v1.0.0-rc.153 (#63)

This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
* jfjoch_broker: Add ROI calculation in non-FPGA workflow
* jfjoch_broker: Fixes to TCP image pusher
* jfjoch_broker: Remove NUMA bindings
* jfjoch_broker: Improvements to indexing
* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results

Reviewed-on: #63

docs/python_client/README.md

@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.152
-- Package version: 1.0.0-rc.152
+- API version: 1.0.0-rc.153
+- Package version: 1.0.0-rc.153
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 

docs/python_client/docs/DatasetSettings.md

@@ -21,7 +21,7 @@ Name | Type | Description | Notes
 **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] 
+**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/user of the HDF5 file.  This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.  | [optional] 
 **image_appendix** | **object** | Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) Not saved in HDF5 file  | [optional] 
 **data_reduction_factor_serialmx** | **float** | Rate at which non-indexed images are accepted to be forwarded to writer.  Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability.  | [optional] [default to 1.0]
 **pixel_value_low_threshold** | **int** | Set all counts lower than the value to zero.  When the value is set, negative numbers other than error pixel value are always set to zero. Setting to zero is equivalent to turning the option off.  | [optional] 

docs/python_client/docs/DefaultApi.md

@@ -2069,9 +2069,9 @@ Should be in `Idle` state.
 Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
 If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
 In the latter case - module gaps are ignored and don't need to be assigned value.
-Mask is expected as TIFF (4-byte; unsigned).
+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 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.
 
 
@@ -2130,6 +2130,7 @@ No authorization required
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
 **200** | All good |  -  |
+**400** | Not a valid single-channel TIFF or size doesn't match the detector |  -  |
 **500** | Error within Jungfraujoch code - see output message. |  -  |
 
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)

docs/python_client/docs/Detector.md

@@ -16,6 +16,7 @@ Name | Type | Description | Notes
 **min_count_time_ns** | **int** | Minimum count time available for the detector. | [optional] 
 **min_frame_time_ns** | **int** | Minimum frame time available for the detector. | [optional] 
 **calibration_file** | **List[str]** | Can be empty for all detectors - default calibration used. For JUNGFRAU: list of gain files, one entry per module. For EIGER: one directory (with detector settings) or list of trim bit files, one entry per half-module.  | [optional] 
+**trim_energies_e_v** | **List[int]** | List of energies at which trimming calibration is provided. Only needed for PSI EIGER and compulsory in this case  | [optional] 
 **hostname** | **List[str]** | Hostname for detector module. One entry per module One entry per module. Either empty or number of module entries.  | [optional] 
 **sensor_material** | **str** |  | [optional] [default to 'Si']
 **tx_delay** | **List[int]** |  | [optional] 

docs/python_client/docs/JfjochSettings.md

@@ -19,7 +19,7 @@ Name | Type | Description | Notes
 **image_buffer_mi_b** | **int** | Size of internal buffer in MiB for images before they are sent to a stream | [optional] [default to 2048]
 **verbose** | **bool** | Print extra debug information | [optional] [default to False]
 **receiver_threads** | **int** | Number of threads used by the receiver | [optional] [default to 64]
-**numa_policy** | **str** | NUMA policy to bind CPUs | [optional] 
+**numa_policy** | **str** | Ignored value | [optional] 
 **frontend_directory** | **str** | Location of built JavaScript web frontend | 
 **spot_finding** | [**SpotFindingSettings**](SpotFindingSettings.md) |  | [optional] 
 **image_pusher** | [**ImagePusherType**](ImagePusherType.md) |  | [default to ImagePusherType.NONE]

docs/python_client/docs/RoiAzimuthal.md

@@ -1,6 +1,6 @@
 # RoiAzimuthal
 
-ROI as Q-range (or resolution range)
+ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector
 
 ## Properties
 
@@ -9,6 +9,8 @@ Name | Type | Description | Notes
 **name** | **str** | Name for the ROI; used in the plots | 
 **q_min_recip_a** | **float** | Minimum Q-range for the ROI | 
 **q_max_recip_a** | **float** | Maximum Q-range for the ROI | 
+**phi_min_deg** | **float** | 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.  | [optional] 
+**phi_max_deg** | **float** | Upper azimuthal-angle bound of the sector [degrees]. Optional; see phi_min_deg.  | [optional] 
 
 ## Example