Merge branch '2406-crmx' into 'main'

Release 1.0.0_rc.9

See merge request jungfraujoch/nextgendcu!70

.gitlab-ci.yml

@@ -316,11 +316,8 @@ release:
     - export PACKAGE_VERSION=`head -n1 VERSION`
     - export PACKAGE_REGISTRY_URL="${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/jungfraujoch/${PACKAGE_VERSION}"
     - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm"'
-    - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms.el8.noarch.rpm"'
     - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm"'
-    - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-writer.el8.x86_64.rpm"'
     - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm"'
-    - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm "${PACKAGE_REGISTRY_URL}/jfjoch.el8.x86_64.rpm"'
     - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch_driver.tar.gz "${PACKAGE_REGISTRY_URL}/jfjoch_driver.tar.gz"'
     - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch_frontend.tar.gz "${PACKAGE_REGISTRY_URL}/jfjoch_frontend.tar.gz"'
     - 'curl --header "JOB-TOKEN: $CI_JOB_TOKEN" --upload-file jfjoch_fpga_pcie_100g.mcs "${PACKAGE_REGISTRY_URL}/jfjoch_fpga_pcie_100g.mcs"'
@@ -331,9 +328,6 @@ release:
       --assets-link "{\"name\":\"jfjoch_frontend.tar.gz\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch_frontend.tar.gz\"}"
       --assets-link "{\"name\":\"jfjoch_fpga_pcie_8x10g.mcs\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch_fpga_pcie_8x10g.mcs\"}"
       --assets-link "{\"name\":\"jfjoch_fpga_pcie_100g.mcs\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch_fpga_pcie_100g.mcs\"}"
-      --assets-link "{\"name\":\"jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm\"}"
-      --assets-link "{\"name\":\"jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm\"}"
-      --assets-link "{\"name\":\"jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm\"}"
-      --assets-link "{\"name\":\"jfjoch.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch.el8.x86_64.rpm\"}"
-      --assets-link "{\"name\":\"jfjoch-writer.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-writer.el8.x86_64.rpm\"}"
-      --assets-link "{\"name\":\"jfjoch-driver-dkms.el8.noarch.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms.el8.noarch.rpm\"}"
+      --assets-link "{\"name\":\"jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"link_type\":\"package\"}"
+      --assets-link "{\"name\":\"jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-writer-${PACKAGE_VERSION}-1.el8.x86_64.rpm\",\"link_type\":\"package\"}"
+      --assets-link "{\"name\":\"jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm\",\"url\":\"${PACKAGE_REGISTRY_URL}/jfjoch-driver-dkms-${PACKAGE_VERSION}-1.el8.noarch.rpm\",\"link_type\":\"package\"}"

CMakeLists.txt

@@ -161,6 +161,7 @@ SET(CPACK_RPM_DRIVER-DKMS_PACKAGE_REQUIRES "dkms, gcc, bash, sed")
 SET(CPACK_RPM_DRIVER-DKMS_PACKAGE_ARCHITECTURE "noarch")
 SET(CPACK_RPM_DRIVER-DKMS_POST_INSTALL_SCRIPT_FILE ${CMAKE_CURRENT_SOURCE_DIR}/fpga/pcie_driver/postinstall.sh)
 SET(CPACK_RPM_DRIVER-DKMS_PRE_UNINSTALL_SCRIPT_FILE ${CMAKE_CURRENT_SOURCE_DIR}/fpga/pcie_driver/preuninstall.sh)
+SET(CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION /usr/src)
 
 # Set The Vendor Name
 SET(CPACK_PACKAGE_VENDOR "Paul Scherrer Institut")

README.md

@@ -7,6 +7,7 @@ Citation: F. Leonarski, M. Bruckner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadle
 The project is supported by :
 * Innosuisse via Innovation Project "NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications" (101.535.1 IP-ENG; Apr 2023 - Sep 2025).
 * ETH Domain via Open Research Data Contribute project (Jan - Dec 2023)
+* AMD University Program with donation of licenses of Ethernet IP cores and Vivado software
 
 ## License
 

VERSION

@@ -1 +1 @@
-1.0.0_rc.6
+1.0.0_rc.9

broker/JFJochBrokerHttp.cpp

@@ -4,6 +4,7 @@
 #include <nlohmann/json.hpp>
 #include "JFJochBrokerHttp.h"
 #include "gen/model/Error_message.h"
+#include "../preview/JFJochTIFF.h"
 
 // From https://en.cppreference.com/w/cpp/string/byte/tolower
 inline std::string str_tolower(std::string s) {
@@ -22,6 +23,10 @@ inline SpotFindingSettings Convert(const org::openapitools::server::model::Spot_
     ret.enable = input.isEnable();
     ret.indexing = input.isIndexing();
     ret.indexing_tolerance = input.getIndexingTolerance();
+    if (input.filterPowderRingsIsSet())
+        ret.filter_spots_powder_ring = input.isFilterPowderRings();
+    if (input.minSpotCountPowderRingIsSet())
+        ret.min_spot_count_powder_ring = input.getMinSpotCountPowderRing();
     return ret;
 }
 
@@ -36,6 +41,8 @@ inline org::openapitools::server::model::Spot_finding_settings Convert(const Spo
     ret.setEnable(input.enable);
     ret.setIndexing(input.indexing);
     ret.setIndexingTolerance(input.indexing_tolerance);
+    ret.setFilterPowderRings(input.filter_spots_powder_ring);
+    ret.setMinSpotCountPowderRing(input.min_spot_count_powder_ring);
     return ret;
 }
 
@@ -45,6 +52,7 @@ inline org::openapitools::server::model::Measurement_statistics Convert(const Me
     if (!input.file_prefix.empty())
         ret.setFilePrefix(input.file_prefix);
 
+    ret.setExperimentGroup(input.experiment_group);
     ret.setImagesExpected(input.images_expected);
     ret.setImagesCollected(input.images_collected);
     ret.setImagesSent(input.images_sent);
@@ -68,7 +76,7 @@ inline org::openapitools::server::model::Measurement_statistics Convert(const Me
     if (input.bkg_estimate)
         ret.setBkgEstimate(input.bkg_estimate.value());
     ret.setUnitCell(input.unit_cell);
-
+    ret.setRunNumber(input.run_number);
     return ret;
 }
 
@@ -185,10 +193,10 @@ inline org::openapitools::server::model::Detector_status Convert(const DetectorS
     output.setHighVoltageV(input.high_voltage_V);
     switch (input.power_state) {
         case DetectorPowerState::ON:
-            output.setPowerchip("On");
+            output.setPowerchip("PowerOn");
             break;
         case DetectorPowerState::OFF:
-            output.setPowerchip("Off");
+            output.setPowerchip("PowerOff");
             break;
         case DetectorPowerState::PARTIAL:
             output.setPowerchip("Partial");
@@ -317,6 +325,7 @@ inline PreviewJPEGSettings Convert(const org::openapitools::server::model::Previ
     ret.saturation_value = input.getSaturation();
     ret.show_roi = input.isShowRoi();
     ret.show_indexed = input.isShowIndexed();
+    ret.show_user_mask = input.isShowUserMask();
     if (input.resolutionRingIsSet())
         ret.resolution_ring = input.getResolutionRing();
     return ret;
@@ -328,6 +337,10 @@ inline DatasetSettings Convert(const org::openapitools::server::model::Dataset_s
     ret.ImagesPerTrigger(input.getImagesPerTrigger());
     ret.NumTriggers(input.getNtrigger());
 
+    if (input.runNumberIsSet())
+        ret.RunNumber(input.getRunNumber());
+    ret.ExperimentGroup(input.getExperimentGroup());
+
     if (!input.fpgaOutputIsSet())
         ret.FPGAOutputMode(FPGAPixelOutput::Auto);
     else {
@@ -350,9 +363,8 @@ inline DatasetSettings Convert(const org::openapitools::server::model::Dataset_s
     ret.BeamX_pxl(input.getBeamXPxl());
     ret.BeamY_pxl(input.getBeamYPxl());
     ret.DetectorDistance_mm(input.getDetectorDistanceMm());
-    ret.PhotonEnergy_keV(input.getPhotonEnergyKeV());
-
-    ret.PhotonEnergyMultiplayer(input.getPhotonEnergyMultiplier());
+    ret.PhotonEnergy_keV(input.getIncidentEnergyKeV());
+    ret.PhotonEnergyMultiplayer(input.getEnergyMultiplier());
 
     ret.FilePrefix(input.getFilePrefix());
 
@@ -387,12 +399,15 @@ inline DatasetSettings Convert(const org::openapitools::server::model::Dataset_s
     if (input.transmissionIsSet())
         ret.AttenuatorTransmission(input.getTransmission());
 
-    if (input.omegaIsSet()) {
-        ret.OmegaStep(input.getOmega().getStep());
-        ret.OmegaStart(input.getOmega().getStart());
-        if (input.getOmega().getVector().size() == 3) {
-            auto v = input.getOmega().getVector();
-            ret.OmegaAxis(Coord(v[0], v[1], v[2]));
+    if (input.goniometerIsSet()) {
+        ret.Goniometer(GoniometerAxis{
+                .name = input.getGoniometer().getName(),
+                .increment = input.getGoniometer().getStep(),
+                .start = input.getGoniometer().getStart()
+        });
+        if (input.getGoniometer().getVector().size() == 3) {
+            auto v = input.getGoniometer().getVector();
+            ret.RotationAxis(Coord(v[0], v[1], v[2]));
         }
     }
 
@@ -655,18 +670,33 @@ void JFJochBrokerHttp::preview_image_tiff_get(Pistache::Http::ResponseWriter &re
 void JFJochBrokerHttp::config_internal_generator_image_put(const Pistache::Rest::Request &request,
                                                            Pistache::Http::ResponseWriter &response) {
     int64_t image_number = 0;
-    auto number_query = request.query().get("number");
+    auto number_query = request.query().get("id");
     if (number_query)
         image_number = std::stoi(number_query.value());
 
     if ((image_number < 0) || (image_number > 127))
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "image_number must be in range 0-127");
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "id must be in range 0-127");
 
     state_machine.LoadInternalGeneratorImage(request.body().data(), request.body().size(), image_number);
     logger.Info("Internal generator image #{} loaded", image_number);
     response.send(Pistache::Http::Code::Ok);
 }
 
+
+void JFJochBrokerHttp::config_internal_generator_image_tiff_put(const Pistache::Rest::Request &request,
+                                                                Pistache::Http::ResponseWriter &response) {
+    int64_t image_number = 0;
+    auto number_query = request.query().get("id");
+    if (number_query)
+        image_number = std::stoi(number_query.value());
+
+    if ((image_number < 0) || (image_number > 127))
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "id must be in range 0-127");
+
+    state_machine.LoadInternalGeneratorImageTIFF(request.body(), image_number);
+    response.send(Pistache::Http::Code::Ok);
+}
+
 void JFJochBrokerHttp::roi_box_get(Pistache::Http::ResponseWriter &response) {
     ProcessOutput(Convert(state_machine.GetBoxROI()), response);
 }
@@ -782,3 +812,19 @@ void JFJochBrokerHttp::plot_strong_pixel_get(const std::optional<int32_t> &binni
                                              Pistache::Http::ResponseWriter &response) {
     GenericPlot(PlotType::StrongPixels, binning, response);
 }
+
+void JFJochBrokerHttp::config_mask_tiff_get(Pistache::Http::ResponseWriter &response) {
+    std::string s = state_machine.GetFullPixelMaskTIFF();
+    response.send(Pistache::Http::Code::Ok, s, Pistache::Http::Mime::MediaType::fromString("image/tiff"));
+}
+
+void JFJochBrokerHttp::config_user_mask_tiff_get(Pistache::Http::ResponseWriter &response) {
+    std::string s = state_machine.GetUserPixelMaskTIFF();
+    response.send(Pistache::Http::Code::Ok, s, Pistache::Http::Mime::MediaType::fromString("image/tiff"));
+}
+
+void JFJochBrokerHttp::config_user_mask_tiff_put(const Pistache::Rest::Request &request,
+                                                  Pistache::Http::ResponseWriter &response) {
+    state_machine.SetUserPixelMask(request.body());
+    response.send(Pistache::Http::Code::Ok);
+}

broker/JFJochBrokerHttp.h

@@ -118,6 +118,16 @@ class JFJochBrokerHttp : public org::openapitools::server::api::DefaultApi {
     void xfel_event_code_get(Pistache::Http::ResponseWriter &response) override;
     void xfel_pulse_id_get(Pistache::Http::ResponseWriter &response) override;
 
+    void config_mask_tiff_get(Pistache::Http::ResponseWriter &response) override;
+
+    void config_user_mask_tiff_get(Pistache::Http::ResponseWriter &response) override;
+
+    void config_user_mask_tiff_put(const Pistache::Rest::Request &request,
+                                    Pistache::Http::ResponseWriter &response) override;
+
+    void config_internal_generator_image_tiff_put(const Pistache::Rest::Request &request,
+                                                  Pistache::Http::ResponseWriter &response) override;
+
     void GetStaticFile(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     std::pair<Pistache::Http::Code, std::string> handleOperationException(const std::exception &ex) const noexcept override;
 

broker/JFJochBrokerParser.cpp

@@ -304,19 +304,21 @@ void ParseFacilityConfiguration(const nlohmann::json &input, const std::string&
         auto j = input[tag];
         experiment.SourceName(GET_STR(j, "source_name"));
         experiment.SourceNameShort(GET_STR(j, "source_name_short"));
+        experiment.SourceType(GET_STR(j, "source_type", ""));
+
         experiment.InstrumentName(GET_STR(j, "instrument_name"));
         experiment.InstrumentNameShort(GET_STR(j, "instrument_name_short"));
 
         experiment.PulsedSource(GET_BOOL(j, "pulsed_source", false));
 
-        if (j.contains("omega_axis")) {
-            if (j["omega_axis"].is_array() && (j["omega_axis"].size() == 3))
-                experiment.DefaultOmegaAxis(Coord(j["omega_axis"][0].get<float>(),
-                                                  j["omega_axis"][1].get<float>(),
-                                                  j["omega_axis"][2].get<float>()));
+        if (j.contains("rotation_axis")) {
+            if (j["rotation_axis"].is_array() && (j["rotation_axis"].size() == 3))
+                experiment.DefaultRotationAxis(Coord(j["rotation_axis"][0].get<float>(),
+                                                     j["rotation_axis"][1].get<float>(),
+                                                     j["rotation_axis"][2].get<float>()));
             else
                 throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                                      "omega_axis must be float array of 3");
+                                      "rotation_axis must be float array of 3");
         }
 
         if (j.contains("pedestal_g0_frames"))

broker/JFJochServices.cpp

@@ -5,15 +5,17 @@
 
 JFJochServices::JFJochServices(Logger &in_logger) : logger(in_logger) {}
 
-void JFJochServices::Start(const DiffractionExperiment& experiment, const JFCalibration &calibration) {
+void JFJochServices::Start(const DiffractionExperiment& experiment,
+                           const PixelMask &pixel_mask,
+                           const JFCalibration &calibration) {
     logger.Info("Measurement start for: {}", experiment.GetFilePrefix());
 
     if (receiver != nullptr) {
         logger.Info("   ... receiver start");
         if (experiment.GetDetectorMode() == DetectorMode::Conversion)
-            receiver->Start(experiment, &calibration);
+            receiver->Start(experiment, pixel_mask, &calibration);
         else
-            receiver->Start(experiment, nullptr);
+            receiver->Start(experiment, pixel_mask, nullptr);
 
         if (detector && !experiment.IsUsingInternalPacketGen()) {
             logger.Info("   ... detector start");

broker/JFJochServices.h

@@ -23,7 +23,9 @@ public:
     void On(const DiffractionExperiment& experiment);
     void Off();
     void ConfigureDetector(const DiffractionExperiment& experiment);
-    void Start(const DiffractionExperiment& experiment, const JFCalibration &calibration);
+    void Start(const DiffractionExperiment& experiment,
+               const PixelMask &pixel_mask,
+               const JFCalibration &calibration);
     JFJochServicesOutput Stop();
     void Cancel();
     void Trigger();

broker/JFJochStateMachine.cpp

@@ -3,7 +3,7 @@
 #include <thread>
 
 #include "JFJochStateMachine.h"
-#include "../preview/WriteTIFF.h"
+#include "../preview/JFJochTIFF.h"
 
 void ApplyDetectorSettings(DiffractionExperiment& experiment, const DetectorSettings &settings) {
     auto tmp = experiment;
@@ -66,8 +66,10 @@ void ApplyRadialIntegrationSettings(DiffractionExperiment& experiment, const Rad
 }
 
 JFJochStateMachine::JFJochStateMachine(JFJochServices &in_services, Logger &in_logger)
-: services(in_services), logger(in_logger),
-data_processing_settings(DiffractionExperiment::DefaultDataProcessingSettings()) {
+        : services(in_services),
+          logger(in_logger),
+          data_processing_settings(DiffractionExperiment::DefaultDataProcessingSettings()),
+          pixel_mask(experiment) {
 
 }
 
@@ -126,6 +128,7 @@ void JFJochStateMachine::TakePedestalInternalAll(std::unique_lock<std::mutex> &u
             }
         }
         services.ConfigureDetector(experiment);
+        pixel_mask.LoadDetectorBadPixelMask(calibration->CalculateMask());
     } catch (const std::exception &e) {
         logger.Error("Pedestal sequence error {}", e.what());
         state = JFJochState::Error;
@@ -158,7 +161,7 @@ void JFJochStateMachine::TakePedestalInternalG0(std::unique_lock<std::mutex> &ul
 
     state = JFJochState::Pedestal;
     services.ConfigureDetector(local_experiment);
-    services.Start(local_experiment, *calibration);
+    services.Start(local_experiment, pixel_mask, *calibration);
 
     services.Trigger();
 
@@ -197,7 +200,7 @@ void JFJochStateMachine::TakePedestalInternalG1(std::unique_lock<std::mutex> &ul
 
     state = JFJochState::Pedestal;
     services.ConfigureDetector(local_experiment);
-    services.Start(local_experiment, *calibration);
+    services.Start(local_experiment, pixel_mask, *calibration);
 
     services.Trigger();
 
@@ -236,7 +239,7 @@ void JFJochStateMachine::TakePedestalInternalG2(std::unique_lock<std::mutex> &ul
 
     state = JFJochState::Pedestal;
     services.ConfigureDetector(local_experiment);
-    services.Start(local_experiment, *calibration);
+    services.Start(local_experiment, pixel_mask, *calibration);
 
     services.Trigger();
 
@@ -321,12 +324,12 @@ void JFJochStateMachine::Start(const DatasetSettings& settings) {
     else
         experiment.StorageCellStart(0);
 
-    experiment.IncrementSeriesID();
+    experiment.IncrementRunNumber();
 
     try {
         state = JFJochState::Busy;
         services.SetSpotFindingSettings(GetSpotFindingSettings());
-        services.Start(experiment, *calibration);
+        services.Start(experiment, pixel_mask, *calibration);
 
         state = JFJochState::Measuring;
         measurement = std::async(std::launch::async, &JFJochStateMachine::MeasurementThread, this);
@@ -398,6 +401,9 @@ void JFJochStateMachine::SetFullMeasurementOutput(const JFJochServicesOutput &ou
     MeasurementStatistics tmp{}; // reset last measurement statistics
 
     tmp.file_prefix = experiment.GetFilePrefix();
+    tmp.run_number = experiment.GetRunNumber();
+    tmp.experiment_group = experiment.GetExperimentGroup();
+
     tmp.detector_width = experiment.GetXPixelsNum();
     tmp.detector_height = experiment.GetYPixelsNum();
     tmp.detector_pixel_depth = experiment.GetPixelDepth();
@@ -424,6 +430,9 @@ void JFJochStateMachine::ClearAndSetMeasurementStatistics() {
     MeasurementStatistics tmp{};
 
     tmp.file_prefix = experiment.GetFilePrefix();
+    tmp.run_number = experiment.GetRunNumber();
+    tmp.experiment_group = experiment.GetExperimentGroup();
+
     tmp.detector_height = experiment.GetXPixelsNum();
     tmp.detector_width = experiment.GetYPixelsNum();
     tmp.detector_pixel_depth = experiment.GetPixelDepth();
@@ -445,6 +454,9 @@ std::optional<MeasurementStatistics> JFJochStateMachine::GetMeasurementStatistic
         MeasurementStatistics tmp;
 
         tmp.file_prefix = experiment.GetFilePrefix();
+        tmp.run_number = experiment.GetRunNumber();
+        tmp.experiment_group = experiment.GetExperimentGroup();
+
         tmp.detector_width = experiment.GetXPixelsNum();
         tmp.detector_height = experiment.GetYPixelsNum();
         tmp.detector_pixel_depth = experiment.GetPixelDepth();
@@ -562,6 +574,7 @@ void JFJochStateMachine::AddDetectorSetup(const DetectorSetup &setup) {
         experiment.Detector(setup);
         gain_calibration = setup.GetGainCalibration();
         current_detector_setup = 0;
+        pixel_mask = PixelMask(setup);
     }
     detector_setup.emplace_back(setup);
 }
@@ -599,6 +612,7 @@ void JFJochStateMachine::SelectDetector(int64_t id) {
     try {
         experiment.Detector(detector_setup[id]);
         gain_calibration = detector_setup[id].GetGainCalibration();
+        pixel_mask = PixelMask(detector_setup[id]);
         state = JFJochState::Inactive;
         current_detector_setup = id;
     } catch (JFJochException &e) {
@@ -705,6 +719,21 @@ void JFJochStateMachine::LoadInternalGeneratorImage(const void *data, size_t siz
     services.LoadInternalGeneratorImage(experiment, image, image_number);
 }
 
+void JFJochStateMachine::LoadInternalGeneratorImageTIFF(const std::string &s, uint64_t image_number) {
+    std::unique_lock<std::mutex> ul(m);
+
+    if (state != JFJochState::Idle)
+        throw WrongDAQStateException ("Can change internal generator image only when detector in Idle state");
+
+    uint32_t cols, lines;
+    auto v = ReadTIFFFromString16(s, cols, lines);
+    if (((cols == experiment.GetXPixelsNum()) && (lines == experiment.GetYPixelsNum()))
+        || ((cols == RAW_MODULE_SIZE) && (lines == RAW_MODULE_LINES * experiment.GetModulesNum())))
+        services.LoadInternalGeneratorImage(experiment, v, image_number);
+    else
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image size doesn't match current detector");
+}
+
 void JFJochStateMachine::SetBoxROI(const std::vector<ROIBox> &input) {
     std::unique_lock<std::mutex> ul(m);
 
@@ -744,3 +773,33 @@ std::vector<uint64_t> JFJochStateMachine::GetXFELEventCode() const {
     services.GetXFELEventCode(ret);
     return ret;
 }
+
+std::string JFJochStateMachine::GetFullPixelMaskTIFF() const {
+    std::unique_lock<std::mutex> ul(m);
+    std::vector v = pixel_mask.GetMask(experiment);
+    return WriteTIFFToString(v.data(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum(),
+                             sizeof(uint32_t), false);
+}
+
+std::string JFJochStateMachine::GetUserPixelMaskTIFF() const {
+    std::unique_lock<std::mutex> ul(m);
+    std::vector v = pixel_mask.GetUserMask(experiment);
+    return WriteTIFFToString(v.data(), experiment.GetXPixelsNum(), experiment.GetYPixelsNum(),
+                             sizeof(uint32_t), false);
+}
+
+void JFJochStateMachine::SetUserPixelMask(const std::string &s) {
+    std::unique_lock<std::mutex> ul(m);
+
+    if (state != JFJochState::Idle)
+        throw WrongDAQStateException ("User mask can be only modified in Idle state");
+
+    try {
+        uint32_t cols, lines;
+        auto v = ReadTIFFFromString32(s, cols, lines);
+        pixel_mask.LoadUserMask(experiment, v);
+    } catch (const JFJochException &e) {
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "Problem handling user mask " + std::string(e.what()));
+    }
+}

broker/JFJochStateMachine.h

@@ -37,6 +37,9 @@ struct DetectorList {
 
 struct MeasurementStatistics {
     std::string file_prefix;
+    std::string experiment_group;
+    int64_t run_number;
+
     int64_t images_expected;
     int64_t images_collected;
     int64_t images_sent;
@@ -98,6 +101,8 @@ class JFJochStateMachine {
     volatile JFJochState state = JFJochState::Inactive;
     volatile bool cancel_sequence = false;
     std::unique_ptr<JFCalibration> calibration;
+    PixelMask pixel_mask;
+
     std::vector<JFModuleGainCalibration> gain_calibration;
     std::vector<DetectorSetup> detector_setup;
     int64_t current_detector_setup;
@@ -172,6 +177,7 @@ public:
     std::string GetPedestalTIFF(size_t gain_level, size_t sc) const;
 
     void LoadInternalGeneratorImage(const void *data, size_t size, uint64_t image_number);
+    void LoadInternalGeneratorImageTIFF(const std::string &s, uint64_t image_number);
 
     // Not thread safe - only for configuration in serial context
     DiffractionExperiment& NotThreadSafe_Experiment();
@@ -187,6 +193,10 @@ public:
 
     std::vector<uint64_t> GetXFELPulseID() const;
     std::vector<uint64_t> GetXFELEventCode() const;
+
+    std::string GetFullPixelMaskTIFF() const;
+    std::string GetUserPixelMaskTIFF() const;
+    void SetUserPixelMask(const std::string &v);
 };
 
 

broker/gen/api/DefaultApi.cpp

@@ -37,12 +37,16 @@ void DefaultApi::setupRoutes() {
     Routes::Get(*router, base + "/config/detector", Routes::bind(&DefaultApi::config_detector_get_handler, this));
     Routes::Put(*router, base + "/config/detector", Routes::bind(&DefaultApi::config_detector_put_handler, this));
     Routes::Put(*router, base + "/config/internal_generator_image", Routes::bind(&DefaultApi::config_internal_generator_image_put_handler, this));
+    Routes::Put(*router, base + "/config/internal_generator_image.tiff", Routes::bind(&DefaultApi::config_internal_generator_image_tiff_put_handler, this));
+    Routes::Get(*router, base + "/config/mask.tiff", Routes::bind(&DefaultApi::config_mask_tiff_get_handler, this));
     Routes::Get(*router, base + "/config/rad_int", Routes::bind(&DefaultApi::config_rad_int_get_handler, this));
     Routes::Put(*router, base + "/config/rad_int", Routes::bind(&DefaultApi::config_rad_int_put_handler, this));
     Routes::Get(*router, base + "/config/select_detector", Routes::bind(&DefaultApi::config_select_detector_get_handler, this));
     Routes::Put(*router, base + "/config/select_detector", Routes::bind(&DefaultApi::config_select_detector_put_handler, this));
     Routes::Get(*router, base + "/config/spot_finding", Routes::bind(&DefaultApi::config_spot_finding_get_handler, this));
     Routes::Put(*router, base + "/config/spot_finding", Routes::bind(&DefaultApi::config_spot_finding_put_handler, this));
+    Routes::Get(*router, base + "/config/user_mask.tiff", Routes::bind(&DefaultApi::config_user_mask_tiff_get_handler, this));
+    Routes::Put(*router, base + "/config/user_mask.tiff", Routes::bind(&DefaultApi::config_user_mask_tiff_put_handler, this));
     Routes::Post(*router, base + "/deactivate", Routes::bind(&DefaultApi::deactivate_post_handler, this));
     Routes::Get(*router, base + "/detector/status", Routes::bind(&DefaultApi::detector_status_get_handler, this));
     Routes::Post(*router, base + "/initialize", Routes::bind(&DefaultApi::initialize_post_handler, this));
@@ -192,6 +196,45 @@ void DefaultApi::config_internal_generator_image_put_handler(const Pistache::Res
         response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
     }
 
+}
+void DefaultApi::config_internal_generator_image_tiff_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response) {
+    try {
+
+    try {
+      this->config_internal_generator_image_tiff_put(request, response);
+    } catch (Pistache::Http::HttpError &e) {
+        response.send(static_cast<Pistache::Http::Code>(e.code()), e.what());
+        return;
+    } catch (std::exception &e) {
+        const std::pair<Pistache::Http::Code, std::string> errorInfo = this->handleOperationException(e);
+        response.send(errorInfo.first, errorInfo.second);
+        return;
+    }
+
+    } catch (std::exception &e) {
+        response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
+    }
+
+}
+void DefaultApi::config_mask_tiff_get_handler(const Pistache::Rest::Request &, Pistache::Http::ResponseWriter response) {
+    try {
+
+
+    try {
+        this->config_mask_tiff_get(response);
+    } catch (Pistache::Http::HttpError &e) {
+        response.send(static_cast<Pistache::Http::Code>(e.code()), e.what());
+        return;
+    } catch (std::exception &e) {
+        const std::pair<Pistache::Http::Code, std::string> errorInfo = this->handleOperationException(e);
+        response.send(errorInfo.first, errorInfo.second);
+        return;
+    }
+
+    } catch (std::exception &e) {
+        response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
+    }
+
 }
 void DefaultApi::config_rad_int_get_handler(const Pistache::Rest::Request &, Pistache::Http::ResponseWriter response) {
     try {
@@ -351,6 +394,45 @@ void DefaultApi::config_spot_finding_put_handler(const Pistache::Rest::Request &
         response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
     }
 
+}
+void DefaultApi::config_user_mask_tiff_get_handler(const Pistache::Rest::Request &, Pistache::Http::ResponseWriter response) {
+    try {
+
+
+    try {
+        this->config_user_mask_tiff_get(response);
+    } catch (Pistache::Http::HttpError &e) {
+        response.send(static_cast<Pistache::Http::Code>(e.code()), e.what());
+        return;
+    } catch (std::exception &e) {
+        const std::pair<Pistache::Http::Code, std::string> errorInfo = this->handleOperationException(e);
+        response.send(errorInfo.first, errorInfo.second);
+        return;
+    }
+
+    } catch (std::exception &e) {
+        response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
+    }
+
+}
+void DefaultApi::config_user_mask_tiff_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response) {
+    try {
+
+    try {
+      this->config_user_mask_tiff_put(request, response);
+    } catch (Pistache::Http::HttpError &e) {
+        response.send(static_cast<Pistache::Http::Code>(e.code()), e.what());
+        return;
+    } catch (std::exception &e) {
+        const std::pair<Pistache::Http::Code, std::string> errorInfo = this->handleOperationException(e);
+        response.send(errorInfo.first, errorInfo.second);
+        return;
+    }
+
+    } catch (std::exception &e) {
+        response.send(Pistache::Http::Code::Internal_Server_Error, e.what());
+    }
+
 }
 void DefaultApi::deactivate_post_handler(const Pistache::Rest::Request &, Pistache::Http::ResponseWriter response) {
     try {

broker/gen/api/DefaultApi.h

@@ -61,12 +61,16 @@ private:
     void config_detector_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_detector_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_internal_generator_image_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
+    void config_internal_generator_image_tiff_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
+    void config_mask_tiff_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_rad_int_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_rad_int_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_select_detector_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_select_detector_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_spot_finding_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void config_spot_finding_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
+    void config_user_mask_tiff_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
+    void config_user_mask_tiff_put_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void deactivate_post_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void detector_status_get_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
     void initialize_post_handler(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter response);
@@ -150,6 +154,20 @@ private:
     /// </remarks>
     virtual void config_internal_generator_image_put(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter &response) = 0;
     /// <summary>
+    /// Load TIFF image for internal FPGA generator
+    /// </summary>
+    /// <remarks>
+    /// Load image for internal FPGA generator. This can only happen in Idle state of the detector. Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates  (depending on detector settings). 
+    /// </remarks>
+    virtual void config_internal_generator_image_tiff_put(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter &response) = 0;
+    /// <summary>
+    /// Get mask of the detector
+    /// </summary>
+    /// <remarks>
+    /// Get full pixel mask of the detector See NXmx standard for meaning of pixel values 
+    /// </remarks>
+    virtual void config_mask_tiff_get(Pistache::Http::ResponseWriter &response) = 0;
+    /// <summary>
     /// Get radial integration configuration
     /// </summary>
     /// <remarks>
@@ -195,6 +213,20 @@ private:
     /// <param name="spotFindingSettings"> (optional)</param>
     virtual void config_spot_finding_put(const org::openapitools::server::model::Spot_finding_settings &spotFindingSettings, Pistache::Http::ResponseWriter &response) = 0;
     /// <summary>
+    /// Get user mask of the detector
+    /// </summary>
+    /// <remarks>
+    /// Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
+    /// </remarks>
+    virtual void config_user_mask_tiff_get(Pistache::Http::ResponseWriter &response) = 0;
+    /// <summary>
+    /// Upload user mask of the detector
+    /// </summary>
+    /// <remarks>
+    /// Should be in &#x60;Idle&#x60; state. Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions. If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates. In the latter case - module gaps are ignored and don&#39;t need to be assigned value. Mask is expected as TIFF (4-byte; unsigned). 0 - good pixel, other value - masked User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.  User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images. 
+    /// </remarks>
+    virtual void config_user_mask_tiff_put(const Pistache::Rest::Request &request, Pistache::Http::ResponseWriter &response) = 0;
+    /// <summary>
     /// Prepare detector to turn off
     /// </summary>
     /// <remarks>

broker/gen/model/Dataset_settings.cpp

@@ -30,7 +30,7 @@ Dataset_settings::Dataset_settings()
     m_Beam_x_pxl = 0.0f;
     m_Beam_y_pxl = 0.0f;
     m_Detector_distance_mm = 0.0f;
-    m_Photon_energy_keV = 0.0f;
+    m_Incident_energy_keV = 0.0f;
     m_File_prefix = "";
     m_File_prefixIsSet = false;
     m_Images_per_file = 1000L;
@@ -46,15 +46,19 @@ Dataset_settings::Dataset_settings()
     m_Total_fluxIsSet = false;
     m_Transmission = 0.0f;
     m_TransmissionIsSet = false;
-    m_OmegaIsSet = false;
+    m_GoniometerIsSet = false;
     m_Header_appendix = "";
     m_Header_appendixIsSet = false;
     m_Image_appendix = "";
     m_Image_appendixIsSet = false;
-    m_Photon_energy_multiplier = 1.0f;
-    m_Photon_energy_multiplierIsSet = false;
+    m_Energy_multiplier = 1.0f;
+    m_Energy_multiplierIsSet = false;
     m_Data_reduction_factor_serialmx = 1.0f;
     m_Data_reduction_factor_serialmxIsSet = false;
+    m_Run_number = 0L;
+    m_Run_numberIsSet = false;
+    m_Experiment_group = "";
+    m_Experiment_groupIsSet = false;
     m_Unit_cellIsSet = false;
     
 }
@@ -141,9 +145,9 @@ bool Dataset_settings::validate(std::stringstream& msg, const std::string& pathP
     }
          
