
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properties:
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images_per_trigger:
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type: integer
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format: int64
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minimum: 1
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default: 1
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description: |
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For standard synchrotron data collection - this is number of images collected per one TTL trigger
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For XFEL (pulsed source) - this number is ignored and set to 1
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For storage cell mode - this number is ignored and set to number of storage cells
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ntrigger:
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type: integer
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format: int64
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default: 1
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minimum: 1
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description: |
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Number of TTL trigger that the detector is expected to receive during data collection
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image_time_us:
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type: integer
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format: int64
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minimum: 0
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description: |
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Image time.
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If not provided (or zero value) the frame time is assumed as default.
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For JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.
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In XFEL mode: summation happens for frames collected with multiple triggers.
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Ignored for storage cells and if raw data are saved.
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beam_x_pxl:
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type: number
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format: float
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description: |
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/entry/detector/beam_center_x in NXmx
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Beam center in X direction [pixels]
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beam_y_pxl:
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type: number
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format: float
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description: |
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/entry/detector/beam_center_y in NXmx
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Beam center in X direction [pixels]
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detector_distance_mm:
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type: number
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format: float
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minimum: 0
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description:
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/entry/detector/distance in NXmx
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Detector distance [mm]
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incident_energy_keV:
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type: number
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format: float
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minimum: 0.001
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maximum: 500.0
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description: |
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Used to calculate /entry/beam/incident_wavelength in NXmx
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Incident particle (photon, electron) energy in keV
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file_prefix:
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type: string
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default: ""
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description: Prefix for filenames. If left empty, no file will be saved.
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images_per_file:
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type: integer
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format: int64
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minimum: 0
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default: 1000
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description: Number of files in a single HDF5 data file (0 = write all images to a single data file).
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space_group_number:
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type: integer
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format: int64
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minimum: 1
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maximum: 194
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description: Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.
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sample_name:
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type: string
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default: ""
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description: |
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/entry/sample/name in NXmx
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Sample name
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compression:
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type: string
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enum: [
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"bslz4",
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"bszstd",
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"bszstd_rle",
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"bszstd_rlehuf",
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"none"
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]
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default: "bslz4"
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description: |
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Compression type for the images transferred over ZeroMQ and saved to HDF5 file.
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total_flux:
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type: number
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format: float
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description: |
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/entry/beam/total_flux in NXmx
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Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]
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transmission:
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type: number
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format: float
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minimum: 0.0
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maximum: 1.0
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description: |
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/entry/instrument/attenuator/attenuator_transmission
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Transmission of attenuator (filter) [no units]
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goniometer:
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$ref: "#/components/schemas/rotation_axis"
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grid_scan:
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$ref: "#/components/schemas/grid_scan"
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header_appendix:
|
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description: |
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Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)
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In general, it is not saved in HDF5 file.
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However, if values are placed in "hdf5" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file.
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This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.
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For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.
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image_appendix:
|
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description: |
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Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)
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Not saved in HDF5 file
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data_reduction_factor_serialmx:
|
|
type: number
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format: float
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|
default: 1.0
|
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minimum: 0.0
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maximum: 1.0
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|
description: |
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Rate at which non-indexed images are accepted to be forwarded to writer.
|
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Value of 1.0 (default) means that all images are written.
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Values below zero mean that non-indexed images will be accepted with a given probability.
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pixel_value_low_threshold:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
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description: |
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Set all counts lower than the value to zero.
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When the value is set, negative numbers other than error pixel value are always set to zero.
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Setting to zero is equivalent to turning the option off.
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|
run_number:
|
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type: integer
|
|
format: int64
|
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minimum: 0
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description: |
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|
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:
|
|
type: string
|
|
description: |
|
|
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:
|
|
type: string
|
|
description: |
|
|
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:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
maximum: 16
|
|
description: |
|
|
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:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments
|
|
and to turn off for other experiments.
|
|
save_calibration:
|
|
type: boolean
|
|
description: |
|
|
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:
|
|
type: number
|
|
description: Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization
|
|
format: float
|
|
minimum: -1.0
|
|
maximum: 1.0
|
|
ring_current_mA:
|
|
type: number
|
|
format: float
|
|
description: Ring current at the beginning of the data collection
|
|
minimum: 0.0
|
|
sample_temperature_K:
|
|
type: number
|
|
format: float
|
|
description: Sample temperature in Kelvin
|
|
minimum: 0.0
|
|
poni_rot1_rad:
|
|
type: number
|
|
description: PONI angle rot1 (see PyFAI documentation for details) in radians
|
|
format: float
|
|
minimum: -6.28318530718
|
|
maximum: 6.28318530718
|
|
default: 0.0
|
|
poni_rot2_rad:
|
|
type: number
|
|
description: PONI angle rot2 (see PyFAI documentation for details) in radians
|
|
format: float
|
|
minimum: -6.28318530718
|
|
maximum: 6.28318530718
|
|
default: 0.0
|
|
poni_rot3_rad:
|
|
type: number
|
|
description: PONI angle rot3 (see PyFAI documentation for details) in radians
|
|
format: float
|
|
minimum: -6.28318530718
|
|
maximum: 6.28318530718
|
|
default: 0.0
|
|
unit_cell:
|
|
$ref: '#/components/schemas/unit_cell'
|
|
spot_finding:
|
|
type: boolean
|
|
description: Enable spot finding and save spots
|
|
default: true
|
|
smargon:
|
|
type: object
|
|
description: |
|
|
Geometry of Smargon goniometer at SLS 2.0 / MX beamlines.
|
|
Assuming that Smargon is used as static positioner and not moving during the scan, allowing to reconstruct geometry.
|
|
required:
|
|
- phi_deg
|
|
- chi_deg
|
|
properties:
|
|
phi_deg:
|
|
type: number
|
|
format: float
|
|
description: Phi angle in degrees
|
|
chi_deg:
|
|
minimum: 0.0
|
|
maximum: 90.0
|
|
type: number
|
|
format: float
|
|
description: Chi angle in degrees
|
|
phi_axis:
|
|
type: array
|
|
description: Phi rotation axis
|
|
default: [ 1, 0, 0 ]
|
|
example: [ 1, 0, 0 ]
|
|
items:
|
|
type: number
|
|
format: float
|
|
minItems: 3
|
|
maxItems: 3
|
|
chi_axis:
|
|
type: array
|
|
description: Chi rotation axis
|
|
default: [ 0, 0, 1 ]
|
|
example: [ 0, 0, 1 ]
|
|
items:
|
|
type: number
|
|
format: float
|
|
minItems: 3
|
|
maxItems: 3
|
|
max_spot_count:
|
|
type: integer
|
|
minimum: 10
|
|
maximum: 2000
|
|
default: 250
|
|
description: Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected
|
|
detect_ice_rings:
|
|
type: boolean
|
|
description: Flag spots as ice rings and reduce their effect on indexing
|
|
async_start:
|
|
type: boolean
|
|
default: false
|
|
description: When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement.
|
|
xray_fluorescence_spectrum:
|
|
type: object
|
|
required:
|
|
- energy_eV
|
|
- data
|
|
properties:
|
|
energy_eV:
|
|
type: array
|
|
items:
|
|
type: number
|
|
format: float
|
|
description: X-ray fluorescence scan energy for each measurement point
|
|
data:
|
|
type: array
|
|
items:
|
|
type: number
|
|
format: float
|
|
description: X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV
|
|
crystal_lattice:
|
|
type: array
|
|
items:
|
|
type: number
|
|
format: float
|
|
minItems: 9
|
|
maxItems: 9
|
|
description: |
|
|
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)
|
|
unit_cell:
|
|
type: object
|
|
description: Unit cell parameters. Necessary to run indexing. Units of angstrom and degree
|
|
required:
|
|
- a
|
|
- b
|
|
- c
|
|
- alpha
|
|
- beta
|
|
- gamma
|
|
properties:
|
|
a:
|
|
type: number
|
|
format: float
|
|
example: 37
|
|
minimum: 0
|
|
b:
|
|
type: number
|
|
format: float
|
|
example: 37
|
|
minimum: 0
|
|
c:
|
|
type: number
|
|
format: float
|
|
example: 78
|
|
minimum: 0
|
|
alpha:
|
|
type: number
|
|
format: float
|
|
example: 90
|
|
minimum: 0
|
|
maximum: 360
|
|
beta:
|
|
type: number
|
|
format: float
|
|
example: 90
|
|
minimum: 0
|
|
maximum: 360
|
|
gamma:
|
|
type: number
|
|
format: float
|
|
example: 90
|
|
minimum: 0
|
|
maximum: 360
|
|
file_writer_format:
|
|
type: string
|
|
enum:
|
|
- "NXmxOnlyData"
|
|
- "NXmxLegacy"
|
|
- "NXmxVDS"
|
|
- "NXmxIntegrated"
|
|
- "CBF"
|
|
- "TIFF"
|
|
- "NoFileWritten"
|
|
default: "NXmxLegacy"
|
|
description: |
|
|
NoFileWritten - no files are written at all
|
|
NXmxOnlyData - only data files are written, no master file
|
|
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
|
|
NXmxIntegrated - single HDF5 per dataset
|
|
CBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
|
|
TIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
|
|
file_writer_settings:
|
|
type: object
|
|
properties:
|
|
overwrite:
|
|
type: boolean
|
|
default: false
|
|
description: |
|
|
Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.
|
|
format:
|
|
$ref: '#/components/schemas/file_writer_format'
|
|
pixel_mask_statistics:
|
|
type: object
|
|
properties:
|
|
user_mask:
|
|
description: Number of pixels masked using the user mask
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
too_high_pedestal_rms:
|
|
description: Number of pixels with G0 pedestal RMS higher than provided threshold
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
wrong_gain:
|
|
description: Number of pixels that show wrong gain level during the pedestal procedure
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
image_buffer_status:
|
|
type: object
|
|
required:
|
|
- image_numbers
|
|
- total_slots
|
|
- in_preparation_slots
|
|
- in_sending_slots
|
|
- available_slots
|
|
- max_image_number
|
|
- min_image_number
|
|
properties:
|
|
min_image_number:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: Smallest image number available in the buffer
|
|
max_image_number:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: Largest image number available in the buffer
|
|
image_numbers:
|
|
type: array
|
|
description: Image numbers currently present in the buffer.
