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v1.0.0-rc.40

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1
docs/python_client/docs/DatasetSettings.md
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@@ -20,6 +20,7 @@ Name | Type | Description | Notes
**total_flux** | **float** | /entry/beam/total_flux in NXmx Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s] | [optional]
**transmission** | **float** | /entry/instrument/attenuator/attenuator_transmission Transmission of attenuator (filter) [no units] | [optional]
**goniometer** | [**RotationAxis**](RotationAxis.md) | | [optional]
**grid_scan** | [**GridScan**](GridScan.md) | | [optional]
**header_appendix** | **object** | Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file. However, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/data of the HDF5 file. This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2. | [optional]
**image_appendix** | **object** | Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) Not saved in HDF5 file | [optional]
**data_reduction_factor_serialmx** | **float** | Rate at which non-indexed images are accepted to be forwarded to writer. Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability. | [optional] [default to 1.0]

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docs/python_client/docs/DefaultApi.md
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docs/python_client/docs/DetectorListDetectorsInner.md
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@@ -13,9 +13,6 @@ Name | Type | Description | Notes
**nmodules** | **int** | |
**width** | **int** | |
**height** | **int** | |
**readout_time_us** | **int** | |
**min_frame_time_us** | **int** | |
**min_count_time_us** | **int** | |
## Example

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# GridPlot
## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**data** | **List[float]** | |
**width** | **int** | |
## Example
```python
from jfjoch_client.models.grid_plot import GridPlot
# TODO update the JSON string below
json = "{}"
# create an instance of GridPlot from a JSON string
grid_plot_instance = GridPlot.from_json(json)
# print the JSON string representation of the object
print(GridPlot.to_json())
# convert the object into a dict
grid_plot_dict = grid_plot_instance.to_dict()
# create an instance of GridPlot from a dict
grid_plot_from_dict = GridPlot.from_dict(grid_plot_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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# GridPlots
## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**plots** | [**List[GridPlot]**](GridPlot.md) | |
**width** | **int** | |
## Example
```python
from jfjoch_client.models.grid_plots import GridPlots
# TODO update the JSON string below
json = "{}"
# create an instance of GridPlots from a JSON string
grid_plots_instance = GridPlots.from_json(json)
# print the JSON string representation of the object
print(GridPlots.to_json())
# convert the object into a dict
grid_plots_dict = grid_plots_instance.to_dict()
# create an instance of GridPlots from a dict
grid_plots_from_dict = GridPlots.from_dict(grid_plots_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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# GridScan
Definition of a grid scan (mutually exclusive with `rotation_axis`)
## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**n_fast** | **int** | Number of elements in the fast direction |
**step_x_um** | **float** | Step in grid along the fast direction. Can be negative. Positive number: left to right Negative number: right to left |
**step_y_um** | **float** | Step in grid along the slow direction. Can be negative. Positive number: top to bottom Negative number: bottom to top |
**vertical** | **bool** | If disabled: fast direction = X, slow direction = Y If enabled: fast direction = Y, slow direction = X | [optional] [default to False]
**snake** | **bool** | Flip fast direction for every second row | [optional] [default to False]
## Example
```python
from jfjoch_client.models.grid_scan import GridScan
# TODO update the JSON string below
json = "{}"
# create an instance of GridScan from a JSON string
grid_scan_instance = GridScan.from_json(json)
# print the JSON string representation of the object
print(GridScan.to_json())