     
-    /* Photon_energy_keV */ {
-        const float& value = m_Photon_energy_keV;
-        const std::string currentValuePath = _pathPrefix + ".photonEnergyKeV";
+    /* Incident_energy_keV */ {
+        const float& value = m_Incident_energy_keV;
+        const std::string currentValuePath = _pathPrefix + ".incidentEnergyKeV";
                 
         
         if (value < static_cast<float>(0))
@@ -206,10 +210,10 @@ bool Dataset_settings::validate(std::stringstream& msg, const std::string& pathP
 
     }
                      
-    if (photonEnergyMultiplierIsSet())
+    if (energyMultiplierIsSet())
     {
-        const float& value = m_Photon_energy_multiplier;
-        const std::string currentValuePath = _pathPrefix + ".photonEnergyMultiplier";
+        const float& value = m_Energy_multiplier;
+        const std::string currentValuePath = _pathPrefix + ".energyMultiplier";
                 
         
         if (value < static_cast<float>(0.015625))
@@ -243,7 +247,21 @@ bool Dataset_settings::validate(std::stringstream& msg, const std::string& pathP
         }
 
     }
+         
+    if (runNumberIsSet())
+    {
+        const int64_t& value = m_Run_number;
+        const std::string currentValuePath = _pathPrefix + ".runNumber";
+                
         
+        if (value < 0ll)
+        {
+            success = false;
+            msg << currentValuePath << ": must be greater than or equal to 0;";
+        }
+
+    }
+            
     return success;
 }
 
@@ -270,7 +288,7 @@ bool Dataset_settings::operator==(const Dataset_settings& rhs) const
     (getDetectorDistanceMm() == rhs.getDetectorDistanceMm())
      &&
     
-    (getPhotonEnergyKeV() == rhs.getPhotonEnergyKeV())
+    (getIncidentEnergyKeV() == rhs.getIncidentEnergyKeV())
      &&
     
     
@@ -298,7 +316,7 @@ bool Dataset_settings::operator==(const Dataset_settings& rhs) const
     ((!transmissionIsSet() && !rhs.transmissionIsSet()) || (transmissionIsSet() && rhs.transmissionIsSet() && getTransmission() == rhs.getTransmission())) &&
     
     
-    ((!omegaIsSet() && !rhs.omegaIsSet()) || (omegaIsSet() && rhs.omegaIsSet() && getOmega() == rhs.getOmega())) &&
+    ((!goniometerIsSet() && !rhs.goniometerIsSet()) || (goniometerIsSet() && rhs.goniometerIsSet() && getGoniometer() == rhs.getGoniometer())) &&
     
     
     ((!headerAppendixIsSet() && !rhs.headerAppendixIsSet()) || (headerAppendixIsSet() && rhs.headerAppendixIsSet() && getHeaderAppendix() == rhs.getHeaderAppendix())) &&
@@ -307,12 +325,18 @@ bool Dataset_settings::operator==(const Dataset_settings& rhs) const
     ((!imageAppendixIsSet() && !rhs.imageAppendixIsSet()) || (imageAppendixIsSet() && rhs.imageAppendixIsSet() && getImageAppendix() == rhs.getImageAppendix())) &&
     
     
-    ((!photonEnergyMultiplierIsSet() && !rhs.photonEnergyMultiplierIsSet()) || (photonEnergyMultiplierIsSet() && rhs.photonEnergyMultiplierIsSet() && getPhotonEnergyMultiplier() == rhs.getPhotonEnergyMultiplier())) &&
+    ((!energyMultiplierIsSet() && !rhs.energyMultiplierIsSet()) || (energyMultiplierIsSet() && rhs.energyMultiplierIsSet() && getEnergyMultiplier() == rhs.getEnergyMultiplier())) &&
     
     
     ((!dataReductionFactorSerialmxIsSet() && !rhs.dataReductionFactorSerialmxIsSet()) || (dataReductionFactorSerialmxIsSet() && rhs.dataReductionFactorSerialmxIsSet() && getDataReductionFactorSerialmx() == rhs.getDataReductionFactorSerialmx())) &&
     
     
+    ((!runNumberIsSet() && !rhs.runNumberIsSet()) || (runNumberIsSet() && rhs.runNumberIsSet() && getRunNumber() == rhs.getRunNumber())) &&
+    
+    
+    ((!experimentGroupIsSet() && !rhs.experimentGroupIsSet()) || (experimentGroupIsSet() && rhs.experimentGroupIsSet() && getExperimentGroup() == rhs.getExperimentGroup())) &&
+    
+    
     ((!unitCellIsSet() && !rhs.unitCellIsSet()) || (unitCellIsSet() && rhs.unitCellIsSet() && getUnitCell() == rhs.getUnitCell()))
     
     ;
@@ -335,7 +359,7 @@ void to_json(nlohmann::json& j, const Dataset_settings& o)
     j["beam_x_pxl"] = o.m_Beam_x_pxl;
     j["beam_y_pxl"] = o.m_Beam_y_pxl;
     j["detector_distance_mm"] = o.m_Detector_distance_mm;
-    j["photon_energy_keV"] = o.m_Photon_energy_keV;
+    j["incident_energy_keV"] = o.m_Incident_energy_keV;
     if(o.filePrefixIsSet())
         j["file_prefix"] = o.m_File_prefix;
     if(o.imagesPerFileIsSet())
@@ -351,16 +375,20 @@ void to_json(nlohmann::json& j, const Dataset_settings& o)
         j["total_flux"] = o.m_Total_flux;
     if(o.transmissionIsSet())
         j["transmission"] = o.m_Transmission;
-    if(o.omegaIsSet())
-        j["omega"] = o.m_Omega;
+    if(o.goniometerIsSet())
+        j["goniometer"] = o.m_Goniometer;
     if(o.headerAppendixIsSet())
         j["header_appendix"] = o.m_Header_appendix;
     if(o.imageAppendixIsSet())
         j["image_appendix"] = o.m_Image_appendix;
-    if(o.photonEnergyMultiplierIsSet())
-        j["photon_energy_multiplier"] = o.m_Photon_energy_multiplier;
+    if(o.energyMultiplierIsSet())
+        j["energy_multiplier"] = o.m_Energy_multiplier;
     if(o.dataReductionFactorSerialmxIsSet())
         j["data_reduction_factor_serialmx"] = o.m_Data_reduction_factor_serialmx;
+    if(o.runNumberIsSet())
+        j["run_number"] = o.m_Run_number;
+    if(o.experimentGroupIsSet())
+        j["experiment_group"] = o.m_Experiment_group;
     if(o.unitCellIsSet())
         j["unit_cell"] = o.m_Unit_cell;
     
@@ -386,7 +414,7 @@ void from_json(const nlohmann::json& j, Dataset_settings& o)
     j.at("beam_x_pxl").get_to(o.m_Beam_x_pxl);
     j.at("beam_y_pxl").get_to(o.m_Beam_y_pxl);
     j.at("detector_distance_mm").get_to(o.m_Detector_distance_mm);
-    j.at("photon_energy_keV").get_to(o.m_Photon_energy_keV);
+    j.at("incident_energy_keV").get_to(o.m_Incident_energy_keV);
     if(j.find("file_prefix") != j.end())
     {
         j.at("file_prefix").get_to(o.m_File_prefix);
@@ -423,10 +451,10 @@ void from_json(const nlohmann::json& j, Dataset_settings& o)
         j.at("transmission").get_to(o.m_Transmission);
         o.m_TransmissionIsSet = true;
     } 
-    if(j.find("omega") != j.end())
+    if(j.find("goniometer") != j.end())
     {
-        j.at("omega").get_to(o.m_Omega);
-        o.m_OmegaIsSet = true;
+        j.at("goniometer").get_to(o.m_Goniometer);
+        o.m_GoniometerIsSet = true;
     } 
     if(j.find("header_appendix") != j.end())
     {
@@ -438,16 +466,26 @@ void from_json(const nlohmann::json& j, Dataset_settings& o)
         j.at("image_appendix").get_to(o.m_Image_appendix);
         o.m_Image_appendixIsSet = true;
     } 
-    if(j.find("photon_energy_multiplier") != j.end())
+    if(j.find("energy_multiplier") != j.end())
     {
-        j.at("photon_energy_multiplier").get_to(o.m_Photon_energy_multiplier);
-        o.m_Photon_energy_multiplierIsSet = true;
+        j.at("energy_multiplier").get_to(o.m_Energy_multiplier);
+        o.m_Energy_multiplierIsSet = true;
     } 
     if(j.find("data_reduction_factor_serialmx") != j.end())
     {
         j.at("data_reduction_factor_serialmx").get_to(o.m_Data_reduction_factor_serialmx);
         o.m_Data_reduction_factor_serialmxIsSet = true;
     } 
+    if(j.find("run_number") != j.end())
+    {
+        j.at("run_number").get_to(o.m_Run_number);
+        o.m_Run_numberIsSet = true;
+    } 
+    if(j.find("experiment_group") != j.end())
+    {
+        j.at("experiment_group").get_to(o.m_Experiment_group);
+        o.m_Experiment_groupIsSet = true;
+    } 
     if(j.find("unit_cell") != j.end())
     {
         j.at("unit_cell").get_to(o.m_Unit_cell);
@@ -531,13 +569,13 @@ void Dataset_settings::setDetectorDistanceMm(float const value)
 {
     m_Detector_distance_mm = value;
 }
-float Dataset_settings::getPhotonEnergyKeV() const
+float Dataset_settings::getIncidentEnergyKeV() const
 {
-    return m_Photon_energy_keV;
+    return m_Incident_energy_keV;
 }
-void Dataset_settings::setPhotonEnergyKeV(float const value)
+void Dataset_settings::setIncidentEnergyKeV(float const value)
 {
-    m_Photon_energy_keV = value;
+    m_Incident_energy_keV = value;
 }
 std::string Dataset_settings::getFilePrefix() const
 {
@@ -666,22 +704,22 @@ void Dataset_settings::unsetTransmission()
 {
     m_TransmissionIsSet = false;
 }
-org::openapitools::server::model::Rotation_axis Dataset_settings::getOmega() const
+org::openapitools::server::model::Rotation_axis Dataset_settings::getGoniometer() const
 {
-    return m_Omega;
+    return m_Goniometer;
 }
-void Dataset_settings::setOmega(org::openapitools::server::model::Rotation_axis const& value)
+void Dataset_settings::setGoniometer(org::openapitools::server::model::Rotation_axis const& value)
 {
-    m_Omega = value;
-    m_OmegaIsSet = true;
+    m_Goniometer = value;
+    m_GoniometerIsSet = true;
 }
-bool Dataset_settings::omegaIsSet() const
+bool Dataset_settings::goniometerIsSet() const
 {
-    return m_OmegaIsSet;
+    return m_GoniometerIsSet;
 }
-void Dataset_settings::unsetOmega()
+void Dataset_settings::unsetGoniometer()
 {
-    m_OmegaIsSet = false;
+    m_GoniometerIsSet = false;
 }
 std::string Dataset_settings::getHeaderAppendix() const
 {
@@ -717,22 +755,22 @@ void Dataset_settings::unsetImage_appendix()
 {
     m_Image_appendixIsSet = false;
 }
-float Dataset_settings::getPhotonEnergyMultiplier() const
+float Dataset_settings::getEnergyMultiplier() const
 {
-    return m_Photon_energy_multiplier;
+    return m_Energy_multiplier;
 }
-void Dataset_settings::setPhotonEnergyMultiplier(float const value)
+void Dataset_settings::setEnergyMultiplier(float const value)
 {
-    m_Photon_energy_multiplier = value;
-    m_Photon_energy_multiplierIsSet = true;
+    m_Energy_multiplier = value;
+    m_Energy_multiplierIsSet = true;
 }
-bool Dataset_settings::photonEnergyMultiplierIsSet() const
+bool Dataset_settings::energyMultiplierIsSet() const
 {
-    return m_Photon_energy_multiplierIsSet;
+    return m_Energy_multiplierIsSet;
 }
-void Dataset_settings::unsetPhoton_energy_multiplier()
+void Dataset_settings::unsetEnergy_multiplier()
 {
-    m_Photon_energy_multiplierIsSet = false;
+    m_Energy_multiplierIsSet = false;
 }
 float Dataset_settings::getDataReductionFactorSerialmx() const
 {
@@ -751,6 +789,40 @@ void Dataset_settings::unsetData_reduction_factor_serialmx()
 {
     m_Data_reduction_factor_serialmxIsSet = false;
 }
+int64_t Dataset_settings::getRunNumber() const
+{
+    return m_Run_number;
+}
+void Dataset_settings::setRunNumber(int64_t const value)
+{
+    m_Run_number = value;
+    m_Run_numberIsSet = true;
+}
+bool Dataset_settings::runNumberIsSet() const
+{
+    return m_Run_numberIsSet;
+}
+void Dataset_settings::unsetRun_number()
+{
+    m_Run_numberIsSet = false;
+}
+std::string Dataset_settings::getExperimentGroup() const
+{
+    return m_Experiment_group;
+}
+void Dataset_settings::setExperimentGroup(std::string const& value)
+{
+    m_Experiment_group = value;
+    m_Experiment_groupIsSet = true;
+}
+bool Dataset_settings::experimentGroupIsSet() const
+{
+    return m_Experiment_groupIsSet;
+}
+void Dataset_settings::unsetExperiment_group()
+{
+    m_Experiment_groupIsSet = false;
+}
 org::openapitools::server::model::Dataset_settings_unit_cell Dataset_settings::getUnitCell() const
 {
     return m_Unit_cell;

broker/gen/model/Dataset_settings.h

@@ -97,10 +97,10 @@ public:
     float getDetectorDistanceMm() const;
     void setDetectorDistanceMm(float const value);
     /// <summary>
-    /// Used to calculate /entry/beam/incident_wavelength in NXmx Incident photon energy in keV 
+    /// Used to calculate /entry/beam/incident_wavelength in NXmx Incident particle (photon, electron) energy in keV 
     /// </summary>
-    float getPhotonEnergyKeV() const;
-    void setPhotonEnergyKeV(float const value);
+    float getIncidentEnergyKeV() const;
+    void setIncidentEnergyKeV(float const value);
     /// <summary>
     /// Prefix for filenames. If left empty, no file will be saved.
     /// </summary>
@@ -158,10 +158,10 @@ public:
     /// <summary>
     /// 
     /// </summary>
-    org::openapitools::server::model::Rotation_axis getOmega() const;
-    void setOmega(org::openapitools::server::model::Rotation_axis const& value);
-    bool omegaIsSet() const;
-    void unsetOmega();
+    org::openapitools::server::model::Rotation_axis getGoniometer() const;
+    void setGoniometer(org::openapitools::server::model::Rotation_axis const& value);
+    bool goniometerIsSet() const;
+    void unsetGoniometer();
     /// <summary>
     /// Header appendix, added as user_data to start message
     /// </summary>
@@ -177,12 +177,12 @@ public:
     bool imageAppendixIsSet() const;
     void unsetImage_appendix();
     /// <summary>
-    /// For JUNGFRAU conversion it is possible to multiply energy by a given factor to get fractional/multiplied photon counts
+    /// For JUNGFRAU conversion it is possible to multiply incident energy by a given factor to get fractional/multiplied particle counts
     /// </summary>
-    float getPhotonEnergyMultiplier() const;
-    void setPhotonEnergyMultiplier(float const value);
-    bool photonEnergyMultiplierIsSet() const;
-    void unsetPhoton_energy_multiplier();
+    float getEnergyMultiplier() const;
+    void setEnergyMultiplier(float const value);
+    bool energyMultiplierIsSet() const;
+    void unsetEnergy_multiplier();
     /// <summary>
     /// Rate at which non-indexed images are accepted to be forwarded to writer.  Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability. 
     /// </summary>
@@ -191,6 +191,20 @@ public:
     bool dataReductionFactorSerialmxIsSet() const;
     void unsetData_reduction_factor_serialmx();
     /// <summary>
+    /// Number of run within an experimental session.  Transferred over CBOR stream as \&quot;series ID\&quot;, though not saved in HDF5 file. It is highly recommended to keep this number unique for each data collection during experimental series. If not provided, the number will be automatically incremented. 
+    /// </summary>
+    int64_t getRunNumber() const;
+    void setRunNumber(int64_t const value);
+    bool runNumberIsSet() const;
+    void unsetRun_number();
+    /// <summary>
+    /// Name of group owning the data (e.g. p-group or proposal number).  Transferred over CBOR stream, though not saved in HDF5 file. 
+    /// </summary>
+    std::string getExperimentGroup() const;
+    void setExperimentGroup(std::string const& value);
+    bool experimentGroupIsSet() const;
+    void unsetExperiment_group();
+    /// <summary>
     /// 
     /// </summary>
     org::openapitools::server::model::Dataset_settings_unit_cell getUnitCell() const;
@@ -213,7 +227,7 @@ protected:
 
     float m_Detector_distance_mm;
 
-    float m_Photon_energy_keV;
+    float m_Incident_energy_keV;
 
     std::string m_File_prefix;
     bool m_File_prefixIsSet;
@@ -231,16 +245,20 @@ protected:
     bool m_Total_fluxIsSet;
     float m_Transmission;
     bool m_TransmissionIsSet;
-    org::openapitools::server::model::Rotation_axis m_Omega;
-    bool m_OmegaIsSet;
+    org::openapitools::server::model::Rotation_axis m_Goniometer;
+    bool m_GoniometerIsSet;
     std::string m_Header_appendix;
     bool m_Header_appendixIsSet;
     std::string m_Image_appendix;
     bool m_Image_appendixIsSet;
-    float m_Photon_energy_multiplier;
-    bool m_Photon_energy_multiplierIsSet;
+    float m_Energy_multiplier;
+    bool m_Energy_multiplierIsSet;
     float m_Data_reduction_factor_serialmx;
     bool m_Data_reduction_factor_serialmxIsSet;
+    int64_t m_Run_number;
+    bool m_Run_numberIsSet;
+    std::string m_Experiment_group;
+    bool m_Experiment_groupIsSet;
     org::openapitools::server::model::Dataset_settings_unit_cell m_Unit_cell;
     bool m_Unit_cellIsSet;
     

broker/gen/model/Measurement_statistics.cpp

@@ -23,6 +23,10 @@ Measurement_statistics::Measurement_statistics()
 {
     m_File_prefix = "";
     m_File_prefixIsSet = false;
+    m_Run_number = 0L;
+    m_Run_numberIsSet = false;
+    m_Experiment_group = "";
+    m_Experiment_groupIsSet = false;
     m_Images_expected = 0L;
     m_Images_expectedIsSet = false;
     m_Images_collected = 0L;
@@ -75,7 +79,7 @@ bool Measurement_statistics::validate(std::stringstream& msg, const std::string&
     bool success = true;
     const std::string _pathPrefix = pathPrefix.empty() ? "Measurement_statistics" : pathPrefix;
 
-                                 
+                                         
     if (collectionEfficiencyIsSet())
     {
         const float& value = m_Collection_efficiency;
@@ -121,6 +125,12 @@ bool Measurement_statistics::operator==(const Measurement_statistics& rhs) const
     ((!filePrefixIsSet() && !rhs.filePrefixIsSet()) || (filePrefixIsSet() && rhs.filePrefixIsSet() && getFilePrefix() == rhs.getFilePrefix())) &&
     
     
+    ((!runNumberIsSet() && !rhs.runNumberIsSet()) || (runNumberIsSet() && rhs.runNumberIsSet() && getRunNumber() == rhs.getRunNumber())) &&
+    
+    
+    ((!experimentGroupIsSet() && !rhs.experimentGroupIsSet()) || (experimentGroupIsSet() && rhs.experimentGroupIsSet() && getExperimentGroup() == rhs.getExperimentGroup())) &&
+    
+    
     ((!imagesExpectedIsSet() && !rhs.imagesExpectedIsSet()) || (imagesExpectedIsSet() && rhs.imagesExpectedIsSet() && getImagesExpected() == rhs.getImagesExpected())) &&
     
     
@@ -178,6 +188,10 @@ void to_json(nlohmann::json& j, const Measurement_statistics& o)
     j = nlohmann::json();
     if(o.filePrefixIsSet())
         j["file_prefix"] = o.m_File_prefix;
+    if(o.runNumberIsSet())
+        j["run_number"] = o.m_Run_number;
+    if(o.experimentGroupIsSet())
+        j["experiment_group"] = o.m_Experiment_group;
     if(o.imagesExpectedIsSet())
         j["images_expected"] = o.m_Images_expected;
     if(o.imagesCollectedIsSet())
@@ -218,6 +232,16 @@ void from_json(const nlohmann::json& j, Measurement_statistics& o)
         j.at("file_prefix").get_to(o.m_File_prefix);
         o.m_File_prefixIsSet = true;
     } 
+    if(j.find("run_number") != j.end())
+    {
+        j.at("run_number").get_to(o.m_Run_number);
+        o.m_Run_numberIsSet = true;
+    } 
+    if(j.find("experiment_group") != j.end())
+    {
+        j.at("experiment_group").get_to(o.m_Experiment_group);
+        o.m_Experiment_groupIsSet = true;
+    } 
     if(j.find("images_expected") != j.end())
     {
         j.at("images_expected").get_to(o.m_Images_expected);
@@ -313,6 +337,40 @@ void Measurement_statistics::unsetFile_prefix()
 {
     m_File_prefixIsSet = false;
 }
+int64_t Measurement_statistics::getRunNumber() const
+{
+    return m_Run_number;
+}
+void Measurement_statistics::setRunNumber(int64_t const value)
+{
+    m_Run_number = value;
+    m_Run_numberIsSet = true;
+}
+bool Measurement_statistics::runNumberIsSet() const
+{
+    return m_Run_numberIsSet;
+}
+void Measurement_statistics::unsetRun_number()
+{
+    m_Run_numberIsSet = false;
+}
+std::string Measurement_statistics::getExperimentGroup() const
+{
+    return m_Experiment_group;
+}
+void Measurement_statistics::setExperimentGroup(std::string const& value)
+{
+    m_Experiment_group = value;
+    m_Experiment_groupIsSet = true;
+}
+bool Measurement_statistics::experimentGroupIsSet() const
+{
+    return m_Experiment_groupIsSet;
+}
+void Measurement_statistics::unsetExperiment_group()
+{
+    m_Experiment_groupIsSet = false;
+}
 int64_t Measurement_statistics::getImagesExpected() const
 {
     return m_Images_expected;

broker/gen/model/Measurement_statistics.h

@@ -66,6 +66,20 @@ public:
     bool filePrefixIsSet() const;
     void unsetFile_prefix();
     /// <summary>
+    /// Number of data collection run. This can be either automatically incremented or provided externally for each data collection. 
+    /// </summary>
+    int64_t getRunNumber() const;
+    void setRunNumber(int64_t const value);
+    bool runNumberIsSet() const;
+    void unsetRun_number();
+    /// <summary>
+    /// Name of group owning the data (e.g. p-group or proposal number). 
+    /// </summary>
+    std::string getExperimentGroup() const;
+    void setExperimentGroup(std::string const& value);
+    bool experimentGroupIsSet() const;
+    void unsetExperiment_group();
+    /// <summary>
     /// 
     /// </summary>
     int64_t getImagesExpected() const;
@@ -176,6 +190,10 @@ public:
 protected:
     std::string m_File_prefix;
     bool m_File_prefixIsSet;
+    int64_t m_Run_number;
+    bool m_Run_numberIsSet;
+    std::string m_Experiment_group;
+    bool m_Experiment_groupIsSet;
     int64_t m_Images_expected;
     bool m_Images_expectedIsSet;
     int64_t m_Images_collected;

broker/gen/model/Preview_settings.cpp

@@ -26,11 +26,13 @@ Preview_settings::Preview_settings()
     m_Show_spotsIsSet = false;
     m_Show_roi = false;
     m_Show_roiIsSet = false;
-    m_Jpeg_quality = 0L;
+    m_Jpeg_quality = 100L;
     m_Jpeg_qualityIsSet = false;
     m_Show_indexed = false;
     m_Show_indexedIsSet = false;
-    m_Resolution_ring = 0.0f;
+    m_Show_user_mask = false;
+    m_Show_user_maskIsSet = false;
+    m_Resolution_ring = 0.1f;
     m_Resolution_ringIsSet = false;
     
 }
@@ -92,7 +94,7 @@ bool Preview_settings::validate(std::stringstream& msg, const std::string& pathP
         }
 
     }
-             
+                 
     if (resolutionRingIsSet())
     {
         const float& value = m_Resolution_ring;
@@ -136,6 +138,9 @@ bool Preview_settings::operator==(const Preview_settings& rhs) const
     ((!showIndexedIsSet() && !rhs.showIndexedIsSet()) || (showIndexedIsSet() && rhs.showIndexedIsSet() && isShowIndexed() == rhs.isShowIndexed())) &&
     
     
+    ((!showUserMaskIsSet() && !rhs.showUserMaskIsSet()) || (showUserMaskIsSet() && rhs.showUserMaskIsSet() && isShowUserMask() == rhs.isShowUserMask())) &&
+    
+    
     ((!resolutionRingIsSet() && !rhs.resolutionRingIsSet()) || (resolutionRingIsSet() && rhs.resolutionRingIsSet() && getResolutionRing() == rhs.getResolutionRing()))
     
     ;
@@ -158,6 +163,8 @@ void to_json(nlohmann::json& j, const Preview_settings& o)
         j["jpeg_quality"] = o.m_Jpeg_quality;
     if(o.showIndexedIsSet())
         j["show_indexed"] = o.m_Show_indexed;
+    if(o.showUserMaskIsSet())
+        j["show_user_mask"] = o.m_Show_user_mask;
     if(o.resolutionRingIsSet())
         j["resolution_ring"] = o.m_Resolution_ring;
     
@@ -186,6 +193,11 @@ void from_json(const nlohmann::json& j, Preview_settings& o)
         j.at("show_indexed").get_to(o.m_Show_indexed);
         o.m_Show_indexedIsSet = true;
     } 
+    if(j.find("show_user_mask") != j.end())
+    {
+        j.at("show_user_mask").get_to(o.m_Show_user_mask);
+        o.m_Show_user_maskIsSet = true;
+    } 
     if(j.find("resolution_ring") != j.end())
     {
         j.at("resolution_ring").get_to(o.m_Resolution_ring);
@@ -270,6 +282,23 @@ void Preview_settings::unsetShow_indexed()
 {
     m_Show_indexedIsSet = false;
 }
+bool Preview_settings::isShowUserMask() const
+{
+    return m_Show_user_mask;
+}
+void Preview_settings::setShowUserMask(bool const value)
+{
+    m_Show_user_mask = value;
+    m_Show_user_maskIsSet = true;
+}
+bool Preview_settings::showUserMaskIsSet() const
+{
+    return m_Show_user_maskIsSet;
+}
+void Preview_settings::unsetShow_user_mask()
+{
+    m_Show_user_maskIsSet = false;
+}
 float Preview_settings::getResolutionRing() const
 {
     return m_Resolution_ring;

broker/gen/model/Preview_settings.h

@@ -91,6 +91,13 @@ public:
     bool showIndexedIsSet() const;
     void unsetShow_indexed();
     /// <summary>
+    /// Show user mask
+    /// </summary>
+    bool isShowUserMask() const;
+    void setShowUserMask(bool const value);
+    bool showUserMaskIsSet() const;
+    void unsetShow_user_mask();
+    /// <summary>
     /// 
     /// </summary>
     float getResolutionRing() const;
@@ -111,6 +118,8 @@ protected:
     bool m_Jpeg_qualityIsSet;
     bool m_Show_indexed;
     bool m_Show_indexedIsSet;
+    bool m_Show_user_mask;
+    bool m_Show_user_maskIsSet;
     float m_Resolution_ring;
     bool m_Resolution_ringIsSet;
     

broker/gen/model/Rotation_axis.cpp

@@ -21,6 +21,8 @@ namespace org::openapitools::server::model
 
 Rotation_axis::Rotation_axis()
 {
+    m_Name = "omega";
+    m_NameIsSet = false;
     m_Step = 0.0f;
     m_Start = 0.0f;
     m_StartIsSet = false;
@@ -47,6 +49,20 @@ bool Rotation_axis::validate(std::stringstream& msg, const std::string& pathPref
     bool success = true;
     const std::string _pathPrefix = pathPrefix.empty() ? "Rotation_axis" : pathPrefix;
 
+         
+    if (nameIsSet())
+    {
+        const std::string& value = m_Name;
+        const std::string currentValuePath = _pathPrefix + ".name";
+                
+        
+        if (value.length() < 1)
+        {
+            success = false;
+            msg << currentValuePath << ": must be at least 1 characters long;";
+        }
+
+    }
                  
     if (vectorIsSet())
     {
@@ -87,6 +103,9 @@ bool Rotation_axis::operator==(const Rotation_axis& rhs) const
     return
     
     
+    
+    ((!nameIsSet() && !rhs.nameIsSet()) || (nameIsSet() && rhs.nameIsSet() && getName() == rhs.getName())) &&
+    
     (getStep() == rhs.getStep())
      &&
     
@@ -107,6 +126,8 @@ bool Rotation_axis::operator!=(const Rotation_axis& rhs) const
 void to_json(nlohmann::json& j, const Rotation_axis& o)
 {
     j = nlohmann::json();
+    if(o.nameIsSet())
+        j["name"] = o.m_Name;
     j["step"] = o.m_Step;
     if(o.startIsSet())
         j["start"] = o.m_Start;
@@ -117,6 +138,11 @@ void to_json(nlohmann::json& j, const Rotation_axis& o)
 
 void from_json(const nlohmann::json& j, Rotation_axis& o)
 {
+    if(j.find("name") != j.end())
+    {
+        j.at("name").get_to(o.m_Name);
+        o.m_NameIsSet = true;
+    } 
     j.at("step").get_to(o.m_Step);
     if(j.find("start") != j.end())
     {
@@ -131,6 +157,23 @@ void from_json(const nlohmann::json& j, Rotation_axis& o)
     
 }
 
+std::string Rotation_axis::getName() const
+{
+    return m_Name;
+}
+void Rotation_axis::setName(std::string const& value)
+{
+    m_Name = value;
+    m_NameIsSet = true;
+}
+bool Rotation_axis::nameIsSet() const
+{
+    return m_NameIsSet;
+}
+void Rotation_axis::unsetName()
+{
+    m_NameIsSet = false;
+}
 float Rotation_axis::getStep() const
 {
     return m_Step;

broker/gen/model/Rotation_axis.h

@@ -19,6 +19,7 @@
 #define Rotation_axis_H_
 
 
+#include <string>
 #include <vector>
 #include <nlohmann/json.hpp>
 
@@ -58,6 +59,13 @@ public:
     /////////////////////////////////////////////
     /// Rotation_axis members
 
+    /// <summary>
+    /// Name of rotation axis (e.g., omega, phi)
+    /// </summary>
+    std::string getName() const;
+    void setName(std::string const& value);
+    bool nameIsSet() const;
+    void unsetName();
     /// <summary>
     /// Angle step in degrees
     /// </summary>
@@ -81,6 +89,8 @@ public:
     friend void to_json(nlohmann::json& j, const Rotation_axis& o);
     friend void from_json(const nlohmann::json& j, Rotation_axis& o);
 protected:
+    std::string m_Name;
+    bool m_NameIsSet;
     float m_Step;
 
     float m_Start;

broker/gen/model/Spot_finding_settings.cpp

@@ -23,6 +23,10 @@ Spot_finding_settings::Spot_finding_settings()
 {
     m_Enable = true;
     m_Indexing = true;
+    m_Filter_powder_rings = false;
+    m_Filter_powder_ringsIsSet = false;
+    m_Min_spot_count_powder_ring = 0L;
+    m_Min_spot_count_powder_ringIsSet = false;
     m_Signal_to_noise_threshold = 0.0f;
     m_Photon_count_threshold = 0L;
     m_Min_pix_per_spot = 0L;
@@ -52,7 +56,21 @@ bool Spot_finding_settings::validate(std::stringstream& msg, const std::string&
     bool success = true;
     const std::string _pathPrefix = pathPrefix.empty() ? "Spot_finding_settings" : pathPrefix;
 
-                 
+                     
+    if (minSpotCountPowderRingIsSet())
+    {
+        const int64_t& value = m_Min_spot_count_powder_ring;
+        const std::string currentValuePath = _pathPrefix + ".minSpotCountPowderRing";
+                
+        
+        if (value < 5ll)
+        {
+            success = false;
+            msg << currentValuePath << ": must be greater than or equal to 5;";
+        }
+
+    }
+         
     
     /* Signal_to_noise_threshold */ {
         const float& value = m_Signal_to_noise_threshold;
@@ -142,6 +160,12 @@ bool Spot_finding_settings::operator==(const Spot_finding_settings& rhs) const
     (isIndexing() == rhs.isIndexing())
      &&
     
+    
+    ((!filterPowderRingsIsSet() && !rhs.filterPowderRingsIsSet()) || (filterPowderRingsIsSet() && rhs.filterPowderRingsIsSet() && isFilterPowderRings() == rhs.isFilterPowderRings())) &&
+    
+    
+    ((!minSpotCountPowderRingIsSet() && !rhs.minSpotCountPowderRingIsSet()) || (minSpotCountPowderRingIsSet() && rhs.minSpotCountPowderRingIsSet() && getMinSpotCountPowderRing() == rhs.getMinSpotCountPowderRing())) &&
+    
     (getSignalToNoiseThreshold() == rhs.getSignalToNoiseThreshold())
      &&
     