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
total_slots:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
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:
|
|
type: integer
|
|
format: int64
|
|
description: Slots available for the data collection
|
|
in_preparation_slots:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Number of slots in the image buffer that are currently in preparation for sending.
|
|
in_sending_slots:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Number of slots in the image buffer that are currently sending/writing data.
|
|
current_counter:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
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
|
|
image_format_settings:
|
|
type: object
|
|
required:
|
|
- summation
|
|
- jungfrau_conversion
|
|
- geometry_transform
|
|
- mask_chip_edges
|
|
- mask_module_edges
|
|
- apply_mask
|
|
properties:
|
|
summation:
|
|
type: boolean
|
|
description: |
|
|
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:
|
|
type: boolean
|
|
description: |
|
|
Place module read-out into their location on composed detector and extend multipixels
|
|
jungfrau_conversion:
|
|
type: boolean
|
|
description: |
|
|
Convert pixel value in ADU to photon counts/energy
|
|
Only affects JUNGFRAU detector
|
|
jungfrau_conversion_factor_keV:
|
|
type: number
|
|
format: float
|
|
minimum: 0.001
|
|
maximum: 500.0
|
|
description: |
|
|
Used to convert energy deposited into pixel to counts
|
|
If not provided incident_energy_keV is used
|
|
bit_depth_image:
|
|
type: integer
|
|
format: int64
|
|
enum: [8, 16, 32]
|
|
description: |
|
|
Bit depth of resulting image (it doesn't affect the detector read-out value)
|
|
If not provided value is adjusted automatically
|
|
signed_output:
|
|
type: boolean
|
|
description: |
|
|
Controls if pixels have signed output
|
|
If not provided value is adjusted automatically
|
|
mask_module_edges:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
Mask 1 pixel on the module boundary
|
|
mask_chip_edges:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
Mask multipixels on chip boundary
|
|
jungfrau_mask_pixels_without_g0:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
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:
|
|
type: boolean
|
|
default: false
|
|
description: |
|
|
Masked pixels are set to special value in the images produced by Jungfraujoch
|
|
jungfrau_pedestal_g0_rms_limit:
|
|
type: integer
|
|
format: int64
|
|
default: 100
|
|
minimum: 0
|
|
description: Pixels with pedestal G0 RMS above the threshold are marked as masked pixels
|
|
detector_power_state:
|
|
type: string
|
|
description: Power on of ASICs
|
|
enum: [ "PowerOn", "PowerOff", "Partial" ]
|
|
detector_state:
|
|
type: string
|
|
description: Current state of the detector
|
|
enum: [ "Idle", "Waiting", "Busy", "Error", "Not connected"]
|
|
detector_status:
|
|
type: object
|
|
required:
|
|
- state
|
|
- powerchip
|
|
- server_version
|
|
- number_of_triggers_left
|
|
- fpga_temp_degC
|
|
- high_voltage_V
|
|
properties:
|
|
state:
|
|
$ref: '#/components/schemas/detector_state'
|
|
powerchip:
|
|
$ref: '#/components/schemas/detector_power_state'
|
|
server_version:
|
|
type: string
|
|
description: Detector server (on read-out boards) version
|
|
number_of_triggers_left:
|
|
type: integer
|
|
format: int64
|
|
description: Remaining triggers to the detector (max of all modules)
|
|
fpga_temp_degC:
|
|
type: array
|
|
description: Temperature of detector FPGAs
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
high_voltage_V:
|
|
type: array
|
|
description: High voltage for detector modules
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
detector_timing:
|
|
type: string
|
|
enum: [auto, trigger, burst, gated]
|
|
default: trigger
|
|
detector_settings:
|
|
type: object
|
|
required:
|
|
- frame_time_us
|
|
properties:
|
|
frame_time_us:
|
|
type: integer
|
|
description: |
|
|
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
|
|
format: int64
|
|
minimum: 1
|
|
count_time_us:
|
|
type: integer
|
|
description: |
|
|
Integration time of the detector.
|
|
If not provided count time will be set to maximum value for a given frame time.
|
|
format: int64
|
|
internal_frame_generator:
|
|
type: boolean
|
|
default: false
|
|
description: Use internal frame generator in FPGA instead of getting data from a real detector
|
|
internal_frame_generator_images:
|
|
type: integer
|
|
format: int64
|
|
default: 1
|
|
minimum: 1
|
|
maximum: 64
|
|
description: Number of images stored in the internal frame generator.
|
|
detector_trigger_delay_ns:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
default: 0
|
|
description: Delay between TTL trigger and acquisition start [ns]
|
|
timing:
|
|
$ref: '#/components/schemas/detector_timing'
|
|
eiger_threshold_keV:
|
|
type: number
|
|
format: float
|
|
minimum: 1.0
|
|
maximum: 100.0
|
|
description: |
|
|
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:
|
|
type: integer
|
|
format: int64
|
|
enum: [ 8, 16, 32 ]
|
|
description: |
|
|
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:
|
|
type: integer
|
|
format: int64
|
|
default: 2000
|
|
minimum: 0
|
|
jungfrau_pedestal_g1_frames:
|
|
type: integer
|
|
format: int64
|
|
default: 300
|
|
minimum: 0
|
|
jungfrau_pedestal_g2_frames:
|
|
type: integer
|
|
format: int64
|
|
default: 300
|
|
minimum: 0
|
|
jungfrau_pedestal_min_image_count:
|
|
type: integer
|
|
format: int64
|
|
default: 128
|
|
minimum: 32
|
|
description: Minimum number of collected images for pedestal to consider it viable
|
|
jungfrau_storage_cell_count:
|
|
type: integer
|
|
format: int64
|
|
default: 1
|
|
minimum: 1
|
|
maximum: 16
|
|
jungfrau_storage_cell_delay_ns:
|
|
type: integer
|
|
format: int64
|
|
minimum: 2100
|
|
default: 5000
|
|
description: Delay between two storage cells [ns]
|
|
jungfrau_fixed_gain_g1:
|
|
type: boolean
|
|
default: false
|
|
description: Fix gain to G1 (can be useful for storage cells)
|
|
jungfrau_use_gain_hg0:
|
|
type: boolean
|
|
default: false
|
|
description: Use high G0 (for low energy applications)
|
|
spot_finding_settings:
|
|
type: object
|
|
required:
|
|
- enable
|
|
- indexing
|
|
- signal_to_noise_threshold
|
|
- photon_count_threshold
|
|
- max_pix_per_spot
|
|
- min_pix_per_spot
|
|
- low_resolution_limit
|
|
- quick_integration
|
|
- high_resolution_limit_for_spot_count_low_res
|
|
- ice_ring_width_q_recipA
|
|
properties:
|
|
enable:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
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:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.
|
|
signal_to_noise_threshold:
|
|
type: number
|
|
format: float
|
|
minimum: 0
|
|
photon_count_threshold:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
min_pix_per_spot:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
max_pix_per_spot:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
high_resolution_limit:
|
|
type: number
|
|
format: float
|
|
description: |
|
|
High resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding extends
|
|
as far as the detector reaches, i.e. the detection is not clipped in resolution.
|
|
low_resolution_limit:
|
|
type: number
|
|
format: float
|
|
description: Low resolution limit for spot finding [Angstrom]
|
|
high_resolution_limit_for_spot_count_low_res:
|
|
type: number
|
|
format: float
|
|
description: High resolution threshold to consider spot "low resolution" [Angstrom]
|
|
minimum: 2.0
|
|
maximum: 8.0
|
|
quick_integration:
|
|
type: boolean
|
|
default: false
|
|
description: |
|
|
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:
|
|
type: number
|
|
format: float
|
|
minimum: 0.0
|
|
maximum: 1.0
|
|
default: 0.03
|
|
description: Half-width of the ice ring band in q (1/A). Matches the offline default in
|
|
image_analysis/spot_finding/SpotFindingSettings.h, which was set from a measured ring
|
|
FWHM of ~0.06; the two must agree or the same data gets a narrower ice band online.
|
|
high_res_gap_Q_recipA:
|
|
type: number
|
|
format: float
|
|
minimum: 0.1
|
|
maximum: 5.0
|
|
default: 1.5
|
|
description: |
|
|
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.