# convert the object into a dict
grid_scan_dict = grid_scan_instance.to_dict()
# create an instance of GridScan from a dict
grid_scan_from_dict = GridScan.from_dict(grid_scan_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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docs/python_client/docs/IndexingAlgorithm.md Normal file
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# IndexingAlgorithm
Selection of an indexing algorithm used by Jungfraujoch
## Enum
* `FFBIDX` (value: `'FFBIDX'`)
* `FFT` (value: `'FFT'`)
* `NONE` (value: `'None'`)
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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docs/python_client/docs/IndexingSettings.md Normal file
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# IndexingSettings
Settings for crystallography indexing
## Properties
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**algorithm** | [**IndexingAlgorithm**](IndexingAlgorithm.md) | | [default to IndexingAlgorithm.FFBIDX]
**fft_max_unit_cell_a** | **float** | Largest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT | [default to 250]
**fft_min_unit_cell_a** | **float** | Smallest unit cell to be indexed by FFT algorithm; parameter value affects execution time of FFT | [default to 10.0]
**fft_high_resolution_a** | **float** | Highest resolution of spots used for FFT algorithm; parameter value affects execution time of FFT. There is also correlation between smallest unit cell and max resolution, which need to be checked for very small systems. | [default to 2.0]
**fft_num_vectors** | **int** | Number of search directions for the FFT algorithm; parameter value affects execution time of FFT. | [default to 16384]
**tolerance** | **float** | Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted |
## Example
```python
from jfjoch_client.models.indexing_settings import IndexingSettings
# TODO update the JSON string below
json = "{}"
# create an instance of IndexingSettings from a JSON string
indexing_settings_instance = IndexingSettings.from_json(json)
# print the JSON string representation of the object
print(IndexingSettings.to_json())
# convert the object into a dict
indexing_settings_dict = indexing_settings_instance.to_dict()
# create an instance of IndexingSettings from a dict
indexing_settings_from_dict = IndexingSettings.from_dict(indexing_settings_dict)
```
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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docs/python_client/docs/JfjochSettings.md
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@@ -11,6 +11,7 @@ Name | Type | Description | Notes
**instrument** | [**InstrumentMetadata**](InstrumentMetadata.md) | | [optional]
**file_writer** | [**FileWriterSettings**](FileWriterSettings.md) | | [optional]
**detector** | [**List[Detector]**](Detector.md) | |
**indexing** | [**IndexingSettings**](IndexingSettings.md) | | [optional]
**detector_settings** | [**DetectorSettings**](DetectorSettings.md) | | [optional]
**azim_int** | [**AzimIntSettings**](AzimIntSettings.md) | | [optional]
**image_format** | [**ImageFormatSettings**](ImageFormatSettings.md) | | [optional]

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docs/python_client/docs/JfjochStatistics.md
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@@ -23,6 +23,7 @@ Name | Type | Description | Notes
**roi** | [**RoiDefinitions**](RoiDefinitions.md) | | [optional]
**az_int** | [**AzimIntSettings**](AzimIntSettings.md) | | [optional]
**buffer** | [**ImageBufferStatus**](ImageBufferStatus.md) | | [optional]
**indexing** | [**IndexingSettings**](IndexingSettings.md) | | [optional]
## Example

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docs/python_client/docs/Plot.md
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@@ -9,6 +9,7 @@ Name | Type | Description | Notes
**title** | **str** | | [default to '']
**x** | **List[float]** | |
**y** | **List[float]** | |
**z** | **List[float]** | | [optional]
## Example

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# PlotTypeEnum
## Enum
* `BKG_ESTIMATE` (value: `'bkg_estimate'`)
* `AZINT` (value: `'azint'`)
* `SPOT_COUNT` (value: `'spot_count'`)
* `INDEXING_RATE` (value: `'indexing_rate'`)
* `INDEXING_UNIT_CELL_LENGTH` (value: `'indexing_unit_cell_length'`)
