v1.0.0-rc.81

reader/JFJochHDF5Reader.cpp

@@ -52,6 +52,7 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
     try {
         auto dataset = std::make_shared<JFJochReaderDataset>();
         master_file = std::make_unique<HDF5ReadOnlyFile>(filename);
+        dataset->experiment.DetectIceRings(true);
 
         std::filesystem::path fsPath(filename);
         dataset->experiment.FilePrefix(dataset_name(filename));
@@ -171,6 +172,10 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
                 dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
         }
 
+        auto ring_current_A = master_file->GetOptFloat("/entry/source/current");
+        if (ring_current_A) dataset->experiment.RingCurrent_mA(ring_current_A.value() * 1000.0);
+
+        dataset->experiment.DetectIceRings(master_file->GetOptBool("/entry/instrument/detector/detectorSpecific/detect_ice_rings").value_or(false));
         dataset->experiment.PoniRot1_rad(master_file->GetOptFloat("/entry/instrument/detector/transformations/rot1").value_or(0.0));
         dataset->experiment.PoniRot2_rad(master_file->GetOptFloat("/entry/instrument/detector/transformations/rot2").value_or(0.0));
         dataset->experiment.PoniRot3_rad(master_file->GetOptFloat("/entry/instrument/detector/transformations/rot3").value_or(0.0));
@@ -254,6 +259,14 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
             }
         }
 
+        // Read fluorescence spectrum if present
+        if (master_file->Exists("/entry/instrument/fluorescence")) {
+            auto energy = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/energy");
+            auto data = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/data");
+            if (!energy.empty() && energy.size() == data.size())
+                dataset->experiment.FluorescenceSpectrum(XrayFluorescenceSpectrum(energy, data));
+        }
+
         auto detector_name = master_file->GetString("/entry/instrument/detector/description");
 
         DetectorSetup detector = DetDECTRIS(image_size_x, image_size_y, detector_name, {});
@@ -431,6 +444,11 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
                 s.ice_ring = (spot_ice.at(i) != 0);
             message.spots.emplace_back(s);
         }
+
+        message.spot_count = source_file->ReadElement<uint32_t>("/entry/MX/peakCountUnfiltered", image_id);
+        message.spot_count_ice_rings = source_file->ReadElement<uint32_t>("/entry/MX/peakCountIceRingRes", image_id);
+        message.spot_count_low_res = source_file->ReadElement<uint32_t>("/entry/MX/peakCountLowRes", image_id);
+        message.spot_count_indexed = source_file->ReadElement<uint32_t>("/entry/MX/peakCountIndexed", image_id);
     }
 
     if (!dataset->az_int_bin_to_q.empty()) {

reader/JFJochHttpReader.cpp

@@ -57,6 +57,7 @@ std::shared_ptr<JFJochReaderDataset>  JFJochHttpReader::UpdateDataset_i() {
             return {};
 
         auto dataset = std::make_shared<JFJochReaderDataset>();
+        dataset->experiment.DetectIceRings(true);
 
         // JFJochReader is always using int32_t
         dataset->experiment.BitDepthImage(32);
@@ -65,6 +66,7 @@ std::shared_ptr<JFJochReaderDataset>  JFJochHttpReader::UpdateDataset_i() {
         dataset->experiment.BeamX_pxl(msg->start_message->beam_center_x);
         dataset->experiment.BeamY_pxl(msg->start_message->beam_center_y);
         dataset->experiment.DetectorDistance_mm(msg->start_message->detector_distance * 1000.0);
+        dataset->experiment.DetectIceRings(msg->start_message->detect_ice_rings.value_or(false));
         dataset->az_int_bin_to_q = msg->start_message->az_int_bin_to_q;
         dataset->az_int_bin_to_phi = msg->start_message->az_int_bin_to_phi;
         dataset->q_bins = msg->start_message->az_int_q_bin_count.value_or(0);

reader/JFJochReader.cpp

@@ -72,6 +72,8 @@ void JFJochReader::UpdateGeomMetadata(const DiffractionExperiment &experiment) {
         return;
 
     auto new_dataset = std::make_shared<JFJochReaderDataset>(*dataset);
+    // At the moment subset of options is limited to safe ones...need to change it in the future
+
     new_dataset->experiment.BeamX_pxl(experiment.GetBeamX_pxl());
     new_dataset->experiment.BeamY_pxl(experiment.GetBeamY_pxl());
     new_dataset->experiment.DetectorDistance_mm(experiment.GetDetectorDistance_mm());
@@ -80,7 +82,9 @@ void JFJochReader::UpdateGeomMetadata(const DiffractionExperiment &experiment) {
     new_dataset->experiment.PoniRot2_rad(experiment.GetDatasetSettings().GetPoniRot2_rad());
     new_dataset->experiment.PoniRot3_rad(experiment.GetDatasetSettings().GetPoniRot3_rad());
     new_dataset->experiment.SetUnitCell(experiment.GetUnitCell());
-
+    new_dataset->experiment.ImportIndexingSettings(experiment.GetIndexingSettings());
+    new_dataset->experiment.ImportBraggIntegrationSettings(experiment.GetBraggIntegrationSettings());
+    new_dataset->experiment.DetectIceRings(experiment.IsDetectIceRings());
     dataset = new_dataset;
 }
 

reader/JFJochReaderImage.cpp

@@ -241,3 +241,9 @@ std::vector<float> JFJochReaderImage::GetAzInt1D_BinToQ() const {
     } else
         return {};
 }
+
+std::shared_ptr<JFJochReaderDataset> JFJochReaderImage::CreateMutableDataset() {
+    std::shared_ptr<JFJochReaderDataset> new_dataset = std::make_shared<JFJochReaderDataset>(*dataset);
+    dataset = new_dataset;
+    return new_dataset;
+}

reader/JFJochReaderImage.h

@@ -17,7 +17,7 @@ constexpr static int32_t ERROR_PXL_VALUE = INT32_MIN;
 constexpr static int32_t SATURATED_PXL_VALUE = INT32_MAX;
 
 class JFJochReaderImage {
-    const std::shared_ptr<const JFJochReaderDataset> dataset;
+    std::shared_ptr<const JFJochReaderDataset> dataset;
 
     std::vector<int32_t> image; // Image in the reader must be 32-bit signed, uncompressed
     DataMessage message;
@@ -51,6 +51,8 @@ public:
 
     // Functions that change the content
     void CalcROI(const ROIElement *input);
+
+    std::shared_ptr<JFJochReaderDataset> CreateMutableDataset();
 };
 
 #endif //JFJOCH_JFJOCHREADERIMAGE_H