|
|
adaptive_threshold:
|
|
type: boolean
|
|
default: false
|
|
description: |
|
|
Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring
|
|
threshold derived from each image's own noise, so the same setting works across datasets without
|
|
per-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the
|
|
operating point instead.
|
|
Only available on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow).
|
|
The JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold,
|
|
so enabling this there is rejected rather than silently ignored.
|
|
false_pixels_per_frame:
|
|
type: number
|
|
format: float
|
|
minimum: 1.0
|
|
maximum: 100000.0
|
|
default: 100.0
|
|
description: |
|
|
Operating point of the adaptive threshold: the number of noise pixels tolerated per frame.
|
|
About 100 suits a multi-megapixel detector. Ignored unless adaptive_threshold is set.
|
|
azim_int_settings:
|
|
type: object
|
|
required:
|
|
- solid_angle_corr
|
|
- polarization_corr
|
|
- low_q_recipA
|
|
- q_spacing
|
|
properties:
|
|
polarization_corr:
|
|
type: boolean
|
|
description: Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)
|
|
default: true
|
|
solid_angle_corr:
|
|
type: boolean
|
|
description: Apply solid angle correction for azimuthal integration
|
|
default: true
|
|
high_q_recipA:
|
|
type: number
|
|
minimum: 2e-5
|
|
maximum: 10.0
|
|
format: float
|
|
description: |
|
|
Upper q limit of the azimuthal integration [1/Angstrom]. Optional: if omitted, the integration
|
|
(and the adaptive spot detection that shares these q bins) extends to the highest q the
|
|
detector reaches.
|
|
low_q_recipA:
|
|
type: number
|
|
format: float
|
|
minimum: 1e-5
|
|
maximum: 10
|
|
q_spacing:
|
|
type: number
|
|
format: float
|
|
minimum: 1e-5
|
|
azimuthal_bins:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
maximum: 512
|
|
default: 1
|
|
description: Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration
|
|
force_cpu:
|
|
type: boolean
|
|
default: false
|
|
description: |
|
|
Force CPU processing of azimuthal integration in the FPGA data acquisition workflow.
|
|
This allows to extend number of azimuthal integration bins, as well as to calculate standard deviation
|
|
of the azimuthal integration results.
|
|
detector_list_element:
|
|
type: object
|
|
required:
|
|
- id
|
|
- nmodules
|
|
- description
|
|
- width
|
|
- height
|
|
- serial_number
|
|
- base_ipv4_addr
|
|
- udp_interface_count
|
|
- readout_time_ns
|
|
- min_frame_time_ns
|
|
- min_count_time_ns
|
|
properties:
|
|
id:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description:
|
|
type: string
|
|
example: "JUNGFRAU 4 Mpixel"
|
|
serial_number:
|
|
type: string
|
|
example: "JF17T16V01"
|
|
base_ipv4_addr:
|
|
type: string
|
|
example: "10.10.10.1"
|
|
udp_interface_count:
|
|
type: integer
|
|
format: int64
|
|
example: 2
|
|
description: Number of UDP interfaces per detector module
|
|
nmodules:
|
|
type: integer
|
|
format: int64
|
|
example: 18
|
|
width:
|
|
type: integer
|
|
format: int64
|
|
example: 2068
|
|
height:
|
|
type: integer
|
|
format: int64
|
|
example: 2164
|
|
pixel_size_mm:
|
|
type: number
|
|
format: float
|
|
example: 0.075
|
|
readout_time_ns:
|
|
type: integer
|
|
format: int64
|
|
min_frame_time_ns:
|
|
type: integer
|
|
format: int64
|
|
min_count_time_ns:
|
|
type: integer
|
|
format: int64
|
|
type:
|
|
$ref: "#/components/schemas/detector_type"
|
|
detector_list:
|
|
type: object
|
|
required:
|
|
- detectors
|
|
- current_id
|
|
properties:
|
|
detectors:
|
|
type: array
|
|
items:
|
|
$ref: '#/components/schemas/detector_list_element'
|
|
current_id:
|
|
type: integer
|
|
format: int64
|
|
example: 0
|
|
detector_selection:
|
|
type: object
|
|
required:
|
|
- id
|
|
properties:
|
|
id:
|
|
type: integer
|
|
format: int64
|
|
example: 1
|
|
measurement_statistics:
|
|
type: object
|
|
properties:
|
|
file_prefix:
|
|
type: string
|
|
run_number:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Number of data collection run. This can be either automatically incremented or provided externally for each data collection.
|
|
experiment_group:
|
|
type: string
|
|
description: |
|
|
Name of group owning the data (e.g. p-group or proposal number).
|
|
images_expected:
|
|
type: integer
|
|
format: int64
|
|
images_collected:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.
|
|
images_sent:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
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.
|
|
images_written:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Images successfully written to disk.
|
|
The value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.
|
|
images_discarded_lossy_compression:
|
|
type: integer
|
|
format: int64
|
|
description: Images discarded by the lossy compression filter
|
|
max_image_number_sent:
|
|
type: integer
|
|
format: int64
|
|
collection_efficiency:
|
|
type: number
|
|
format: float
|
|
example: 1.0
|
|
minimum: 0.0
|
|
maximum: 1.0
|
|
compression_ratio:
|
|
type: number
|
|
format: float
|
|
example: 5.3
|
|
minimum: 0.0
|
|
cancelled:
|
|
type: boolean
|
|
max_receiver_delay:
|
|
type: integer
|
|
format: int64
|
|
indexing_rate:
|
|
type: number
|
|
format: float
|
|
detector_width:
|
|
type: integer
|
|
format: int64
|
|
detector_height:
|
|
type: integer
|
|
format: int64
|
|
detector_pixel_depth:
|
|
type: integer
|
|
format: int64
|
|
enum: [2, 4]
|
|
bkg_estimate:
|
|
type: number
|
|
format: float
|
|
unit_cell:
|
|
type: string
|
|
error_pixels:
|
|
type: number
|
|
format: float
|
|
description: Moving average of 1000 images counting number of error pixels on the detector
|
|
saturated_pixels:
|
|
type: number
|
|
format: float
|
|
description: Moving average of 1000 images counting number of saturated pixels on the detector
|
|
roi_beam_pixels:
|
|
type: number
|
|
format: float
|
|
description: |
|
|
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
|
|
roi_beam_sum:
|
|
type: number
|
|
format: float
|
|
description: |
|
|
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
|
|
fpga_status:
|
|
type: array
|
|
items:
|
|
type: object
|
|
required:
|
|
- pci_dev_id
|
|
- serial_number
|
|
- base_mac_addr
|
|
- eth_link_status
|
|
- eth_link_count
|
|
- eth_link_speed
|
|
- power_usage_W
|
|
- fpga_temp_C
|
|
- hbm_temp_C
|
|
- packets_sls
|
|
- packets_udp
|
|
- idle
|
|
- fw_version
|
|
- pcie_link_speed
|
|
- pcie_link_width
|
|
properties:
|
|
pci_dev_id:
|
|
type: string
|
|
serial_number:
|
|
type: string
|
|
fw_version:
|
|
type: string
|
|
base_mac_addr:
|
|
type: string
|
|
eth_link_count:
|
|
type: integer
|
|
format: int64
|
|
eth_link_status:
|
|
type: integer
|
|
format: int64
|
|
power_usage_W:
|
|
type: number
|
|
format: float
|
|
fpga_temp_C:
|
|
type: number
|
|
format: float
|
|
hbm_temp_C:
|
|
type: number
|
|
format: float
|
|
packets_udp:
|
|
type: integer
|
|
format: int64
|
|
packets_sls:
|
|
type: integer
|
|
format: int64
|
|
idle:
|
|
type: boolean
|
|
pcie_link_speed:
|
|
type: integer
|
|
format: int64
|
|
description: PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)
|
|
pcie_link_width:
|
|
type: integer
|
|
format: int64
|
|
description: PCIe link width (expected value is 8 == x8)
|
|
broker_status:
|
|
type: object
|
|
required:
|
|
- state
|
|
properties:
|
|
state:
|
|
type: string
|
|
enum: ["Inactive", "Idle", "Busy", "Measuring", "Pedestal", "Error"]
|
|
progress:
|
|
type: number
|
|
format: float
|
|
description: Progress of data collection (only available if receiving is running)
|
|
example: 1.0
|
|
minimum: 0.0
|
|
maximum: 1.0
|
|
message:
|
|
type: string
|
|
description: |
|
|
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.
|
|
message_severity:
|
|
type: string
|
|
enum: ["success", "info", "warning", "error"]
|
|
default: "error"
|
|
description: Level of the message to display
|
|
gpu_count:
|
|
type: integer
|
|
format: int32
|
|
description: Number of installed GPUs
|
|
broker_version:
|
|
type: string
|
|
description: Version of the jfjoch_broker
|
|
example: "1.0.0-rc.128"
|
|
image_pusher_status:
|
|
type: object
|
|
required:
|
|
- pusher_type
|
|
- addr
|
|
- connected_writers
|
|
description: |
|
|
Informs about status of the image pusher.
|
|
properties:
|
|
pusher_type:
|
|
$ref: "#/components/schemas/image_pusher_type"
|
|
addr:
|
|
type: array
|
|
items:
|
|
type: string
|
|
example: [ "tcp://1.2.3.4:5000", "tcp://1.2.3.4:5001" ]
|
|
description: |
|
|
List of addresses of image pushers.