* `INDEXING_UNIT_CELL_ANGLE` (value: `'indexing_unit_cell_angle'`)
* `ERROR_PIXELS` (value: `'error_pixels'`)
* `IMAGE_COLLECTION_EFFICIENCY` (value: `'image_collection_efficiency'`)
* `RECEIVER_DELAY` (value: `'receiver_delay'`)
* `RECEIVER_FREE_SEND_BUF` (value: `'receiver_free_send_buf'`)
* `STRONG_PIXELS` (value: `'strong_pixels'`)
* `ROI_SUM` (value: `'roi_sum'`)
* `ROI_MEAN` (value: `'roi_mean'`)
* `ROI_MAX_COUNT` (value: `'roi_max_count'`)
* `ROI_PIXELS` (value: `'roi_pixels'`)
* `ROI_WEIGHTED_X` (value: `'roi_weighted_x'`)
* `ROI_WEIGHTED_Y` (value: `'roi_weighted_y'`)
* `PACKETS_RECEIVED` (value: `'packets_received'`)
* `MAX_PIXEL_VALUE` (value: `'max_pixel_value'`)
* `RESOLUTION_ESTIMATE` (value: `'resolution_estimate'`)
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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# PlotUnitX
## Enum
* `IMAGE_NUMBER` (value: `'image_number'`)
* `Q_RECIP_A` (value: `'q_recipA'`)
* `ANGLE_DEG` (value: `'angle_deg'`)
* `ADU` (value: `'ADU'`)
* `GRID_UM` (value: `'grid_um'`)
[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)

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docs/python_client/docs/Plots.md
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Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**title** | **str** | | [optional]
**unit_x** | [**PlotUnitX**](PlotUnitX.md) | | [default to PlotUnitX.IMAGE_NUMBER]
**size_x** | **float** | Max X range of the plot | [optional]
**size_y** | **float** | Max Y range of the plot | [optional]
**plot** | [**List[Plot]**](Plot.md) | |
## Example

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@@ -10,9 +10,9 @@ Name | Type | Description | Notes
**show_spots** | **bool** | Show spot finding results on the image | [optional] [default to True]
**show_roi** | **bool** | Show ROI areas on the image | [optional] [default to False]
**jpeg_quality** | **int** | Quality of JPEG image (100 - highest; 0 - lowest) | [optional] [default to 100]
**show_indexed** | **bool** | Preview indexed images only | [optional] [default to False]
**show_user_mask** | **bool** | Show user mask | [optional] [default to False]
**resolution_ring** | **float** | | [optional] [default to 0.1]
**scale** | [**ColorScale**](ColorScale.md) | | [optional] [default to ColorScale.INDIGO]
## Example

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docs/python_client/docs/RotationAxis.md
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@@ -7,9 +7,10 @@ Definition of a crystal rotation axis
Name | Type | Description | Notes
------------ | ------------- | ------------- | -------------
**name** | **str** | Name of rotation axis (e.g., omega, phi) | [optional] [default to 'omega']
**step** | **float** | Angle step in degrees |
**step** | **float** | Angle step (per image) in degrees |
**start** | **float** | Start angle in degrees | [optional] [default to 0]
**vector** | **List[float]** | Rotation axis |
**helical_step_um** | **List[float]** | Translation (per image) for helical scan | [optional]
## Example

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docs/python_client/docs/SpotFindingSettings.md
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@@ -15,8 +15,8 @@ Name | Type | Description | Notes
**max_pix_per_spot** | **int** | |
**high_resolution_limit** | **float** | |
**low_resolution_limit** | **float** | |
**indexing_tolerance** | **float** | Acceptance tolerance for spots after the indexing run - the larger the number, the more spots will be accepted |
**resolution_estimate** | **bool** | Diffraction image resolution estimation using ML model from SSRL; `jfjoch_broker` must be compiled with libtorch support and path to .pt file configured in `jfjoch_broker` configuration file. | [optional] [default to True]
**resolution_estimate** | **bool** | Diffraction image resolution estimation using ML model from SSRL; `jfjoch_broker` must be compiled with libtorch support and path to .pt file configured in `jfjoch_broker` configuration file. If enabled it will likely reduce performance of Jungfraujoch to below 100 Hz. (experimental feature) | [optional] [default to True]
**quick_integration** | **bool** | Quick integration of collected diffraction images. If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate. (experimental feature) | [default to False]
## Example