@@ -176,6 +200,10 @@ void to_json(nlohmann::json& j, const Spot_finding_settings& o)
     j = nlohmann::json();
     j["enable"] = o.m_Enable;
     j["indexing"] = o.m_Indexing;
+    if(o.filterPowderRingsIsSet())
+        j["filter_powder_rings"] = o.m_Filter_powder_rings;
+    if(o.minSpotCountPowderRingIsSet())
+        j["min_spot_count_powder_ring"] = o.m_Min_spot_count_powder_ring;
     j["signal_to_noise_threshold"] = o.m_Signal_to_noise_threshold;
     j["photon_count_threshold"] = o.m_Photon_count_threshold;
     j["min_pix_per_spot"] = o.m_Min_pix_per_spot;
@@ -190,6 +218,16 @@ void from_json(const nlohmann::json& j, Spot_finding_settings& o)
 {
     j.at("enable").get_to(o.m_Enable);
     j.at("indexing").get_to(o.m_Indexing);
+    if(j.find("filter_powder_rings") != j.end())
+    {
+        j.at("filter_powder_rings").get_to(o.m_Filter_powder_rings);
+        o.m_Filter_powder_ringsIsSet = true;
+    } 
+    if(j.find("min_spot_count_powder_ring") != j.end())
+    {
+        j.at("min_spot_count_powder_ring").get_to(o.m_Min_spot_count_powder_ring);
+        o.m_Min_spot_count_powder_ringIsSet = true;
+    } 
     j.at("signal_to_noise_threshold").get_to(o.m_Signal_to_noise_threshold);
     j.at("photon_count_threshold").get_to(o.m_Photon_count_threshold);
     j.at("min_pix_per_spot").get_to(o.m_Min_pix_per_spot);
@@ -216,6 +254,40 @@ void Spot_finding_settings::setIndexing(bool const value)
 {
     m_Indexing = value;
 }
+bool Spot_finding_settings::isFilterPowderRings() const
+{
+    return m_Filter_powder_rings;
+}
+void Spot_finding_settings::setFilterPowderRings(bool const value)
+{
+    m_Filter_powder_rings = value;
+    m_Filter_powder_ringsIsSet = true;
+}
+bool Spot_finding_settings::filterPowderRingsIsSet() const
+{
+    return m_Filter_powder_ringsIsSet;
+}
+void Spot_finding_settings::unsetFilter_powder_rings()
+{
+    m_Filter_powder_ringsIsSet = false;
+}
+int64_t Spot_finding_settings::getMinSpotCountPowderRing() const
+{
+    return m_Min_spot_count_powder_ring;
+}
+void Spot_finding_settings::setMinSpotCountPowderRing(int64_t const value)
+{
+    m_Min_spot_count_powder_ring = value;
+    m_Min_spot_count_powder_ringIsSet = true;
+}
+bool Spot_finding_settings::minSpotCountPowderRingIsSet() const
+{
+    return m_Min_spot_count_powder_ringIsSet;
+}
+void Spot_finding_settings::unsetMin_spot_count_powder_ring()
+{
+    m_Min_spot_count_powder_ringIsSet = false;
+}
 float Spot_finding_settings::getSignalToNoiseThreshold() const
 {
     return m_Signal_to_noise_threshold;

broker/gen/model/Spot_finding_settings.h

@@ -58,16 +58,30 @@ public:
     /// Spot_finding_settings members
 
     /// <summary>
-    /// Enable spot finding
+    /// Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection.  Even if disabled spot finding information will still be send and written, though always with zero spots. 
     /// </summary>
     bool isEnable() const;
     void setEnable(bool const value);
     /// <summary>
-    /// Enable indexing
+    /// Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection. 
     /// </summary>
     bool isIndexing() const;
     void setIndexing(bool const value);
     /// <summary>
+    /// Filter spots which form powder rings (e.g., ice rings)
+    /// </summary>
+    bool isFilterPowderRings() const;
+    void setFilterPowderRings(bool const value);
+    bool filterPowderRingsIsSet() const;
+    void unsetFilter_powder_rings();
+    /// <summary>
+    /// Minimum number of spots to consider a thin resolution shell (0.01 A^-1) a powder ring and filter out.
+    /// </summary>
+    int64_t getMinSpotCountPowderRing() const;
+    void setMinSpotCountPowderRing(int64_t const value);
+    bool minSpotCountPowderRingIsSet() const;
+    void unsetMin_spot_count_powder_ring();
+    /// <summary>
     /// 
     /// </summary>
     float getSignalToNoiseThreshold() const;
@@ -110,6 +124,10 @@ protected:
 
     bool m_Indexing;
 
+    bool m_Filter_powder_rings;
+    bool m_Filter_powder_ringsIsSet;
+    int64_t m_Min_spot_count_powder_ring;
+    bool m_Min_spot_count_powder_ringIsSet;
     float m_Signal_to_noise_threshold;
 
     int64_t m_Photon_count_threshold;

broker/jfjoch_api.yaml

@@ -11,6 +11,11 @@ components:
       required:
         - step
       properties:
+        name:
+          type: string
+          default: omega
+          minLength: 1
+          description: Name of rotation axis (e.g., omega, phi)
         step:
           type: number
           format: float
@@ -37,7 +42,7 @@ components:
         - beam_x_pxl
         - beam_y_pxl
         - detector_distance_mm
-        - photon_energy_keV
+        - incident_energy_keV
         - sample_name
       properties:
         images_per_trigger:
@@ -86,13 +91,13 @@ components:
           description:
             /entry/detector/distance in NXmx
             Detector distance [mm]
-        photon_energy_keV:
+        incident_energy_keV:
           type: number
           format: float
           minimum: 0
           description: |
             Used to calculate /entry/beam/incident_wavelength in NXmx
-            Incident photon energy in keV
+            Incident particle (photon, electron) energy in keV
         file_prefix:
           type: string
           default: ""
@@ -148,7 +153,7 @@ components:
           description: |
             /entry/instrument/attenuator/attenuator_transmission
             Transmission of attenuator (filter) [no units]
-        omega:
+        goniometer:
           $ref: "#/components/schemas/rotation_axis"
         header_appendix:
           type: string
@@ -156,13 +161,13 @@ components:
         image_appendix:
           type: string
           description: Image appendix, added as user_data to image message
-        photon_energy_multiplier:
+        energy_multiplier:
           type: number
           format: float
           default: 1.0
           minimum: 0.015625
           maximum: 4.0
-          description: For JUNGFRAU conversion it is possible to multiply energy by a given factor to get fractional/multiplied photon counts
+          description: For JUNGFRAU conversion it is possible to multiply incident energy by a given factor to get fractional/multiplied particle counts
         data_reduction_factor_serialmx:
           type: number
           format: float
@@ -173,6 +178,20 @@ components:
             Rate at which non-indexed images are accepted to be forwarded to writer. 
             Value of 1.0 (default) means that all images are written.
             Values below zero mean that non-indexed images will be accepted with a given probability.
+        run_number:
+          type: integer
+          format: int64
+          minimum: 0
+          description: |
+            Number of run within an experimental session. 
+            Transferred over CBOR stream as "series ID", though not saved in HDF5 file.
+            It is highly recommended to keep this number unique for each data collection during experimental series.
+            If not provided, the number will be automatically incremented.
+        experiment_group:
+          type: string
+          description: |
+            Name of group owning the data (e.g. p-group or proposal number). 
+            Transferred over CBOR stream, though not saved in HDF5 file.
         unit_cell:
           type: object
           description: Units of angstrom and degree
@@ -235,7 +254,7 @@ components:
         powerchip:
           type: string
           description: Power on of ASICs
-          enum: ["On", "Off", "Partial"]
+          enum: ["PowerOn", "PowerOff", "Partial"]
         server_version:
           type: string
           description: Detector server (on read-out boards) version
@@ -333,11 +352,23 @@ components:
         enable:
           type: boolean
           default: true
-          description: Enable spot finding
+          description: |
+            Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. 
+            Even if disabled spot finding information will still be send and written, though always with zero spots.
         indexing:
           type: boolean
           default: true
-          description: Enable indexing
+          description: |
+            Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.
+        filter_powder_rings:
+          type: boolean
+          default: false
+          description: Filter spots which form powder rings (e.g., ice rings)
+        min_spot_count_powder_ring:
+          type: integer
+          format: int64
+          minimum: 5
+          description: Minimum number of spots to consider a thin resolution shell (0.01 A^-1) a powder ring and filter out.
         signal_to_noise_threshold:
           type: number
           format: float
@@ -447,6 +478,15 @@ components:
       properties:
         file_prefix:
           type: string
+        run_number:
+          type: integer
+          format: int64
+          description: |
+            Number of data collection run. This can be either automatically incremented or provided externally for each data collection.
+        experiment_group:
+          type: string
+          description: |
+            Name of group owning the data (e.g. p-group or proposal number).
         images_expected:
           type: integer
           format: int64
@@ -620,14 +660,21 @@ components:
           type: integer
           description: "Quality of JPEG image (100 - highest; 0 - lowest)"
           format: int64
+          default: 100
           minimum: 0
           maximum: 100
         show_indexed:
           type: boolean
           description: "Preview indexed images only"
+          default: false
+        show_user_mask:
+          type: boolean
+          description: "Show user mask"
+          default: false
         resolution_ring:
           type: number
           format: float
+          default: 0.1
           minimum: 0.1
           maximum: 100.0
     error_message:
@@ -967,9 +1014,9 @@ paths:
         Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates 
         (depending on detector settings).
       parameters:
-        - name: number
+        - name: id
           in: query
-          description: Image number to upload
+          description: Image id to upload
           required: false
           schema:
             type: integer
@@ -992,6 +1039,38 @@ paths:
               schema:
                 type: string
                 description: Exception error
+  /config/internal_generator_image.tiff:
+    put:
+      summary: Load TIFF image for internal FPGA generator
+      description: |
+        Load image for internal FPGA generator. This can only happen in Idle state of the detector.
+        Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates 
+        (depending on detector settings).
+      parameters:
+        - in: query
+          name: id
+          description: Image ID to upload
+          required: false
+          schema:
+            type: integer
+            minimum: 0
+            maximum: 127
+      requestBody:
+        content:
+          image/tiff:
+            schema:
+              type: string
+              format: binary
+      responses:
+        "200":
+          description: Everything OK
+        "400":
+          description: Input parsing or validation error
+          content:
+            text/plain:
+              schema:
+                type: string
+                description: Exception error
   /config/select_detector:
     put:
       summary: Select detector
@@ -1564,6 +1643,63 @@ paths:
                 format: binary
         "404":
           description: No preview image recorded so far
+  /config/mask.tiff:
+    get:
+      summary: Get mask of the detector
+      description: |
+        Get full pixel mask of the detector
+        See NXmx standard for meaning of pixel values
+      responses:
+        "200":
+          description: Pixel mask in TIFF format (4 byte; unsigned)
+          content:
+            image/tiff:
+              schema:
+                type: string
+                format: binary
+  /config/user_mask.tiff:
+    get:
+      summary: Get user mask of the detector
+      description: "Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked"
+      responses:
+        "200":
+          description: User mask in TIFF format (4 byte; unsigned)
+          content:
+            image/tiff:
+              schema:
+                type: string
+                format: binary
+    put:
+      summary: Upload user mask of the detector
+      description: |
+        Should be in `Idle` state.
+        Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
+        If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
+        In the latter case - module gaps are ignored and don't need to be assigned value.
+        Mask is expected as TIFF (4-byte; unsigned).
+        0 - good pixel, other value - masked
+        User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration. 
+        User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
+      requestBody:
+        content:
+          application/octet-stream:
+            schema:
+              type: string
+              format: binary
+      responses:
+        "200":
+          description: All good
+          content:
+            image/tiff:
+              schema:
+                type: string
+                format: binary
+        "500":
+          description: Error within Jungfraujoch code - see output message.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/error_message'
   /preview/pedestal.tiff:
     get:
       parameters:

broker/jfjoch_broker.cpp

@@ -115,9 +115,9 @@ int main (int argc, char **argv) {
 
     logger.Info("Source {} Instrument {} Default rotation axis {:.2f},{:.2f},{:.2f}",
                 experiment.GetSourceName(), experiment.GetInstrumentName(),
-                experiment.GetDefaultOmegaAxis().x,
-                experiment.GetDefaultOmegaAxis().y,
-                experiment.GetDefaultOmegaAxis().z);
+                experiment.GetDefaultRotationAxis().x,
+                experiment.GetDefaultRotationAxis().y,
+                experiment.GetDefaultRotationAxis().z);
 
     Pistache::Address addr(Pistache::Ipv4::any(), Pistache::Port(http_port));
 

common/DatasetSettings.cpp

@@ -24,7 +24,6 @@ DatasetSettings::DatasetSettings() {
     space_group_number = 0; // not set
     compression = CompressionAlgorithm::BSHUF_LZ4;
     photon_energy_multiplier = 1.0f;
-    omega_start = 0.0f;
     images_per_file = 1000;
     data_reduction_factor_serialmx = 1.0;
 }
@@ -151,31 +150,25 @@ DatasetSettings &DatasetSettings::TotalFlux(const std::optional<float> &input) {
     return *this;
 }
 
-DatasetSettings &DatasetSettings::OmegaStep(const std::optional<float> &input) {
+DatasetSettings &DatasetSettings::Goniometer(const std::optional<GoniometerAxis> &input) {
     if (input) {
-        check_finite("Omega step", input.value());
+        check_finite("Rotation angle increment", input->increment);
+        if (input->increment == 0.0f)
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "Angle increment cannot be zero");
+        check_finite("Rotation angle start", input->start);
+        goniometer = input;
     }
-
-    if (input && (input == 0.0f))
-        omega_step.reset();
-    else
-        omega_step = input;
     return *this;
 }
 
-DatasetSettings &DatasetSettings::OmegaStart(float input) {
-    check_finite("Omega start", input);
-    omega_start = input;
-    return *this;
-}
-
-DatasetSettings &DatasetSettings::OmegaAxis(const std::optional<Coord> &c) {
+DatasetSettings &DatasetSettings::RotationAxis(const std::optional<Coord> &c) {
     if (c) {
         if (c->Length() == 0.0)
             throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Cannot use empty vector for omega");
-        omega_rotation_axis = c->Normalize();
+        rotation_axis = c->Normalize();
     } else
-        omega_rotation_axis = c;
+        rotation_axis = c;
     return *this;
 }
 
@@ -228,16 +221,12 @@ std::optional<float> DatasetSettings::GetTotalFlux() const {
     return total_flux;
 }
 
-std::optional<float> DatasetSettings::GetOmegaStep() const {
-    return omega_step;
+std::optional<GoniometerAxis> DatasetSettings::GetGoniometer() const {
+    return goniometer;
 }
 
-float DatasetSettings::GetOmegaStart() const {
-    return omega_start;
-}
-
-std::optional<Coord> DatasetSettings::GetOmegaAxis() const {
-    return omega_rotation_axis;
+std::optional<Coord> DatasetSettings::GetRotationAxis() const {
+    return rotation_axis;
 }
 
 std::string DatasetSettings::GetHeaderAppendix() const {
@@ -332,3 +321,25 @@ DatasetSettings &DatasetSettings::DataReductionFactorSerialMX(float input) {
 float DatasetSettings::GetDataReductionFactorSerialMX() const {
     return data_reduction_factor_serialmx;
 }
+
+DatasetSettings &DatasetSettings::RunNumber(const std::optional<uint64_t> &input) {
+    if (input) {
+        check_min("Run number", input, 0);
+        check_max("Run number", input, INT64_MAX);
+    }
+    run_number = input;
+    return *this;
+}
+
+DatasetSettings &DatasetSettings::ExperimentGroup(const std::string &input) {
+    group = input;
+    return *this;
+}
+
+std::optional<uint64_t> DatasetSettings::GetRunNumber() const {
+    return run_number;
+}
+
+std::string DatasetSettings::GetExperimentGroup() const {
+    return group;
+}

common/DatasetSettings.h

@@ -40,14 +40,16 @@ class DatasetSettings {
 
     std::optional<float> total_flux;
     std::optional<float> attenuator_transmission;
-    std::optional<float> omega_step;
-    float omega_start;
+    std::optional<GoniometerAxis> goniometer;
     std::string image_appendix;
     std::string header_appendix;
 
-    std::optional<Coord> omega_rotation_axis;
+    std::optional<Coord> rotation_axis;
 
     float data_reduction_factor_serialmx;
+
+    std::optional<uint64_t> run_number;
+    std::string group;
 public:
 
     DatasetSettings();
@@ -65,9 +67,8 @@ public:
     DatasetSettings& SampleName(std::string input);
     DatasetSettings& AttenuatorTransmission(const std::optional<float> &input);
     DatasetSettings& TotalFlux(const std::optional<float> &input);
-    DatasetSettings& OmegaStep(const std::optional<float> &input);
-    DatasetSettings& OmegaStart(float input);
-    DatasetSettings& OmegaAxis(const std::optional<Coord> &c);
+    DatasetSettings& Goniometer(const std::optional<GoniometerAxis>& input);
+    DatasetSettings& RotationAxis(const std::optional<Coord> &c);
     DatasetSettings& HeaderAppendix(const std::string& input);
     DatasetSettings& ImageAppendix(const std::string& input);
     DatasetSettings& PhotonEnergyMultiplayer(float input);
@@ -75,12 +76,13 @@ public:
     DatasetSettings& FPGAOutputMode(FPGAPixelOutput input);
     DatasetSettings& ImagesPerFile(int64_t input);
     DatasetSettings& DataReductionFactorSerialMX(float input);
+    DatasetSettings& RunNumber(const std::optional<uint64_t> &run_number);
+    DatasetSettings& ExperimentGroup(const std::string &group);
 
     std::optional<float> GetAttenuatorTransmission() const;
     std::optional<float> GetTotalFlux() const;
-    std::optional<float> GetOmegaStep() const;
-    float GetOmegaStart() const;
-    std::optional<Coord> GetOmegaAxis() const;
+    std::optional<GoniometerAxis> GetGoniometer() const;
+    std::optional<Coord> GetRotationAxis() const;
     std::string GetHeaderAppendix() const;
     std::string GetImageAppendix() const;
     float GetPhotonEnergyMultiplier() const;
@@ -104,6 +106,9 @@ public:
     int64_t GetImageNumPerTrigger() const;
     int64_t GetImagesPerFile() const;
     float GetDataReductionFactorSerialMX() const;
+
+    std::optional<uint64_t> GetRunNumber() const;
+    std::string GetExperimentGroup() const;
 };
 
 #endif //JUNGFRAUJOCH_DATASETSETTINGS_H

common/Definitions.h

@@ -12,10 +12,12 @@
 #define CONVERTED_MODULE_SIZE   (CONVERTED_MODULE_LINES * CONVERTED_MODULE_COLS)
 #define JUNGFRAU_PACKET_SIZE_BYTES  (8192)
 
-#define MIN_COUNT_TIME_IN_US 5
 #define MIN_FRAME_TIME_HALF_SPEED_IN_US 1000
 #define MIN_FRAME_TIME_FULL_SPEED_IN_US 470
-#define MAX_FRAME_TIME 2000
+
+#define MAX_COUNT_TIME_IN_US 1980
+#define MIN_COUNT_TIME_IN_US 3
+
 #define MIN_STORAGE_CELL_DELAY_IN_NS 2100
 #define READOUT_TIME_IN_US 20
 

common/DiffractionExperiment.cpp

@@ -10,6 +10,7 @@
 #include "RawToConvertedGeometry.h"
 #include "../fpga/pcie_driver/jfjoch_fpga.h"
 #include "../include/spdlog/fmt/fmt.h"
+#include "GitInfo.h"
 
 using namespace std::literals::chrono_literals;
 
@@ -29,8 +30,6 @@ DiffractionExperiment::DiffractionExperiment(const DetectorSetup& det_setup)
     internal_fpga_packet_generator = false;
     internal_fpga_packet_generator_images = 1;
 
-    debug_pixel_mask = false;
-
     ndatastreams = 1;
 
     frame_time = std::chrono::microseconds(MIN_FRAME_TIME_HALF_SPEED_IN_US);
@@ -102,10 +101,13 @@ DiffractionExperiment &DiffractionExperiment::NumTriggers(int64_t input) {
 DiffractionExperiment &DiffractionExperiment::FrameTime(std::chrono::microseconds in_frame_time,
                                                         std::chrono::microseconds in_count_time) {
     check_min("Frame time (us)", in_frame_time.count(), MIN_FRAME_TIME_FULL_SPEED_IN_US);
-    check_max("Frame time (us)", in_frame_time.count(), MAX_FRAME_TIME);
     check_max("Count time (us)", in_count_time.count(), in_frame_time.count() - READOUT_TIME_IN_US);
     if (in_count_time.count() != 0) {
         check_min("Count time (us)", in_count_time.count(), MIN_COUNT_TIME_IN_US);
+        check_max("Count time (us)", in_count_time.count(), MAX_COUNT_TIME_IN_US);
+    } else {
+        check_max("Count time (us)", in_frame_time.count() - READOUT_TIME_IN_US,
+                  MAX_COUNT_TIME_IN_US);
     }
 
     frame_time = in_frame_time;
@@ -684,6 +686,7 @@ void DiffractionExperiment::CheckDataProcessingSettings(const SpotFindingSetting
         check_min("Spot finding low resolution limit", settings.low_resolution_limit, 1.0);
         check_max("Spot finding low resolution limit", settings.low_resolution_limit, 50.0);
     }
+    check_min("min spot count for powder ring detection", settings.min_spot_count_powder_ring, 5);
     check_min("indexing tolerance", settings.indexing_tolerance, 0.0);
     check_max("indexing tolerance", settings.indexing_tolerance, 1.0);
 }
@@ -730,6 +733,7 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
 
     message.source_name = GetSourceName();
     message.source_name_short = GetSourceNameShort();
+    message.source_type = GetSourceType();
 
     message.instrument_name = GetInstrumentName();
     message.instrument_name_short = GetInstrumentNameShort();
@@ -739,14 +743,16 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
     message.countrate_correction_enabled = false;
     message.flatfield_enabled = false;
 
-    if (GetOmegaStep())
-        message.omega = GoniometerAxis{.increment = GetOmegaStep().value(), .start = GetOmegaStart(),
-                .axis = {GetOmegaAxis().x, GetOmegaAxis().y, GetOmegaAxis().z}};
-    else
-        message.omega = GoniometerAxis{.increment = 0.0f};
+    auto goniometer = dataset.GetGoniometer();
+    if (goniometer) {
+        message.goniometer = goniometer;
+        message.rotation_axis[0] = GetRotationAxis().x;
+        message.rotation_axis[1] = GetRotationAxis().y;
+        message.rotation_axis[2] = GetRotationAxis().z;
+    }
 
-    message.series_id = GetSeriesID();
-    message.series_unique_id = GetSeriesIDString();
+    message.series_id = GetRunNumber();
+    message.series_unique_id = GetRunName();
 
     message.gain_file_names = detector.GetGainFileNames();
 
@@ -754,6 +760,8 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
         message.roi_names.emplace_back(x);
 
     message.data_reduction_factor_serialmx = GetDataReductionFactorSerialMX();
+    message.experiment_group = dataset.GetExperimentGroup();
+    message.jfjoch_release = jfjoch_version();
 }
 
 float DiffractionExperiment::GetPixelSize_mm() const {
@@ -770,6 +778,11 @@ DiffractionExperiment &DiffractionExperiment::SourceNameShort(std::string input)
     return *this;
 }
 
+DiffractionExperiment &DiffractionExperiment::SourceType(std::string input) {
+    source_type = input;
+    return *this;
+}
+
 DiffractionExperiment &DiffractionExperiment::InstrumentName(std::string input) {
     instrument_name = input;
     return *this;
@@ -788,6 +801,10 @@ std::string DiffractionExperiment::GetSourceNameShort() const {
     return source_name_short;
 }
 
+std::string DiffractionExperiment::GetSourceType() const {
+    return source_type;
+}
+
 std::string DiffractionExperiment::GetInstrumentName() const {
     return instrument_name;
 }
@@ -950,22 +967,13 @@ std::optional<float> DiffractionExperiment::GetTotalFlux() const {
     return dataset.GetTotalFlux();
 }
 
-DiffractionExperiment &DiffractionExperiment::OmegaStep(const std::optional<float> &input) {
-    dataset.OmegaStep(input);
+DiffractionExperiment &DiffractionExperiment::Goniometer(const std::optional<GoniometerAxis> &input) {
+    dataset.Goniometer(input);
     return *this;
 }
 
-DiffractionExperiment &DiffractionExperiment::OmegaStart(float input) {
-    dataset.OmegaStart(input);
-    return *this;
-}
-
-std::optional<float> DiffractionExperiment::GetOmegaStep() const {
-    return dataset.GetOmegaStep();
-}
-
-float DiffractionExperiment::GetOmegaStart() const {
-    return dataset.GetOmegaStart();
+std::optional<GoniometerAxis> DiffractionExperiment::GetGoniometer() const {
+    return dataset.GetGoniometer();
 }
 
 DiffractionExperiment &DiffractionExperiment::UsingGainHG0(bool input) {
@@ -1004,45 +1012,42 @@ std::string DiffractionExperiment::GetImageAppendix() const {
     return dataset.GetImageAppendix();
 }
 
-DiffractionExperiment &DiffractionExperiment::OmegaAxis(const Coord &c) {
-    dataset.OmegaAxis(c);
+DiffractionExperiment &DiffractionExperiment::RotationAxis(const std::optional<Coord> &c) {
+    dataset.RotationAxis(c);
     return *this;
 }
 
-DiffractionExperiment &DiffractionExperiment::OmegaAxis() {
-    dataset.OmegaAxis({});
-    return *this;
-}
-
-Coord DiffractionExperiment::GetOmegaAxis() const {
-    auto tmp = dataset.GetOmegaAxis();
+Coord DiffractionExperiment::GetRotationAxis() const {
+    auto tmp = dataset.GetRotationAxis();
     if (tmp)
         return tmp.value();
     else
         return default_omega_axis;
 }
 
-DiffractionExperiment &DiffractionExperiment::DefaultOmegaAxis(const Coord &c) {
+DiffractionExperiment &DiffractionExperiment::DefaultRotationAxis(const Coord &c) {
     if (c.Length() == 0.0)
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Cannot use empty vector for omega axis");
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Cannot use empty vector for goniometer axis");
 
     default_omega_axis = c.Normalize();
     return *this;
 }
 
-Coord DiffractionExperiment::GetDefaultOmegaAxis() const {
+Coord DiffractionExperiment::GetDefaultRotationAxis() const {
     return default_omega_axis;
 }
 
-uint64_t DiffractionExperiment::GetSeriesID() const {
+uint64_t DiffractionExperiment::GetRunNumber() const {
+    if (dataset.GetRunNumber())
+        return dataset.GetRunNumber().value();
     return series_id;
 }
 
-std::string DiffractionExperiment::GetSeriesIDString() const {
+std::string DiffractionExperiment::GetRunName() const {
     return std::to_string(series_id) + ": " + dataset.GetFilePrefix();
 }
 
-DiffractionExperiment &DiffractionExperiment::IncrementSeriesID() {
+DiffractionExperiment &DiffractionExperiment::IncrementRunNumber() {
     series_id++;
     return *this;
 }
@@ -1069,6 +1074,7 @@ bool DiffractionExperiment::IsConversionOnFPGA() const {
 }
 
 DiffractionExperiment &DiffractionExperiment::DetectorDelay(std::chrono::nanoseconds input) {
+    check_min("Detector delay (us)", input.count(), 0);
     detector_delay = input;
     return *this;
 }
@@ -1185,3 +1191,7 @@ DiffractionExperiment &DiffractionExperiment::DataReductionFactorSerialMX(float
     dataset.DataReductionFactorSerialMX(input);
     return *this;
 }
+
+std::string DiffractionExperiment::GetExperimentGroup() const {
+    return dataset.GetExperimentGroup();
+}

common/DiffractionExperiment.h

@@ -78,11 +78,11 @@ class DiffractionExperiment {
 
     std::string source_name;
     std::string source_name_short;
+    std::string source_type;
     std::string instrument_name;
     std::string instrument_name_short;
     bool pulsed_source;
 
-    bool debug_pixel_mask;
     Coord default_omega_axis;
 
     bool conversion_on_fpga;
@@ -133,14 +133,15 @@ public:
     DiffractionExperiment& StorageCellStart(int64_t input = 15);
 
     DiffractionExperiment& SourceName(std::string input);
+    DiffractionExperiment& SourceType(std::string input);
     DiffractionExperiment& SourceNameShort(std::string input);
     DiffractionExperiment& InstrumentName(std::string input);
     DiffractionExperiment& InstrumentNameShort(std::string input);
-    DiffractionExperiment& DefaultOmegaAxis(const Coord &c);
+    DiffractionExperiment& DefaultRotationAxis(const Coord &c);
 
     DiffractionExperiment& UsingGainHG0(bool input);
     DiffractionExperiment& FixedGainG1(bool input);
-    DiffractionExperiment& IncrementSeriesID();
+    DiffractionExperiment& IncrementRunNumber();
     DiffractionExperiment& ConversionOnFPGA(bool input);
     DiffractionExperiment& PulsedSource(bool input);
 
@@ -157,10 +158,8 @@ public:
     DiffractionExperiment& SampleName(std::string input);
     DiffractionExperiment& AttenuatorTransmission(const std::optional<float> &input);
     DiffractionExperiment& TotalFlux(const std::optional<float> &input);
-    DiffractionExperiment& OmegaStep(const std::optional<float> &input);
-    DiffractionExperiment& OmegaStart(float input);
-    DiffractionExperiment& OmegaAxis(const Coord &c);
-    DiffractionExperiment& OmegaAxis();
+    DiffractionExperiment& Goniometer(const std::optional<GoniometerAxis> &input);
+    DiffractionExperiment& RotationAxis(const std::optional<Coord> &c);
     DiffractionExperiment& HeaderAppendix(const std::string& input);
     DiffractionExperiment& ImageAppendix(const std::string& input);
     DiffractionExperiment& PhotonEnergyMultiplayer(float input);
@@ -253,6 +252,7 @@ public:
 
     float GetPixelSize_mm() const;
     std::string GetSourceName() const;
+    std::string GetSourceType() const;
     std::string GetSourceNameShort() const;
     std::string GetInstrumentName() const;
     std::string GetInstrumentNameShort() const;
@@ -269,13 +269,13 @@ public:
 
     int64_t GetUDPInterfaceCount() const;
     std::vector<DetectorModuleConfig> GetDetectorModuleConfig(const std::vector<AcquisitionDeviceNetConfig>& net_config) const;
-    Coord GetDefaultOmegaAxis() const;
+    Coord GetDefaultRotationAxis() const;
 
     bool IsFixedGainG1() const;
     bool IsUsingGainHG0() const;
 
-    uint64_t GetSeriesID() const;
-    std::string GetSeriesIDString() const;
+    uint64_t GetRunNumber() const;
+    std::string GetRunName() const;
     bool IsConversionOnFPGA() const;
 
     const DetectorSetup& GetDetectorSetup() const;
@@ -288,9 +288,9 @@ public:
 
     std::optional<float> GetAttenuatorTransmission() const;
     std::optional<float> GetTotalFlux() const;
-    std::optional<float> GetOmegaStep() const;
-    float GetOmegaStart() const;
-    Coord GetOmegaAxis() const;
+    std::optional<GoniometerAxis> GetGoniometer() const;
+
+    Coord GetRotationAxis() const;
     std::string GetHeaderAppendix() const;
     std::string GetImageAppendix() const;
     float GetPhotonEnergyMultiplier() const;
@@ -321,6 +321,7 @@ public:
     int64_t GetImagesPerFile() const;
 
     float GetDataReductionFactorSerialMX() const;
+    std::string GetExperimentGroup() const;
 };
 
 #endif //DIFFRACTIONEXPERIMENT_H

common/PixelMask.cpp

@@ -12,7 +12,7 @@ PixelMask::PixelMask(const DetectorSetup &detector)
 PixelMask::PixelMask(const DiffractionExperiment& experiment)
         : PixelMask(experiment.GetDetectorSetup()) {}
 
-void PixelMask::LoadDetectorBadPixelMask(const std::vector<uint32_t> &input_mask, uint8_t bit) {
+void PixelMask::LoadMask(const std::vector<uint32_t> &input_mask, uint8_t bit) {
     if (input_mask.size() != mask.size())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Input match doesn't fit the detector ");
@@ -25,7 +25,11 @@ void PixelMask::LoadDetectorBadPixelMask(const std::vector<uint32_t> &input_mask
     }
 }
 
-std::vector<uint32_t> PixelMask::GetMask(const DiffractionExperiment &experiment) {
+void PixelMask::LoadDetectorBadPixelMask(const std::vector<uint32_t> &input_mask) {
+    LoadMask(input_mask, ErrorPixelBit);
+}
+
+std::vector<uint32_t> PixelMask::GetMask(const DiffractionExperiment &experiment, bool conv) const {
     std::vector<uint32_t> mask_out = mask;
 
     // apply edge mask
@@ -39,7 +43,7 @@ std::vector<uint32_t> PixelMask::GetMask(const DiffractionExperiment &experiment
                         || (line == RAW_MODULE_LINES - 1)
                         || (col == 0)
                         || (col == RAW_MODULE_COLS - 1))
-                        mask_out[pixel] |= (1 << 30);
+                        mask_out[pixel] |= (1 << ModuleEdgePixelBit);
                 }
 
                 if (experiment.GetMaskChipEdges()) {
@@ -47,33 +51,39 @@ std::vector<uint32_t> PixelMask::GetMask(const DiffractionExperiment &experiment
                         || (col == 511) || (col == 512)
                         || (col == 767) || (col == 768)
                         || (line == 255) || (line== 256))
-                        mask_out[pixel] |= (1 << 31);
+                        mask_out[pixel] |= (1 << ChipGapPixelBit);
                 }
             }
         }
     }
 
-    if (experiment.GetDetectorMode() == DetectorMode::Conversion) {
-        std::vector<uint32_t> tmp(experiment.GetPixelsNum(), 1); // nonfuctional areas (i.e. gaps) are filled with 1
+    if (conv && (experiment.GetDetectorMode() == DetectorMode::Conversion)) {
+        std::vector<uint32_t> tmp(experiment.GetPixelsNum(), 1<<ModuleGapPixelBit); // nonfunctional areas (i.e. gaps) are filled with 1
         RawToConvertedGeometry<uint32_t, uint32_t>(experiment, tmp.data(), mask_out.data());
         return tmp;
     } else
         return mask_out;
 }
 
+std::vector<uint32_t> PixelMask::GetUserMask(const DiffractionExperiment &experiment, bool conv) const {
+    std::vector<uint32_t> ret = GetMask(experiment, conv);
+    for (auto &i: ret)
+        i = ((i & (1 << UserMaskedPixelBit)) != 0) ? 1 : 0;
+    return ret;
+}
+
 void PixelMask::LoadUserMask(const DiffractionExperiment &experiment,
-                             const std::vector<uint32_t> &in_mask,
-                             uint8_t bit) {
+                             const std::vector<uint32_t> &in_mask) {
     if (experiment.GetModulesNum() != nmodules)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Mismatch in module size");
 
     if (in_mask.size() == nmodules * RAW_MODULE_SIZE) {
-        LoadDetectorBadPixelMask(in_mask, bit);
+        LoadMask(in_mask, UserMaskedPixelBit);
     } else if (in_mask.size() == experiment.GetPixelsNum()) {
         std::vector<uint32_t> raw_mask(nmodules * RAW_MODULE_SIZE);
         ConvertedToRawGeometry(experiment, raw_mask.data(), in_mask.data());
-        LoadDetectorBadPixelMask(in_mask, bit);
+        LoadMask(raw_mask, UserMaskedPixelBit);
     } else
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                               "Size of input user mask invalid");

common/PixelMask.h

@@ -9,12 +9,21 @@
 class PixelMask {
     size_t nmodules;
     std::vector<uint32_t> mask;
+    void LoadMask(const std::vector<uint32_t>& mask, uint8_t bit);
 public:
+    // NXmx bits
+    constexpr static const uint8_t ModuleGapPixelBit = 0;
+    constexpr static const uint8_t ErrorPixelBit = 1;
+    constexpr static const uint8_t UserMaskedPixelBit = 8;
+    constexpr static const uint8_t ChipGapPixelBit = 31;
+    constexpr static const uint8_t ModuleEdgePixelBit = 30;
+
     PixelMask(const DetectorSetup& detector);
     PixelMask(const DiffractionExperiment& experiment);
-    void LoadUserMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask, uint8_t bit);
-    void LoadDetectorBadPixelMask(const std::vector<uint32_t>& mask, uint8_t bit);
-    std::vector<uint32_t> GetMask(const DiffractionExperiment& experiment);
+    void LoadUserMask(const DiffractionExperiment& experiment, const std::vector<uint32_t>& mask);
+    void LoadDetectorBadPixelMask(const std::vector<uint32_t>& mask);
+    std::vector<uint32_t> GetMask(const DiffractionExperiment& experiment, bool conv = true) const;
+    std::vector<uint32_t> GetUserMask(const DiffractionExperiment& experiment, bool conv = true) const;
 };
 