|
|
For HDF5 socket - no addresses will be returned.
|
|
For ZeroMQ - list of addresses for each socket will be provided.
|
|
For TCP/IP - single address to connect all writers will be provided.
|
|
connected_writers:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: |
|
|
Number of connected writers
|
|
For ZeroMQ image socket: number is constant
|
|
For TCP/IP image socket: number is updated live during operation
|
|
images_written:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: |
|
|
Number of images written to the image socket.
|
|
This number is updated live during operation for TCP/IP image socket and direct HDF5 writer.
|
|
It is updated at the end of experiment for ZeroMQ image socket.
|
|
images_write_error:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: |
|
|
Number of images that could not be written to the image socket.
|
|
This number is updated live during operation for TCP/IP image socket.
|
|
No other socket use it.
|
|
writer_fifo_utilization:
|
|
type: array
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: |
|
|
Utilization of internal writer FIFO.
|
|
This number is updated live during operation for TCP/IP image socket.
|
|
No other socket use it.
|
|
plot:
|
|
type: object
|
|
required:
|
|
- x
|
|
- y
|
|
- title
|
|
description: x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly
|
|
properties:
|
|
title:
|
|
type: string
|
|
default: ""
|
|
x:
|
|
type: array
|
|
items:
|
|
type: number
|
|
format: float
|
|
y:
|
|
type: array
|
|
items:
|
|
type: number
|
|
format: float
|
|
nullable: true
|
|
z:
|
|
type: array
|
|
items:
|
|
type: number
|
|
format: float
|
|
nullable: true
|
|
plot_unit_x:
|
|
type: string
|
|
enum:
|
|
- "image_number"
|
|
- "q_recipA"
|
|
- "d_A"
|
|
- "angle_deg"
|
|
- "ADU"
|
|
- "grid_um"
|
|
default: "image_number"
|
|
plots:
|
|
type: object
|
|
required:
|
|
- plot
|
|
- unit_x
|
|
properties:
|
|
title:
|
|
type: string
|
|
unit_x:
|
|
$ref: '#/components/schemas/plot_unit_x'
|
|
size_x:
|
|
type: number
|
|
format: float
|
|
description: Max X range of the plot
|
|
size_y:
|
|
type: number
|
|
format: float
|
|
description: Max Y range of the plot
|
|
plot:
|
|
type: array
|
|
items:
|
|
$ref: '#/components/schemas/plot'
|
|
scan_result:
|
|
type: object
|
|
description: Results of a scan
|
|
required:
|
|
- images
|
|
properties:
|
|
file_prefix:
|
|
type: string
|
|
rotation_unit_cell:
|
|
$ref: '#/components/schemas/unit_cell'
|
|
rotation_crystal_lattice:
|
|
$ref: '#/components/schemas/crystal_lattice'
|
|
rotation_bravais:
|
|
type: string
|
|
description: |
|
|
Bravais lattice type of the global rotation-indexing solution: crystal-system
|
|
letter + centering, e.g. "tP", "oC", "cF", "hR", "mP". Empty if not determined.
|
|
images:
|
|
type: array
|
|
items:
|
|
type: object
|
|
required:
|
|
- efficiency
|
|
- number
|
|
properties:
|
|
efficiency:
|
|
type: number
|
|
format: float
|
|
number:
|
|
type: integer
|
|
format: int64
|
|
description: Detector image number for a given cell
|
|
nx:
|
|
type: integer
|
|
format: int64
|
|
description: Cell position in X for grid scan
|
|
ny:
|
|
type: integer
|
|
format: int64
|
|
description: Cell position in Y for grid scan
|
|
angle:
|
|
type: number
|
|
format: float
|
|
description: Rotation angle associated with the image
|
|
bkg:
|
|
type: number
|
|
format: float
|
|
description: Background estimate
|
|
spots:
|
|
type: integer
|
|
format: int64
|
|
description: Spot count
|
|
spots_low_res:
|
|
type: integer
|
|
format: int64
|
|
description: Spot count in low resolution range
|
|
spots_indexed:
|
|
type: integer
|
|
format: int64
|
|
description: Spot count within indexing tolerance
|
|
spots_ice:
|
|
type: integer
|
|
format: int64
|
|
description: Spot count within common ice ring resolutions
|
|
ice:
|
|
type: number
|
|
format: float
|
|
description: Strongest hexagonal-ice ring intensity over the smooth radial background (1 = no ice)
|
|
index:
|
|
type: integer
|
|
format: int64
|
|
description: Indexing solution
|
|
latt_count:
|
|
type: integer
|
|
format: int64
|
|
description: Indexing lattice count
|
|
pr:
|
|
type: number
|
|
format: float
|
|
description: Profile radius, i.e. how far reflections are from the Ewald sphere
|
|
b:
|
|
type: number
|
|
format: float
|
|
description: B-Factor estimate
|
|
uc:
|
|
$ref: '#/components/schemas/unit_cell'
|
|
xfel_pulseid:
|
|
type: integer
|
|
format: int64
|
|
description: XFEL pulse ID
|
|
pixel_sum:
|
|
type: integer
|
|
format: int64
|
|
description: Total sum of all pixels
|
|
max:
|
|
type: integer
|
|
format: int64
|
|
description: Max viable pixel
|
|
sat:
|
|
type: integer
|
|
format: int64
|
|
description: Number of saturated pixels
|
|
err:
|
|
type: integer
|
|
format: int64
|
|
description: Number of error pixels
|
|
res:
|
|
type: number
|
|
format: float
|
|
description: Diffraction resolution estimate
|
|
calibration_statistics:
|
|
type: array
|
|
items:
|
|
required:
|
|
- module_number
|
|
- storage_cell_number
|
|
- pedestal_g0_mean
|
|
- pedestal_g1_mean
|
|
- pedestal_g2_mean
|
|
- gain_g0_mean
|
|
- gain_g1_mean
|
|
- gain_g2_mean
|
|
- masked_pixels
|
|
type: object
|
|
properties:
|
|
module_number:
|
|
type: integer
|
|
format: int64
|
|
storage_cell_number:
|
|
type: integer
|
|
format: int64
|
|
pedestal_g0_mean:
|
|
type: number
|
|
format: float
|
|
pedestal_g1_mean:
|
|
type: number
|
|
format: float
|
|
pedestal_g2_mean:
|
|
type: number
|
|
format: float
|
|
gain_g0_mean:
|
|
type: number
|
|
format: float
|
|
gain_g1_mean:
|
|
type: number
|
|
format: float
|
|
gain_g2_mean:
|
|
type: number
|
|
format: float
|
|
masked_pixels:
|
|
type: integer
|
|
format: int64
|
|
jfjoch_statistics:
|
|
type: object
|
|
description: "Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker"
|
|
properties:
|
|
detector:
|
|
$ref: '#/components/schemas/detector_status'
|
|
detector_list:
|
|
$ref: '#/components/schemas/detector_list'
|
|
detector_settings:
|
|
$ref: '#/components/schemas/detector_settings'
|
|
image_format_settings:
|
|
$ref: '#/components/schemas/image_format_settings'
|
|
instrument_metadata:
|
|
$ref: '#/components/schemas/instrument_metadata'
|
|
file_writer_settings:
|
|
$ref: '#/components/schemas/file_writer_settings'
|
|
data_processing_settings:
|
|
$ref: '#/components/schemas/spot_finding_settings'
|
|
measurement:
|
|
$ref: '#/components/schemas/measurement_statistics'
|
|
broker:
|
|
$ref: '#/components/schemas/broker_status'
|
|
fpga:
|
|
$ref: '#/components/schemas/fpga_status'
|
|
calibration:
|
|
$ref: '#/components/schemas/calibration_statistics'
|
|
zeromq_preview:
|
|
$ref: '#/components/schemas/zeromq_preview_settings'
|
|
zeromq_metadata:
|
|
$ref: '#/components/schemas/zeromq_metadata_settings'
|
|
dark_mask:
|
|
$ref: '#/components/schemas/dark_mask_settings'
|
|
pixel_mask:
|
|
$ref: '#/components/schemas/pixel_mask_statistics'
|
|
roi:
|
|
$ref: '#/components/schemas/roi_definitions'
|
|
az_int:
|
|
$ref: '#/components/schemas/azim_int_settings'
|
|
buffer:
|
|
$ref: '#/components/schemas/image_buffer_status'
|
|
indexing:
|
|
$ref: '#/components/schemas/indexing_settings'
|
|
bragg_integration:
|
|
$ref: '#/components/schemas/bragg_integration_settings'
|
|
image_pusher:
|
|
$ref: '#/components/schemas/image_pusher_status'
|
|
error_message:
|
|
type: object
|
|
required:
|
|
- msg
|
|
- reason
|
|
properties:
|
|
msg:
|
|
type: string
|
|
description: "Human readable message"
|
|
example: "Detector in wrong state"
|
|
reason:
|
|
type: string
|
|
description: "Enumerate field for automated analysis"
|
|
enum: ["WrongDAQState", "Other"]
|
|
roi_azimuthal:
|
|
type: object
|
|
description: "ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector"
|
|
required:
|
|
- name
|
|
- q_min_recipA
|
|
- q_max_recipA
|
|
properties:
|
|
name:
|
|
type: string
|
|
minLength: 1
|
|
description: "Name for the ROI; used in the plots"
|
|
q_min_recipA:
|
|
type: number
|
|
format: float
|
|
minimum: 0.00001
|
|
description: "Minimum Q-range for the ROI"
|
|
q_max_recipA:
|
|
type: number
|
|
format: float
|
|
minimum: 0.00001
|
|
description: "Maximum Q-range for the ROI"
|
|
phi_min_deg:
|
|
type: number
|
|
format: float
|
|
description: >
|
|
Lower azimuthal-angle bound of the sector [degrees]. Optional: provide both
|
|
phi_min_deg and phi_max_deg to restrict the ROI to an angular sector, or omit
|
|
both for a full ring. A sector with phi_min_deg > phi_max_deg wraps across 0.
