v1.0.0-rc.158 (#68)

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.

* Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation.
* jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window.
* rugnux: Accept an absolute `-o` output prefix in offline processing.
* Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed).
* Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

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.157
-- Package version: 1.0.0-rc.157
+- API version: 1.0.0-rc.158
+- Package version: 1.0.0-rc.158
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 

docs/python_client/docs/DefaultApi.md

@@ -2862,7 +2862,7 @@ No authorization required
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
 # **image_buffer_image_jpeg_get**
-> bytearray image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
+> bytearray image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_predictions=show_predictions, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
 
 Get preview image in JPEG format using custom settings
 
@@ -2889,6 +2889,7 @@ with jfjoch_client.ApiClient(configuration) as api_client:
     show_user_mask = False # bool | Show user mask (optional) (default to False)
     show_roi = False # bool | Show ROI areas on the image (optional) (default to False)
     show_spots = True # bool | Show spot finding results on the image (optional) (default to True)
+    show_predictions = False # bool | Show Bragg spot predictions on the image (if available for the image) (optional) (default to False)
     show_beam_center = True # bool | Show beam center on the image (optional) (default to True)
     saturation = 3.4 # float | Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used (optional)
     jpeg_quality = 100 # int | Quality of JPEG image (100 - highest; 0 - lowest) (optional) (default to 100)
@@ -2898,7 +2899,7 @@ with jfjoch_client.ApiClient(configuration) as api_client:
 
     try:
         # Get preview image in JPEG format using custom settings
-        api_response = api_instance.image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
+        api_response = api_instance.image_buffer_image_jpeg_get(id=id, show_user_mask=show_user_mask, show_roi=show_roi, show_spots=show_spots, show_predictions=show_predictions, show_beam_center=show_beam_center, saturation=saturation, jpeg_quality=jpeg_quality, show_res_ring=show_res_ring, color=color, show_res_est=show_res_est)
         print("The response of DefaultApi->image_buffer_image_jpeg_get:\n")
         pprint(api_response)
     except Exception as e:
@@ -2916,6 +2917,7 @@ Name | Type | Description  | Notes
  **show_user_mask** | **bool**| Show user mask | [optional] [default to False]
  **show_roi** | **bool**| Show ROI areas on the image | [optional] [default to False]
  **show_spots** | **bool**| Show spot finding results on the image | [optional] [default to True]
+ **show_predictions** | **bool**| Show Bragg spot predictions on the image (if available for the image) | [optional] [default to False]
  **show_beam_center** | **bool**| Show beam center on the image | [optional] [default to True]
  **saturation** | **float**| Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used | [optional] 
  **jpeg_quality** | **int**| Quality of JPEG image (100 - highest; 0 - lowest) | [optional] [default to 100]