 

common/Plot.h

@@ -7,9 +7,12 @@
 #include <cstdint>
 #include <string>
 
-enum class PlotType {BkgEstimate, RadInt, RadIntPerTimePoint, SpotCount, IndexingRate, IndexingRatePerTimePoint,
-                     ErrorPixels, ImageCollectionEfficiency, ReceiverDelay, ReceiverFreeSendBuf, StrongPixels,
-                     ROISum, ROIMaxCount, ROIPixels};
+enum class PlotType {
+    BkgEstimate, RadInt, RadIntPerTimePoint, SpotCount, SpotCountInRings,
+    IndexingRate, IndexingRatePerTimePoint,
+    ErrorPixels, ImageCollectionEfficiency, ReceiverDelay, ReceiverFreeSendBuf, StrongPixels,
+    ROISum, ROIMaxCount, ROIPixels
+};
 
 struct PlotRequest {
     PlotType type;

common/StatusVector.h

@@ -7,6 +7,7 @@
 #include <map>
 #include <mutex>
 #include <cmath>
+#include <optional>
 
 #include "Plot.h"
 
@@ -37,6 +38,11 @@ template <class T> class StatusVector {
         return ret;
     }
 public:
+    void AddElement(uint32_t id, std::optional<T> val) {
+        if (val.has_value())
+            AddElement(id, val.value());
+    }
+
     void AddElement(uint32_t id, T val) {
         std::unique_lock<std::mutex> ul(m);
         if (id >= content.size()) {

fpga/hls/spot_finder.cpp

@@ -13,13 +13,18 @@
 struct spot_finder_packet {
     ap_uint<768> data;
     ap_uint<32> mask;
+    ap_uint<32> strong_pixel;
+    ap_int<32> count_threshold;
+    ap_uint<32> snr_threshold;
     ap_uint<1> user;
     ap_uint<1> last;
 };
 
 void spot_finder_in_stream(STREAM_768 &data_in,
                            hls::stream<ap_uint<32>> &mask_in,
-                           hls::stream<spot_finder_packet> &data_out) {
+                           hls::stream<spot_finder_packet> &data_out,
+                           volatile ap_int<32> &in_count_threshold,
+                           volatile ap_uint<32> &in_snr_threshold) {
     ap_uint<32> mask;
     packet_768_t packet_in;
     {
@@ -33,12 +38,53 @@ void spot_finder_in_stream(STREAM_768 &data_in,
     while (!packet_in.user) {
 #pragma HLS PIPELINE II=1
         mask_in >> mask;
-        data_out << spot_finder_packet{.data = packet_in.data, .mask = mask, .user = packet_in.user, .last = packet_in.last};
+        data_out << spot_finder_packet{
+            .data = packet_in.data,
+                .mask = mask,
+                .strong_pixel = 0,
+                .count_threshold = in_count_threshold,
+                .snr_threshold = in_snr_threshold,
+                .user = packet_in.user,
+                .last = packet_in.last
+        };
         data_in >> packet_in;
     }
     data_out << spot_finder_packet{.data = packet_in.data, .mask = 0, .user = packet_in.user, .last = packet_in.last};
 }
 
+void spot_finder_out_stream(hls::stream<spot_finder_packet> &data_in,
+                            STREAM_768 &data_out,
+                            hls::stream<ap_axiu<32,1,1,1>> &strong_pixel_out) {
+    spot_finder_packet packet_in;
+    {
+#pragma HLS PROTOCOL fixed
+        data_in >> packet_in;
+        ap_wait();
+        data_out << packet_768_t{.data = packet_in.data, .user = packet_in.user, .last = packet_in.last};
+        ap_wait();
+    }
+
+    data_in >> packet_in;
+    while (!packet_in.user) {
+        ap_uint<32> count_threshold = packet_in.count_threshold;
+        ap_uint<32> snr_threshold_u32 = packet_in.snr_threshold;
+        for (int i = 0; i < RAW_MODULE_SIZE * sizeof(uint16_t) / 64; i++) {
+#pragma HLS PIPELINE II=1
+            data_out << packet_768_t{.data = packet_in.data, .user = packet_in.user, .last = packet_in.last};
+            strong_pixel_out << ap_axiu<32,1,1,1>{.data = packet_in.strong_pixel, .user = 0};
+            data_in >> packet_in;
+        }
+
+        // Save module statistics
+        strong_pixel_out << ap_axiu<32,1,1,1>{.data = count_threshold, .user = 0};
+        strong_pixel_out << ap_axiu<32,1,1,1>{.data = snr_threshold_u32, .user = 0};
+        for (int i = 0; i < 14;i++)
+            strong_pixel_out << ap_axiu<32,1,1,1>{.data =  0, .user = 0};
+    }
+    strong_pixel_out << ap_axiu<32,1,1,1>{.data = 0, .user = 1};
+    data_out << packet_768_t{.data = packet_in.data, .user = packet_in.user, .last = packet_in.last};
+}
+
 ap_int<SUM_BITWIDTH> calc_sum(ap_int<24> val[32], ap_uint<32> mask) {
 #pragma HLS PIPELINE II=1
     ap_int<SUM_BITWIDTH> ret = 0;
@@ -73,6 +119,8 @@ void spot_finder_prepare(hls::stream<spot_finder_packet> &data_in,
                          hls::stream<ap_int<SUM_BITWIDTH>> &sum_out,
                          hls::stream<ap_int<SUM2_BITWIDTH>> &sum2_out,
                          hls::stream<ap_int<VALID_BITWIDTH>> &valid_out) {
+    ap_uint<32> strong_pixel;
+
     spot_finder_packet packet;
     {
 #pragma HLS PROTOCOL fixed
@@ -95,6 +143,7 @@ void spot_finder_prepare(hls::stream<spot_finder_packet> &data_in,
         for (ap_uint<15> i = 0; i < RAW_MODULE_SIZE * sizeof(uint16_t) / 64; i++) {
 #pragma HLS PIPELINE II=1
             data_out << packet;
+
             ap_int<24> val[32];
             unpack32(packet.data, val);
             ap_uint<32> mask = packet.mask;
@@ -167,31 +216,28 @@ ap_uint<32> spot_finder_count_threshold(ap_int<24> val[32], ap_int<32> &count_th
 }
 
 void spot_finder_apply_threshold(hls::stream<spot_finder_packet> &data_in,
-                                 STREAM_768 &data_out,
+                                 hls::stream<spot_finder_packet> &data_out,
                                  hls::stream<ap_int<SUM_BITWIDTH>> &sum_in,
                                  hls::stream<ap_int<SUM2_BITWIDTH>> &sum2_in,
-                                 hls::stream<ap_int<VALID_BITWIDTH>> &valid_in,
-                                 hls::stream<ap_axiu<32,1,1,1>> &strong_pixel_out,
-                                 volatile ap_int<32> &in_count_threshold,
-                                 volatile ap_uint<32> &in_snr_threshold) {
+                                 hls::stream<ap_int<VALID_BITWIDTH>> &valid_in) {
+    ap_uint<32> strong_pixel_prev;
     spot_finder_packet packet_in;
     {
 #pragma HLS PROTOCOL fixed
         data_in >> packet_in;
         ap_wait();
-        data_out << packet_768_t{.data = packet_in.data, .user = packet_in.user, .last = packet_in.last};
+        data_out << packet_in;
         ap_wait();
     }
 
-
     ap_int<SUM_BITWIDTH> sum[32];
     ap_int<SUM2_BITWIDTH> sum2[32];
     ap_int<VALID_BITWIDTH> valid[32];
 
     data_in >> packet_in;
     while (!packet_in.user) {
-        ap_int<32> count_threshold = in_count_threshold;
-        ap_uint<32> snr_threshold_u32 = in_snr_threshold;
+        ap_int<32> count_threshold = packet_in.count_threshold;
+        ap_uint<32> snr_threshold_u32 = packet_in.snr_threshold;
         float_uint32 thr;
         thr.u = snr_threshold_u32;
         ap_ufixed<10,8, AP_RND_CONV> snr_threshold = thr.f;
@@ -212,34 +258,28 @@ void spot_finder_apply_threshold(hls::stream<spot_finder_packet> &data_in,
                 valid_in >> valid[i % 32];
             }
 
-            data_out << packet_768_t{.data = packet_in.data, .user = packet_in.user, .last = packet_in.last};
             ap_int<24> data_unpacked[32];
             unpack32(packet_in.data, data_unpacked);
 
             ap_uint<32> strong_pixel = spot_finder_count_threshold(data_unpacked, count_threshold) &
-                    spot_finder_snr_threshold(data_unpacked, snr_threshold_2,
-                                              sum[i % 32], sum2[i % 32], valid[i % 32]);
-
-            strong_pixel = strong_pixel & packet_in.mask;
+                                       spot_finder_snr_threshold(data_unpacked, snr_threshold_2,
+                                                                 sum[i % 32], sum2[i % 32], valid[i % 32]);
 
             if ((snr_threshold == 0) && (count_threshold <= 0))
                 strong_pixel = 0;
 
-            strong_pixel_out << ap_axiu<32,1,1,1>{.data = strong_pixel, .user = 0};
+            strong_pixel = strong_pixel & packet_in.mask;
+
+            packet_in.mask |= strong_pixel; // mask strong pixels
+            packet_in.strong_pixel |= strong_pixel; // add strong pixels to the output
+
+            data_out << packet_in;
             data_in >> packet_in;
         }
-
-        // Save module statistics
-       strong_pixel_out << ap_axiu<32,1,1,1>{.data = count_threshold, .user = 0};
-       strong_pixel_out << ap_axiu<32,1,1,1>{.data = snr_threshold_u32, .user = 0};
-       	  for (int i = 0; i < 14;i++)
-              strong_pixel_out << ap_axiu<32,1,1,1>{.data =  0, .user = 0};
     }
-    strong_pixel_out << ap_axiu<32,1,1,1>{.data = 0, .user = 1};
-    data_out << packet_768_t{.data = packet_in.data, .user = packet_in.user, .last = packet_in.last};
+    data_out << packet_in;
 }
 
-
 void spot_finder(STREAM_768 &data_in,
                  hls::stream<ap_uint<32>> &mask_in,
                  STREAM_768 &data_out,
@@ -256,22 +296,38 @@ void spot_finder(STREAM_768 &data_in,
 
     hls::stream<spot_finder_packet, 2> data_0;
     hls::stream<spot_finder_packet, 1080> data_1;
+    hls::stream<spot_finder_packet, 8> data_2;
+    hls::stream<spot_finder_packet, 1080> data_3;
+    hls::stream<spot_finder_packet, 8> data_4;
+
 #pragma HLS BIND_STORAGE variable=data_1 type=fifo impl=bram
+#pragma HLS BIND_STORAGE variable=data_3 type=fifo impl=bram
+
     hls::stream<ap_int<SUM_BITWIDTH>, 24> sum_0;
     hls::stream<ap_int<SUM2_BITWIDTH>, 24> sum2_0;
     hls::stream<ap_int<VALID_BITWIDTH>, 24> valid_0;
+
+    hls::stream<ap_int<SUM_BITWIDTH>, 24> sum_1;
+    hls::stream<ap_int<SUM2_BITWIDTH>, 24> sum2_1;
+    hls::stream<ap_int<VALID_BITWIDTH>, 24> valid_1;
+
 #ifndef JFJOCH_HLS_NOSYNTH
-    spot_finder_in_stream(data_in, mask_in, data_0);
+    spot_finder_in_stream(data_in, mask_in, data_0, in_count_threshold, in_snr_threshold);
     spot_finder_prepare(data_0, data_1, sum_0, sum2_0, valid_0);
-    spot_finder_apply_threshold(data_1, data_out, sum_0, sum2_0, valid_0, strong_pixel_out,
-                                in_count_threshold, in_snr_threshold);
+    spot_finder_apply_threshold(data_1, data_2, sum_0, sum2_0, valid_0);
+    spot_finder_prepare(data_2, data_3, sum_1, sum2_1, valid_1);
+    spot_finder_apply_threshold(data_3, data_4, sum_1, sum2_1, valid_1);
+    spot_finder_out_stream(data_4, data_out, strong_pixel_out);
 #else
     std::vector<std::thread> spot_finder_cores;
-    spot_finder_cores.emplace_back([&] {spot_finder_in_stream(data_in, mask_in, data_0);});
+    spot_finder_cores.emplace_back([&] {spot_finder_in_stream(data_in, mask_in, data_0, in_count_threshold,
+                                                              in_snr_threshold);});
     spot_finder_cores.emplace_back([&] {spot_finder_prepare(data_0, data_1, sum_0, sum2_0, valid_0);});
-    spot_finder_cores.emplace_back([&] {spot_finder_apply_threshold(data_1, data_out, sum_0, sum2_0, valid_0,
-                                                                    strong_pixel_out, in_count_threshold,
-                                                                    in_snr_threshold);});
+    spot_finder_cores.emplace_back([&] {spot_finder_apply_threshold(data_1, data_2, sum_0, sum2_0, valid_0);});
+    spot_finder_cores.emplace_back([&] {spot_finder_prepare(data_2, data_3, sum_1, sum2_1, valid_1);});
+    spot_finder_cores.emplace_back([&] {spot_finder_apply_threshold(data_3, data_4, sum_1, sum2_1, valid_1);});
+    spot_finder_cores.emplace_back([&] {spot_finder_out_stream(data_4, data_out, strong_pixel_out);});
+
     for (auto &i : spot_finder_cores)
         i.join();
 #endif

fpga/hls/spot_finder_mask.cpp

@@ -74,8 +74,8 @@ void spot_finder_mask(STREAM_768 &data_in,
                     || (((col == 0) || (col == 8) || (col == 16) || (col == 24)) && (j ==  0))
                     || (pixel_val[j] == INT24_MIN)
                     || (pixel_val[j] == INT24_MAX)
-                    || ((d[j] != 0) && (d[j] < min_d_value))
-                    || ((d[j] != 0) && (d[j] > max_d_value)))
+                    || (d[j] < min_d_value)
+                    || (d[j] > max_d_value))
                     mask_val[j] = 0;
                 else
                     mask_val[j] = 1;

fpga/pcie_driver/jfjoch_pcie_setup.c

@@ -54,12 +54,13 @@ int jfjoch_check_version(struct pci_dev *pdev) {
     release_level = ioread32(drvdata->bar0 + ACTION_CONFIG_OFFSET + ADDR_RELEASE_LEVEL);
 
     if (action_type != JFJOCH_FPGA_MAGIC) {
-        dev_err(dev, "Mismatch in JFJoch action type (%x)\n", action_type);
+        dev_err(dev, "Very likely the FPGA is not flashed with Jungfraujoch design, given that action type register value is wrong (%x).\n", action_type);
         return -EINVAL;
     }
 
     if (release_level != JFJOCH_FPGA_RELEASE) {
-        dev_err(dev, "Mismatch in JFJoch release level (%x)\n", release_level);
+        dev_err(dev, "Jungfraujoch FPGA is flashed with design made with release %x, while driver is compiled with release %x.\n", release_level, JFJOCH_FPGA_RELEASE);
+        dev_err(dev, "Given FPGA releases have braking changes in FPGA-driver interface (register map, data structure size, etc.)\n it is not safe and not supported at the moment to operate multiple releases with one driver.\n");
         return -EINVAL;
     }
     return 0;

frame_serialize/CBORStream2Deserializer.cpp

@@ -456,6 +456,8 @@ namespace {
                     message.user_data = GetCBORString(value);
                 else if (key == "spots")
                     GetCBORSpots(message, value);
+                else if (key == "spot_count_in_rings")
+                    message.spot_count_in_rings = GetCBORUInt(value);
                 else if (key == "az_int_profile")
                     GetCBORFloatArray(value, message.az_int_profile);
                 else if (key == "indexing_result")
@@ -526,30 +528,38 @@ namespace {
         cborErr(cbor_value_leave_container(&value, &array_value));
     }
 
-    void ProcessGoniometerOmega(StartMessage &message, CborValue &value) {
+    GoniometerAxis ProcessGoniometerOmega(std::string &name, CborValue &value) {
+        GoniometerAxis ret;
+        ret.name = name;
+
         CborValue map_value;
 
         cborErr(cbor_value_enter_container(&value, &map_value));
         while (!cbor_value_at_end(&map_value)) {
             auto key = GetCBORString(map_value);
             if (key == "increment")
-                message.omega.increment = GetCBORFloat(map_value);
+                ret.increment = GetCBORFloat(map_value);
             else if (key == "start")
-                message.omega.start = GetCBORFloat(map_value);
+                ret.start = GetCBORFloat(map_value);
             else
                 cbor_value_advance(&value);
         }
         cborErr(cbor_value_leave_container(&value, &map_value));
+
+        return ret;
     }
 
     void ProcessGoniometerMap(StartMessage &message, CborValue &value) {
         CborValue map_value;
 
+        if (GetCBORMapLen(value) > 1)
+            throw JFJochException(JFJochExceptionCategory::CBORError, "Max one rotation angle allowed");
+
         cborErr(cbor_value_enter_container(&value, &map_value));
         while (!cbor_value_at_end(&map_value)) {
+            GoniometerAxis axis;
             auto key = GetCBORString(map_value);
-            if (key == "omega")
-                ProcessGoniometerOmega(message, map_value);
+            message.goniometer = ProcessGoniometerOmega(key, map_value);
         }
         cborErr(cbor_value_leave_container(&value, &map_value));
     }
@@ -613,6 +623,8 @@ namespace {
                 message.sample_name = j["sample_name"];
             if (j.contains("source_name"))
                 message.source_name = j["source_name"];
+            if (j.contains("source_type"))
+                message.source_type = j["source_type"];
             if (j.contains("source_name_short"))
                 message.source_name_short = j["source_name_short"];
             if (j.contains("instrument_name"))
@@ -623,10 +635,10 @@ namespace {
                 message.total_flux = j["total_flux"];
             if (j.contains("attenuator_transmission"))
                 message.attenuator_transmission = j["attenuator_transmission"];
-            if (j.contains("omega_rotation_axis") && j["omega_rotation_axis"].is_array() &&
-                (j["omega_rotation_axis"].size() == 3)) {
+            if (j.contains("rotation_axis") && j["rotation_axis"].is_array() &&
+                (j["rotation_axis"].size() == 3)) {
                 for (int i = 0; i < 3; i++)
-                    message.omega.axis[i] = j["omega_rotation_axis"][i];
+                    message.rotation_axis[i] = j["rotation_axis"][i];
             }
             if (j.contains("space_group_number"))
                 message.space_group_number = j["space_group_number"];
@@ -638,6 +650,11 @@ namespace {
                 message.write_master_file = j["write_master_file"];
             if (j.contains("data_reduction_factor_serialmx"))
                 message.data_reduction_factor_serialmx = j["data_reduction_factor_serialmx"];
+            if (j.contains("experiment_group"))
+                message.experiment_group = j["experiment_group"];
+            if (j.contains("jfjoch_release"))
+                message.jfjoch_release = j["jfjoch_release"];
+
         } catch (const std::exception &e) {
             throw JFJochException(JFJochExceptionCategory::CBORError,
                                   "Cannot parse user_data as valid JSON " + std::string(e.what()));

frame_serialize/CBORStream2Serializer.cpp

@@ -215,10 +215,10 @@ inline void CBOR_ENC_AXIS(CborEncoder &encoder, const char* key, const float det
     cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
 }
 
-inline void CBOR_ENC_GONIOMETER(CborEncoder &encoder, const char* key, const GoniometerAxis &g) {
+inline void CBOR_ENC_GONIOMETER(CborEncoder &encoder, const GoniometerAxis &g) {
     CborEncoder mapEncoder;
 
-    cborErr(cbor_encode_text_stringz(&encoder, key));
+    cborErr(cbor_encode_text_stringz(&encoder, g.name.c_str()));
     cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 2));
     CBOR_ENC(mapEncoder, "increment", g.increment);
     CBOR_ENC(mapEncoder, "start", g.start);
@@ -228,11 +228,12 @@ inline void CBOR_ENC_GONIOMETER(CborEncoder &encoder, const char* key, const Gon
 inline void CBOR_ENC_GONIOMETER_MAP(CborEncoder &encoder, const char* key, const StartMessage &msg) {
     CborEncoder mapEncoder;
 
-    cborErr(cbor_encode_text_stringz(&encoder, key));
-    cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 1));
-    CBOR_ENC_GONIOMETER(mapEncoder, "omega", msg.omega);
-
-    cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
+    if (msg.goniometer) {
+        cborErr(cbor_encode_text_stringz(&encoder, key));
+        cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 1));
+        CBOR_ENC_GONIOMETER(mapEncoder, msg.goniometer.value());
+        cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
+    }
 }
 
 inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<std::string> &v) {
@@ -302,6 +303,8 @@ inline void CBOR_ENC_START_USER_DATA(CborEncoder& encoder, const char* key,
     j["images_per_file"] = message.images_per_file;
     j["source_name"] = message.source_name;
     j["source_name_short"] = message.source_name_short;
+    if (!message.source_type.empty())
+        j["source_type"] = message.source_type;
     j["instrument_name"] = message.instrument_name;
     j["instrument_name_short"] = message.instrument_name_short;
     j["sample_name"] = message.sample_name;
@@ -310,7 +313,7 @@ inline void CBOR_ENC_START_USER_DATA(CborEncoder& encoder, const char* key,
         j["attenuator_transmission"] = message.attenuator_transmission.value();
     if (message.total_flux)
         j["total_flux"] = message.total_flux.value();
-    j["omega_rotation_axis"] = {message.omega.axis[0], message.omega.axis[1], message.omega.axis[2]};
+    j["rotation_axis"] = {message.rotation_axis[0], message.rotation_axis[1], message.rotation_axis[2]};
     j["space_group_number"] = message.space_group_number;
     j["roi_names"] = message.roi_names;
     j["gain_file_names"] = message.gain_file_names;
@@ -318,7 +321,9 @@ inline void CBOR_ENC_START_USER_DATA(CborEncoder& encoder, const char* key,
         j["write_master_file"] = message.write_master_file.value();
     if (message.data_reduction_factor_serialmx)
         j["data_reduction_factor_serialmx"] = message.data_reduction_factor_serialmx.value();
-
+    if (message.experiment_group)
+        j["experiment_group"] = message.experiment_group.value();
+    j["jfjoch_release"] = message.jfjoch_release;
     auto str = j.dump();
 
     CBOR_ENC(encoder, key, str);
@@ -450,6 +455,8 @@ void CBORStream2Serializer::SerializeImage(const DataMessage& message) {
     CBOR_ENC_RATIONAL(mapEncoder, "end_time", message.timestamp + message.exptime, message.timestamp_base);
 
     CBOR_ENC(mapEncoder, "spots", message.spots);
+    CBOR_ENC(mapEncoder, "spot_count_in_rings", message.spot_count_in_rings);
+
     CBOR_ENC(mapEncoder, "az_int_profile", message.az_int_profile);
     CBOR_ENC(mapEncoder, "indexing_result", message.indexing_result);
     if (!message.indexing_lattice.empty())

frame_serialize/JFJochMessages.h

@@ -45,6 +45,7 @@ struct DataMessage {
     float image_collection_efficiency;
 
     std::vector<SpotToSave> spots;
+    std::optional<uint64_t> spot_count_in_rings = 0;
 
     std::vector<float> az_int_profile;
     float bkg_estimate;
@@ -84,9 +85,9 @@ struct DataMessage {
 };
 
 struct GoniometerAxis {
+    std::string name;
     float increment;
     float start;
-    float axis[3];
 };
 
 struct StartMessage {
@@ -143,9 +144,11 @@ struct StartMessage {
 
     std::vector<std::string> roi_names;
 
-    GoniometerAxis omega;
+    std::optional<GoniometerAxis> goniometer;
+    float rotation_axis[3];
     float detector_translation[3];
 
+    std::string source_type;
     std::string source_name;
     std::string source_name_short;
     std::string instrument_name;
@@ -170,6 +173,9 @@ struct StartMessage {
     std::string user_data;
 
     std::optional<float> data_reduction_factor_serialmx;
+    std::optional<std::string> experiment_group;
+
+    std::string jfjoch_release;
 };
 
 struct EndMessage {

frame_serialize/README.md

@@ -13,96 +13,98 @@ There are minor differences at the moment:
 
 ## Start message
 
-| Field name                | Type                            | Description                                                                                                                       | Present in DECTRIS format |
-|---------------------------|---------------------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:|
-| type                      | String                          | value "start"                                                                                                                     |             X             |
-| magic_number              | uint64                          | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver |                           |
-| detector_distance         | float                           | Detector distance \[m\]                                                                                                           |                           |
-| detector_translation      | float                           | Detector translation vector \[m\]                                                                                                 |             X             |
-| beam_center_x             | float                           | Beam center in X direction \[pixels\]                                                                                             |             X             |
-| beam_center_y             | float                           | Beam center in Y direction \[pixels\]                                                                                             |             X             |
-| number_of_images          | uint64                          | Number of images in the series                                                                                                    |             X             |
-| image_size_x              | uint64                          | Image width \[pixels\]                                                                                                            |             X             |
-| image_size_y              | uint64                          | Image height \[pixels\]                                                                                                           |             X             |
-| incident_energy           | float                           | X-ray energy \[eV\]                                                                                                               |             X             |
-| incident_wavelength       | float                           | X-ray wavelength \[Angstrom\]                                                                                                     |             X             |
-| frame_time                | float                           | Frame time, if multiple frames per trigger \[s\]                                                                                  |             X             |
-| count_time                | float                           | Exposure time \[s\]                                                                                                               |             X             |
-| saturation_value          | int64                           | Maximum valid sample value                                                                                                        |             X             |
-| error_value               | int64                           | Value used in images to describe pixels that are in error state or missing                                                        |                           |
-| pixel_size_x              | float                           | Pixel width \[m\]                                                                                                                 |             X             |
-| pixel_size_y              | float                           | Pixel height \[m\]                                                                                                                |             X             |
-| sensor_thickness          | float                           | Sensor thickness \[m\]                                                                                                            |             X             |
-| sensor_material           | string                          | Sensor material                                                                                                                   |             X             |
-| arm_data                  | data                            | Approximate date of arming                                                                                                        |             X             |
-| pixel_mask_enabled        | bool                            | Pixel mask applied on images                                                                                                      |             X             |
-| detector_description      | string                          | Name of the detector                                                                                                              |             X             |
-| series_unique_id          | string                          | Unique text ID of the series                                                                                                      |             X             |
-| series_id                 | uint64                          | Unique numeric ID of the series                                                                                                   |             X             |
-| goniometer                | Map                             | See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/stream_v2) - only "omega" axis is supported        |             X             |
-| pixel_mask                | Map(string -> Image)            | Pixel mask - multiple in case of storage cells                                                                                    |             X             |
-| channels                  | Array(string)                   | List of image channels                                                                                                            |             X             |
-| max_spot_count            | uint64                          | Maximum number of spots identified in spot finding                                                                                |                           |
-| storage_cell_number       | uint64                          | Number of storage cells used by JUNGFRAU                                                                                          |                           |
-| image_dtype               | string                          | Pixel bit type (e.g. uint16)                                                                                                      |             X             |
-| unit_cell                 | Array(6 * float) (optional)     | Unit cell of the system: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]                                                   |                           |
-| az_int_bin_number         | uint64                          | Number of azimuthal integration bins                                                                                              |                           |
-| az_int_bin_to_q           | Array(float)                    | Q value for each azimuthal integration bin \[angstrom^-1\]                                                                        |                           |
-| summation                 | uint64                          | Factor of frame summation                                                                                                         |                           |
-| user_data                 | string                          | JSON string that can contain the following fields (among others):                                                                 |             X             |
-| - source_name             | string                          | Facility name                                                                                                                     |                           |
-| - source_name_short       | string                          | Facility name (short)                                                                                                             |                           |
-| - instrument_name         | string                          | Instrument name                                                                                                                   |                           |
-| - instrument_name_short   | string                          | Instrument name (short                                                                                                            |                           |
-| - attenuator_transmission | float (optional)                | Attenuator transmission \[\]                                                                                                      |                           |
-| - total_flux              | float (optional)                | Total flux \[ph/s\]                                                                                                               |                           |
-| - data_file_count         | uint64                          | Number of used data files                                                                                                         |                           |
-| - file_prefix             | string                          | File prefix                                                                                                                       |                           |
-| - sample_name             | string                          | Name of the sample                                                                                                                |                           |
-| - omega_rotation_axis     | Array(float)                    | Omega rotation axis (array of size 3)                                                                                             |                           |
-| - space_group_number      | uint64                          | Space group number                                                                                                                |                           |
-| - write_master_file       | bool                            | With multiple sockets, it selects which socket will provide master file                                                           |                           |
+| Field name                | Type                        | Description                                                                                                                       | Present in DECTRIS format |
+|---------------------------|-----------------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:|
+| type                      | String                      | value "start"                                                                                                                     |             X             |
+| magic_number              | uint64                      | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver |                           |
+| detector_distance         | float                       | Detector distance \[m\]                                                                                                           |                           |
+| detector_translation      | float                       | Detector translation vector \[m\]                                                                                                 |             X             |
+| beam_center_x             | float                       | Beam center in X direction \[pixels\]                                                                                             |             X             |
+| beam_center_y             | float                       | Beam center in Y direction \[pixels\]                                                                                             |             X             |
+| number_of_images          | uint64                      | Number of images in the series                                                                                                    |             X             |
+| image_size_x              | uint64                      | Image width \[pixels\]                                                                                                            |             X             |
+| image_size_y              | uint64                      | Image height \[pixels\]                                                                                                           |             X             |
+| incident_energy           | float                       | X-ray energy \[eV\]                                                                                                               |             X             |
+| incident_wavelength       | float                       | X-ray wavelength \[Angstrom\]                                                                                                     |             X             |
+| frame_time                | float                       | Frame time, if multiple frames per trigger \[s\]                                                                                  |             X             |
+| count_time                | float                       | Exposure time \[s\]                                                                                                               |             X             |
+| saturation_value          | int64                       | Maximum valid sample value                                                                                                        |             X             |
+| error_value               | int64                       | Value used in images to describe pixels that are in error state or missing                                                        |                           |
+| pixel_size_x              | float                       | Pixel width \[m\]                                                                                                                 |             X             |
+| pixel_size_y              | float                       | Pixel height \[m\]                                                                                                                |             X             |
+| sensor_thickness          | float                       | Sensor thickness \[m\]                                                                                                            |             X             |
+| sensor_material           | string                      | Sensor material                                                                                                                   |             X             |
+| arm_data                  | data                        | Approximate date of arming                                                                                                        |             X             |
+| pixel_mask_enabled        | bool                        | Pixel mask applied on images                                                                                                      |             X             |
+| detector_description      | string                      | Name of the detector                                                                                                              |             X             |
+| series_unique_id          | string                      | Unique text ID of the series                                                                                                      |             X             |
+| series_id                 | uint64                      | Unique numeric ID of the series                                                                                                   |             X             |
+| goniometer                | Map                         | See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/stream_v2) - only one axis is supported            |             X             |
+| pixel_mask                | Map(string -> Image)        | Pixel mask - multiple in case of storage cells                                                                                    |             X             |
+| channels                  | Array(string)               | List of image channels                                                                                                            |             X             |
+| max_spot_count            | uint64                      | Maximum number of spots identified in spot finding                                                                                |                           |
+| storage_cell_number       | uint64                      | Number of storage cells used by JUNGFRAU                                                                                          |                           |
+| image_dtype               | string                      | Pixel bit type (e.g. uint16)                                                                                                      |             X             |
+| unit_cell                 | Array(6 * float) (optional) | Unit cell of the system: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]                                                   |                           |
+| az_int_bin_number         | uint64                      | Number of azimuthal integration bins                                                                                              |                           |
+| az_int_bin_to_q           | Array(float)                | Q value for each azimuthal integration bin \[angstrom^-1\]                                                                        |                           |
+| summation                 | uint64                      | Factor of frame summation                                                                                                         |                           |
+| user_data                 | string                      | JSON string that can contain the following fields (among others):                                                                 |             X             |
+| - source_name             | string                      | Facility name                                                                                                                     |                           |
+| - source_name_short       | string                      | Facility name (short)                                                                                                             |                           |
+| - source_type             | string (optional)           | Type of X-ray source (use NXsource/type values, for example "Synchrotron X-ray Source" or "Free-Electron Laser")                  |                           |
+| - instrument_name         | string                      | Instrument name                                                                                                                   |                           |
+| - instrument_name_short   | string                      | Instrument name (short)                                                                                                           |                           |
+| - attenuator_transmission | float (optional)            | Attenuator transmission \[\]                                                                                                      |                           |
+| - total_flux              | float (optional)            | Total flux \[ph/s\]                                                                                                               |                           |
+| - data_file_count         | uint64                      | Number of used data files                                                                                                         |                           |
+| - file_prefix             | string                      | File prefix                                                                                                                       |                           |
+| - sample_name             | string                      | Name of the sample                                                                                                                |                           |
+| - rotation_axis           | Array(float)                | Rotation axis vector (array of size 3)                                                                                            |                           |
+| - space_group_number      | uint64                      | Space group number                                                                                                                |                           |
+| - write_master_file       | bool                        | With multiple sockets, it selects which socket will provide master file                                                           |                           |
+| - experiment_group        | string                      | ID of instrument user, e.g., p-group (SLS/SwissFEL) or proposal number                                                            |                           |
 
 See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/stream_v2) for definition of Image as MultiDimArray with optional compression.
 