|
|
phi_max_deg:
|
|
type: number
|
|
format: float
|
|
description: >
|
|
Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.
|
|
roi_circle:
|
|
type: object
|
|
description: "Circular ROI"
|
|
required:
|
|
- name
|
|
- center_x_pxl
|
|
- center_y_pxl
|
|
- radius_pxl
|
|
properties:
|
|
name:
|
|
type: string
|
|
minLength: 1
|
|
description: "Name for the ROI; used in the plots"
|
|
center_x_pxl:
|
|
type: number
|
|
format: float
|
|
description: "X coordinate of center of the circle [pixels]"
|
|
center_y_pxl:
|
|
type: number
|
|
format: float
|
|
description: "Y coordinate of center of the circle [pixels]"
|
|
radius_pxl:
|
|
type: number
|
|
format: float
|
|
minimum: 0.0
|
|
exclusiveMinimum: true
|
|
description: "Radius of the circle [pixels]"
|
|
roi_box:
|
|
type: object
|
|
description: "Box ROI"
|
|
required:
|
|
- name
|
|
- min_x_pxl
|
|
- max_x_pxl
|
|
- min_y_pxl
|
|
- max_y_pxl
|
|
properties:
|
|
name:
|
|
type: string
|
|
minLength: 1
|
|
description: "Name for the ROI; used in the plots"
|
|
min_x_pxl:
|
|
type: integer
|
|
format: int64
|
|
description: "Lower bound (inclusive) in X coordinate for the box"
|
|
minimum: 0
|
|
max_x_pxl:
|
|
type: integer
|
|
format: int64
|
|
description: "Upper bound (inclusive) in X coordinate for the box"
|
|
minimum: 0
|
|
min_y_pxl:
|
|
type: integer
|
|
format: int64
|
|
description: "Lower bound (inclusive) in Y coordinate for the box"
|
|
minimum: 0
|
|
max_y_pxl:
|
|
type: integer
|
|
format: int64
|
|
description: "Upper bound (inclusive) in Y coordinate for the box"
|
|
minimum: 0
|
|
roi_circle_list:
|
|
type: object
|
|
description: "List of circular ROIs"
|
|
required:
|
|
- rois
|
|
properties:
|
|
rois:
|
|
type: array
|
|
maxItems: 12
|
|
items:
|
|
$ref: "#/components/schemas/roi_circle"
|
|
roi_box_list:
|
|
type: object
|
|
description: "List of box ROIs"
|
|
properties:
|
|
rois:
|
|
type: array
|
|
maxItems: 12
|
|
items:
|
|
$ref: "#/components/schemas/roi_box"
|
|
roi_azim_list:
|
|
type: object
|
|
description: "List of azimuthal ROIs"
|
|
properties:
|
|
rois:
|
|
type: array
|
|
maxItems: 12
|
|
items:
|
|
$ref: "#/components/schemas/roi_azimuthal"
|
|
roi_definitions:
|
|
type: object
|
|
required:
|
|
- box
|
|
- circle
|
|
- azim
|
|
description: "ROI defintions"
|
|
properties:
|
|
box:
|
|
$ref: '#/components/schemas/roi_box_list'
|
|
circle:
|
|
$ref: '#/components/schemas/roi_circle_list'
|
|
azim:
|
|
$ref: '#/components/schemas/roi_azim_list'
|
|
dark_mask_settings:
|
|
type: object
|
|
description: "Settings for collection of dark images to be used for mask calculation"
|
|
required:
|
|
- detector_threshold_keV
|
|
- frame_threshold_keV
|
|
- max_allowed_pixel_count
|
|
- max_frames_with_signal
|
|
- frame_time_us
|
|
- number_of_frames
|
|
properties:
|
|
detector_threshold_keV:
|
|
type: number
|
|
format: float
|
|
description: "Energy threshold for dark image collection"
|
|
minimum: 2.5
|
|
default: 3.5
|
|
maximum: 100.0
|
|
frame_time_us:
|
|
type: integer
|
|
format: int64
|
|
description: "Time between frames for dark image collection"
|
|
minimum: 500
|
|
default: 10000
|
|
maximum: 100000
|
|
number_of_frames:
|
|
type: integer
|
|
format: int64
|
|
description: "Number of frames for dark image collection; zero means no dark collection"
|
|
minimum: 0
|
|
default: 1000
|
|
max_allowed_pixel_count:
|
|
type: integer
|
|
format: int64
|
|
description: "Maximum count in a pixel considered normal (not-masked)"
|
|
minimum: 0
|
|
default: 1
|
|
max_frames_with_signal:
|
|
type: integer
|
|
format: int64
|
|
description: "Maximum number of frames with signal in a pixel considered normal (not-masked)"
|
|
minimum: 0
|
|
default: 10
|
|
indexing_settings:
|
|
type: object
|
|
description: "Settings for crystallography indexing"
|
|
required:
|
|
- algorithm
|
|
- geom_refinement_algorithm
|
|
- fft_high_resolution_A
|
|
- fft_max_unit_cell_A
|
|
- fft_min_unit_cell_A
|
|
- fft_num_vectors
|
|
- tolerance
|
|
- thread_count
|
|
- unit_cell_dist_tolerance
|
|
- index_ice_rings
|
|
- viable_cell_min_spots
|
|
- rotation_indexing
|
|
- rotation_indexing_min_angular_range_deg
|
|
- rotation_indexing_angular_stride_deg
|
|
- blocking
|
|
properties:
|
|
algorithm:
|
|
$ref: "#/components/schemas/indexing_algorithm"
|
|
fft_max_unit_cell_A:
|
|
type: number
|
|
format: float
|
|
default: 250
|
|
maximum: 500
|
|
minimum: 50
|
|
description: Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT
|
|
fft_min_unit_cell_A:
|
|
type: number
|
|
format: float
|
|
default: 10.0
|
|
minimum: 5
|
|
maximum: 40
|
|
description: Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT
|
|
fft_high_resolution_A:
|
|
type: number
|
|
format: float
|
|
default: 2.0
|
|
minimum: 0.5
|
|
maximum: 6.0
|
|
description: |
|
|
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:
|
|
type: integer
|
|
format: int64
|
|
minimum: 128
|
|
default: 16384
|
|
description: Number of search directions for the FFT algorithm; parameter value affects execution time of FFT.
|
|
tolerance:
|
|
type: number
|
|
format: float
|
|
minimum: 0.0
|
|
maximum: 0.5
|
|
description: Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted
|
|
thread_count:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
maximum: 64
|
|
description: Thread count for indexing algorithm
|
|
geom_refinement_algorithm:
|
|
$ref: '#/components/schemas/geom_refinement_algorithm'
|
|
unit_cell_dist_tolerance:
|
|
type: number
|
|
format: float
|
|
minimum: 0.0001
|
|
maximum: 0.2001
|
|
default: 0.05
|
|
description: Relative distance tolerance for unit cell vs. reference; Lattices outside given tolerance will be ignored
|
|
viable_cell_min_spots:
|
|
type: integer
|
|
format: int64
|
|
minimum: 5
|
|
default: 10
|
|
description: Minimum number of indexed spots required for a cell to be considered viable
|
|
index_ice_rings:
|
|
type: boolean
|
|
default: false
|
|
description: |
|
|
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:
|
|
type: boolean
|
|
default: false
|
|
rotation_indexing_min_angular_range_deg:
|
|
type: number
|
|
format: float
|
|
default: 20.0
|
|
minimum: 1.0
|
|
rotation_indexing_angular_stride_deg:
|
|
type: number
|
|
format: float
|
|
default: 0.5
|
|
minimum: 0
|
|
blocking:
|
|
type: boolean
|
|
default: true
|
|
description: |
|
|
Indexing in Jungfraujoch goes with a dedicated thread pool.
|
|
If set to false, the thread pool is non-blocking, i.e. if there are no threads available, image indexing will be skipped. This option is recommended for real-time processing at high frame rates.
|
|
If set to true, the thread pool will block until a thread is available.
