v1.0.0-rc.156 (#66)

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_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output.
* jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling.
* Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool.
* jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection.
* jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata.
* CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66

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

image_analysis/MXAnalysisWithoutFPGA.cpp

@@ -13,12 +13,14 @@
 #include "azint/AzIntEngineCPU.h"
 #include "roi/ROIIntegrationCPU.h"
 #include "spot_finding/ImageSpotFinderCPU.h"
+#include "bragg_integration/BraggIntegrationEngineCPU.h"
 #ifdef JFJOCH_USE_CUDA
 #include "azint/AzIntEngineGPU.h"
 #include "roi/ROIIntegrationGPU.h"
 #include "spot_finding/ImageSpotFinderGPU.h"
 #include "image_preprocessing/ImagePreprocessorGPU.h"
 #include "image_preprocessing/ImagePreprocessorBufferGPU.h"
+#include "bragg_integration/BraggIntegrationEngineGPU.h"
 #include "../common/CUDAWrapper.h"
 #endif
 
@@ -44,6 +46,7 @@ MXAnalysisWithoutFPGA::MXAnalysisWithoutFPGA(const DiffractionExperiment &in_exp
         spotFinder = std::make_unique<ImageSpotFinderCPU>(experiment.GetXPixelsNum(), experiment.GetYPixelsNum());
         azint = std::make_unique<AzIntEngineCPU>(integration);
         preprocessor = std::make_unique<ImagePreprocessorCPU>(in_experiment, in_mask);
+        bragg_engine = std::make_unique<BraggIntegrationEngineCPU>(in_experiment);
         if (experiment.ROI().size() >= 1)
             roi = std::make_unique<ROIIntegrationCPU>(experiment);
 #ifdef JFJOCH_USE_CUDA
@@ -53,6 +56,7 @@ MXAnalysisWithoutFPGA::MXAnalysisWithoutFPGA(const DiffractionExperiment &in_exp
         preprocessor = std::make_unique<ImagePreprocessorGPU>(in_experiment, in_mask, stream);
         spotFinder = std::make_unique<ImageSpotFinderGPU>(experiment.GetXPixelsNum(), experiment.GetYPixelsNum(), stream);
         azint = std::make_unique<AzIntEngineGPU>(integration, stream);
+        bragg_engine = std::make_unique<BraggIntegrationEngineGPU>(in_experiment, stream);
         if (experiment.ROI().size() >= 1)
             roi = std::make_unique<ROIIntegrationGPU>(experiment, stream);
     }
@@ -99,9 +103,10 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
         output.spot_finding_time_s = std::chrono::duration<float>(spot_finding_end_time - spot_finding_start_time).count();
 
         if (spot_finding_settings.indexing)
-            indexer.ProcessImage(output, spot_finding_settings,
-                CompressedImage(preprocessor_buffer->getBuffer(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum()),
-                *prediction);
+            indexer.ProcessImage(output, spot_finding_settings, *prediction,
+                [this](const std::vector<Reflection> &predicted, size_t npredicted, int64_t image_number) {
+                    return bragg_engine->Run(*preprocessor_buffer, predicted, npredicted, image_number);
+                });
     }
 
     output.max_viable_pixel_value = ret.max_value;
@@ -113,6 +118,8 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
     output.az_int_profile_std = profile.GetStd();
 
     output.bkg_estimate = profile.GetBkgEstimate(integration.Settings());
+    output.ice_ring_score = profile.GetIceRingScore(integration.Settings(),
+                                                    spot_finding_settings.ice_ring_width_Q_recipA);
 }
 
 void MXAnalysisWithoutFPGA::RebuildROI() {