 ## Image message
 
-| Field name                 | Type                        | Description                                                                                                                       | Present in DECTRIS format | Optional |
-|----------------------------|-----------------------------|-----------------------------------------------------------------------------------------------------------------------------------|:-------------------------:|:--------:|
-| type                       | String                      | value "image"                                                                                                                     |             X             |          |
+| Field name                 | Type                        | Description                                                                                                                    | Present in DECTRIS format | Optional |
+|----------------------------|-----------------------------|--------------------------------------------------------------------------------------------------------------------------------|:-------------------------:|:--------:|
+| type                       | String                      | value "image"                                                                                                                  |             X             |          |
 | magic_number               | uint64                      | Number used to describe version of the Jungfraujoch data interface - to allow to detect inconsistency between sender and receiver |                           |          |
-| series_unique_id           | string                      | Unique text ID of the series                                                                                                      |             X             |          |
-| series_id                  | uint64                      | Unique numeric ID of the series                                                                                                   |             X             |          |
-| image_id                   | uint64                      | Number of image within the series                                                                                                 |             X             |          |
-| real_time                  | Rational                    | Exposure time                                                                                                                     |             X             |          |
-| start_time                 | Rational                    | Exposure start time (highly approximate)                                                                                          |             X             |          |
-| end_time                   | Rational                    | Exposure end time (highly approximate)                                                                                            |             X             |          |
-| spots                      | Array(object)               | Spots:                                                                                                                            |                           |          |
-| - x                        | float                       | position in x (pixels)                                                                                                            |                           |          |
-| - y                        | float                       | position in y (pixels)                                                                                                            |                           |          |
-| - I                        | float                       | intensity (photons)                                                                                                               |                           |          |
-| - indexed                  | bool                        | indexed solution                                                                                                                  |                           |          |
-| az_int_profile             | Array(float)                | Azimuthal integration results, use az_int_bin_to_q from start message for legend                                                  |                           |          |
-| indexing_result            | bool                        | Indexing successful                                                                                                               |                           |          |
-| indexing_lattice           | Array(float * 9) (optional) | Indexing result real lattice; present only if indexed                                                                             |                           |          |
-| xfel_pulse_id              | uint64                      | Bunch ID (for SwissFEL)                                                                                                           |                           |    X     |
-| xfel_event_code            | uint64                      | Event code (for SwissFEL)                                                                                                         |                           |    X     |
-| jf_info                    | uint64                      | Detector info field                                                                                                               |                           |          |
-| receiver_aq_dev_delay      | uint64                      | Receiver internal delay                                                                                                           |                           |          |
-| receiver_free_send_buf     | uint64                      | Receiver internal number of available send buffers                                                                                |                           |          |
-| storage_cell               | uint64                      | Storage cell number                                                                                                               |                           |          |
-| saturated_pixel_count      | uint64                      | Saturated pixel count                                                                                                             |                           |          |
-| error_pixel_count          | uint64                      | Error pixel count                                                                                                                 |                           |          |
-| strong_pixel_count         | uint64                      | Strong pixel count (first stage of spot finding)                                                                                  |                           |          |
-| data_collection_efficiency | float                       | Image collection efficiency \[\]                                                                                                  |                           |          |
-| bkg_estimate               | float                       | Mean value for pixels in resolution range from 3.0 to 5.0 A [\photons\]                                                           |                           |          |
-| adu_histogram              | Array(uint64)               | ADU histogram                                                                                                                     |                           |          |
-| corr_beam_x_pxl            | float                       | Difference between provided and calculated beam center X (pixels) - requires indexing                                             |                           |    X     |
-| corr_beam_y_pxl            | float                       | Difference between provided and calculated beam center Y (pixels) - requires indexing                                             |                           |    X     |
-| corr_det_dist_mm           | float                       | Difference between provided and calculated detector distance (mm) - requires indexing                                             |                           |    X     |
-| user_data                  | string                      | Optional user defined text information                                                                                            |                           |          |
-| roi_sum                    | int64                       | Sum of ROI rectangle \[photons\]                                                                                                  |                           |    X     |
-| image                      | Map(string -> Image)        | Image                                                                                                                             |                           |          |
+| series_unique_id           | string                      | Unique text ID of the series                                                                                                   |             X             |          |
+| series_id                  | uint64                      | Unique numeric ID of the series                                                                                                |             X             |          |
+| image_id                   | uint64                      | Number of image within the series                                                                                              |             X             |          |
+| real_time                  | Rational                    | Exposure time                                                                                                                  |             X             |          |
+| start_time                 | Rational                    | Exposure start time (highly approximate)                                                                                       |             X             |          |
+| end_time                   | Rational                    | Exposure end time (highly approximate)                                                                                         |             X             |          |
+| spots                      | Array(object)               | Spots:                                                                                                                         |                           |          |
+| - x                        | float                       | position in x (pixels)                                                                                                         |                           |          |
+| - y                        | float                       | position in y (pixels)                                                                                                         |                           |          |
+| - I                        | float                       | intensity (photons)                                                                                                            |                           |          |
+| - indexed                  | bool                        | indexed solution                                                                                                               |                           |          |
+| az_int_profile             | Array(float)                | Azimuthal integration results, use az_int_bin_to_q from start message for legend                                               |                           |          |
+| indexing_result            | bool                        | Indexing successful                                                                                                            |                           |          |
+| indexing_lattice           | Array(float * 9) (optional) | Indexing result real lattice; present only if indexed                                                                          |                           |          |
+| xfel_pulse_id              | uint64                      | Bunch ID (for pulsed source, e.g., SwissFEL)                                                                                   |                           |    X     |
+| xfel_event_code            | uint64                      | Event code (for pulsed source, e.g., SwissFEL)                                                                                 |                           |    X     |
+| jf_info                    | uint64                      | Detector info field                                                                                                            |                           |          |
+| receiver_aq_dev_delay      | uint64                      | Receiver internal delay                                                                                                        |                           |          |
+| receiver_free_send_buf     | uint64                      | Receiver internal number of available send buffers                                                                             |                           |          |
+| storage_cell               | uint64                      | Storage cell number                                                                                                            |                           |          |
+| saturated_pixel_count      | uint64                      | Saturated pixel count                                                                                                          |                           |          |
+| error_pixel_count          | uint64                      | Error pixel count                                                                                                              |                           |          |
+| strong_pixel_count         | uint64                      | Strong pixel count (first stage of spot finding)                                                                               |                           |          |
+| data_collection_efficiency | float                       | Image collection efficiency \[\]                                                                                               |                           |          |
+| bkg_estimate               | float                       | Mean value for pixels in resolution range from 3.0 to 5.0 A [\photons\]                                                        |                           |          |
+| adu_histogram              | Array(uint64)               | ADU histogram                                                                                                                  |                           |          |
+| corr_beam_x_pxl            | float                       | Difference between provided and calculated beam center X (pixels) - requires indexing                                          |                           |    X     |
+| corr_beam_y_pxl            | float                       | Difference between provided and calculated beam center Y (pixels) - requires indexing                                          |                           |    X     |
+| corr_det_dist_mm           | float                       | Difference between provided and calculated detector distance (mm) - requires indexing                                          |                           |    X     |
+| user_data                  | string                      | Optional user defined text information                                                                                         |                           |          |
+| roi_sum                    | int64                       | Sum of ROI rectangle \[photons\]                                                                                               |                           |    X     |
+| image                      | Map(string -> Image)        | Image                                                                                                                          |                           |          |
 
 ## End message
 

frontend_ui/package-lock.json

@@ -1,13 +1,13 @@
 {
-  "name": "jungfrau-frontend",
-  "version": "0.1.0",
+  "name": "jungfraujoch-frontend",
+  "version": "1.0.0",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "name": "jungfrau-frontend",
-      "version": "0.1.0",
-      "license": "GPL-3.0",
+      "name": "jungfraujoch-frontend",
+      "version": "1.0.0",
+      "license": "Proprietary",
       "dependencies": {
         "@emotion/react": "^11.10.4",
         "@emotion/styled": "^11.10.4",

frontend_ui/package.json

@@ -1,7 +1,7 @@
 {
-  "name": "jungfrau-frontend",
-  "version": "0.1.0",
-  "license": "GPL-3.0",
+  "name": "jungfraujoch-frontend",
+  "version": "1.0.0",
+  "license": "Proprietary",
   "private": true,
   "homepage": "/frontend",
   "dependencies": {
@@ -29,7 +29,7 @@
     "redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=build/openapi.html",
     "test": "react-scripts test",
     "eject": "react-scripts eject",
-    "openapi": "openapi --input ../broker/jfjoch_api.yaml --output ./src/openapi"
+    "openapi": "./node_modules/openapi-typescript-codegen/bin/index.js -i ../broker/jfjoch_api.yaml --output ./src/openapi"
   },
   "eslintConfig": {
     "extends": "react-app"

frontend_ui/src/App.tsx

@@ -9,7 +9,6 @@ import Calibration from "./components/Calibration";
 import StatusBar from "./components/StatusBar";
 import DataProcessingPlots from "./components/DataProcessingPlots";
 import DetectorSelection from "./components/DetectorSelection";
-import BkgEstimatePlot from "./components/BkgEstimatePlot";
 import MeasurementStatistics from "./components/MeasurementStatistics";
 import DetectorStatus from "./components/DetectorStatus";
 import Paper from "@mui/material/Paper";
@@ -91,13 +90,13 @@ class App extends Component<MyProps, MyState> {
                       spacing={3}
                       sx={{width: "95%"}}>
                     <Grid item xs={8}>
-                        <BkgEstimatePlot/>
+                        <DataProcessingPlots default_tab={"12"} height={550}/>
                     </Grid>
                     <Grid item xs={4}>
                         <MeasurementStatistics/>
                     </Grid>
                     <Grid item xs={8}>
-                        <DataProcessingPlots/>
+                        <DataProcessingPlots default_tab={"1"} height={700}/>
                     </Grid>
                     <Grid item xs={4}>
                         <DataProcessingSettings/>

frontend_ui/src/components/BkgEstimatePlot.tsx

@@ -1,25 +0,0 @@
-import Paper from "@mui/material/Paper";
-import DataProcessingPlot, {PlotType} from "./DataProcessingPlot";
-import React, {Component} from "react";
-import {Box} from "@mui/material";
-
-type MyProps = {};
-
-
-class BkgEstimatePlot extends Component<MyProps> {
-
-    render() {
-        return <Paper style={{textAlign: 'center'}} sx={{height: 500, width: "100%"}}>
-            <Box sx={{width: "100%", height: 50}}>
-                <br/>
-                <center><strong>Background estimate</strong></center>
-            </Box>
-            <Box sx={{width: "95%", height: 350}}>
-                <DataProcessingPlot type={PlotType.BKG_ESTIMATE} xlabel={"Image Number"}
-                                    ylabel={"Photon count"} binning={0}/><br/>
-            </Box>
-        </Paper>
-    }
-}
-
-export default BkgEstimatePlot;

frontend_ui/src/components/DataProcessingPlots.tsx

@@ -9,7 +9,9 @@ import FormControl from "@mui/material/FormControl";
 import Select, {SelectChangeEvent} from "@mui/material/Select";
 
 type MyProps = {
-};
+    default_tab: string,
+    height: number
+}
 
 type MyState = {
     type: PlotType,
@@ -28,7 +30,7 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
         xlabel: "Image number",
         ylabel: "Indexing rate",
         binning: "0",
-        tab: "1",
+        tab: this.props.default_tab,
         connection_error: true
     }
 
@@ -69,6 +71,9 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
             case "11":
                 this.setState({type: PlotType.ROI_SUM, xlabel: "Image number", ylabel: "Photon count"});
                 break;
+            case "12":
+                this.setState({type: PlotType.BKG_ESTIMATE, xlabel: "Image number", ylabel: "Photon count"});
+                break;
             case "13":
                 this.setState({type: PlotType.RECEIVER_FREE_SEND_BUFS, xlabel: "Image number", ylabel: "Number of buffers"});
                 break;
@@ -80,7 +85,7 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
     };
 
     render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 630, width: "100%" }}>
+        return <Paper style={{textAlign: 'center'}} sx={{ height: this.props.height, width: "100%" }}>
             <Toolbar>
 
                 <Grid container sx={{ minWidth: 500 }} >
@@ -95,6 +100,7 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
                             <MenuItem value={1}>Indexing rate</MenuItem>
                             <MenuItem value={2}>Spot count</MenuItem>
                             <MenuItem value={3}>Azimuthal integration profile</MenuItem>
+                            <MenuItem value={12}>Background estimate</MenuItem>
                             <MenuItem value={11}>ROI area sum</MenuItem>
                             <MenuItem value={6}>ROI area max count</MenuItem>
                             <MenuItem value={4}>Indexing rate (per time point)</MenuItem>
@@ -129,7 +135,7 @@ class DataProcessingPlots extends Component<MyProps, MyState> {
                     </FormControl>
                 </Grid>
             </Toolbar>
-            <Box sx={{width:"95%", height: 550}} >
+            <Box sx={{width:"95%", height: this.props.height - 150}} >
                 <DataProcessingPlot type={this.state.type} xlabel={this.state.xlabel} ylabel={this.state.ylabel}
                                     binning={Number(this.state.binning)}/>
             </Box>

frontend_ui/src/components/DataProcessingSettings.tsx

@@ -17,6 +17,8 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
         s: {
             enable: true,
             indexing: true,
+            filter_powder_rings: false,
+            min_spot_count_powder_ring: 20,
             photon_count_threshold: 8,
             signal_to_noise_threshold: 3.0,
             min_pix_per_spot: 2,
@@ -50,10 +52,6 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
         this.interval = setInterval(() => this.getValues(), 1000);
     }
 
-    componentWillUnmount() {
-        clearInterval(this.interval);
-    }
-
     setPhotonCountThreshold = (event: Event, newValue: number | number[]) => {
         this.setState(prevState => (
             {
@@ -64,6 +62,7 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
             }
         ));
         this.putValues();
+        this.getValues();
     }
 
     setSignalToNoiseThreshold = (event: Event, newValue: number | number[]) => {
@@ -132,8 +131,28 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
         this.getValues();
     }
 
+    enableFilterPowderRingToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
+        let x = this.state;
+        x.s.filter_powder_rings = event.target.checked;
+        this.putValues2(x);
+        this.getValues();
+    }
+
+    setMinSpotCountPowderRing = (event: Event, newValue: number | number[]) => {
+        this.setState(prevState => (
+            {
+                s : {
+                    ...prevState.s,
+                    min_spot_count_powder_ring: newValue as number
+                }
+            }
+        ));
+        this.putValues();
+        this.getValues();
+    }
+
     render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 630, width: '100%' }}>
+        return <Paper style={{textAlign: 'center'}} sx={{ height: 700, width: '100%' }}>
                     <Grid container spacing={0}>
 
                         <Grid item xs={1}/>
@@ -141,43 +160,53 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
                             <br/><strong>Spot finding parameters</strong><br/><br/>
                             <Switch onChange={this.enableSpotFindingToggle} checked={this.state.s.enable}
                                     disabled={this.state.connection_error}/>
-                            Enable spot finding &nbsp;
-                            <Switch onChange={this.enableIndexingToggle} checked={this.state.s.indexing}
-                                    disabled={this.state.connection_error || !this.state.s.enable}/>
-                            Enable indexing <br/><br/>
+                            Spot finding
+                            <br/><br/>
 
                             <Typography gutterBottom> Count threshold </Typography>
                             <Slider disabled={this.state.connection_error || !this.state.s.enable}
                                     value={Number(this.state.s.photon_count_threshold)}
                                     onChange={this.setPhotonCountThreshold}
-                                    min={1} max={50} step={1} valueLabelDisplay="auto" />
+                                    min={1} max={50} step={1} valueLabelDisplay="auto"/>
 
                             <br/><Typography> Signal-to-noise threshold </Typography>
                             <Slider disabled={this.state.connection_error || !this.state.s.enable}
                                     value={Number(this.state.s.signal_to_noise_threshold)}
                                     onChange={this.setSignalToNoiseThreshold}
-                                    min={2} max={10} step={0.5} valueLabelDisplay="auto" />
+                                    min={2} max={10} step={0.5} valueLabelDisplay="auto"/>
 
                             <br/><Typography> Minimum pixel / spot </Typography>
                             <Slider disabled={this.state.connection_error || !this.state.s.enable}
                                     value={Number(this.state.s.min_pix_per_spot)}
                                     onChange={this.setMinPixPerSpot}
-                                    min={1} max={8} step={1} valueLabelDisplay="auto"  />
+                                    min={1} max={8} step={1} valueLabelDisplay="auto"/>
                             <Typography> High resolution limit [&#8491;] </Typography>
                             <Slider disabled={this.state.connection_error || !this.state.s.enable}
                                     value={Number(this.state.s.high_resolution_limit)}
                                     onChange={this.setHighResolutionLimit}
-                                    min={1} max={5} step={0.2} valueLabelDisplay="auto"  />
+                                    min={1} max={5} step={0.2} valueLabelDisplay="auto"/>
+                            <br/><br/>
+                            <Switch onChange={this.enableFilterPowderRingToggle}
+                                    checked={this.state.s.filter_powder_rings}
+                                    disabled={this.state.connection_error || !this.state.s.enable}/>
+                            Filter spots in powder rings (<i>e.g.</i>, ice)
+                            <br/><br/>
+                            <Typography> Min spots to filter powder ring </Typography>
+                            <Slider disabled={this.state.connection_error || !this.state.s.enable || !this.state.s.filter_powder_rings}
+                                    value={Number(this.state.s.filter_powder_rings)}
+                                    onChange={this.setMinSpotCountPowderRing}
+                                    min={5} max={50} step={1} valueLabelDisplay="auto"/>
+                            <br/> <br/>
+                            <Switch onChange={this.enableIndexingToggle} checked={this.state.s.indexing}
+                                    disabled={this.state.connection_error || !this.state.s.enable}/>
+                            Indexing <br/><br/>
                             <Typography> Indexing spot acceptance tolerance </Typography>
-                            <Slider disabled={this.state.connection_error || !this.state.s.enable}
+                            <Slider disabled={this.state.connection_error || !this.state.s.enable || !this.state.s.indexing}
                                     value={Number(this.state.s.indexing_tolerance)}
                                     onChange={this.setIndexingTolerance}
-                                    min={0.0} max={0.3} step={0.01} valueLabelDisplay="auto"  />
-                            <br/><br/>
+                                    min={0.0} max={0.3} step={0.01} valueLabelDisplay="auto"/>
                         </Grid>
                         <Grid item xs={1}/>
-
-
                     </Grid>
                 </Paper>
     }

frontend_ui/src/components/DetectorSettings.tsx

@@ -65,12 +65,12 @@ class DetectorSettings extends Component<MyProps, MyState> {
         }
 
         if (!frame_err) {
-            if ((Number(frame_time) < 470) || (Number(frame_time) > 2000))
+            if (Number(frame_time) < 470)
                 frame_err = true;
         }
 
         if (!count_err) {
-            if (Number(count_time) < 5)
+            if ((Number(count_time) < 3) || (Number(count_time) > 1980))
                 count_err = true;
         }
 

frontend_ui/src/components/DetectorStatus.tsx

@@ -3,8 +3,8 @@ import React, {Component} from 'react';
 import Paper from '@mui/material/Paper';
 import {Grid, Table, TableBody, TableCell, TableContainer, TableRow,} from "@mui/material";
 import {DefaultService, detector_status} from "../openapi";
-import powerchip = detector_status.powerchip;
 import state = detector_status.state;
+import powerchip = detector_status.powerchip;
 
 type MyProps = {}
 
@@ -13,16 +13,28 @@ type MyState = {
     connection_error: boolean
 }
 
+function powerchipToString(s : detector_status) : string {
+    if (s.powerchip === undefined)
+        return "";
+    switch (s.powerchip) {
+        case powerchip.POWER_ON:
+            return "On";
+        case powerchip.POWER_OFF:
+            return "Off";
+        case powerchip.PARTIAL:
+            return "Partially on";
+    }
+}
 class DetectorStatus extends Component<MyProps, MyState> {
     interval : NodeJS.Timer | undefined;
     state : MyState = {
         s: {
             state: state.IDLE,
-            powerchip: powerchip.OFF,
+            powerchip: powerchip.POWER_OFF,
             server_version: "Detector off",
             number_of_triggers_left: 0,
-            fpga_temp_degC: [0,0,0,0,0,1],
-            high_voltage_V: [1,0,0,0,-1]
+            fpga_temp_degC: [-1],
+            high_voltage_V: [-1]
         },
         connection_error: true
     }
@@ -37,11 +49,11 @@ class DetectorStatus extends Component<MyProps, MyState> {
                 this.setState({
                     s: {
                         state: state.IDLE,
-                        powerchip: powerchip.OFF,
+                        powerchip: powerchip.POWER_OFF,
                         server_version: "Detector off",
                         number_of_triggers_left: 0,
-                        fpga_temp_degC: [30,29,35,40,32],
-                        high_voltage_V: [120,120,110,115]
+                        fpga_temp_degC: [-1],
+                        high_voltage_V: [-1]
                     },
                     connection_error: true
                 });
@@ -72,7 +84,7 @@ class DetectorStatus extends Component<MyProps, MyState> {
                                 </TableRow>
                                 <TableRow>
                                     <TableCell component="th" scope="row"> Detector ASIC power: </TableCell>
-                                    <TableCell align="right">{this.state.s.powerchip.toString()}</TableCell>
+                                    <TableCell align="right">{powerchipToString(this.state.s)}</TableCell>
                                 </TableRow>
                                 <TableRow>
                                     <TableCell component="th" scope="row"> Triggers remaining: </TableCell>

frontend_ui/src/components/MeasurementStatistics.tsx

@@ -15,7 +15,9 @@ class MeasurementStatistics extends Component<MyProps, MyState> {
     interval : NodeJS.Timer | undefined;
     state : MyState = {
         s: {
+            run_number: undefined,
             file_prefix: undefined,
+            experiment_group: undefined,
             images_expected: 0,
             images_collected: 0,
             images_sent: 0,
@@ -48,7 +50,7 @@ class MeasurementStatistics extends Component<MyProps, MyState> {
     }
 
     render() {
-        return <Paper style={{textAlign: 'center'}} sx={{ height: 500, width: '100%' }}>
+        return <Paper style={{textAlign: 'center'}} sx={{ height: 550, width: '100%' }}>
             <Grid container spacing={0}>
                 <Grid item xs={1}/>
                 <Grid item xs={10}>
@@ -57,10 +59,19 @@ class MeasurementStatistics extends Component<MyProps, MyState> {
                     <TableContainer component={Paper} style={{marginLeft: "auto", marginRight: "auto"}}>
                         <Table size="small" aria-label="simple table">
                             <TableBody>
-                                    <TableRow>
-                                        <TableCell component="th" scope="row"> File prefix: </TableCell>
-                                        <TableCell align="right">{(this.state.s.file_prefix !== undefined) ? this.state.s.file_prefix : "(images not written)"}</TableCell>
-                                    </TableRow>
+                                <TableRow>
+                                    <TableCell component="th" scope="row"> File prefix: </TableCell>
+                                    <TableCell align="right">{(this.state.s.file_prefix !== undefined) ? this.state.s.file_prefix : "(images not written)"}</TableCell>
+                                </TableRow>
+                                <TableRow>
+                                    <TableCell component="th" scope="row"> Run number: </TableCell>
+                                    <TableCell align="right">{(this.state.s.run_number !== undefined) ? this.state.s.run_number : "(not set)"}</TableCell>
+                                </TableRow>
+                                <TableRow>
+                                    <TableCell component="th" scope="row"> Experiment group: </TableCell>
+                                    <TableCell align="right">{this.state.s.experiment_group}</TableCell>
+                                </TableRow>
+
                                 <TableRow>
                                     <TableCell component="th" scope="row"> Images expected: </TableCell>
                                     <TableCell align="right">{this.state.s.images_expected}</TableCell>

frontend_ui/src/components/PreviewImage.tsx

@@ -26,6 +26,7 @@ class PreviewImage extends Component<MyProps, MyState> {
             show_spots: true,
             show_roi: false,
             show_indexed: false,
+            show_user_mask: false,
             resolution_ring: 0.5
         },
         s_url: null,
@@ -94,6 +95,17 @@ class PreviewImage extends Component<MyProps, MyState> {
         );
     }
 
+    showUserMaskToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
+        this.setState(prevState => (
+            {
+                settings : {
+                    ...prevState.settings,
+                    show_user_mask: event.target.checked
+                }
+            })
+        );
+    }
+
     getValues() {
         if (!this.state.update)
             return;
@@ -125,7 +137,7 @@ class PreviewImage extends Component<MyProps, MyState> {
     }
 
     render() {
-        return <Paper sx={{height: 1050, width: 850, m: 2}}
+        return <Paper sx={{height: 1250, width: 1000, m: 2}}
                       component={Stack}
                       direction="column">
             <br/>
@@ -143,6 +155,9 @@ class PreviewImage extends Component<MyProps, MyState> {
                 <Switch disabled={this.state.connection_error} checked={this.state.settings.show_indexed}
                         onChange={this.showIndexedToggle} name="Show ROI"/>
                 Show only indexed images&nbsp;&nbsp;&nbsp;
+                <Switch disabled={this.state.connection_error} checked={this.state.settings.show_user_mask}
+                        onChange={this.showUserMaskToggle} name="Show user mask"/>
+                Show user mask&nbsp;&nbsp;&nbsp;
                 <Box sx={{width: 200}}>
                     <Slider disabled={this.state.connection_error}
                             value={Number(this.state.settings.saturation)} min={1} max={80}

frontend_ui/src/openapi/models/dataset_settings.ts

@@ -44,10 +44,10 @@ export type dataset_settings = {
     detector_distance_mm: number;
     /**
      * Used to calculate /entry/beam/incident_wavelength in NXmx
-     * Incident photon energy in keV
+     * Incident particle (photon, electron) energy in keV
      *
      */
-    photon_energy_keV: number;
+    incident_energy_keV: number;
     /**
      * Prefix for filenames. If left empty, no file will be saved.
      */
@@ -80,7 +80,7 @@ export type dataset_settings = {
      *
      */
     transmission?: number;
-    omega?: rotation_axis;
+    goniometer?: rotation_axis;
     /**
      * Header appendix, added as user_data to start message
      */
@@ -90,9 +90,9 @@ export type dataset_settings = {
      */
     image_appendix?: string;
     /**
-     * For JUNGFRAU conversion it is possible to multiply energy by a given factor to get fractional/multiplied photon counts
+     * For JUNGFRAU conversion it is possible to multiply incident energy by a given factor to get fractional/multiplied particle counts
      */
-    photon_energy_multiplier?: number;
+    energy_multiplier?: number;
     /**
      * Rate at which non-indexed images are accepted to be forwarded to writer.
      * Value of 1.0 (default) means that all images are written.
@@ -100,6 +100,20 @@ export type dataset_settings = {
      *
      */
     data_reduction_factor_serialmx?: number;
+    /**
+     * Number of run within an experimental session.
+     * Transferred over CBOR stream as "series ID", though not saved in HDF5 file.
+     * It is highly recommended to keep this number unique for each data collection during experimental series.
+     * If not provided, the number will be automatically incremented.
+     *
+     */
+    run_number?: number;
+    /**
+     * Name of group owning the data (e.g. p-group or proposal number).
+     * Transferred over CBOR stream, though not saved in HDF5 file.
+     *
+     */
+    experiment_group?: string;
     /**
      * Units of angstrom and degree
      */

frontend_ui/src/openapi/models/detector_status.ts

@@ -46,8 +46,8 @@ export namespace detector_status {
      * Power on of ASICs
      */
     export enum powerchip {
-        ON = 'On',
-        OFF = 'Off',
+        POWER_ON = 'PowerOn',
+        POWER_OFF = 'PowerOff',
         PARTIAL = 'Partial',
     }
 

frontend_ui/src/openapi/models/measurement_statistics.ts

@@ -5,6 +5,16 @@
 
 export type measurement_statistics = {
     file_prefix?: string;
+    /**
+     * Number of data collection run. This can be either automatically incremented or provided externally for each data collection.
+     *
+     */
+    run_number?: number;
+    /**
+     * Name of group owning the data (e.g. p-group or proposal number).
+     *
+     */
+    experiment_group?: string;
     images_expected?: number;
     /**
      * Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.

frontend_ui/src/openapi/models/preview_settings.ts

@@ -27,6 +27,10 @@ export type preview_settings = {
      * Preview indexed images only
      */
     show_indexed?: boolean;
+    /**
+     * Show user mask
+     */
+    show_user_mask?: boolean;
     resolution_ring?: number;
 };
 

frontend_ui/src/openapi/models/rotation_axis.ts

@@ -7,6 +7,10 @@
  * Definition of a crystal rotation axis
  */
 export type rotation_axis = {
+    /**
+     * Name of rotation axis (e.g., omega, phi)
+     */
+    name?: string;
     /**
      * Angle step in degrees
      */

frontend_ui/src/openapi/models/spot_finding_settings.ts

@@ -5,13 +5,24 @@
 
 export type spot_finding_settings = {
     /**
-     * Enable spot finding
+     * Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection.
+     * Even if disabled spot finding information will still be send and written, though always with zero spots.
+     *
      */
     enable: boolean;
     /**
-     * Enable indexing
+     * Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.
+     *
      */
     indexing: boolean;
+    /**
+     * Filter spots which form powder rings (e.g., ice rings)
+     */
+    filter_powder_rings?: boolean;
+    /**
+     * Minimum number of spots to consider a thin resolution shell (0.01 A^-1) a powder ring and filter out.
+     */
+    min_spot_count_powder_ring?: number;
     signal_to_noise_threshold: number;
     photon_count_threshold: number;
     min_pix_per_spot: number;

frontend_ui/src/openapi/services/DefaultService.ts

@@ -280,20 +280,20 @@ export class DefaultService {
      * Requires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates
      * (depending on detector settings).
      *
-     * @param number Image number to upload
+     * @param id Image id to upload
      * @param requestBody
      * @returns any Everything OK
      * @throws ApiError
      */
     public static putConfigInternalGeneratorImage(
-        number?: number,
+        id?: number,
         requestBody?: Blob,
     ): CancelablePromise<any> {
         return __request(OpenAPI, {
             method: 'PUT',
             url: '/config/internal_generator_image',
             query: {
-                'number': number,
+                'id': id,
             },
             body: requestBody,
             mediaType: 'application/octet-stream',
@@ -303,6 +303,35 @@ export class DefaultService {
         });
     }
 
+    /**
+     * Load TIFF image for internal FPGA generator
+     * Load image for internal FPGA generator. This can only happen in Idle state of the detector.
+     * Requires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates
+     * (depending on detector settings).
+     *
+     * @param id Image ID to upload
+     * @param requestBody
+     * @returns any Everything OK
+     * @throws ApiError
+     */
+    public static putConfigInternalGeneratorImageTiff(
+        id?: number,
+        requestBody?: Blob,
+    ): CancelablePromise<any> {
+        return __request(OpenAPI, {
+            method: 'PUT',
+            url: '/config/internal_generator_image.tiff',
+            query: {
+                'id': id,
+            },
+            body: requestBody,
+            mediaType: 'image/tiff',
+            errors: {
+                400: `Input parsing or validation error`,
+            },
+        });
+    }
+
     /**
      * Select detector
      * Jungfraujoch allows to control multiple detectors and/or region-of-interests.
@@ -847,6 +876,63 @@ export class DefaultService {
         });
     }
 
+    /**
+     * Get mask of the detector
+     * Get full pixel mask of the detector
+     * See NXmx standard for meaning of pixel values
+     *
+     * @returns binary Pixel mask in TIFF format (4 byte; unsigned)
+     * @throws ApiError
+     */
+    public static getConfigMaskTiff(): CancelablePromise<Blob> {
+        return __request(OpenAPI, {
+            method: 'GET',
+            url: '/config/mask.tiff',
+        });
+    }
+
+    /**
+     * Get user mask of the detector
+     * Get user pixel mask of the detector in the actual detector coordinates: 0 - good pixel, 1 - masked
+     * @returns binary User mask in TIFF format (4 byte; unsigned)
+     * @throws ApiError
+     */
+    public static getConfigUserMaskTiff(): CancelablePromise<Blob> {
+        return __request(OpenAPI, {
+            method: 'GET',
+            url: '/config/user_mask.tiff',
+        });
+    }
+
+    /**
+     * Upload user mask of the detector
+     * Should be in `Idle` state.
+     * Upload user mask of the detector - this is for example to account for beam stop shadow or misbehaving regions.
+     * If detector is conversion mode the mask can be both in raw (1024x512; stacked modules) or converted coordinates.
+     * In the latter case - module gaps are ignored and don't need to be assigned value.
+     * Mask is expected as TIFF (4-byte; unsigned).
+     * 0 - good pixel, other value - masked
+     * User mask is stored in NXmx pixel mask (bit 8), as well as used in spot finding and azimuthal integration.
+     * User mask is not automatically applied - i.e. pixels with user mask will have a valid pixel value in the images.
+     *
+     * @param requestBody
+     * @returns binary All good
+     * @throws ApiError
+     */
+    public static putConfigUserMaskTiff(
+        requestBody?: Blob,
+    ): CancelablePromise<Blob> {
+        return __request(OpenAPI, {
+            method: 'PUT',
+            url: '/config/user_mask.tiff',
+            body: requestBody,
+            mediaType: 'application/octet-stream',
+            errors: {
+                500: `Error within Jungfraujoch code - see output message.`,
+            },
+        });
+    }
+
     /**
      * Get pedestal G0 in TIFF format
      * @param gainLevel Gain level (0, 1, 2)

image_analysis/CPUSpotFinder.cpp

@@ -1,86 +1,125 @@
 // Copyright (2019-2024) Paul Scherrer Institute
 
 #include "CPUSpotFinder.h"
+#define NUM_PASS 2
 
 template <int N>
 void FindSpots(DeviceOutput &output,
                int big_column, int big_row,
                const SpotFindingSettings& settings,
-               const float *d_array) {
+               const float *d_array,
+               float *arr_mean,
+               float *arr_stddev,
+               uint32_t *arr_valid_count,
+               uint32_t *arr_strong_pixel) {
     auto image = (int16_t *) output.pixels;
 
-    int64_t sum = 0;
-    int64_t sum2 = 0;
-    int64_t valid_count = 0;
+    std::vector<uint8_t> mask(N * N, 0);
 
     for (int y = 0; y < N; y++) {
+        size_t line = big_row * N + y;
         for (int x = 0; x < N; x++) {
-            size_t coord = (big_row * N + y) * RAW_MODULE_COLS + big_column * N + x;
-            if ((image[coord] != INT16_MIN) || (image[coord] != INT16_MAX)) {
-                sum += image[coord];
-                sum2 += image[coord] * image[coord];
-                valid_count++;
-            }
-        }
-    }
-
-    int64_t variance = valid_count * sum2 - sum * sum;
-    float threshold = variance * settings.signal_to_noise_threshold * settings.signal_to_noise_threshold;
-
-    for (int y = 0; y < N; y++) {
-        for (int x = 0; x < N; x++) {
-            size_t line = big_row * N + y;
             size_t col = big_column * N + x;
             size_t coord = line * RAW_MODULE_COLS + col;
 