|
|
instrument_metadata:
|
|
type: object
|
|
description: "Metadata for a measurement instrument"
|
|
required:
|
|
- source_name
|
|
- instrument_name
|
|
properties:
|
|
source_name:
|
|
type: string
|
|
example: Swiss Light Source
|
|
source_type:
|
|
type: string
|
|
description: |
|
|
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
|
|
example: Synchrotron X-ray Source
|
|
default: ""
|
|
instrument_name:
|
|
type: string
|
|
example: CristallinaMX
|
|
pulsed_source:
|
|
type: boolean
|
|
description: |
|
|
Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)
|
|
default: false
|
|
electron_source:
|
|
type: boolean
|
|
description: |
|
|
Settings specific to electron source (e.g., wavelength definition)
|
|
default: false
|
|
detector_module_direction:
|
|
type: string
|
|
enum: [Xp, Xn, Yp, Yn]
|
|
detector_type:
|
|
type: string
|
|
enum: [EIGER, JUNGFRAU, DECTRIS]
|
|
image_pusher_type:
|
|
type: string
|
|
default: None
|
|
enum: [ZeroMQ, HDF5, CBOR, TCP, None]
|
|
standard_detector_geometry:
|
|
type: object
|
|
description: Regular rectangular geometry, first module is in the bottom left corner of the detector
|
|
required:
|
|
- nmodules
|
|
properties:
|
|
nmodules:
|
|
type: integer
|
|
minimum: 1
|
|
description: Number of modules in the detector
|
|
gap_x:
|
|
type: integer
|
|
default: 8
|
|
minimum: 0
|
|
description: Gap size in X direction [pixels]
|
|
gap_y:
|
|
type: integer
|
|
minimum: 0
|
|
default: 36
|
|
description: Gap size in Y direction [pixels]
|
|
modules_in_row:
|
|
type: integer
|
|
minimum: 1
|
|
default: 1
|
|
description: Number of modules in one row
|
|
detector_module:
|
|
type: object
|
|
required:
|
|
- x0
|
|
- y0
|
|
- fast_axis
|
|
- slow_axis
|
|
properties:
|
|
x0:
|
|
type: number
|
|
y0:
|
|
type: number
|
|
fast_axis:
|
|
$ref: '#/components/schemas/detector_module_direction'
|
|
slow_axis:
|
|
$ref: '#/components/schemas/detector_module_direction'
|
|
detector:
|
|
type: object
|
|
required:
|
|
- description
|
|
properties:
|
|
description:
|
|
type: string
|
|
minLength: 1
|
|
serial_number:
|
|
type: string
|
|
default: "Unknown"
|
|
minLength: 1
|
|
type:
|
|
$ref: '#/components/schemas/detector_type'
|
|
high_voltage_V:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
maximum: 200
|
|
default: 0
|
|
udp_interface_count:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
maximum: 2
|
|
default: 1
|
|
module_sync:
|
|
type: boolean
|
|
default: true
|
|
description: Use module 0 as master for timing. Only applies to JUNGFRAU detector (this cannot be turned off for EIGER).
|
|
sensor_thickness_um:
|
|
type: number
|
|
format: float
|
|
minimum: 0
|
|
default: 320
|
|
readout_time_ns:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
description: |
|
|
Minimum difference between frame time and count time in microseconds
|
|
Defaults are 3'000 ns for EIGER and 20'000 ns for JUNGFRAU
|
|
min_count_time_ns:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: Minimum count time available for the detector.
|
|
min_frame_time_ns:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
description: Minimum frame time available for the detector.
|
|
calibration_file:
|
|
type: array
|
|
description: |
|
|
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.
|
|
items:
|
|
type: string
|
|
trim_energies_eV:
|
|
type: array
|
|
description: |
|
|
List of energies at which trimming calibration is provided.
|
|
Only needed for PSI EIGER and compulsory in this case
|
|
items:
|
|
type: integer
|
|
format: int32
|
|
minimum: 100
|
|
hostname:
|
|
type: array
|
|
description: |
|
|
Hostname for detector module. One entry per module
|
|
One entry per module. Either empty or number of module entries.
|
|
items:
|
|
type: string
|
|
sensor_material:
|
|
type: string
|
|
default: Si
|
|
tx_delay:
|
|
type: array
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
base_data_ipv4_address:
|
|
type: string
|
|
example: 10.10.10.50
|
|
standard_geometry:
|
|
$ref: '#/components/schemas/standard_detector_geometry'
|
|
custom_geometry:
|
|
type: array
|
|
items:
|
|
$ref: '#/components/schemas/detector_module'
|
|
roi_mode:
|
|
type: string
|
|
default: ""
|
|
description: ROI setting for DECTRIS detectors
|
|
mirror_y:
|
|
type: boolean
|
|
default: true
|
|
description: Mirror detector in Y direction to account for MX convention of (0,0) point in top left corner
|
|
temp_thresold_degC:
|
|
type: integer
|
|
format: int64
|
|
description: Temperature threshold for JUNGFRAU detector modules
|
|
minimum: 40
|
|
maximum: 70
|
|
default: 55
|
|
default_settings:
|
|
$ref: '#/components/schemas/detector_settings'
|
|
zeromq_settings:
|
|
type: object
|
|
description: |
|
|
ZeroMQ configuration for Jungfraujoch software.
|
|
This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
|
|
properties:
|
|
send_watermark:
|
|
type: integer
|
|
format: int64
|
|
minimum: 2
|
|
maximum: 16384
|
|
default: 100
|
|
description: Watermark for ZeroMQ send queue (number of outstanding messages queued on Jungfraujoch server per queue)
|
|
send_buffer_size:
|
|
type: integer
|
|
format: int64
|
|
description: Send buffer size for ZeroMQ socket
|
|
image_socket:
|
|
type: array
|
|
items:
|
|
type: string
|
|
example: ["tcp://1.2.3.4:5000", "tcp://1.2.3.4:5001"]
|
|
description: |
|
|
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.
|
|
writer_notification_socket:
|
|
type: string
|
|
example: "tcp://1.3.4.6:7000"
|
|
description: |
|
|
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.
|
|
tcp_settings:
|
|
type: object
|
|
description: |
|
|
TCP image stream configuration for Jungfraujoch software.
|
|
This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
|
|
required:
|
|
- addr
|
|
properties:
|
|
send_buffer_size:
|
|
type: integer
|
|
format: int64
|
|
description: Send buffer size for TCP/IP socket
|
|
image_socket:
|
|
type: string
|
|
example: "tcp://1.2.3.4:5000"
|
|
description: |
|
|
tcp://<IP address>:<port>
|
|
0.0.0.0 instead of IP address is accepted and means listening on all network interfaces
|
|
nwriters:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
maximum: 100
|
|
default: 32
|
|
description: Number of TCP/IP writers to be used for streaming images
|
|
peer_liveness_timeout_ms:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Max time (in milliseconds) a send may block with no sign of life from the
|
|
writer (no BUSY heartbeat or ACK) before the connection is declared dead.
|
|
Optional; the built-in default is used when unset.
|
|
max_backpressure_timeout_ms:
|
|
type: integer
|
|
format: int64
|
|
description: |
|
|
Hard upper bound (in milliseconds) on backpressure: if no bytes can be sent to
|
|
the writer for this long the connection is declared dead even while the writer
|
|
keeps heartbeating, so a wedged writer cannot block the run or its
|
|
finalization. Optional; the built-in default is used when unset.
|
|
pcie_devices:
|
|
type: array
|
|
minLength: 1
|
|
items:
|
|
type: object
|
|
required:
|
|
- block_device
|
|
properties:
|
|
blk:
|
|
type: string
|
|
example: "/dev/jfjoch0"
|
|
description: Block device name
|
|
ipv4:
|
|
type: string
|
|
example: 10.1.1.7
|
|
description: IPv4 address of the block device
|
|
bragg_integration_settings:
|
|
type: object
|
|
description: "Settings for Bragg spot integration"
|
|
required:
|
|
- integration_model
|
|
properties:
|
|
integration_model:
|
|
$ref: '#/components/schemas/integration_model'
|
|
max_hkl:
|
|
type: integer
|
|
minimum: 1
|
|
maximum: 511
|
|
default: 100
|
|
description: |
|
|
How far the Bragg predictor walks the lattice: reflections with |h|,|k|,|l| above this are
|
|
never predicted. An axis is truncated once a/d_min exceeds it, so a long axis - or a short
|
|
one taken to high resolution - loses its outermost reflections. The cost grows as the cube
|
|
(2n+1)^3 of candidates per image, which is why online keeps a fixed, predictable value
|
|
instead of taking it from whichever crystal is mounted.
|
|
|
|
Omitting the field selects the default above; it is never interpreted as "choose per
|
|
crystal". The offline tools (rugnux, viewer) do derive it from the refined cell when it is
|
|
left unset there, but that is their own default and is not reachable through this API.
|
|
jfjoch_settings:
|
|
type: object
|
|
required:
|
|
- detector
|
|
- frontend_directory
|
|
- image_pusher
|
|
description: |
|
|
Default settings for Jungfraujoch software.
|
|
This structure is used to provide default settings using configuration JSON file and is not used in HTTP.
