v1.0.0-rc.157 (#67)

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.

* rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`.
* rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling.
* rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics.
* rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1.
* rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group.
* rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix.
* jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation.
* jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning.
* jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint.
* jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed).
* jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types.
* jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails.
* jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak.
* Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation.
* CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67

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

docs/python_client/docs/DefaultApi.md

@@ -7,6 +7,8 @@ Method | HTTP request | Description
 [**cancel_post**](DefaultApi.md#cancel_post) | **POST** /cancel | Cancel running data collection
 [**config_azim_int_get**](DefaultApi.md#config_azim_int_get) | **GET** /config/azim_int | Get azimuthal integration configuration
 [**config_azim_int_put**](DefaultApi.md#config_azim_int_put) | **PUT** /config/azim_int | Configure azimuthal integration
+[**config_bragg_integration_get**](DefaultApi.md#config_bragg_integration_get) | **GET** /config/bragg_integration | Get Bragg integration configuration
+[**config_bragg_integration_put**](DefaultApi.md#config_bragg_integration_put) | **PUT** /config/bragg_integration | Change Bragg integration settings
 [**config_dark_mask_get**](DefaultApi.md#config_dark_mask_get) | **GET** /config/dark_mask | Get settings for dark data collection to calculate mask
 [**config_dark_mask_put**](DefaultApi.md#config_dark_mask_put) | **PUT** /config/dark_mask | Set configuration for dark data collection to calculate mask
 [**config_detector_get**](DefaultApi.md#config_detector_get) | **GET** /config/detector | Get detector configuration
@@ -266,6 +268,139 @@ 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)
 
+# **config_bragg_integration_get**
+> BraggIntegrationSettings config_bragg_integration_get()
+
+Get Bragg integration configuration
+
+Can be done anytime
+
+### Example
+
+
+```python
+import jfjoch_client
+from jfjoch_client.models.bragg_integration_settings import BraggIntegrationSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get Bragg integration configuration
+        api_response = api_instance.config_bragg_integration_get()
+        print("The response of DefaultApi->config_bragg_integration_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_bragg_integration_get: %s\n" % e)
+```
+
+
+
+### Parameters
+
+This endpoint does not need any parameter.
+
+### Return type
+
+[**BraggIntegrationSettings**](BraggIntegrationSettings.md)
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: application/json
+
+### HTTP response details
+
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | Everything OK |  -  |
+
+[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
+
+# **config_bragg_integration_put**
+> config_bragg_integration_put(bragg_integration_settings=bragg_integration_settings)
+
+Change Bragg integration settings
+
+This can only be done when detector is `Idle`, `Error` or `Inactive` states.
+
+
+### Example
+
+
+```python
+import jfjoch_client
+from jfjoch_client.models.bragg_integration_settings import BraggIntegrationSettings
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    bragg_integration_settings = jfjoch_client.BraggIntegrationSettings() # BraggIntegrationSettings |  (optional)
+
+    try:
+        # Change Bragg integration settings
+        api_instance.config_bragg_integration_put(bragg_integration_settings=bragg_integration_settings)
+    except Exception as e:
+        print("Exception when calling DefaultApi->config_bragg_integration_put: %s\n" % e)
+```
+
+
+
+### Parameters
+
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **bragg_integration_settings** | [**BraggIntegrationSettings**](BraggIntegrationSettings.md)|  | [optional] 
+
+### Return type
+
+void (empty response body)
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+ - **Content-Type**: application/json
+ - **Accept**: text/plain, application/json
+
+### HTTP response details
+
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | Everything OK |  -  |
+**400** | Input parsing or validation error |  -  |
+**500** | Error within Jungfraujoch code - see output message. |  -  |
+
+[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
+
 # **config_dark_mask_get**
 > DarkMaskSettings config_dark_mask_get()
 

docs/python_client/docs/JfjochSettings.md

@@ -13,6 +13,7 @@ Name | Type | Description | Notes
 **file_writer** | [**FileWriterSettings**](FileWriterSettings.md) |  | [optional] 
 **detector** | [**List[Detector]**](Detector.md) |  | 
 **indexing** | [**IndexingSettings**](IndexingSettings.md) |  | [optional] 
+**bragg_integration** | [**BraggIntegrationSettings**](BraggIntegrationSettings.md) |  | [optional] 
 **detector_settings** | [**DetectorSettings**](DetectorSettings.md) |  | [optional] 
 **azim_int** | [**AzimIntSettings**](AzimIntSettings.md) |  | [optional] 
 **image_format** | [**ImageFormatSettings**](ImageFormatSettings.md) |  | [optional] 

docs/python_client/docs/JfjochStatistics.md

@@ -25,6 +25,7 @@ Name | Type | Description | Notes
 **az_int** | [**AzimIntSettings**](AzimIntSettings.md) |  | [optional] 
 **buffer** | [**ImageBufferStatus**](ImageBufferStatus.md) |  | [optional] 
 **indexing** | [**IndexingSettings**](IndexingSettings.md) |  | [optional] 
+**bragg_integration** | [**BraggIntegrationSettings**](BraggIntegrationSettings.md) |  | [optional] 
 **image_pusher** | [**ImagePusherStatus**](ImagePusherStatus.md) |  | [optional] 
 
 ## Example

docs/python_client/docs/ScanResult.md

@@ -9,6 +9,7 @@ Name | Type | Description | Notes
 **file_prefix** | **str** |  | [optional] 
 **rotation_unit_cell** | [**UnitCell**](UnitCell.md) |  | [optional] 
 **rotation_crystal_lattice** | **List[float]** | Real-space crystal lattice 3D vectors in Angstrom. Order is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)  | [optional] 
+**rotation_bravais** | **str** | Bravais lattice type of the global rotation-indexing solution: crystal-system letter + centering, e.g. \"tP\", \"oC\", \"cF\", \"hR\", \"mP\". Empty if not determined.  | [optional] 
 **images** | [**List[ScanResultImagesInner]**](ScanResultImagesInner.md) |  | 
 
 ## Example

docs/python_client/docs/ScanResultImagesInner.md

@@ -15,6 +15,7 @@ Name | Type | Description | Notes
 **spots_low_res** | **int** | Spot count in low resolution range | [optional] 
 **spots_indexed** | **int** | Spot count within indexing tolerance | [optional] 
 **spots_ice** | **int** | Spot count within common ice ring resolutions | [optional] 
+**ice** | **float** | Strongest hexagonal-ice ring intensity over the smooth radial background (1 = no ice) | [optional] 
 **index** | **int** | Indexing solution | [optional] 
 **latt_count** | **int** | Indexing lattice count | [optional] 
 **pr** | **float** | Profile radius, i.e. how far reflections are from the Ewald sphere | [optional]