-            bool strong_pixel = true;
-
+            uint8_t bad_pixel = 0;
             if ((line == 255) || (line == 256)
                 || (col == 255) || (col == 256)
                 || (col == 511) || (col == 512)
                 || (col == 767) || (col == 768))
-                strong_pixel = false;
+                bad_pixel = 1;
 
-            if (d_array[coord] != 0) {
-                if ((d_array[coord] < settings.high_resolution_limit)
-                    || (d_array[coord] > settings.low_resolution_limit))
+            if ((d_array[coord] < settings.high_resolution_limit)
+                || (d_array[coord] > settings.low_resolution_limit))
+                bad_pixel = 1;
+
+            if ((image[coord] == INT16_MIN) || (image[coord] > 32760))
+                bad_pixel = 1;
+
+            mask[y * N + x] = bad_pixel;
+        }
+    }
+
+    for (int i = 0; i < NUM_PASS; i++) {
+        int64_t sum = 0;
+        int64_t sum2 = 0;
+        int64_t valid_count = 0;
+
+        for (int y = 0; y < N; y++) {
+            for (int x = 0; x < N; x++) {
+                size_t coord = (big_row * N + y) * RAW_MODULE_COLS + big_column * N + x;
+                if (mask[y * N + x] == 0) {
+                    sum += image[coord];
+                    sum2 += image[coord] * image[coord];
+                    valid_count++;
+                }
+            }
+        }
+
+        int64_t variance = valid_count * sum2 - sum * sum;
+        float threshold = variance * settings.signal_to_noise_threshold * settings.signal_to_noise_threshold;
+
+        for (int y = 0; y < N; y++) {
+            size_t line = big_row * N + y;
+            for (int x = 0; x < N; x++) {
+                size_t col = big_column * N + x;
+                size_t coord = line * RAW_MODULE_COLS + col;
+
+                arr_valid_count[coord] = valid_count;
+                if (valid_count > 0) {
+                    arr_mean[coord] = static_cast<float>(sum) / static_cast<float>(valid_count);
+                    arr_stddev[coord] = sqrtf(
+                            static_cast<float>(variance) / static_cast<float>(valid_count * valid_count));
+                } else {
+                    arr_mean[coord] = -1;
+                    arr_stddev[coord] = -1;
+                }
+
+                bool strong_pixel = true;
+
+                if (mask[y * N + x])
                     strong_pixel = false;
-            }
 
-            if ((settings.photon_count_threshold < 0)
-                && (settings.signal_to_noise_threshold <= 0))
-                strong_pixel = false;
-
-            if ((settings.photon_count_threshold >= 0)
-                && (image[coord] <= settings.photon_count_threshold)) {
-                strong_pixel = false;
-            }
-
-            if (image[coord] > 32760)
-                strong_pixel = false;
-
-            if (settings.signal_to_noise_threshold > 0) {
-                int64_t in_minus_mean = image[coord] * valid_count - sum;
-                if ((in_minus_mean * in_minus_mean <= threshold)
-                    || (in_minus_mean <= 0)
-                    || (valid_count < N * N / 2))
+                if ((settings.photon_count_threshold < 0)
+                    && (settings.signal_to_noise_threshold <= 0))
                     strong_pixel = false;
-            }
 
-            if (strong_pixel) {
-                output.spot_finding_result.strong_pixel[coord / 8] |= (1 << (coord % 8));
-                output.spot_finding_result.strong_pixel_count++;
+                if ((settings.photon_count_threshold >= 0)
+                    && (image[coord] <= settings.photon_count_threshold)) {
+                    strong_pixel = false;
+                }
+
+                if (settings.signal_to_noise_threshold > 0) {
+                    int64_t in_minus_mean = image[coord] * valid_count - sum;
+                    if ((in_minus_mean * in_minus_mean <= threshold)
+                        || (in_minus_mean <= 0)
+                        || (valid_count <= N * N / 2))
+                        strong_pixel = false;
+                }
+
+                if (strong_pixel) {
+                    mask[y * N + x] = 1;
+                    arr_strong_pixel[coord]++;
+                    output.spot_finding_result.strong_pixel[coord / 8] |= (1 << (coord % 8));
+                    output.spot_finding_result.strong_pixel_count++;
+                }
             }
         }
     }
 }
 
-void FindSpots(DeviceOutput &output, const SpotFindingSettings& settings, const float *d_array) {
+void FindSpots(DeviceOutput &output,
+               const SpotFindingSettings& settings,
+               const float *d_array,
+               float *arr_mean,
+               float *arr_stddev,
+               uint32_t *arr_valid_count,
+               uint32_t *arr_strong_pixel) {
     for (auto &i: output.spot_finding_result.strong_pixel)
         i = 0;
 
     for (int i = 0; i < RAW_MODULE_LINES / 32; i++) {
         for (int j = 0; j < RAW_MODULE_COLS / 32; j++)
-            FindSpots<32>(output, j, i, settings, d_array);
+            FindSpots<32>(output, j, i, settings, d_array, arr_mean, arr_stddev, arr_valid_count, arr_strong_pixel);
     }
 }

image_analysis/CPUSpotFinder.h

@@ -7,6 +7,13 @@
 #include "SpotFindingSettings.h"
 #include "StrongPixelSet.h"
 
-void FindSpots(DeviceOutput &output, const SpotFindingSettings& settings, const float *d_array);
+void FindSpots(DeviceOutput &output,
+               const SpotFindingSettings& settings,
+               const float *d_array,
+               float *arr_mean,
+               float *arr_stddev,
+               uint32_t *arr_valid_count,
+               uint32_t *arr_strong_pixel);
+
 
 #endif //JUNGFRAUJOCH_CPUSPOTFINDER_H

image_analysis/IndexerWrapper.cpp

@@ -8,13 +8,17 @@ void IndexerWrapper::Setup(const UnitCell &cell) {
 #endif
 }
 
-std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord, float indexing_threshold) {
+std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord, float indexing_threshold, int nspots) {
 #ifdef JFJOCH_USE_CUDA
     std::vector<IndexingResult> ret;
 
-    if (coord.size() <= viable_cell_min_spots)
+    if (nspots > coord.size())
+        nspots = coord.size();
+
+    if (nspots <= viable_cell_min_spots)
         return ret;
 
+    assert(nspots <= MAX_SPOT_COUNT);
     assert(coord.size() <= MAX_SPOT_COUNT);
 
     for (int i = 0; i < coord.size(); i++) {
@@ -24,9 +28,9 @@ std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord,
     }
 
     // Index
-    indexer.index(1, coord.size());
+    indexer.index(1, nspots);
 
-    fast_feedback::refine::indexer_ifssr<float>::refine(indexer.spotM().topRows(coord.size()),
+    fast_feedback::refine::indexer_ifssr<float>::refine(indexer.spotM().topRows(nspots),
                                                         indexer.oCellM(),
                                                         indexer.oScoreV(),
                                                         cifssr);
@@ -38,30 +42,28 @@ std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord,
     // Get best cell
     auto id = fast_feedback::refine::best_cell(indexer.oScoreV());
 
-    bool indexed = fast_feedback::refine::is_viable_cell(indexer.oCell(id), indexer.Spots(),
-                                                         indexing_threshold, viable_cell_min_spots,
-                                                         false);
+    auto cell = indexer.oCell(id).colwise().reverse();
+    fast_feedback::refine::make_right_handed(cell);
 
-    // Check if result is viable
-    if (indexed) {
-        auto cell = indexer.oCell(id).colwise().reverse();
-        fast_feedback::refine::make_right_handed(cell);
+    using M3x = Eigen::MatrixX3<float>;
+    M3x resid = indexer.spotM().topRows(coord.size()) * cell.transpose();
+    const M3x miller = round(resid.array());
+    resid -= miller;
 
-        // get indexed spots
-        using M3x = Eigen::MatrixX3<float>;
-        M3x resid = indexer.spotM().topRows(coord.size()) * cell.transpose();
-        const M3x miller = round(resid.array());
-        const M3x predicted = miller * cell.transpose().inverse();
+    auto indexed_spots = (resid.rowwise().norm().array() < indexing_threshold);
+    auto indexed_spot_count = indexed_spots.topRows(nspots).count();
 
+    // Conditions for indexing:
+    // * There must be 9 AND 20% of all spots indexed
+    // * Decision is only based on spots used for indexing (not all spots)
+    if ((indexed_spot_count > viable_cell_min_spots) && (indexed_spot_count > 0.20 * nspots)) {
         IndexingResult result;
         result.l = CrystalLattice(cell);
 
-        result.predicted_spots.resize(coord.size());
+        result.indexed_spot.resize(coord.size());
 
         for (int i = 0; i < coord.size(); i++)
-            result.predicted_spots[i] = Coord(predicted.coeff(i, 0),
-                                              predicted.coeff(i, 1),
-                                              predicted.coeff(i, 2));
+            result.indexed_spot[i] = indexed_spots(i);
 
         ret.emplace_back(result);
     }

image_analysis/IndexerWrapper.h

@@ -15,7 +15,7 @@
 
 struct IndexingResult {
     CrystalLattice l;
-    std::vector<Coord> predicted_spots;
+    std::vector<uint8_t> indexed_spot;
 };
 
 class IndexerWrapper {
@@ -36,7 +36,7 @@ class IndexerWrapper {
     constexpr const static uint32_t viable_cell_min_spots = 9;
 public:
     void Setup(const UnitCell &cell);
-    std::vector<IndexingResult> Run(const std::vector<Coord> &coord, float indexing_threshold);
+    std::vector<IndexingResult> Run(const std::vector<Coord> &coord, float indexing_threshold, int nspots = -1);
 };
 
 

image_analysis/MXAnalyzer.cpp

@@ -34,9 +34,9 @@ MXAnalyzer::MXAnalyzer(const DiffractionExperiment &in_experiment)
             throw JFJochException(JFJochExceptionCategory::GPUCUDAError, e.what());
         }
     }
+
     if (experiment.IsSpotFindingEnabled())
         find_spots = true;
-
 }
 
 void MXAnalyzer::ReadFromFPGA(const DeviceOutput *output, const SpotFindingSettings &settings, size_t module_number) {
@@ -60,18 +60,70 @@ void MXAnalyzer::ReadFromCPU(const int16_t *image, const SpotFindingSettings &se
 
     CalcSpotFinderResolutionMap(d_map.data(), experiment, module_number);
 
-    FindSpots(output, settings, d_map.data());
+    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);
 }
 
+uint32_t MXAnalyzer::FilterSpotsInPowderRings(const std::vector<DiffractionSpot> &spots_filter,
+                                              std::vector<DiffractionSpot> &spots_out,
+                                              int64_t min_spot_count_ring) {
+    uint32_t ret = 0;
+
+    double high_q = 5.0;
+    double low_q = 0;
+    double q_spacing = 0.01;
+
+    size_t bin_count = (high_q - low_q) / q_spacing + 1;
+
+    std::vector<std::vector<uint32_t> > bins(bin_count);
+
+    for (int i = 0; i < spots_filter.size(); i++) {
+        double q = 2 * M_PI / spots_filter[i].GetResolution(experiment);
+        if ((q >= low_q) && (q < high_q)) {
+            int32_t q_bin = std::floor((q - low_q) / q_spacing);
+            bins[q_bin].push_back(i);
+        } else // spots outside of azim. int. range are not filtered
+            spots_out.push_back(spots_filter[i]);
+    }
+
+    for (auto & bin : bins) {
+        if (bin.size() > min_spot_count_ring)
+            ret += bin.size();
+        else {
+            for (auto &iter: bin)
+                spots_out.push_back(spots_filter[iter]);
+        }
+    }
+    return ret;
+}
+
 void MXAnalyzer::Process(DataMessage &message, const SpotFindingSettings& settings) {
     message.indexing_result = false;
     if (!find_spots)
         return;
 
     std::vector<DiffractionSpot> spots_out;
-    FilterSpotsByCount(experiment, spots, spots_out);
+    if (settings.filter_spots_powder_ring) {
+        std::vector<DiffractionSpot> spots_no_rings;
+        message.spot_count_in_rings = FilterSpotsInPowderRings(spots,
+                                                               spots_no_rings,
+                                                               settings.min_spot_count_powder_ring);
+        FilterSpotsByCount(experiment, spots_no_rings, spots_out);
+    } else
+        FilterSpotsByCount(experiment, spots, spots_out);
+
     spots.clear();
 
     for (const auto &spot: spots_out)
@@ -83,22 +135,39 @@ void MXAnalyzer::Process(DataMessage &message, const SpotFindingSettings& settin
         for (const auto &i: spots_out)
             recip.push_back(i.ReciprocalCoord(experiment));
 
-        auto indexer_result = indexer->Run(recip, settings.indexing_tolerance);
+        std::vector<IndexingResult> indexer_result;
+
+        // If there is a really large number of spots detected, it is better to start with a smaller subset
+        if (recip.size() > 80)
+            indexer_result = indexer->Run(recip, settings.indexing_tolerance, 50);
+        if (indexer_result.empty())
+            indexer_result = indexer->Run(recip, settings.indexing_tolerance);
 
         if (!indexer_result.empty()) {
             message.indexing_result = true;
+            assert(indexer_result[0].indexed_spot.size() == recip.size());
 
             // identify indexed spots
-            for (int i = 0; i < recip.size(); i++) {
-                auto predicted_pos = RecipToDector(experiment, indexer_result[0].predicted_spots[i]);
-                float x_diff = predicted_pos.first - spots_out[i].RawCoord().x;
-                float y_diff = predicted_pos.second - spots_out[i].RawCoord().y;
-                message.spots[i].indexed = (x_diff * x_diff + y_diff * y_diff
-                                            < spot_distance_threshold_pxl * spot_distance_threshold_pxl);
-            }
+            for (int i = 0; i < recip.size(); i++)
+                message.spots[i].indexed = indexer_result[0].indexed_spot[i];
 
             indexer_result[0].l.Save(message.indexing_lattice);
-            message.indexing_unit_cell = indexer_result[0].l.GetUnitCell();
         }
     }
 }
+
+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;
+}

image_analysis/MXAnalyzer.h

@@ -13,7 +13,17 @@ class MXAnalyzer {
     bool find_spots = false;
     std::vector<DiffractionSpot> spots;
     constexpr static const float spot_distance_threshold_pxl = 2.0f;
+
+    std::vector<float> arr_mean;
+    std::vector<float> arr_sttdev;
+    std::vector<uint32_t> arr_valid_count;
+    std::vector<uint32_t> arr_strong_pixel;
 public:
+    const std::vector<float> &GetCPUMean() const;
+    const std::vector<float> &GetCPUStdDev() const;
+    const std::vector<uint32_t> &GetCPUValidCount() const;
+    const std::vector<uint32_t> &GetCPUStrongPixel() const;
+
     explicit MXAnalyzer(const DiffractionExperiment& experiment);
 
     void ReadFromFPGA(const DeviceOutput* output,
@@ -26,6 +36,10 @@ public:
 
     void Process(DataMessage &message,
                  const SpotFindingSettings& settings);
+
+    uint32_t FilterSpotsInPowderRings(const std::vector<DiffractionSpot> &spots_filter,
+                                      std::vector<DiffractionSpot> &spots_out,
+                                      int64_t min_spot_count_ring);
 };
 
 

image_analysis/SpotFindingSettings.h

@@ -7,14 +7,17 @@
 
 struct SpotFindingSettings {
     bool enable = true;
-    bool indexing = true;
     float signal_to_noise_threshold = 3;  // STRONG_PIXEL in XDS
     int64_t photon_count_threshold = 10;  // Threshold in photon counts
     int64_t min_pix_per_spot = 2;         // Minimum pixels per spot
     int64_t max_pix_per_spot = 50;        // Maximum pixels per spot
-    float high_resolution_limit = 2.5;
+    float high_resolution_limit = 2.0;
     float low_resolution_limit = 50.0;
 
+    bool filter_spots_powder_ring = false;
+    int64_t min_spot_count_powder_ring = 20;
+
+    bool indexing = true;
     float indexing_tolerance = 0.1;
 };
 

jungfrau/JFCalibration.cpp

@@ -3,7 +3,7 @@
 #include "JFCalibration.h"
 
 #include <cstring>
-#include "../preview/WriteTIFF.h"
+#include "../preview/JFJochTIFF.h"
 
 JFCalibration::JFCalibration(size_t in_nmodules, size_t in_nstorage_cells) :
         nmodules(in_nmodules),

preview/CMakeLists.txt

@@ -1,8 +1,8 @@
 FIND_PACKAGE(JPEG REQUIRED)
 
 ADD_LIBRARY(JFJochPreview STATIC
-        WriteTIFF.cpp WriteTIFF.h
-        WriteJPEG.cpp WriteJPEG.h
+        JFJochTIFF.cpp JFJochTIFF.h
+        JFJochJPEG.cpp JFJochJPEG.h
         PreviewCounter.cpp PreviewCounter.h
         PreviewImage.cpp PreviewImage.h)
 

preview/JFJochJPEG.cpp

@@ -7,7 +7,7 @@
 #include <jpeglib.h>
 
 #include "../common/JFJochException.h"
-#include "WriteJPEG.h"
+#include "JFJochJPEG.h"
 
 
 std::string WriteJPEGToMem(const std::vector<uint8_t> &input, size_t width, size_t height, int quality) {

preview/JFJochTIFF.cpp

@@ -0,0 +1,110 @@
+// Copyright (2019-2024) Paul Scherrer Institute
+
+#include <tiffio.h>
+#include <tiffio.hxx>
+#include <sstream>
+
+#include "JFJochTIFF.h"
+#include "../common/JFJochException.h"
+
+
+void WriteTIFF(TIFF *tiff, void *buff, size_t cols, size_t lines, size_t elem_size, bool is_signed) {
+
+    if (tiff == nullptr)
+        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFStreamOpen error");
+
+    TIFFSetField(tiff, TIFFTAG_IMAGEWIDTH, cols);  // set the width of the image
+    TIFFSetField(tiff, TIFFTAG_IMAGELENGTH, lines);    // set the height of the image
+    TIFFSetField(tiff, TIFFTAG_SAMPLESPERPIXEL, 1);   // set number of channels per pixel
+    TIFFSetField(tiff, TIFFTAG_BITSPERSAMPLE, elem_size * 8);    // set the size of the channels
+    TIFFSetField(tiff, TIFFTAG_COMPRESSION, COMPRESSION_NONE); // setc ompression to LZW
+    TIFFSetField(tiff, TIFFTAG_ROWSPERSTRIP, lines);
+    if (is_signed)
+        TIFFSetField(tiff, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_INT);
+    else
+        TIFFSetField(tiff, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_UINT);
+
+    if (TIFFWriteEncodedStrip(tiff, 0, buff, cols * lines * elem_size) < 0)
+        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFWriteEncodedStrip error");
+}
+
+std::string WriteTIFFToString(void *buff, size_t cols, size_t lines, size_t elem_size, bool is_signed) {
+    std::stringstream os;
+
+    TIFF *tiff = TIFFStreamOpen("x", (std::ostream *) &os);
+    WriteTIFF(tiff, buff, cols, lines, elem_size, is_signed);
+    TIFFClose(tiff);
+
+    return os.str();
+}
+
+void WriteTIFFToFile(const std::string &filename, void *buff, size_t cols, size_t lines, size_t elem_size,
+                     bool is_signed) {
+    TIFF *tiff = TIFFOpen(filename.c_str(), "w");
+
+    WriteTIFF(tiff, buff, cols, lines, elem_size, is_signed);
+
+    TIFFClose(tiff);
+}
+
+std::vector<uint32_t> ReadTIFFFromString32(const std::string &s, uint32_t &cols, uint32_t &lines) {
+    uint32_t rows_per_string = 0;
+
+    std::vector<uint32_t> ret;
+
+    uint16_t elem_size;
+
+    std::istringstream input_TIFF_stream(s);
+    TIFF* tiff = TIFFStreamOpen("MemTIFF", &input_TIFF_stream);
+    TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &cols);  // get the width of the image
+    TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &lines);    // get the height of the image
+    TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &elem_size);    // get the size of the channels
+    TIFFGetField(tiff, TIFFTAG_ROWSPERSTRIP, &rows_per_string);
+
+    if (elem_size != 32)
+        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "Only 32-bit format supported");
+
+    ret.resize(cols * lines);
+
+    if (cols * sizeof(uint32_t) != TIFFScanlineSize(tiff))
+        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFScanlineSize mismatch");
+
+    for (int i = 0; i < lines; i++) {
+        if (TIFFReadScanline(tiff, ret.data() + i * cols, i, 0) < 0)
+            throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFReadScanline error");
+    }
+
+    TIFFClose(tiff);
+    return ret;
+}
+
+std::vector<uint16_t> ReadTIFFFromString16(const std::string &s, uint32_t &cols, uint32_t &lines) {
+    uint32_t rows_per_string = 0;
+
+    std::vector<uint16_t> ret;
+
+    uint16_t elem_size;
+
+    std::istringstream input_TIFF_stream(s);
+    TIFF* tiff = TIFFStreamOpen("MemTIFF", &input_TIFF_stream);
+    TIFFGetField(tiff, TIFFTAG_IMAGEWIDTH, &cols);  // get the width of the image
+    TIFFGetField(tiff, TIFFTAG_IMAGELENGTH, &lines);    // get the height of the image
+    TIFFGetField(tiff, TIFFTAG_BITSPERSAMPLE, &elem_size);    // get the size of the channels
+    TIFFGetField(tiff, TIFFTAG_ROWSPERSTRIP, &rows_per_string);
+
+    if (elem_size != 16)
+        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "Only 16-bit format supported");
+
+    ret.resize(cols * lines);
+
+    if (cols * sizeof(uint16_t) != TIFFScanlineSize(tiff))
+        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFScanlineSize mismatch");
+
+    for (int i = 0; i < lines; i++) {
+        if (TIFFReadScanline(tiff, ret.data() + i * cols, i, 0) < 0)
+            throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFReadScanline error");
+    }
+
+    TIFFClose(tiff);
+    return ret;
+}

preview/JFJochTIFF.h

@@ -4,9 +4,12 @@
 #define JUNGFRAUJOCH_WRITETIFF_H
 
 #include <string>
+#include <vector>
 
 std::string WriteTIFFToString(void *buff, size_t cols, size_t lines, size_t elem_size, bool is_signed = false);
 void WriteTIFFToFile(const std::string &filename, void *buff, size_t cols, size_t lines, size_t elem_size,
                      bool is_signed = false);
+std::vector<uint32_t> ReadTIFFFromString32(const std::string& s, uint32_t &cols, uint32_t &lines);
+std::vector<uint16_t> ReadTIFFFromString16(const std::string& s, uint32_t &cols, uint32_t &lines);
 
 #endif //JUNGFRAUJOCH_WRITETIFF_H

preview/PreviewImage.cpp

@@ -4,8 +4,8 @@
 
 #include <cmath>
 
-#include "WriteJPEG.h"
-#include "WriteTIFF.h"
+#include "JFJochJPEG.h"
+#include "JFJochTIFF.h"
 #include "../common/JFJochException.h"
 #include "../common/DiffractionGeometry.h"
 
@@ -31,28 +31,7 @@ constexpr const static rgb plotly[] = {{0x1f, 0x77, 0xb4},
 constexpr const static rgb indigo = {.r = 0x3f, .g = 0x51, .b = 0xb5};
 constexpr const static rgb gray = {.r = 0xbe, .g = 0xbe, .b = 0xbe};
 
-PreviewImage::PreviewImage(const DiffractionExperiment &in_experiment) :
-        experiment(in_experiment),
-        initialized(false),
-        xpixel(experiment.GetXPixelsNum()),
-        ypixel(experiment.GetYPixelsNum()),
-        beam_x(experiment.GetBeamX_pxl()),
-        beam_y(experiment.GetBeamY_pxl()),
-        pixel_depth_bytes(experiment.GetPixelDepth()),
-        pixel_is_signed(experiment.IsPixelSigned()),
-        uncompressed_image(experiment.GetPixelsNum() * experiment.GetPixelDepth()),
-        roi_map(experiment.ROI()),
-        counter(experiment.GetPreviewPeriod()) {}
-
-void PreviewImage::UpdateImage(const void *in_uncompressed_image,
-                               const std::vector<SpotToSave> &in_spots) {
-    if (counter.GeneratePreview()) {
-        std::unique_lock<std::mutex> ul(m);
-        initialized = true;
-        memcpy(uncompressed_image.data(), in_uncompressed_image, xpixel * ypixel * pixel_depth_bytes);
-        spots = in_spots;
-    }
-}
+PreviewImage::PreviewImage(std::chrono::microseconds period) : counter(period) {}
 
 void colormap(std::vector<unsigned char>& ret, float v, size_t pixel) {
     if ((v < 0.0) || (v > 1.0)) {
@@ -106,55 +85,6 @@ std::vector<unsigned char> GenerateRGB(const T* value, size_t npixel, uint32_t s
     return ret;
 }
 
-std::string PreviewImage::GenerateJPEG(const PreviewJPEGSettings &settings) const {
-    std::vector<unsigned char> v;
-    {
-        // JPEG compression is outside the critical loop protected by m
-        std::unique_lock<std::mutex> ul(m);
-
-        if (!initialized)
-            return {};
-
-        if (!pixel_is_signed) {
-            if (pixel_depth_bytes == 2)
-                v = GenerateRGB<uint16_t>((uint16_t *) uncompressed_image.data(), xpixel * ypixel,
-                                         settings.saturation_value, UINT16_MAX);
-            else
-                v = GenerateRGB<uint32_t>((uint32_t *) uncompressed_image.data(), xpixel * ypixel,
-                                         settings.saturation_value, UINT32_MAX);
-        } else {
-            if (pixel_depth_bytes == 2)
-                v = GenerateRGB<int16_t>((int16_t *) uncompressed_image.data(), xpixel * ypixel,
-                                         settings.saturation_value, INT16_MIN);
-            else
-                v = GenerateRGB<int32_t>((int32_t *) uncompressed_image.data(), xpixel * ypixel,
-                                         settings.saturation_value, INT32_MIN);
-        }
-        if (settings.show_spots)
-            AddSpots(v);
-    }
-
-    if (settings.show_roi)
-        AddROI(v);
-
-    if (settings.resolution_ring)
-        AddResolutionRing(v, settings.resolution_ring.value());
-
-    AddBeamCenter(v);
-
-    return WriteJPEGToMem(v, xpixel, ypixel, settings.jpeg_quality);
-}
-
-std::string PreviewImage::GenerateTIFF() const {
-    std::unique_lock<std::mutex> ul(m);
-    if (!initialized)
-        return {};
-
-    std::string s = WriteTIFFToString(const_cast<uint8_t *>(uncompressed_image.data()),
-                                      xpixel, ypixel, pixel_depth_bytes, pixel_is_signed);
-    return s;
-}
-
 template <class T>
 std::vector<uint16_t> GenerateDioptasPreview(const void* input, size_t xpixel, size_t ypixel, T special_value) {
     auto input_ptr = (T *) input;
@@ -174,26 +104,6 @@ std::vector<uint16_t> GenerateDioptasPreview(const void* input, size_t xpixel, s
     return vec;
 }
 
-std::string PreviewImage::GenerateTIFFDioptas() const {
-    std::unique_lock<std::mutex> ul(m);
-    if (!initialized)
-        return {};
-
-    std::vector<uint16_t> vec;
-    if (pixel_is_signed) {
-        if (pixel_depth_bytes == 2)
-            vec = GenerateDioptasPreview<int16_t>(uncompressed_image.data(), xpixel, ypixel, INT16_MIN);
-        else
-            vec = GenerateDioptasPreview<int32_t>(uncompressed_image.data(), xpixel, ypixel, INT32_MIN);
-    } else {
-        if (pixel_depth_bytes == 2)
-            vec = GenerateDioptasPreview<uint16_t>(uncompressed_image.data(), xpixel, ypixel, UINT16_MAX);
-        else
-            vec = GenerateDioptasPreview<uint32_t>(uncompressed_image.data(), xpixel, ypixel, UINT32_MAX);
-    }
-    return WriteTIFFToString(vec.data(), xpixel, ypixel, 2, false);
-}
-
 void PreviewImage::AddBeamCenter(std::vector<uint8_t> &rgb_image) const {
     size_t beam_x_int = std::lround(beam_x);
     size_t beam_y_int = std::lround(beam_y);
@@ -230,7 +140,7 @@ void PreviewImage::AddSpots(std::vector<uint8_t> &rgb_image) const {
 void PreviewImage::AddROI(std::vector<uint8_t> &rgb_image) const {
     int64_t roi_counter = 0;
 
-    for (const auto &box: roi_map.GetROIBox()) {
+    for (const auto &box: experiment.ROI().GetROIBox()) {
         int rectangle_width = 5;
 
         for (auto x = box.GetXMin() - rectangle_width; x <= box.GetXMax() + rectangle_width; x++) {
@@ -249,7 +159,7 @@ void PreviewImage::AddROI(std::vector<uint8_t> &rgb_image) const {
         roi_counter++;
     }
 
-    for (const auto &circle: roi_map.GetROICircle()) {
+    for (const auto &circle: experiment.ROI().GetROICircle()) {
         int width = 5;
 
         for (int64_t y = std::floor(circle.GetY() - circle.GetRadius_pxl() - width);
@@ -281,3 +191,132 @@ void PreviewImage::AddResolutionRing(std::vector<uint8_t> &rgb_image, float d) c
         }
     }
 }
+
+void PreviewImage::AddUserMask(std::vector<uint8_t> &rgb_image) const {
+    for (int y = 0; y < ypixel; y++) {
+        for (int x = 0; x < xpixel; x++) {
+            if (user_mask[y * xpixel + x] != 0)
+                color_pixel(rgb_image, x, y, gray);
+        }
+    }
+}
+
+void PreviewImage::Configure(const DiffractionExperiment &in_experiment, const PixelMask& mask) {
+    std::unique_lock<std::mutex> ul(m);
+
+    experiment = in_experiment;
+    initialized = false;
+    xpixel = experiment.GetXPixelsNum();
+    ypixel = experiment.GetYPixelsNum();
+    beam_x = experiment.GetBeamX_pxl();
+    beam_y = experiment.GetBeamY_pxl();
+    pixel_depth_bytes = experiment.GetPixelDepth();
+    pixel_is_signed = experiment.IsPixelSigned();
+    uncompressed_image.resize(experiment.GetPixelsNum() * experiment.GetPixelDepth());
+    memset(uncompressed_image.data(), 0, experiment.GetPixelsNum() * experiment.GetPixelDepth());
+    user_mask = mask.GetUserMask(experiment);
+    if (user_mask.size() != experiment.GetPixelsNum())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "User pixel mask size incorrect");
+}
+
+void PreviewImage::Configure() {
+    std::unique_lock<std::mutex> ul(m);
+
+    initialized = false;
+    xpixel = 0;
+    ypixel = 0;
+}
+
+void PreviewImage::UpdateImage(const void *in_uncompressed_image,
+                               const std::vector<SpotToSave> &in_spots) {
+    if (counter.GeneratePreview()) {
+        std::unique_lock<std::mutex> ul(m);
+
+        if (xpixel * ypixel == 0)
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Preview not configured");
+
+        initialized = true;
+        memcpy(uncompressed_image.data(), in_uncompressed_image, xpixel * ypixel * pixel_depth_bytes);
+        spots = in_spots;
+    }
+}
+
+std::string PreviewImage::GenerateJPEG(const PreviewJPEGSettings &settings) const {
+    std::vector<unsigned char> v;
+    size_t local_xpixel;
+    size_t local_ypixel;
+
+    {
+        // JPEG compression is outside the critical loop protected by m
+        std::unique_lock<std::mutex> ul(m);
+
+        local_xpixel = xpixel;
+        local_ypixel = ypixel;
+
+        if (!initialized)
+            return {};
+
+        if (!pixel_is_signed) {
+            if (pixel_depth_bytes == 2)
+                v = GenerateRGB<uint16_t>((uint16_t *) uncompressed_image.data(), xpixel * ypixel,
+                                          settings.saturation_value, UINT16_MAX);
+            else
+                v = GenerateRGB<uint32_t>((uint32_t *) uncompressed_image.data(), xpixel * ypixel,
+                                          settings.saturation_value, UINT32_MAX);
+        } else {
+            if (pixel_depth_bytes == 2)
+                v = GenerateRGB<int16_t>((int16_t *) uncompressed_image.data(), xpixel * ypixel,
+                                         settings.saturation_value, INT16_MIN);
+            else
+                v = GenerateRGB<int32_t>((int32_t *) uncompressed_image.data(), xpixel * ypixel,
+                                         settings.saturation_value, INT32_MIN);
+        }
+
+        if (settings.show_user_mask)
+            AddUserMask(v);
+
+        if (settings.show_spots)
+            AddSpots(v);
+
+        if (settings.show_roi)
+            AddROI(v);
+
+        if (settings.resolution_ring)
+            AddResolutionRing(v, settings.resolution_ring.value());
+
+        AddBeamCenter(v);
+    }
+
+    return WriteJPEGToMem(v, local_xpixel, local_ypixel, settings.jpeg_quality);
+}
+
+
+std::string PreviewImage::GenerateTIFF() const {
+    std::unique_lock<std::mutex> ul(m);
+    if (!initialized)
+        return {};
+
+    std::string s = WriteTIFFToString(const_cast<uint8_t *>(uncompressed_image.data()),
+                                      xpixel, ypixel, pixel_depth_bytes, pixel_is_signed);
+    return s;
+}
+
+std::string PreviewImage::GenerateTIFFDioptas() const {
+    std::unique_lock<std::mutex> ul(m);
+    if (!initialized)
+        return {};
+
+    std::vector<uint16_t> vec;
+    if (pixel_is_signed) {
+        if (pixel_depth_bytes == 2)
+            vec = GenerateDioptasPreview<int16_t>(uncompressed_image.data(), xpixel, ypixel, INT16_MIN);
+        else
+            vec = GenerateDioptasPreview<int32_t>(uncompressed_image.data(), xpixel, ypixel, INT32_MIN);
+    } else {
+        if (pixel_depth_bytes == 2)
+            vec = GenerateDioptasPreview<uint16_t>(uncompressed_image.data(), xpixel, ypixel, UINT16_MAX);
+        else
+            vec = GenerateDioptasPreview<uint32_t>(uncompressed_image.data(), xpixel, ypixel, UINT32_MAX);
+    }
+    return WriteTIFFToString(vec.data(), xpixel, ypixel, 2, false);
+}

preview/PreviewImage.h

@@ -8,6 +8,7 @@
 
 #include "../common/SpotToSave.h"
 #include "../common/DiffractionExperiment.h"
+#include "../common/PixelMask.h"
 #include "PreviewCounter.h"
 
 struct PreviewJPEGSettings {
@@ -16,6 +17,7 @@ struct PreviewJPEGSettings {
     bool show_spots = true;
     bool show_roi = false;
     bool show_indexed = false;
+    bool show_user_mask = false;
     std::optional<float> resolution_ring;
 };
 