|
|
properties:
|
|
pcie:
|
|
$ref: '#/components/schemas/pcie_devices'
|
|
zeromq:
|
|
$ref: '#/components/schemas/zeromq_settings'
|
|
tcp:
|
|
$ref: '#/components/schemas/tcp_settings'
|
|
instrument:
|
|
$ref: '#/components/schemas/instrument_metadata'
|
|
file_writer:
|
|
$ref: '#/components/schemas/file_writer_settings'
|
|
detector:
|
|
type: array
|
|
minLength: 1
|
|
items:
|
|
$ref: '#/components/schemas/detector'
|
|
indexing:
|
|
$ref: '#/components/schemas/indexing_settings'
|
|
bragg_integration:
|
|
$ref: '#/components/schemas/bragg_integration_settings'
|
|
detector_settings:
|
|
$ref: '#/components/schemas/detector_settings'
|
|
azim_int:
|
|
$ref: '#/components/schemas/azim_int_settings'
|
|
image_format:
|
|
$ref: '#/components/schemas/image_format_settings'
|
|
image_buffer_MiB:
|
|
type: integer
|
|
minimum: 128
|
|
default: 2048
|
|
description: Size of internal buffer in MiB for images before they are sent to a stream
|
|
verbose:
|
|
type: boolean
|
|
default: false
|
|
description: Print extra debug information
|
|
receiver_threads:
|
|
type: integer
|
|
minimum: 1
|
|
maximum: 512
|
|
default: 64
|
|
description: Number of threads used by the receiver
|
|
numa_policy:
|
|
type: string
|
|
deprecated: true
|
|
description: Ignored value
|
|
frontend_directory:
|
|
type: string
|
|
description: Location of built JavaScript web frontend
|
|
spot_finding:
|
|
$ref: '#/components/schemas/spot_finding_settings'
|
|
image_pusher:
|
|
$ref: '#/components/schemas/image_pusher_type'
|
|
zeromq_preview:
|
|
$ref: '#/components/schemas/zeromq_preview_settings'
|
|
zeromq_metadata:
|
|
$ref: '#/components/schemas/zeromq_metadata_settings'
|
|
dark_mask:
|
|
$ref: '#/components/schemas/dark_mask_settings'
|
|
zeromq_metadata_settings:
|
|
type: object
|
|
required:
|
|
- enabled
|
|
- period_ms
|
|
properties:
|
|
enabled:
|
|
type: boolean
|
|
default: true
|
|
description: ZeroMQ metadata socket is enabled.
|
|
period_ms:
|
|
type: integer
|
|
format: int64
|
|
minimum: 1
|
|
default: 1000
|
|
description: |
|
|
Period for generating metadata package sent to the ZeroMQ interface in milliseconds.
|
|
socket_address:
|
|
type: string
|
|
description: |
|
|
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.
|
|
zeromq_preview_settings:
|
|
type: object
|
|
required:
|
|
- enabled
|
|
- period_ms
|
|
properties:
|
|
enabled:
|
|
type: boolean
|
|
default: true
|
|
description: ZeroMQ preview socket is enabled.
|
|
period_ms:
|
|
type: integer
|
|
format: int64
|
|
default: 1000
|
|
description: |
|
|
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:
|
|
type: string
|
|
description: |
|
|
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.
|
|
paths:
|
|
/initialize:
|
|
post:
|
|
summary: Initialize detector and data acquisition
|
|
description: |
|
|
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:
|
|
"200":
|
|
description: Initialization started
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
|
|
/pedestal:
|
|
post:
|
|
summary: Collect dark current for the detector
|
|
description: |
|
|
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:
|
|
"200":
|
|
description: Everything OK
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/start:
|
|
post:
|
|
summary: Start detector
|
|
description: |
|
|
Start data acquisition.
|
|
Detector must be in `Idle` state.
|
|
Default behavior is for the call to block until detector is ready to accept soft/TTL triggers.
|
|
However, this behavior can be changed by settings `async_start` to true in the request body,
|
|
in which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/dataset_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/wait_until_running:
|
|
post:
|
|
summary: Wait for acquisition running
|
|
parameters:
|
|
- in: query
|
|
name: timeout
|
|
required: false
|
|
schema:
|
|
type: integer
|
|
default: 60
|
|
minimum: 0
|
|
maximum: 3600
|
|
description: Timeout in seconds (0 == immediate response)
|
|
description: |
|
|
Block execution of external script till detector and Jungfraujoch are ready to collect data.
|
|
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.
|
|
responses:
|
|
"200":
|
|
description: Detector in `Measuring` state
|
|
"400":
|
|
description: Timeout parameter out of bounds
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
"502":
|
|
description: Detector is inactive mode
|
|
"504":
|
|
description: Timeout reached, need to restart operation
|
|
/wait_till_done:
|
|
post:
|
|
summary: Wait for acquisition done
|
|
parameters:
|
|
- in: query
|
|
name: timeout
|
|
required: false
|
|
schema:
|
|
type: integer
|
|
default: 60
|
|
minimum: 0
|
|
maximum: 3600
|
|
description: Timeout in seconds (0 == immediate response)
|
|
description: |
|
|
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.
|
|
responses:
|
|
"200":
|
|
description: Detector in `Idle` state, another data collection can start immediately
|
|
"400":
|
|
description: Timeout parameter out of bounds
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
"502":
|
|
description: Detector is inactive mode
|
|
"504":
|
|
description: Timeout reached, need to restart operation
|
|
|
|
/trigger:
|
|
post:
|
|
summary: Send soft trigger to the detector
|
|
description: Generate soft trigger
|
|
responses:
|
|
"200":
|
|
description: Trigger sent
|
|
|
|
/cancel:
|
|
post:
|
|
summary: Cancel running data collection
|
|
description: |
|
|
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:
|
|
"200":
|
|
description: Cancel request sent to FPGAs (or ignored, as data collection is not running)
|
|
|
|
/deactivate:
|
|
post:
|
|
summary: Prepare detector to turn off
|
|
description: |
|
|
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:
|
|
"200":
|
|
description: Detector ready to turn off
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
|
|
/config/detector:
|
|
put:
|
|
summary: Change detector configuration
|
|
description: |
|
|
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.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/detector_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get detector configuration
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/detector_settings'
|
|
/config/indexing:
|
|
put:
|
|
summary: Change indexing algorithm settings
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/indexing_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get indexing configuration
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/indexing_settings'
|
|
/config/bragg_integration:
|
|
put:
|
|
summary: Change Bragg integration settings
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/bragg_integration_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get Bragg integration configuration
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/bragg_integration_settings'
|
|
/config/file_writer:
|
|
put:
|
|
summary: Change file writer settings
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/file_writer_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get file writer settings
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/file_writer_settings'
|
|
/config/instrument:
|
|
put:
|
|
summary: Change instrument metadata
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/instrument_metadata'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get instrument metadata
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/instrument_metadata'
|
|
/config/image_format:
|
|
put:
|
|
summary: Change image output format
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/image_format_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get image output format
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/image_format_settings'
|
|
/config/image_format/raw:
|
|
post:
|
|
summary: Configure format for raw data collection
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/config/image_format/conversion:
|
|
post:
|
|
summary: Configure format for data collection with full conversion
|
|
description: |
|
|
This can only be done when detector is `Idle`, `Error` or `Inactive` states.
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/config/spot_finding:
|
|
put:
|
|
summary: Configure spot finding
|
|
description: Can be done anytime, also while data collection is running
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/spot_finding_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
get:
|
|
summary: Get data processing configuration
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/spot_finding_settings'
|
|
/config/azim_int:
|
|
put:
|
|
summary: Configure azimuthal integration
|
|
description: Can be done when detector is Inactive or Idle
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/azim_int_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get azimuthal integration configuration
|
|
description: Can be done anytime
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/azim_int_settings'
|
|
/config/internal_generator_image:
|
|
put:
|
|
summary: Load binary image for internal FPGA generator
|
|
description: |
|
|
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).
|
|
parameters:
|
|
- name: id
|
|
in: query
|
|
description: Image id to upload
|
|
required: false
|
|
schema:
|
|
type: integer
|
|
format: int64
|
|
minimum: 0
|
|
maximum: 127
|
|
requestBody:
|
|
content:
|
|
application/octet-stream:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
/config/internal_generator_image.tiff:
|
|
put:
|
|
summary: Load TIFF image for internal FPGA generator
|
|
description: |
|
|
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).
|
|
parameters:
|
|
- in: query
|
|
name: id
|
|
description: Image ID to upload
|
|
required: false
|
|
schema:
|
|
type: integer
|
|
minimum: 0
|
|
maximum: 127
|
|
requestBody:
|
|
content:
|
|
image/tiff:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
/config/select_detector:
|
|
put:
|
|
summary: Select detector
|
|
description: |
|
|
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.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/detector_selection'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: List available detectors
|
|
description: Configured detectors that can be selected by used
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/detector_list'
|
|
/config/zeromq_preview:
|
|
put:
|
|
summary: Set ZeroMQ preview settings
|
|
description: |
|
|
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.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/zeromq_preview_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get ZeroMQ preview settings
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/zeromq_preview_settings'
|
|
/config/zeromq_metadata:
|
|
put:
|
|
summary: Set ZeroMQ metadata settings
|
|
description: |
|
|
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.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/zeromq_metadata_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get ZeroMQ metadata socket settings
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/zeromq_metadata_settings'
|
|
/config/dark_mask:
|
|
put:
|
|
summary: Set configuration for dark data collection to calculate mask
|
|
description: |
|
|
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.
