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v1.0.0-rc.71

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leonarski_f
2025-08-28 07:07:01 +02:00
parent 4e3b54f0b0
commit dba807fadd
185 changed files with 267 additions and 1649 deletions
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103
image_analysis/MXAnalyzer.cpp
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@@ -4,9 +4,7 @@
#include "MXAnalyzer.h"
#include "spot_finding/DetModuleSpotFinder_cpu.h"
#include "../common/CUDAWrapper.h"
#include "indexing/IndexerFactory.h"
#include "spot_finding/SpotAnalysis.h"
#include "geom_refinement/XtalOptimizer.h"
#include "SpotAnalyze.h"
double stddev(const std::vector<float> &v) {
if (v.size() <= 1)
@@ -88,106 +86,11 @@ void MXAnalyzer::ReadFromCPU(DeviceOutput *output, const SpotFindingSettings &se
ReadFromFPGA(output, settings, module_number);
}
void MXAnalyzer::ReadFromCPU(const int16_t *image,
const SpotFindingSettings &settings,
size_t module_number) {
std::unique_lock ul(read_from_cpu_mutex);
if (!find_spots)
return;
if (experiment.GetByteDepthImage() != 2)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"CPU spot finder simulation supports only 16-bit images");
std::vector<float> d_map(RAW_MODULE_SIZE);
DeviceOutput output{};
memcpy(output.pixels, image, RAW_MODULE_SIZE * sizeof(int16_t));
experiment.CalcSpotFinderResolutionMap(d_map.data(), module_number);
arr_mean.resize(experiment.GetModulesNum() * RAW_MODULE_SIZE);
arr_sttdev.resize(experiment.GetModulesNum() * RAW_MODULE_SIZE);
arr_valid_count.resize(experiment.GetModulesNum() * RAW_MODULE_SIZE);
arr_strong_pixel.resize(experiment.GetModulesNum() * RAW_MODULE_SIZE);
FindSpots(output,
settings,
d_map.data(),
arr_mean.data() + module_number * RAW_MODULE_SIZE,
arr_sttdev.data() + module_number * RAW_MODULE_SIZE,
arr_valid_count.data() + module_number * RAW_MODULE_SIZE,
arr_strong_pixel.data() + module_number * RAW_MODULE_SIZE);
ReadFromFPGA(&output, settings, module_number);
}
void MXAnalyzer::Process(DataMessage &message, const SpotFindingSettings& settings) {
void MXAnalyzer::Process(DataMessage &message, const SpotFindingSettings& spot_finding_settings) {
if (!find_spots)
return;
std::vector<SpotToSave> spots_out;
auto geom = experiment.GetDiffractionGeometry();
for (const auto &spot: spots)
spots_out.push_back(spot.Export(geom));
CountSpots(message, spots_out, settings.cutoff_spot_count_low_res);
SpotAnalyze(experiment, spot_finding_settings, spots, message.image, indexer, message);
spots.clear();
FilterSpotsByCount(experiment.GetMaxSpotCount(), spots_out, message.spots);
if (indexer && settings.indexing) {
auto latt = indexer->Run(experiment, message).get();
if (latt) {
DiffractionExperiment experiment_copy(experiment);
XtalOptimizerData data{
.geom = experiment_copy.GetDiffractionGeometry(),
.latt = latt.value()
};
switch (experiment.GetIndexingSettings().GetGeomRefinementAlgorithm()) {
case GeomRefinementAlgorithmEnum::None:
break;
case GeomRefinementAlgorithmEnum::BeamCenter:
XtalOptimizer(data, message.spots, false);
experiment_copy.BeamX_pxl(data.geom.GetBeamX_pxl()).BeamY_pxl(data.geom.GetBeamY_pxl());
message.beam_center_x = data.geom.GetBeamX_pxl();
message.beam_center_y = data.geom.GetBeamY_pxl();
message.indexing_lattice = data.latt;
latt = data.latt;
break;
case GeomRefinementAlgorithmEnum::BeamCenterTetragonal:
XtalOptimizer(data, message.spots, true);
experiment_copy.BeamX_pxl(data.geom.GetBeamX_pxl()).BeamY_pxl(data.geom.GetBeamY_pxl());
message.beam_center_x = data.geom.GetBeamX_pxl();
message.beam_center_y = data.geom.GetBeamY_pxl();
message.indexing_lattice = data.latt;
latt = data.latt;
break;
}
if (settings.quick_integration) {
auto res = BraggIntegrate2D(experiment_copy, message.image, latt.value());
message.reflections = res.reflections;
message.b_factor = res.b_factor;
}
}
}
}
const std::vector<float> &MXAnalyzer::GetCPUMean() const {
return arr_mean;
}
const std::vector<float> &MXAnalyzer::GetCPUStdDev() const {
return arr_sttdev;
}
const std::vector<uint32_t> &MXAnalyzer::GetCPUValidCount() const {
return arr_valid_count;
}
const std::vector<uint32_t> &MXAnalyzer::GetCPUStrongPixel() const {
return arr_strong_pixel;
}