@@ -29,21 +31,22 @@ class PreviewImage {
     mutable std::mutex m;
     DiffractionExperiment experiment;
 
-    bool initialized;
-    const ROIMap roi_map;
+    bool initialized = false;
     std::vector<uint8_t> uncompressed_image;
+    std::vector<uint32_t> user_mask;
     std::vector<SpotToSave> spots;
-    size_t xpixel;
-    size_t ypixel;
-    size_t pixel_depth_bytes;
-    bool pixel_is_signed;
-    float beam_x;
-    float beam_y;
+    size_t xpixel = 0;
+    size_t ypixel = 0;
+    size_t pixel_depth_bytes = 2;
+    bool pixel_is_signed = false;
+    float beam_x = 0;
+    float beam_y = 0;
 
     void AddResolutionRing(std::vector<uint8_t> &rgb_image, float d) const;
     void AddBeamCenter(std::vector<uint8_t> &rgb_image) const;
     void AddSpots(std::vector<uint8_t> &rgb_image) const;
     void AddROI(std::vector<uint8_t> &rgb_image) const;
+    void AddUserMask(std::vector<uint8_t> &rgb_image) const;
     PreviewCounter counter;
 
     void color_pixel(std::vector<unsigned char>& ret, int64_t xpixel, int64_t ypixel, const rgb &color) const;
@@ -52,7 +55,9 @@ class PreviewImage {
     void beam_center_mark(std::vector<unsigned char>& ret, int64_t xpixel, int64_t ypixel) const;
 
 public:
-    explicit PreviewImage(const DiffractionExperiment& experiment);
+    explicit PreviewImage(std::chrono::microseconds period = std::chrono::seconds(1));
+    void Configure(const DiffractionExperiment& experiment, const PixelMask& mask);
+    void Configure();
     void UpdateImage(const void *uncompressed_image, const std::vector<SpotToSave> &spots);
     [[nodiscard]] std::string GenerateJPEG(const PreviewJPEGSettings& settings) const;
     [[nodiscard]] std::string GenerateTIFF() const;

preview/WriteTIFF.cpp

@@ -1,48 +0,0 @@
-// Copyright (2019-2024) Paul Scherrer Institute
-
-#include <tiffio.h>
-#include <tiffio.hxx>
-#include <sstream>
-
-#include "WriteTIFF.h"
-#include "../common/JFJochException.h"
-
-
-void WriteTIFF(TIFF *tiff, void *buff, size_t cols, size_t lines, size_t elem_size, bool is_signed) {
-
-    if (tiff == nullptr)
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFStreamOpen error");
-
-    TIFFSetField(tiff, TIFFTAG_IMAGEWIDTH, cols);  // set the width of the image
-    TIFFSetField(tiff, TIFFTAG_IMAGELENGTH, lines);    // set the height of the image
-    TIFFSetField(tiff, TIFFTAG_SAMPLESPERPIXEL, 1);   // set number of channels per pixel
-    TIFFSetField(tiff, TIFFTAG_BITSPERSAMPLE, elem_size * 8);    // set the size of the channels
-    TIFFSetField(tiff, TIFFTAG_COMPRESSION, COMPRESSION_NONE); // setc ompression to LZW
-    TIFFSetField(tiff, TIFFTAG_ROWSPERSTRIP, lines);
-    if (is_signed)
-        TIFFSetField(tiff, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_INT);
-    else
-        TIFFSetField(tiff, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_UINT);
-
-    if (TIFFWriteEncodedStrip(tiff, 0, buff, cols * lines * elem_size) < 0)
-        throw JFJochException(JFJochExceptionCategory::TIFFGeneratorError, "TIFFWriteEncodedStrip error");
-}
-
-std::string WriteTIFFToString(void *buff, size_t cols, size_t lines, size_t elem_size, bool is_signed) {
-    std::stringstream os;
-
-    TIFF *tiff = TIFFStreamOpen("x", (std::ostream *) &os);
-    WriteTIFF(tiff, buff, cols, lines, elem_size, is_signed);
-    TIFFClose(tiff);
-
-    return os.str();
-}
-
-void WriteTIFFToFile(const std::string &filename, void *buff, size_t cols, size_t lines, size_t elem_size,
-                     bool is_signed) {
-    TIFF *tiff = TIFFOpen(filename.c_str(), "w");
-
-    WriteTIFF(tiff, buff, cols, lines, elem_size, is_signed);
-
-    TIFFClose(tiff);
-}

receiver/JFJochReceiver.cpp

@@ -11,12 +11,15 @@
 #include "../common/PixelMask.h"
 
 JFJochReceiver::JFJochReceiver(const DiffractionExperiment& in_experiment,
+                               const PixelMask &pixel_mask,
                                const JFCalibration *in_calibration,
                                AcquisitionDeviceGroup &in_aq_device,
                                ImagePusher &in_image_sender,
                                Logger &in_logger, int64_t in_forward_and_sum_nthreads,
                                const NUMAHWPolicy &in_numa_policy,
                                const SpotFindingSettings &in_spot_finding_settings,
+                               PreviewImage &in_preview_image,
+                               PreviewImage &in_preview_image_indexed,
                                SendBuffer &buf) :
         experiment(in_experiment),
         calibration(nullptr),
@@ -33,9 +36,10 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment& in_experiment,
         az_int_mapping(experiment),
         plots(experiment, az_int_mapping),
         spot_finding_settings(in_spot_finding_settings),
-        preview_image(experiment),
-        preview_image_indexed(experiment),
-        serialmx_filter(experiment)
+        preview_image(in_preview_image),
+        preview_image_indexed(in_preview_image_indexed),
+        serialmx_filter(experiment),
+        user_mask_raw_coord(pixel_mask.GetUserMask(experiment, false))
 {
     if (experiment.GetDetectorSetup().GetDetectorType() == DetectorType::JUNGFRAU)
         calibration = in_calibration;
@@ -60,7 +64,7 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment& in_experiment,
     logger.Info("Data acquisition devices ready");
 
     if (experiment.GetImageNum() > 0) {
-        SendStartMessage();
+        SendStartMessage(pixel_mask);
         SendCalibration();
 
         for (int i = 0; i < experiment.GetImageNum(); i++)
@@ -88,7 +92,7 @@ JFJochReceiver::JFJochReceiver(const DiffractionExperiment& in_experiment,
     logger.Info("Receiving data started");
 }
 
-void JFJochReceiver::SendStartMessage() {
+void JFJochReceiver::SendStartMessage(const PixelMask &pixel_mask) {
     if (!push_images_to_writer)
         return;
 
@@ -99,11 +103,6 @@ void JFJochReceiver::SendStartMessage() {
     message.az_int_bin_to_q = az_int_mapping.GetBinToQ();
     message.write_master_file = true;
 
-    PixelMask pixel_mask(experiment);
-
-    if (calibration)
-        pixel_mask.LoadDetectorBadPixelMask(calibration->CalculateMask(), 1);
-
     std::vector<uint32_t> nexus_mask;
     nexus_mask = pixel_mask.GetMask(experiment);
 
@@ -178,6 +177,10 @@ void JFJochReceiver::AcquireThread(uint16_t data_stream) {
         std::vector<float> tmp(RAW_MODULE_SIZE);
         for (int m = 0; m < experiment.GetModulesNum(data_stream); m++) {
             CalcSpotFinderResolutionMap(tmp.data(), experiment, m_offset + m);
+            for (int i = 0; i < RAW_MODULE_SIZE; i++) {
+                if (user_mask_raw_coord[(m_offset + m) * RAW_MODULE_SIZE + i] != 0)
+                    tmp[i] = 0.0f;
+            }
             acquisition_device[data_stream].InitializeSpotFinderResolutionMap(tmp.data(), m);
 
             CalcAzIntCorrRawCoord(tmp.data(), experiment, m_offset + m);
@@ -294,8 +297,8 @@ void JFJochReceiver::FrameTransformationThread(uint32_t threadid) {
             message.number = image_number;
             message.original_number = image_number;
             message.user_data = experiment.GetImageAppendix();
-            message.series_id = experiment.GetSeriesID();
-            message.series_unique_id = experiment.GetSeriesIDString();
+            message.series_id = experiment.GetRunNumber();
+            message.series_unique_id = experiment.GetRunName();
 
             ImageMetadata metadata(experiment);
 
@@ -449,8 +452,8 @@ void JFJochReceiver::FinalizeMeasurement() {
         message.max_receiver_delay = max_delay;
         message.efficiency = GetEfficiency();
         message.end_date = time_UTC(std::chrono::system_clock::now());
-        message.series_id = experiment.GetSeriesID();
-        message.series_unique_id = experiment.GetSeriesIDString();
+        message.series_id = experiment.GetRunNumber();
+        message.series_unique_id = experiment.GetRunName();
 
         message.az_int_result["dataset"] = plots.GetAzIntProfile();
         for (int i = 0; i < experiment.GetTimePointNumber(); i++)
@@ -573,20 +576,6 @@ JFJochReceiverStatus JFJochReceiver::GetStatus() const {
     return ret;
 }
 
-std::string JFJochReceiver::GetTIFF(bool calibration_run) const {
-    if (calibration_run)
-        return preview_image.GenerateTIFFDioptas();
-    else
-        return preview_image.GenerateTIFF();
-}
-
-std::string JFJochReceiver::GetJPEG(const PreviewJPEGSettings &settings) const {
-    if (settings.show_indexed)
-        return preview_image_indexed.GenerateJPEG(settings);
-    else
-        return preview_image.GenerateJPEG(settings);
-}
-
 void JFJochReceiver::GetXFELEventCode(std::vector<uint64_t> &v) const {
     if (experiment.IsPulsedSource())
         plots.GetXFELEventCode(v);

receiver/JFJochReceiver.h

@@ -19,6 +19,7 @@
 #include "../common/ThreadSafeFIFO.h"
 #include "../common/NUMAHWPolicy.h"
 #include "../common/SendBufferControl.h"
+#include "../common/PixelMask.h"
 
 #include "../image_analysis/StrongPixelSet.h"
 #include "../image_analysis/AzimuthalIntegrationMapping.h"
@@ -108,11 +109,13 @@ class JFJochReceiver {
 
     NUMAHWPolicy numa_policy;
 
-    PreviewImage preview_image;
-    PreviewImage preview_image_indexed;
+    PreviewImage &preview_image;
+    PreviewImage &preview_image_indexed;
 
     LossyFilter serialmx_filter;
 
+    std::vector<uint32_t> user_mask_raw_coord;
+
     void AcquireThread(uint16_t data_stream);
     void FrameTransformationThread(uint32_t threadid);
     void Cancel(const JFJochException &e);
@@ -121,16 +124,19 @@ class JFJochReceiver {
     SpotFindingSettings GetSpotFindingSettings();
     void UpdateMaxImage(uint64_t image_number);
     void UpdateMaxDelay(uint64_t delay);
-    void SendStartMessage();
+    void SendStartMessage(const PixelMask &pixel_mask);
     void SendCalibration();
 public:
     JFJochReceiver(const DiffractionExperiment& experiment,
+                   const PixelMask &pixel_mask,
                    const JFCalibration *calibration,
                    AcquisitionDeviceGroup &acquisition_devices,
                    ImagePusher &image_pusher,
                    Logger &logger, int64_t forward_and_sum_nthreads,
                    const NUMAHWPolicy &numa_policy,
                    const SpotFindingSettings &spot_finding_settings,
+                   PreviewImage &preview_image,
+                   PreviewImage &preview_image_indexed,
                    SendBuffer &buffer);
     ~JFJochReceiver();
     JFJochReceiver(const JFJochReceiver &other) = delete;
@@ -148,9 +154,6 @@ public:
 
     MultiLinePlot GetPlots(const PlotRequest& request);
 
-    std::string GetTIFF(bool calibration) const;
-    std::string GetJPEG(const PreviewJPEGSettings &settings) const;
-
     void GetXFELEventCode(std::vector<uint64_t> &v) const;
     void GetXFELPulseID(std::vector<uint64_t> &v) const;
 };

receiver/JFJochReceiverPlots.cpp

@@ -23,15 +23,15 @@ JFJochReceiverPlots::JFJochReceiverPlots(const DiffractionExperiment &experiment
 void JFJochReceiverPlots::Add(const DataMessage &msg, uint64_t file_number, const AzimuthalIntegrationProfile &profile) {
     bkg_estimate.AddElement(msg.number, msg.bkg_estimate);
     spot_count.AddElement(msg.number, msg.spots.size());
+    spot_count_in_rings.AddElement(msg.number, msg.spot_count_in_rings);
+
     saturated_pixels.AddElement(msg.number, msg.saturated_pixel_count);
     error_pixels.AddElement(msg.number, msg.error_pixel_count);
     strong_pixels.AddElement(msg.number, msg.strong_pixel_count);
 
     image_collection_efficiency.AddElement(msg.number, msg.image_collection_efficiency);
-    if (msg.receiver_aq_dev_delay)
-        receiver_delay.AddElement(msg.number, msg.receiver_aq_dev_delay.value());
-    if (msg.receiver_free_send_buf)
-        receiver_free_send_buf.AddElement(msg.number, msg.receiver_free_send_buf.value());
+    receiver_delay.AddElement(msg.number, msg.receiver_aq_dev_delay);
+    receiver_free_send_buf.AddElement(msg.number, msg.receiver_free_send_buf);
 
     indexing_solution.AddElement(msg.number, msg.indexing_result);
     indexing_solution_per_time_point.Add(file_number, msg.indexing_result);
@@ -39,11 +39,8 @@ void JFJochReceiverPlots::Add(const DataMessage &msg, uint64_t file_number, cons
     az_int_profile += profile;
     az_int_profile_per_time_point.at(file_number) += profile;
 
-    if (msg.xfel_pulse_id)
-        xfel_pulse_id.AddElement(msg.number, msg.xfel_pulse_id.value());
-
-    if (msg.xfel_event_code)
-        xfel_event_code.AddElement(msg.number, msg.xfel_event_code.value());
+    xfel_pulse_id.AddElement(msg.number, msg.xfel_pulse_id);
+    xfel_event_code.AddElement(msg.number, msg.xfel_event_code);
 
     for (const auto &[key, value] : msg.roi) {
         if (roi_sum.contains(key) && roi_sum[key])
@@ -69,7 +66,15 @@ MultiLinePlot JFJochReceiverPlots::GetPlots(const PlotRequest &request) {
         case PlotType::RadInt:
             return az_int_profile.GetPlot();
         case PlotType::SpotCount:
-            return spot_count.GetMeanPlot(nbins);
+            tmp = spot_count.GetMeanPlot(nbins);
+            tmp.at(0).title = "Spots (crystal)";
+            ret.emplace_back(tmp.at(0));
+
+            tmp = spot_count_in_rings.GetMeanPlot(nbins);
+            tmp.at(0).title = "Spots (rings)";
+            ret.emplace_back(tmp.at(0));
+
+            return ret;
         case PlotType::IndexingRate:
             return indexing_solution.GetMeanPlot(nbins);
         case PlotType::BkgEstimate:

receiver/JFJochReceiverPlots.h

@@ -18,6 +18,7 @@ class JFJochReceiverPlots {
 
     StatusVector<float> bkg_estimate;
     StatusVector<uint64_t> spot_count;
+    StatusVector<uint64_t> spot_count_in_rings;
     StatusVector<uint64_t> indexing_solution;
     StatusVector<uint64_t> saturated_pixels;
     StatusVector<uint64_t> error_pixels;
@@ -25,7 +26,6 @@ class JFJochReceiverPlots {
     StatusVector<uint64_t> receiver_delay;
     StatusVector<uint64_t> receiver_free_send_buf;
     StatusVector<float> image_collection_efficiency;
-    StatusVector<float> unit_cell[6];
     SetAverage<uint64_t> indexing_solution_per_time_point;
 
     std::map<std::string, std::unique_ptr<StatusVector<int64_t>>> roi_sum;

receiver/JFJochReceiverService.cpp

@@ -45,18 +45,26 @@ std::optional<JFJochReceiverStatus> JFJochReceiverService::GetStatus() {
         return {};
 }
 
-void JFJochReceiverService::Start(const DiffractionExperiment &experiment, const JFCalibration *calibration) {
+void JFJochReceiverService::Start(const DiffractionExperiment &experiment,
+                                  const PixelMask &pixel_mask,
+                                  const JFCalibration *calibration) {
     std::unique_lock ul_state(state_mutex); // unique lock, as it will destroy and create receiver object
     if (state != ReceiverState::Idle)
         throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Receiver not idle, cannot start");
 
     try {
+        preview_image.Configure(experiment, pixel_mask);
+        preview_image_indexed.Configure(experiment, pixel_mask);
+
         // Thanks to properties of unique_ptr, starting new measurement will call destructor of JFJochReceiver, which will
         // ensure that everything was rolled back
-        receiver = std::make_unique<JFJochReceiver>(experiment, calibration,
+        receiver = std::make_unique<JFJochReceiver>(experiment, pixel_mask,
+                                                    calibration,
                                                     aq_devices, image_pusher,
                                                     logger, nthreads, numa_policy,
                                                     spot_finding_settings,
+                                                    preview_image,
+                                                    preview_image_indexed,
                                                     buffer);
         try {
             // Don't want to stop
@@ -128,19 +136,17 @@ std::vector<AcquisitionDeviceNetConfig> JFJochReceiverService::GetNetworkConfig(
 }
 
 std::string JFJochReceiverService::GetTIFF(bool calibration) const {
-    std::unique_lock ul(state_mutex);
-    if (receiver)
-        return receiver->GetTIFF(calibration);
+    if (calibration)
+        return preview_image.GenerateTIFFDioptas();
     else
-        return "";
+        return preview_image.GenerateTIFF();
 }
 
 std::string JFJochReceiverService::GetJPEG(const PreviewJPEGSettings &settings) const {
-    std::unique_lock ul(state_mutex);
-    if (receiver)
-        return receiver->GetJPEG(settings);
+    if (settings.show_indexed)
+        return preview_image_indexed.GenerateJPEG(settings);
     else
-        return "";
+        return preview_image.GenerateJPEG(settings);
 }
 
 void JFJochReceiverService::LoadInternalGeneratorImage(const DiffractionExperiment &experiment,

receiver/JFJochReceiverService.h

@@ -25,6 +25,9 @@ class JFJochReceiverService {
     std::future<void> measurement;
     void FinalizeMeasurement();
     SpotFindingSettings spot_finding_settings;
+
+    PreviewImage preview_image;
+    PreviewImage preview_image_indexed;
 public:
     JFJochReceiverService(AcquisitionDeviceGroup &aq_devices,
                           Logger &logger,
@@ -37,7 +40,9 @@ public:
     void LoadInternalGeneratorImage(const DiffractionExperiment& experiment,
                                     const std::vector<uint16_t> &raw_expected_image,
                                     uint64_t image_number);
-    void Start(const DiffractionExperiment &experiment, const JFCalibration *calibration);
+    void Start(const DiffractionExperiment &experiment,
+               const PixelMask &pixel_mask,
+               const JFCalibration *calibration);
     void Cancel(bool silent);
     JFJochReceiverOutput Stop();
     void SetSpotFindingSettings(const SpotFindingSettings& settings);

receiver/JFJochReceiverTest.cpp

@@ -54,6 +54,8 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
                         size_t send_buf_size_MiB) {
 
     JFCalibration calib = GeneratePedestalCalibration(x);
+    PixelMask mask(x);
+    mask.LoadDetectorBadPixelMask(calib.CalculateMask());
 
     int64_t image_number = x.GetImageNum() - 1;
 
@@ -75,7 +77,7 @@ bool JFJochReceiverTest(JFJochReceiverOutput &output, Logger &logger,
     settings.max_pix_per_spot = 200;
     service.SetSpotFindingSettings(settings);
 
-    service.Start(x, &calib);
+    service.Start(x, mask, &calib);
     output = service.Stop();
 
     bool no_errors = true;

tests/CBORTest.cpp

@@ -48,12 +48,14 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
             .series_id = 4567,
             .gain_file_names = {"abc" , "def", "/dsadasdsa/dadsadas/dsadsa/M056.bin"},
             .roi_names = {"roi0", "roi1"},
-            .omega = {
+            .goniometer = GoniometerAxis{
+                    .name = "omega",
                     .increment = 0.1f,
-                    .start = 10.0f,
-                    .axis = {0,-1.0, 0.0}
+                    .start = 10.0f
             },
+            .rotation_axis = {0,-1.0, 0.0},
             .detector_translation = {0.5f, 0.0f, 0.5f},
+            .source_type = "Synchrotron X-ray Source",
             .source_name = "Swiss Light Source",
             .source_name_short = "SLS",
             .instrument_name = "X06SA",
@@ -65,7 +67,9 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
             .attenuator_transmission = 0.345,
             .write_master_file = true,
             .user_data = "Some random string 12345",
-            .data_reduction_factor_serialmx = 0.75
+            .data_reduction_factor_serialmx = 0.75,
+            .experiment_group = "p10001",
+            .jfjoch_release = "1.4.98"
     };
 
     REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
@@ -108,6 +112,7 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
     CHECK(output_message.detector_serial_number == message.detector_serial_number);
     CHECK(output_message.series_unique_id == message.series_unique_id);
     CHECK(output_message.series_id == message.series_id);
+    CHECK(output_message.source_type == message.source_type);
     CHECK(output_message.source_name == message.source_name);
     CHECK(output_message.source_name_short == message.source_name_short);
     CHECK(output_message.instrument_name == message.instrument_name);
@@ -127,10 +132,11 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
     CHECK(output_message.unit_cell->beta == message.unit_cell->beta);
     CHECK(output_message.unit_cell->gamma == message.unit_cell->gamma);
 
-    CHECK(output_message.omega.increment == message.omega.increment);
-    CHECK(output_message.omega.start == message.omega.start);
+    CHECK(output_message.goniometer->name == message.goniometer->name);
+    CHECK(output_message.goniometer->increment == message.goniometer->increment);
+    CHECK(output_message.goniometer->start == message.goniometer->start);
     for (int i = 0; i < 3; i++)
-        CHECK(output_message.omega.axis[i] == message.omega.axis[i]);
+        CHECK(output_message.rotation_axis[i] == message.rotation_axis[i]);
 
     REQUIRE (output_message.total_flux);
     CHECK(output_message.total_flux.value() == message.total_flux.value());
@@ -143,6 +149,8 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
     CHECK(output_message.flatfield_enabled == message.flatfield_enabled);
     CHECK(output_message.write_master_file == message.write_master_file);
     CHECK(output_message.data_reduction_factor_serialmx == message.data_reduction_factor_serialmx);
+    CHECK(output_message.experiment_group == message.experiment_group);
+    CHECK(output_message.jfjoch_release == message.jfjoch_release);
 }
 
 TEST_CASE("CBORSerialize_Start_PixelMask", "[CBOR]") {
@@ -345,6 +353,7 @@ TEST_CASE("CBORSerialize_Image", "[CBOR]") {
             .image = image,
             .image_collection_efficiency = 0.11,
             .spots = spots,
+            .spot_count_in_rings = 157,
             .bkg_estimate = 12.345f,
             .indexing_result = 1,
             .adu_histogram = {3, 4, 5, 8},
@@ -401,6 +410,7 @@ TEST_CASE("CBORSerialize_Image", "[CBOR]") {
     REQUIRE(image_array.image_collection_efficiency == message.image_collection_efficiency);
     REQUIRE(image_array.user_data == message.user_data);
     REQUIRE(image_array.original_number == message.original_number);
+    REQUIRE(image_array.spot_count_in_rings == message.spot_count_in_rings);
 }
 
 TEST_CASE("CBORSerialize_Image_2", "[CBOR]") {

tests/DiffractionExperimentTest.cpp

@@ -472,6 +472,18 @@ TEST_CASE("DiffractionExperiment_SaveCalibration", "[DiffractionExperiment]") {
     REQUIRE(!x.GetSaveCalibration());
 }
 
+TEST_CASE("DiffractionExperiment_FrameCountTime","[DiffractionExperiment]") {
+    DiffractionExperiment x;
+    REQUIRE_NOTHROW(x.FrameTime(1000us, 3us));
+    REQUIRE_NOTHROW(x.FrameTime(1000us));
+    REQUIRE(x.GetFrameCountTime() == 1000us - std::chrono::microseconds(READOUT_TIME_IN_US));
+
+    REQUIRE_NOTHROW(x.FrameTime(2000us));
+    REQUIRE_THROWS(x.FrameTime(2500us));
+    REQUIRE_THROWS(x.FrameTime(10000us, 2100us));
+    REQUIRE_NOTHROW(x.FrameTime(10000us, 10us));
+}
+
 //TODO: Update
 /*
 TEST_CASE("DiffractionExperiment_FrameCountTime","[DiffractionExperiment]") {
@@ -774,40 +786,44 @@ TEST_CASE("DiffractionExperiment_Appendix","") {
 TEST_CASE("DiffractionExperiment_OmegaRotationAxis","[DiffractionExperiment]") {
     DiffractionExperiment x;
 
-    x.DefaultOmegaAxis({0,-1,0});
-    REQUIRE(x.GetDefaultOmegaAxis().x == 0);
-    REQUIRE(x.GetDefaultOmegaAxis().y == -1);
+    x.DefaultRotationAxis({0, -1, 0});
+    REQUIRE(x.GetDefaultRotationAxis().x == 0);
+    REQUIRE(x.GetDefaultRotationAxis().y == -1);
 
-    x.OmegaAxis();
-    REQUIRE(x.GetOmegaAxis().x == 0);
-    REQUIRE(x.GetOmegaAxis().y == -1);
+    x.RotationAxis({});
+    REQUIRE(x.GetRotationAxis().x == 0);
+    REQUIRE(x.GetRotationAxis().y == -1);
 
-    x.OmegaAxis({-1, 0, 0});
-    REQUIRE(x.GetOmegaAxis().x == -1);
-    REQUIRE(x.GetOmegaAxis().y == 0);
+    x.RotationAxis(Coord{-1, 0, 0});
+    REQUIRE(x.GetRotationAxis().x == -1);
+    REQUIRE(x.GetRotationAxis().y == 0);
 
-    REQUIRE_THROWS(x.DefaultOmegaAxis({0,0,0}));
-    REQUIRE_THROWS(x.OmegaAxis({0,0,0}));
+    REQUIRE_THROWS(x.DefaultRotationAxis({0, 0, 0}));
+    REQUIRE_THROWS(x.RotationAxis(Coord{0,0,0}));
 }
 
 TEST_CASE("DiffractionExperiment_OmegaStep","[DiffractionExperiment]") {
     DiffractionExperiment x;
     StartMessage msg;
 
-    x.OmegaStep(std::optional<float>());
     x.FillMessage(msg);
-    REQUIRE(!x.GetOmegaStep());
-    REQUIRE(msg.omega.increment == 0.0f);
+    REQUIRE(!x.GetGoniometer());
+    REQUIRE(!msg.goniometer);
 
-    x.OmegaStep(0.0);
-    REQUIRE(!x.GetOmegaStep());
-    x.FillMessage(msg);
-    REQUIRE(msg.omega.increment == 0.0f);
+    DatasetSettings d;
+    d.Goniometer(GoniometerAxis{
+            .name = "omega",
+            .increment = 75.0f,
+            .start = 20.0f
+    });
+    x.ImportDatasetSettings(d);
 
-    x.OmegaStep(1.0);
     x.FillMessage(msg);
-    REQUIRE(x.GetOmegaStep());
-    REQUIRE(msg.omega.increment == 1.0f);
+    REQUIRE(x.GetGoniometer().has_value());
+    REQUIRE(msg.goniometer);
+    REQUIRE(msg.goniometer->name == "omega");
+    REQUIRE(msg.goniometer->increment == 75.0f);
+    REQUIRE(msg.goniometer->start == 20.0f);
 }
 
 TEST_CASE("DiffractionExperiment_ConversionOnFPGA","[DiffractionExperiment]") {
@@ -862,7 +878,23 @@ TEST_CASE("DiffractionExperiment_PhotonEnergyMultiplayer","[DiffractionExperimen
     REQUIRE(x.GetPhotonEnergyForConversion_keV() == 16.0f);
 }
 
-TEST_CASE("DiffractioExperiment_GetDefaultPlotBinning", "[DiffractionExperiment]") {
+TEST_CASE("DiffractionExperiment_SeriesID","[DiffractionExperiment]") {
+    DiffractionExperiment x;
+    REQUIRE(x.GetRunNumber() == 0);
+    x.IncrementRunNumber();
+    REQUIRE(x.GetRunNumber() == 1);
+
+    DatasetSettings d;
+    d.RunNumber(25);
+    x.ImportDatasetSettings(d);
+    REQUIRE(x.GetRunNumber() == 25);
+
+    d.RunNumber({});
+    x.ImportDatasetSettings(d);
+    REQUIRE(x.GetRunNumber() == 1);
+}
+
+TEST_CASE("DiffractionExperiment_GetDefaultPlotBinning", "[DiffractionExperiment]") {
     DiffractionExperiment x;
     x.FrameTime(std::chrono::milliseconds(1));
 
@@ -879,7 +911,7 @@ TEST_CASE("DiffractioExperiment_GetDefaultPlotBinning", "[DiffractionExperiment]
     CHECK(x.GetDefaultPlotBinning() == 1);
 }
 
-TEST_CASE("DiffractioExperiment_ImportDataset_TooManyFrames", "[DiffractionExperiment]") {
+TEST_CASE("DiffractionExperiment_ImportDataset_TooManyFrames", "[DiffractionExperiment]") {
     DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36, true));
     x.ImagesPerTrigger(345).NumTriggers(17);
     DatasetSettings dataset;
@@ -888,7 +920,7 @@ TEST_CASE("DiffractioExperiment_ImportDataset_TooManyFrames", "[DiffractionExper
     REQUIRE(x.GetImageNum() == 345 * 17);
 }
 
-TEST_CASE("DiffractioExperiment_ExportROIMask", "[DiffractionExperiment]") {
+TEST_CASE("DiffractionExperiment_ExportROIMask", "[DiffractionExperiment]") {
     DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36, true));
     x.Mode(DetectorMode::Conversion);
 

tests/FPGAIntegrationTest.cpp

@@ -1513,6 +1513,7 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_count_threshol
 
     HLSSimulatedDevice test(0, 64);
 
+    std::vector<float> d_map(RAW_MODULE_SIZE, 3.0);
     std::vector<uint16_t> frame(RAW_MODULE_SIZE, 0);
     frame [  1*1024 +   1] = 11;
     frame [123*1024 + 578] = 10;
@@ -1520,14 +1521,17 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_count_threshol
     frame [ 89*1024 + 300] =  8;
     frame [300*1024 +   0] =  9;
 
-    for (int m = 0; m < x.GetModulesNum(); m++)
+    for (int m = 0; m < x.GetModulesNum(); m++) {
         test.SetInternalGeneratorFrame(frame.data(), m);
-
+        test.InitializeSpotFinderResolutionMap(d_map.data(), m);
+    }
 
     SpotFindingSettings parameters{
-        .signal_to_noise_threshold = 0.0,
-        .photon_count_threshold = 9,
-        .min_pix_per_spot = 1
+            .signal_to_noise_threshold = 0.0,
+            .photon_count_threshold = 9,
+            .min_pix_per_spot = 1,
+            .high_resolution_limit = 2.5,
+            .low_resolution_limit = 3.1
     };
     test.SetSpotFinderParameters(parameters);
 
@@ -1577,14 +1581,19 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_mask", "[FPGA]
     frame [  256*1024 +  876] = 50;
     frame [  320*1024 +  400] = 50;
 
-    for (int m = 0; m < x.GetModulesNum(); m++)
-        test.SetInternalGeneratorFrame(frame.data(), m);
+    std::vector<float> d_map(RAW_MODULE_SIZE, 3.0);
 
+    for (int m = 0; m < x.GetModulesNum(); m++) {
+        test.SetInternalGeneratorFrame(frame.data(), m);
+        test.InitializeSpotFinderResolutionMap(d_map.data(), m);
+    }
 
     SpotFindingSettings parameters{
             .signal_to_noise_threshold = 0.0,
             .photon_count_threshold = 45,
-            .min_pix_per_spot = 1
+            .min_pix_per_spot = 1,
+            .high_resolution_limit = 2.0,
+            .low_resolution_limit = 4.0
     };
     test.SetSpotFinderParameters(parameters);
 
@@ -1616,6 +1625,8 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_min_pix_per_sp
 
     HLSSimulatedDevice test(0, 64);
 
+    std::vector<float> d_map(RAW_MODULE_SIZE, 3.0);
+
     std::vector<uint16_t> frame(RAW_MODULE_SIZE, 0);
     frame [1*1024 + 1] = 11;
     frame [1*1024 + 2] = 10;
@@ -1630,13 +1641,17 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_min_pix_per_sp
     frame [101*1024+200] = 12;
     frame [RAW_MODULE_SIZE - 1 - 1024] = 20;
 
-    for (int m = 0; m < x.GetModulesNum(); m++)
+    for (int m = 0; m < x.GetModulesNum(); m++) {
+        test.InitializeSpotFinderResolutionMap(d_map.data(), m);
         test.SetInternalGeneratorFrame(frame.data(), m);
+    }
 
     SpotFindingSettings parameters{
             .signal_to_noise_threshold = 0.0,
             .photon_count_threshold = 9,
-            .min_pix_per_spot = 2
+            .min_pix_per_spot = 2,
+            .high_resolution_limit = 2.0,
+            .low_resolution_limit = 4.0
     };
     test.SetSpotFinderParameters(parameters);
 
@@ -1685,9 +1700,10 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_d_min_max", "[
     frame [1024+4] = 12;
 
     test.InitializeSpotFinderResolutionMap(d_map.data(), 0);
-    for (int m = 0; m < x.GetModulesNum(); m++)
+    for (int m = 0; m < x.GetModulesNum(); m++) {
         test.SetInternalGeneratorFrame(frame.data(), m);
-
+        test.InitializeSpotFinderResolutionMap(d_map.data(), m);
+    }
 
     SpotFindingSettings parameters{
             .signal_to_noise_threshold = 0.0,
@@ -1727,6 +1743,7 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_snr_threshold"
 
     HLSSimulatedDevice test(0, 64);
 