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/dark_mask_settings'
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
get:
|
|
summary: Get settings for dark data collection to calculate mask
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/dark_mask_settings'
|
|
/status:
|
|
get:
|
|
summary: Get Jungfraujoch status
|
|
description: Status of the data acquisition
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/broker_status'
|
|
/fpga_status:
|
|
get:
|
|
summary: Get status of FPGA devices
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/fpga_status'
|
|
/xfel/pulse_id:
|
|
get:
|
|
summary: Return XFEL pulse IDs for the current data acquisition
|
|
description: Return array of XFEL pulse IDs - (-1) if image not recorded
|
|
responses:
|
|
"200":
|
|
description: "Pulse ID collected"
|
|
content:
|
|
application/json:
|
|
schema:
|
|
type: array
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
"404":
|
|
description: "Not in XFEL mode or no acquisition recorded"
|
|
/xfel/event_code:
|
|
get:
|
|
summary: Return XFEL event codes for the current data acquisition
|
|
description: Return array of XFEL event codes
|
|
responses:
|
|
"200":
|
|
description: "Event codes collected"
|
|
content:
|
|
application/json:
|
|
schema:
|
|
type: array
|
|
items:
|
|
type: integer
|
|
format: int64
|
|
"404":
|
|
description: "Not in XFEL mode or no acquisition recorded"
|
|
/image_pusher/status:
|
|
get:
|
|
summary: Get status of image pusher
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/image_pusher_status'
|
|
"500":
|
|
description: Error encountered when trying to read status
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
/detector/status:
|
|
get:
|
|
summary: Get detector status
|
|
description: Status of the JUNGFRAU detector
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/detector_status'
|
|
"404":
|
|
description: Running in "simulator" mode - no detector present
|
|
"500":
|
|
description: Error encountered when trying to read status
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
/config/roi:
|
|
get:
|
|
summary: Get ROI definitions
|
|
responses:
|
|
"200":
|
|
description: "OK"
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/roi_definitions'
|
|
put:
|
|
summary: Upload ROI definitions
|
|
requestBody:
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: "#/components/schemas/roi_definitions"
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/statistics:
|
|
get:
|
|
summary: Get general statistics
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/jfjoch_statistics'
|
|
/statistics/data_collection:
|
|
get:
|
|
summary: Get data collection statistics
|
|
description: Results of the last data collection
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/measurement_statistics'
|
|
"404":
|
|
description: No data collection performed so far
|
|
/statistics/calibration:
|
|
get:
|
|
summary: Get calibration statistics
|
|
description: Statistics are provided for each module/storage cell separately
|
|
responses:
|
|
"200":
|
|
description: Everything OK
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/calibration_statistics'
|
|
/config/mask:
|
|
get:
|
|
summary: Get mask of the detector (binary)
|
|
description: |
|
|
Detector must be Initialized.
|
|
Get full pixel mask of the detector.
|
|
See NXmx standard for meaning of pixel values.
|
|
responses:
|
|
"200":
|
|
description: Binary array (4 byte; unsigned)
|
|
content:
|
|
application/octet-stream:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
/config/user_mask:
|
|
get:
|
|
summary: |
|
|
Detector must be Initialized.
|
|
Get user mask of the detector (binary)
|
|
description: "Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked"
|
|
responses:
|
|
"200":
|
|
description: User mask in binary format (4 byte; unsigned)
|
|
content:
|
|
application/octet-stream:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
put:
|
|
summary: Upload user mask of the detector (binary)
|
|
description: |
|
|
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.
|
|
requestBody:
|
|
content:
|
|
application/octet-stream:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
responses:
|
|
"200":
|
|
description: All good
|
|
"400":
|
|
description: Mask is not 4-byte unsigned integer array or empty body
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/config/mask.tiff:
|
|
get:
|
|
summary: Get mask of the detector (TIFF)
|
|
description: |
|
|
Should be in `Idle` state.
|
|
Get full pixel mask of the detector
|
|
See NXmx standard for meaning of pixel values
|
|
responses:
|
|
"200":
|
|
description: Pixel mask in TIFF format (4 byte; unsigned)
|
|
content:
|
|
image/tiff:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
/config/user_mask.tiff:
|
|
get:
|
|
summary: |
|
|
Detector must be Initialized.
|
|
Get user mask of the detector (TIFF)
|
|
description: "Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked"
|
|
responses:
|
|
"200":
|
|
description: User mask in TIFF format (4 byte; unsigned)
|
|
content:
|
|
image/tiff:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
put:
|
|
summary: Upload user mask of the detector
|
|
description: |
|
|
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 a single-channel TIFF (8-, 16- or 32-bit integer, signed or 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.
|
|
requestBody:
|
|
content:
|
|
image/tiff:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
responses:
|
|
"200":
|
|
description: All good
|
|
"400":
|
|
description: Not a valid single-channel TIFF or size doesn't match the detector
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/preview/pedestal.tiff:
|
|
get:
|
|
parameters:
|
|
- in: query
|
|
name: gain_level
|
|
required: true
|
|
schema:
|
|
type: integer
|
|
description: Gain level (0, 1, 2)
|
|
- in: query
|
|
name: sc
|
|
schema:
|
|
type: integer
|
|
description: Storage cell number
|
|
summary: Get pedestal in TIFF format
|
|
responses:
|
|
"200":
|
|
description: Calibration image
|
|
content:
|
|
image/tiff:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
"400":
|
|
description: Invalid gain level or storage cell number
|
|
"404":
|
|
description: No calibration recorded so far
|
|
/preview/plot:
|
|
get:
|
|
summary: Generate 1D plot from Jungfraujoch
|
|
parameters:
|
|
- $ref: "#/components/parameters/binning"
|
|
- $ref: "#/components/parameters/plot_type"
|
|
- $ref: "#/components/parameters/fill_value"
|
|
- $ref: "#/components/parameters/experimental_coord"
|
|
- $ref: "#/components/parameters/azint_unit"
|
|
responses:
|
|
"200":
|
|
description: Everything OK.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/plots'
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
/preview/plot.bin:
|
|
get:
|
|
summary: |
|
|
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.
|
|
parameters:
|
|
- $ref: "#/components/parameters/plot_type"
|
|
- $ref: "#/components/parameters/roi"
|
|
responses:
|
|
"200":
|
|
description: Everything OK.
|
|
content:
|
|
application/octet-stream:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
/result/scan:
|
|
get:
|
|
summary: Get full scan result
|
|
responses:
|
|
"200":
|
|
description: Everything OK.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/scan_result'
|
|
"404":
|
|
description: No grid scan recorded
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/image_buffer/start.cbor:
|
|
get:
|
|
summary: Get Start message in CBOR format
|
|
description: Contains metadata for a dataset (e.g., experimental geometry)
|
|
responses:
|
|
"200":
|
|
description: Return start message
|
|
content:
|
|
application/cbor:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
"404":
|
|
description: No measurement so far
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/image_buffer/image.cbor:
|
|
get:
|
|
summary: Get image message in CBOR format
|
|
description: Contains full image data and metadata. The image must come from the latest data collection.
|
|
parameters:
|
|
- $ref: '#/components/parameters/image_id'
|
|
responses:
|
|
"200":
|
|
description: Return image message
|
|
content:
|
|
application/cbor:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
"404":
|
|
description: Image not present in the buffer - either not yet measured or already replaced by a next image.
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/image_buffer/image.jpeg:
|
|
get:
|
|
summary: Get preview image in JPEG format using custom settings
|
|
parameters:
|
|
- $ref: '#/components/parameters/image_id'
|
|
- $ref: '#/components/parameters/show_user_mask'
|
|
- $ref: '#/components/parameters/show_roi'
|
|
- $ref: '#/components/parameters/show_spots'
|
|
- $ref: '#/components/parameters/show_predictions'
|
|
- $ref: '#/components/parameters/show_beam_center'
|
|
- $ref: '#/components/parameters/saturation'
|
|
- $ref: '#/components/parameters/jpeg_quality'
|
|
- $ref: '#/components/parameters/resolution_ring'
|
|
- $ref: '#/components/parameters/color_scale'
|
|
- $ref: '#/components/parameters/resolution_estimate'
|
|
responses:
|
|
"200":
|
|
description: Preview image
|
|
content:
|
|
image/jpeg:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
"404":
|
|
description: Image not present in the buffer - either not yet measured or already replaced by a next image.
|
|
"400":
|
|
description: Input parsing or validation error
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
description: Exception error
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/image_buffer/image.tiff:
|
|
get:
|
|
summary: Get preview image in TIFF format
|
|
parameters:
|
|
- $ref: '#/components/parameters/image_id'
|
|
responses:
|
|
"200":
|
|
description: Preview image
|
|
content:
|
|
image/tiff:
|
|
schema:
|
|
type: string
|
|
format: binary
|
|
"404":
|
|
description: No preview image recorded so far
|
|
/image_buffer/clear:
|
|
post:
|
|
summary: Clear image buffer
|
|
description: Turns off image buffer for the last data collection. Can be only run when Jungfraujoch is not collecting data.
|
|
responses:
|
|
"200":
|
|
description: Done
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/image_buffer/status:
|
|
get:
|
|
summary: Get status of the image buffers
|
|
description: |
|
|
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:
|
|
"200":
|
|
description: Done
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/image_buffer_status'
|
|
"500":
|
|
description: Error within Jungfraujoch code - see output message.
|
|
content:
|
|
application/json:
|
|
schema:
|
|
$ref: '#/components/schemas/error_message'
|
|
/version:
|
|
get:
|
|
summary: Get Jungfraujoch version of jfjoch_broker
|
|
responses:
|
|
"200":
|
|
description: Release number of Jungfraujoch
|
|
content:
|
|
text/plain:
|
|
schema:
|
|
type: string
|
|
example: 1.0.0-rc.25
|