+    std::vector<float> d_map(RAW_MODULE_SIZE, 3.0);
     std::vector<uint16_t> frame(RAW_MODULE_SIZE);
     for (int i = 0; i < RAW_MODULE_SIZE; i++) {
         frame[i] = ((i / RAW_MODULE_COLS) + (i % RAW_MODULE_COLS)) % 2;
@@ -1741,13 +1758,17 @@ TEST_CASE("HLS_C_Simulation_internal_packet_generator_spot_finder_snr_threshold"
     frame [ 89*1024 + 300] = 7;
     frame [300*1024 +   5] = 3;
 
-    for (int m = 0; m < x.GetModulesNum(); m++)
+    for (int m = 0; m < x.GetModulesNum(); m++) {
         test.SetInternalGeneratorFrame(frame.data(), m);
+        test.InitializeSpotFinderResolutionMap(d_map.data(), m);
+    }
 
     SpotFindingSettings parameters{
             .signal_to_noise_threshold = 10.0,
             .photon_count_threshold = 0,
-            .min_pix_per_spot = 1
+            .min_pix_per_spot = 1,
+            .high_resolution_limit = 2.0,
+            .low_resolution_limit = 3.1
     };
     test.SetSpotFinderParameters(parameters);
 

tests/HDF5WritingTest.cpp

@@ -223,10 +223,17 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
     {
         RegisterHDF5Filter();
         DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
+        x.FrameTime(std::chrono::microseconds(1000), std::chrono::microseconds(100));
+
+        DatasetSettings d;
+        d.FilePrefix("run0345_lysozyme_acq").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION)
+                .HeaderAppendix("{\"z\":567}").DetectorDistance_mm(155).BeamX_pxl(1606.62).BeamY_pxl(1669.59)
+                .PhotonEnergy_keV(12.07).SetUnitCell(UnitCell{.a = 97, .b = 97, .c = 38, .alpha= 90, .beta = 90, .gamma = 90})
+                .SpaceGroupNumber(96).RunNumber(345).ExperimentGroup("p12345").SampleName("lysozyme");
+
+        x.ImportDatasetSettings(d);
         std::vector<SpotToSave> spots;
 
-        x.FilePrefix("test05").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION)
-                .HeaderAppendix("{\"z\":567}");
         StartMessage start_message;
         x.FillMessage(start_message);
 
@@ -259,22 +266,31 @@ TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
         nlohmann::json j;
 
         REQUIRE(s.Receive(msg, true));
+
         j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
-        REQUIRE(j["filename"] == "test05_data_000001.h5");
+        REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000001.h5");
+        REQUIRE(j["file_number"] == 1);
+        REQUIRE(j["nimages"] == 2);
+        REQUIRE(j["photon_energy_eV"] == Catch::Approx(x.GetPhotonEnergy_keV() * 1000.0));
+        REQUIRE(j["space_group_number"] == 96);
+        REQUIRE(j["experiment_group"] == "p12345");
+        REQUIRE(j["run_number"] == 345);
+        REQUIRE(j.contains("user_data"));
+        REQUIRE(j["user_data"]["z"] == 567);
+        std::cout << j.dump(4) << std::endl;
+
+        REQUIRE(s.Receive(msg, true));
+        j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
+        REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000002.h5");
+        REQUIRE(j["file_number"] == 2);
         REQUIRE(j["nimages"] == 2);
         REQUIRE(j.contains("user_data"));
         REQUIRE(j["user_data"]["z"] == 567);
 
         REQUIRE(s.Receive(msg, true));
         j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
-        REQUIRE(j["filename"] == "test05_data_000002.h5");
-        REQUIRE(j["nimages"] == 2);
-        REQUIRE(j.contains("user_data"));
-        REQUIRE(j["user_data"]["z"] == 567);
-
-        REQUIRE(s.Receive(msg, true));
-        j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
-        REQUIRE(j["filename"] == "test05_data_000003.h5");
+        REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000003.h5");
+        REQUIRE(j["file_number"] == 3);
         REQUIRE(j["nimages"] == 1);
         REQUIRE(j.contains("user_data"));
         REQUIRE(j["user_data"]["z"] == 567);

tests/JFJochReceiverIntegrationTest.cpp

@@ -491,6 +491,8 @@ TEST_CASE("JFJochReceiverTest_PacketLost_Raw", "[JFJochReceiver]") {
     x.PedestalG0Frames(0).NumTriggers(1)
             .UseInternalPacketGenerator(false).ImagesPerTrigger(4).PhotonEnergy_keV(12.4);
 
+    PixelMask pixel_mask(x);
+
     AcquisitionDeviceGroup aq_devices;
     for (int i = 0; i < x.GetDataStreamsNum(); i++) {
         auto test = std::make_unique<HLSSimulatedDevice>(i, 64);
@@ -517,7 +519,7 @@ TEST_CASE("JFJochReceiverTest_PacketLost_Raw", "[JFJochReceiver]") {
     JFJochReceiverService service(aq_devices, logger, pusher);
     service.NumThreads(nthreads);
 
-    service.Start(x, &calib);
+    service.Start(x, pixel_mask, &calib);
     auto receiver_out =  service.Stop();
 
     const auto image = pusher.GetImage();
@@ -551,6 +553,8 @@ TEST_CASE("JFJochReceiverTest_Cancel", "[JFJochReceiver]") {
     x.PedestalG0Frames(0).NumTriggers(1)
             .UseInternalPacketGenerator(false).ImagesPerTrigger(4).PhotonEnergy_keV(12.4);
 
+    PixelMask pixel_mask(x);
+
     AcquisitionDeviceGroup aq_devices;
     for (int i = 0; i < x.GetDataStreamsNum(); i++) {
         auto test = std::make_unique<HLSSimulatedDevice>(i, 64);
@@ -570,7 +574,7 @@ TEST_CASE("JFJochReceiverTest_Cancel", "[JFJochReceiver]") {
     JFJochReceiverService service(aq_devices, logger, pusher);
     service.NumThreads(nthreads);
 
-    service.Start(x, &calib);
+    service.Start(x, pixel_mask, &calib);
 
     std::this_thread::sleep_for(std::chrono::seconds(60));
     service.Cancel(false);

tests/JFJochReceiverProcessingTest.cpp

@@ -9,7 +9,7 @@
 #include "../writer/HDF5Objects.h"
 #include "../receiver/JFJochReceiverService.h"
 #include "../common/DiffractionGeometry.h"
-#include "../preview/WriteTIFF.h"
+#include "../preview/JFJochTIFF.h"
 #include "../common/ZMQWrappers.h"
 #include "../frame_serialize/ZMQStream2Pusher.h"
 #include "../writer/StreamWriter.h"
@@ -26,6 +26,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
             .FilePrefix("lyso_test").ConversionOnFPGA(false)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).PhotonEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
+    PixelMask pixel_mask(experiment);
 
     // Load example image
     HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
@@ -64,9 +65,11 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
     settings.photon_count_threshold = 5;
     settings.min_pix_per_spot = 1;
     settings.max_pix_per_spot = 200;
+    settings.high_resolution_limit = 2.0;
+    settings.low_resolution_limit = 50.0;
     service.SetSpotFindingSettings(settings);
 
-    service.Start(experiment, nullptr);
+    service.Start(experiment, pixel_mask, nullptr);
     auto receiver_out = service.Stop();
 
     std::string jpeg;
@@ -80,7 +83,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index", "[JFJochReceiver]
     f.write(jpeg.data(), jpeg.size());
 
     CHECK(receiver_out.efficiency == 1.0);
-    CHECK(receiver_out.status.indexing_rate == 1.0);
+    REQUIRE(receiver_out.status.indexing_rate);
+    CHECK(receiver_out.status.indexing_rate.value() == 1.0);
     CHECK(receiver_out.status.images_sent == experiment.GetImageNum());
     CHECK(!receiver_out.status.cancelled);
 
@@ -99,6 +103,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
             .FilePrefix("lyso_test_min_pix_2").ConversionOnFPGA(false)
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).PhotonEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
+    PixelMask pixel_mask(experiment);
 
     // Load example image
     HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
@@ -138,7 +143,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_lysozyme_spot_and_index_min_pix_2", "[JFJoc
     settings.max_pix_per_spot = 200;
     service.SetSpotFindingSettings(settings);
 
-    service.Start(experiment, nullptr);
+    service.Start(experiment, pixel_mask, nullptr);
     auto receiver_out = service.Stop();
 
     std::string jpeg;
@@ -195,6 +200,8 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
             .DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).PhotonEnergy_keV(12.4)
             .SetUnitCell(UnitCell{.a = 36.9, .b = 78.95, .c = 78.95, .alpha =90, .beta = 90, .gamma = 90});
 
+    PixelMask pixel_mask(experiment);
+
     experiment.ROI().SetROIBox({ROIBox("roi0", 100, 120, 20,30)});
     experiment.ROI().SetROICircle({ROICircle("roi1", 500, 800, 10)});
 
@@ -242,7 +249,7 @@ TEST_CASE("JFJochIntegrationTest_ZMQ_ROI", "[JFJochReceiver]") {
     JFJochReceiverService service(aq_devices, logger, pusher);
     service.NumThreads(nthreads);
 
-    service.Start(experiment, nullptr);
+    service.Start(experiment, pixel_mask, nullptr);
     auto receiver_out = service.Stop();
 
     std::string jpeg;

tests/JPEGTest.cpp

@@ -3,7 +3,7 @@
 #include <catch2/catch_all.hpp>
 
 #include <fstream>
-#include "../preview//WriteJPEG.h"
+#include "../preview//JFJochJPEG.h"
 #include "../preview//PreviewImage.h"
 #include "../writer/HDF5Objects.h"
 #include "../common/RawToConvertedGeometry.h"
@@ -24,7 +24,19 @@ TEST_CASE("JPEGTest","[JPEG]") {
     f.write(s.data(), s.size());
 }
 
+TEST_CASE("PreviewImage_NotConfigured","[JPEG]") {
+    std::vector<int16_t> image_conv_2(67878);
+    std::vector<SpotToSave> spots;
+
+    PreviewImage image;
+    REQUIRE_THROWS(image.UpdateImage(image_conv_2.data(), spots));
+    REQUIRE(image.GenerateJPEG(PreviewJPEGSettings()).empty());
+}
+
+
 TEST_CASE("PreviewImage_GenerateJPEG","[JPEG]") {
+    RegisterHDF5Filter();
+
     DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
             .FilePrefix("lyso_test_min_pix_2").ConversionOnFPGA(false)
@@ -57,7 +69,11 @@ TEST_CASE("PreviewImage_GenerateJPEG","[JPEG]") {
             {.x = 800,  .y = 1000, .indexed = false},
             {.x = 1200, .y = 500, .indexed = true}
     };
-    PreviewImage image(experiment);
+
+    PixelMask mask(experiment);
+
+    PreviewImage image;
+    image.Configure(experiment, mask);
 
     PreviewJPEGSettings preview_settings{
             .saturation_value = 5,
@@ -69,7 +85,6 @@ TEST_CASE("PreviewImage_GenerateJPEG","[JPEG]") {
 
     image.UpdateImage(image_conv_2.data(), spots);
 
-
     std::string s;
     REQUIRE_NOTHROW(s = image.GenerateJPEG(preview_settings));
     std::ofstream f("lyso_diff.jpeg", std::ios::binary);
@@ -77,6 +92,8 @@ TEST_CASE("PreviewImage_GenerateJPEG","[JPEG]") {
 }
 
 TEST_CASE("PreviewImage_GenerateJPEG_ROI","[JPEG]") {
+    RegisterHDF5Filter();
+
     DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
             .FilePrefix("lyso_test_min_pix_2").ConversionOnFPGA(false)
@@ -111,7 +128,11 @@ TEST_CASE("PreviewImage_GenerateJPEG_ROI","[JPEG]") {
             {.x = 800,  .y = 1000, .indexed = false},
             {.x = 1200, .y = 500, .indexed = true}
     };
-    PreviewImage image(experiment);
+    PreviewImage image;
+
+    PixelMask mask(experiment);
+
+    image.Configure(experiment, mask);
     image.UpdateImage(image_conv_2.data(), spots);
 
     PreviewJPEGSettings preview_settings{
@@ -128,6 +149,8 @@ TEST_CASE("PreviewImage_GenerateJPEG_ROI","[JPEG]") {
 }
 
 TEST_CASE("PreviewImage_GenerateJPEG_resolution","[JPEG]") {
+    RegisterHDF5Filter();
+
     DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
             .FilePrefix("lyso_test_min_pix_2").ConversionOnFPGA(false)
@@ -152,8 +175,11 @@ TEST_CASE("PreviewImage_GenerateJPEG_resolution","[JPEG]") {
     ConvertedToRawGeometry(experiment, image_raw_geom.data(), image_conv.data());
     RawToConvertedGeometry(experiment, image_conv_2.data(), image_raw_geom.data());
 
+    PixelMask mask(experiment);
+
     std::vector<SpotToSave> spots = {};
-    PreviewImage image(experiment);
+    PreviewImage image;
+    image.Configure(experiment, mask);
     image.UpdateImage(image_conv_2.data(), spots);
 
     PreviewJPEGSettings preview_settings{

tests/PixelMaskTest.cpp

@@ -57,22 +57,119 @@ TEST_CASE("PixelMask_CalculateNexusMask","[PixelMask]") {
     v[2] = 1;
     v[4] = 1;
     v[5] = 1;
+    v[3 * RAW_MODULE_SIZE + 780] = 1;
 
-    REQUIRE_NOTHROW(mask.LoadDetectorBadPixelMask(v, 2));
+    REQUIRE_NOTHROW(mask.LoadDetectorBadPixelMask(v));
 
     auto mask_v = mask.GetMask(experiment);
 
     REQUIRE(mask_v.size() == experiment.GetPixelsNum() );
     REQUIRE(mask_v[0] == 0);
     REQUIRE(mask_v[1] == 0);
-    REQUIRE(mask_v[2] == 4);
+    REQUIRE(mask_v[2] == (1 << PixelMask::ErrorPixelBit));
     REQUIRE(mask_v[3] == 0);
-    REQUIRE(mask_v[4] == 4);
-    REQUIRE(mask_v[5] == 4);
+    REQUIRE(mask_v[4] == (1 << PixelMask::ErrorPixelBit));
+    REQUIRE(mask_v[5] == (1 << PixelMask::ErrorPixelBit));
     REQUIRE(mask_v[6] == 0);
     REQUIRE(mask_v[1030 * 700 + 300] == 0);
+    REQUIRE(mask_v[(514+36)*1030*3 + 780 + 6] == (1 << PixelMask::ErrorPixelBit));
 }
 
+TEST_CASE("PixelMask_CalculateNexusMask_GetMaskRaw","[PixelMask]") {
+    DiffractionExperiment experiment(DetectorGeometry(4, 1, 8, 36, false));
+    experiment.MaskModuleEdges(false).MaskChipEdges(false);
+
+    PixelMask mask(experiment);
+
+    std::vector<uint32_t> v(4 * RAW_MODULE_SIZE, 0);
+    v[2] = 1;
+    v[4] = 1;
+    v[5] = 1;
+    v[3 * RAW_MODULE_SIZE + 780] = 1;
+
+    REQUIRE_NOTHROW(mask.LoadDetectorBadPixelMask(v));
+
+    auto mask_v = mask.GetMask(experiment, false);
+
+    REQUIRE(mask_v.size() == 4 * RAW_MODULE_SIZE );
+    REQUIRE(mask_v[0] == 0);
+    REQUIRE(mask_v[1] == 0);
+    REQUIRE(mask_v[2] == (1 << PixelMask::ErrorPixelBit));
+    REQUIRE(mask_v[3] == 0);
+    REQUIRE(mask_v[4] == (1 << PixelMask::ErrorPixelBit));
+    REQUIRE(mask_v[5] == (1 << PixelMask::ErrorPixelBit));
+    REQUIRE(mask_v[6] == 0);
+
+    REQUIRE(mask_v[3 * RAW_MODULE_SIZE + 780] == (1 << PixelMask::ErrorPixelBit));
+}
+
+TEST_CASE("PixelMask_CalculateNexusMask_UserMaskRaw","[PixelMask]") {
+    DiffractionExperiment experiment(DetectorGeometry(4, 1, 8, 36, false));
+    experiment.MaskModuleEdges(false).MaskChipEdges(false);
+
+    PixelMask mask(experiment);
+
+    std::vector<uint32_t> v(4 * RAW_MODULE_SIZE, 0);
+    v[2] = 1;
+    v[4] = 1;
+    v[5] = 1;
+
+    REQUIRE_NOTHROW(mask.LoadUserMask(experiment, v));
+
+    auto mask_v = mask.GetMask(experiment);
+
+    REQUIRE(mask_v.size() == experiment.GetPixelsNum() );
+    REQUIRE(mask_v[0] == 0);
+    REQUIRE(mask_v[1] == 0);
+    REQUIRE(mask_v[2] == (1 << PixelMask::UserMaskedPixelBit));
+    REQUIRE(mask_v[3] == 0);
+    REQUIRE(mask_v[4] == (1 << PixelMask::UserMaskedPixelBit));
+    REQUIRE(mask_v[5] == (1 << PixelMask::UserMaskedPixelBit));
+    REQUIRE(mask_v[6] == 0);
+    REQUIRE(mask_v[1030 * 700 + 300] == 0);
+    REQUIRE(mask_v[(1030+8)*514] == (1 << PixelMask::ModuleGapPixelBit));
+
+    auto user_mask_v = mask.GetUserMask(experiment);
+
+    REQUIRE(user_mask_v.size() == experiment.GetPixelsNum() );
+    REQUIRE(user_mask_v[0] == 0);
+    REQUIRE(user_mask_v[1] == 0);
+    REQUIRE(user_mask_v[2] == 1);
+    REQUIRE(user_mask_v[3] == 0);
+    REQUIRE(user_mask_v[4] == 1);
+    REQUIRE(user_mask_v[5] == 1);
+    REQUIRE(user_mask_v[6] == 0);
+    REQUIRE(user_mask_v[1030 * 700 + 300] == 0);
+
+    REQUIRE(user_mask_v[(1030+8)*514] == 0);
+}
+
+TEST_CASE("PixelMask_CalculateNexusMask_UserMaskConv","[PixelMask]") {
+    DiffractionExperiment experiment(DetectorGeometry(4, 1, 8, 36, false));
+    experiment.MaskModuleEdges(false).MaskChipEdges(false);
+
+    PixelMask mask(experiment);
+
+    std::vector<uint32_t> v(experiment.GetPixelsNum(), 0);
+    v[1030 * 700 + 300] = 1;
+
+    REQUIRE_NOTHROW(mask.LoadUserMask(experiment, v));
+
+    auto mask_v = mask.GetMask(experiment);
+
+    REQUIRE(mask_v.size() == experiment.GetPixelsNum() );
+    REQUIRE(mask_v[1030 * 700 + 300] == (1 << PixelMask::UserMaskedPixelBit));
+    REQUIRE(mask_v[(1030+8)*514] == (1 << PixelMask::ModuleGapPixelBit));
+
+    auto user_mask_v = mask.GetUserMask(experiment);
+
+    REQUIRE(user_mask_v.size() == experiment.GetPixelsNum() );
+    REQUIRE(user_mask_v[1030 * 700 + 300] == 1);
+
+    REQUIRE(user_mask_v[(1030+8)*514] == 0);
+}
+
+
 TEST_CASE("PixelMask_MaskDetectorGaps","[PixelMask]") {
     DiffractionExperiment experiment(DetectorGeometry(8, 2, 8, 36, true));
 

tests/StreamWriterTest.cpp

@@ -16,6 +16,8 @@ TEST_CASE("StreamWriterTest_ZMQ","[JFJochWriter]") {
     x.FilePrefix("subdir/JFJochWriterTest").NumTriggers(1).ImagesPerTrigger(5)
             .UseInternalPacketGenerator(true).Mode(DetectorMode::Raw).PedestalG0Frames(0);
 
+    PixelMask pixel_mask(x);
+
     JFModuleGainCalibration gain;
     AcquisitionDeviceGroup aq_devices;
     for (int i = 0; i < x.GetDataStreamsNum(); i++)
@@ -32,7 +34,7 @@ TEST_CASE("StreamWriterTest_ZMQ","[JFJochWriter]") {
     REQUIRE(pusher_addr.size() == 1);
     REQUIRE_NOTHROW(writer = std::make_unique<StreamWriter>(logger, pusher_addr[0]));
     CHECK (writer->GetStatistics().state == StreamWriterState::Idle);
-    REQUIRE_NOTHROW(fpga_receiver_service.Start(x, nullptr));
+    REQUIRE_NOTHROW(fpga_receiver_service.Start(x, pixel_mask, nullptr));
 
     REQUIRE_NOTHROW(writer->Run());
 

tests/TIFFTest.cpp

@@ -4,7 +4,7 @@
 
 #include <fstream>
 
-#include "../preview/WriteTIFF.h"
+#include "../preview/JFJochTIFF.h"
 #include "../preview/PreviewImage.h"
 #include "../writer/HDF5Objects.h"
 #include "../common/RawToConvertedGeometry.h"
@@ -14,6 +14,25 @@ TEST_CASE("TIFFTest","[TIFF]") {
     REQUIRE_NOTHROW(WriteTIFFToString(values.data(), 1024, 512, 2));
 }
 
+#include <iostream>
+
+TEST_CASE("TIFFTest_Write_Read","[TIFF]") {
+    std::vector<uint32_t> values(512*1024), values_out;
+    for (int i = 0; i < values.size(); i++) {
+        values[i] = (i * 17 + 2);
+    }
+
+    std::string s;
+    REQUIRE_NOTHROW(s = WriteTIFFToString(values.data(), 1024, 512, 4));
+    uint32_t lines, cols;
+
+    REQUIRE_NOTHROW(values_out = ReadTIFFFromString32(s, cols, lines));
+    REQUIRE(lines == 512);
+    REQUIRE(cols == 1024);
+    REQUIRE(values.size() == values_out.size());
+    REQUIRE(memcmp(values.data(), values_out.data(), cols * lines * sizeof(uint32_t)) == 0);
+}
+
 TEST_CASE("TIFFTest_File","[TIFF]") {
     std::vector<uint16_t> values(512*1024);
 
@@ -33,6 +52,8 @@ TEST_CASE("TIFFTest_File_signed","[TIFF]") {
 }
 
 TEST_CASE("PreviewImage_GenerateTIFF","[TIFF]") {
+    RegisterHDF5Filter();
+
     DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
             .FilePrefix("lyso_test_min_pix_2").ConversionOnFPGA(false)
@@ -57,8 +78,11 @@ TEST_CASE("PreviewImage_GenerateTIFF","[TIFF]") {
     ConvertedToRawGeometry(experiment, image_raw_geom.data(), image_conv.data());
     RawToConvertedGeometry(experiment, image_conv_2.data(), image_raw_geom.data());
 
+    PixelMask mask(experiment);
+
     std::vector<SpotToSave> spots;
-    PreviewImage image(experiment);
+    PreviewImage image;
+    image.Configure(experiment, mask);
     image.UpdateImage(image_conv_2.data(), spots);
 
     std::string s;
@@ -69,6 +93,8 @@ TEST_CASE("PreviewImage_GenerateTIFF","[TIFF]") {
 
 
 TEST_CASE("PreviewImage_GenerateTIFFDioptas","[TIFF]") {
+    RegisterHDF5Filter();
+
     DiffractionExperiment experiment(DetectorGeometry(8,2,8,36));
     experiment.ImagesPerTrigger(5).NumTriggers(1).UseInternalPacketGenerator(true)
             .FilePrefix("lyso_test_min_pix_2").ConversionOnFPGA(false)
@@ -93,8 +119,11 @@ TEST_CASE("PreviewImage_GenerateTIFFDioptas","[TIFF]") {
     ConvertedToRawGeometry(experiment, image_raw_geom.data(), image_conv.data());
     RawToConvertedGeometry(experiment, image_conv_2.data(), image_raw_geom.data());
 
+    PixelMask mask(experiment);
+
     std::vector<SpotToSave> spots;
-    PreviewImage image(experiment);
+    PreviewImage image;
+    image.Configure(experiment, mask);
     image.UpdateImage(image_conv_2.data(), spots);
 
     std::string s;

tools/jfjoch_spot_finding_test.cpp

@@ -13,10 +13,12 @@
 #include "../image_analysis/MXAnalyzer.h"
 #include "../preview/PreviewImage.h"
 #include "../receiver/LossyFilter.h"
+#include "../preview/JFJochTIFF.h"
 
 Logger logger("jfjoch_spot_finding_test");
 
 bool write_jpeg = false;
+bool write_debug = false;
 
 void print_usage() {
     logger.Info("Usage ./jfjoch_spot_finding_test {options} <name of master dataset> <name of data dataset>");
@@ -34,6 +36,8 @@ void print_usage() {
     logger.Info("-I            enable indexing");
     logger.Info("-t<float>     indexing tolerance (0.0-1.0)");
     logger.Info("-l<float>     lossy filter probability (0.0-1.0)");
+    logger.Info("-r{<int>}     filter powder rings (min spots)");
+    logger.Info("-g            write debug images");
     logger.Info("");
 }
 
@@ -76,12 +80,14 @@ int parse_options(DiffractionExperiment& experiment,
             {"indexing_tolerance",    required_argument, 0, 't'},
             {"nimages",    required_argument, 0, 'n'},
             {"lossy",    required_argument, 0, 'l'},
+            {"filter_rings",    optional_argument, 0, 'r'},
+            {"debug",    no_argument, 0, 'g'},
             {0, 0, 0, 0}
     };
 
     int option_index = 0;
     int opt;
-    while ((opt = getopt_long(argc, argv, "c:s:o:p:d:D:j?hS:Ii:t:l:",long_options, &option_index)) != -1 ) {
+    while ((opt = getopt_long(argc, argv, "c:s:o:p:d:D:j?hS:Ii:t:l:r::g",long_options, &option_index)) != -1 ) {
         switch (opt) {
             case 'j':
                 write_jpeg = true;
@@ -119,7 +125,14 @@ int parse_options(DiffractionExperiment& experiment,
             case 'l':
                 experiment.DataReductionFactorSerialMX(atof(optarg));
                 break;
-            case '?':
+            case 'r':
+                settings.filter_spots_powder_ring = true;
+                if (optarg != nullptr)
+                    settings.min_spot_count_powder_ring = atol(optarg);
+                break;
+            case 'g':
+                write_debug = true;
+                break;
             case 'h':
                 print_usage();
                 exit(EXIT_SUCCESS);
@@ -209,7 +222,11 @@ int main(int argc, char **argv) {
 
     MXAnalyzer analyzer(x);
 
-    PreviewImage preview(x);
+    PixelMask mask(x);
+
+    PreviewImage preview;
+    preview.Configure(x, mask);
+
     uint64_t indexed_images = 0;
 
     LossyFilter filter(x);
@@ -263,6 +280,33 @@ int main(int argc, char **argv) {
                         static_cast<float>(indexed_images) / static_cast<float>(i+1) * 100.0f);
     }
     fileset.reset();
+
+    if (write_debug) {
+        std::vector<float> convg(x.GetPixelsNum());
+        std::vector<int32_t> convg_u32(x.GetPixelsNum());
+
+        if (!analyzer.GetCPUMean().empty()) {
+            RawToConvertedGeometry(x, convg.data(), analyzer.GetCPUMean().data());
+            for (int i = 0; i < convg.size(); i++)
+                convg_u32[i] = std::lround(convg[i] * 10.0f);
+            WriteTIFFToFile("spot_finding_mean.tiff", convg_u32.data(), x.GetXPixelsNum(), x.GetYPixelsNum(), 4, true);
+        }
+
+        if (!analyzer.GetCPUStdDev().empty()) {
+            RawToConvertedGeometry(x, convg.data(), analyzer.GetCPUStdDev().data());
+            for (int i = 0; i < convg.size(); i++)
+                convg_u32[i] = std::lround(convg[i] * 10.0f);
+            WriteTIFFToFile("spot_finding_stddev.tiff", convg_u32.data(), x.GetXPixelsNum(), x.GetYPixelsNum(), 4, true);
+        }
+
+        if (!analyzer.GetCPUStrongPixel().empty()) {
+            RawToConvertedGeometry(x, convg_u32.data(), analyzer.GetCPUStrongPixel().data());
+            WriteTIFFToFile("spot_finding_strong_pixel.tiff", convg_u32.data(), x.GetXPixelsNum(), x.GetYPixelsNum(), 4, true);
+        }
+
+        WriteTIFFToFile("spot_finding_original_image.tiff", original_image.data(), x.GetXPixelsNum(), x.GetYPixelsNum(), 2, true);
+    }
+
     if (settings.indexing)
         logger.Info("Indexing rate: {:0.1f}%", static_cast<float>(indexed_images) / static_cast<float>(nimages) * 100.0f);
 }

writer/CMakeLists.txt

@@ -23,9 +23,6 @@ ADD_LIBRARY(JFJochWriter STATIC
 
 TARGET_LINK_LIBRARIES(JFJochWriter JFJochZMQ JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize)
 
-ADD_EXECUTABLE(HDF5Sum HDF5Sum.cpp)
-TARGET_LINK_LIBRARIES(HDF5Sum JFJochWriter)
-
 AUX_SOURCE_DIRECTORY(gen/model MODEL_SOURCES)
 ADD_LIBRARY(WriterAPI STATIC ${MODEL_SOURCES} gen/api/DefaultApi.cpp gen/api/DefaultApi.h JFJochWriterHttp.h JFJochWriterHttp.cpp)
 

writer/HDF5DataFile.cpp

@@ -11,24 +11,24 @@
 #include "HDF5DataFilePluginXFEL.h"
 #include "HDF5DataFilePluginJUNGFRAU.h"
 #include "../include/spdlog/fmt/fmt.h"
+#include "HDF5NXmx.h"
+
+HDF5DataFile::HDF5DataFile(const StartMessage &msg, uint64_t in_file_number) {
+    file_number = in_file_number;
 
-HDF5DataFile::HDF5DataFile(const std::string &in_filename,
-                           const std::vector<float>& in_rad_int_bin_to_q,
-                           int32_t in_image_low,
-                           size_t in_max_spots) {
     xpixel = 0;
     ypixel = 0;
     max_image_number = 0;
     nimages = 0;
-    filename = in_filename;
-    image_low = in_image_low;
+    filename = HDF5Metadata::DataFileName(msg.file_prefix, file_number);
+    image_low = file_number * msg.images_per_file;
 
     tmp_filename = fmt::format("{}.tmp{:8x}", filename, std::chrono::system_clock::now().time_since_epoch().count());
 
     plugins.emplace_back(std::make_unique<HDF5DataFilePluginJUNGFRAU>());
-    plugins.emplace_back(std::make_unique<HDF5DataFilePluginAzInt>(in_rad_int_bin_to_q));
+    plugins.emplace_back(std::make_unique<HDF5DataFilePluginAzInt>(msg.az_int_bin_to_q));
     plugins.emplace_back(std::make_unique<HDF5DataFilePluginXFEL>());
-    plugins.emplace_back(std::make_unique<HDF5DataFilePluginMX>(in_max_spots));
+    plugins.emplace_back(std::make_unique<HDF5DataFilePluginMX>(msg.max_spot_count));
 }
 
 std::optional<HDF5DataFileStatistics> HDF5DataFile::Close() {
@@ -62,6 +62,7 @@ std::optional<HDF5DataFileStatistics> HDF5DataFile::Close() {
     ret.max_image_number = max_image_number;
     ret.total_images = nimages;
     ret.filename = filename;
+    ret.file_number = file_number + 1;
     return ret;
 }
 

writer/HDF5DataFile.h

@@ -15,6 +15,7 @@
 
 struct HDF5DataFileStatistics {
     std::string filename;
+    uint64_t file_number; // counting from 1!
     size_t max_image_number;
     uint64_t total_images;
 };
@@ -43,10 +44,10 @@ class HDF5DataFile {
 
     bool closed = false;
 
+    int64_t file_number;
     void CreateFile(const DataMessage& msg);
 public:
-    HDF5DataFile(const std::string& name, const std::vector<float>& rad_int_bin_to_q,
-                 int32_t image_low, size_t max_spots = 0);
+    HDF5DataFile(const StartMessage &msg, uint64_t file_number);
     ~HDF5DataFile();
     std::optional<HDF5DataFileStatistics> Close();
     void Write(const DataMessage& msg, uint64_t image_number);

writer/HDF5DataFilePluginMX.cpp

@@ -16,6 +16,7 @@ void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg)
     strong_pixel_count.reserve(RESERVE_IMAGES);
     indexed.reserve(RESERVE_IMAGES);
     indexed_lattice.reserve(9 * RESERVE_IMAGES);
+    spot_count_rings.reserve(RESERVE_IMAGES);
 }
 
 void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number) {
@@ -33,6 +34,9 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
         strong_pixel_count.resize(max_image_number + 1);
         indexed.resize(max_image_number + 1);
         indexed_lattice.resize((max_image_number + 1) * 9);
+
+        if (msg.spot_count_in_rings)
+            spot_count_rings.resize(max_image_number + 1);
     }
 
     uint32_t spot_cnt = std::min(msg.spots.size(), max_spots);
@@ -46,6 +50,9 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
     npeaks[image_number] = spot_cnt;
     strong_pixel_count[image_number] = msg.strong_pixel_count;
     indexed[image_number] = msg.indexing_result;
+    if (msg.spot_count_in_rings)
+        spot_count_rings[image_number] = msg.spot_count_in_rings.value();
+
     if (msg.indexing_lattice.size() == 9) {
         for (int i = 0; i < 9; i++)
             indexed_lattice[image_number * 9 + i] = msg.indexing_lattice[i];
@@ -64,6 +71,9 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
         data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count);
     }
 
+    if (!spot_count_rings.empty())
+        data_file.SaveVector("/entry/MX/nPeaksRingFiltered", spot_count_rings);
+
     if (!indexed.empty())
         data_file.SaveVector("/entry/MX/imageIndexed", indexed);
     if (!indexed_lattice.empty())

writer/HDF5DataFilePluginMX.h

@@ -15,7 +15,7 @@ class HDF5DataFilePluginMX : public HDF5DataFilePlugin {
 
     std::vector<uint32_t> npeaks;
     std::vector<uint32_t> strong_pixel_count;
-
+    std::vector<uint32_t> spot_count_rings;
     // indexing
     std::vector<uint8_t> indexed;
     std::vector<float> indexed_lattice;

writer/HDF5NXmx.cpp

@@ -103,6 +103,8 @@ void NXmx::Detector(const StartMessage &start) {
     HDF5Group det_specific(group, "detectorSpecific");
     det_specific.NXClass("NXcollection");
 
+    if (!start.jfjoch_release.empty())
+        SaveScalar(det_specific, "jfjoch_release", start.jfjoch_release);
     SaveScalar(det_specific, "ntrigger", 1);
 
     SaveScalar(det_specific, "x_pixels_in_detector", static_cast<uint32_t>(start.image_size_x));
@@ -171,6 +173,9 @@ void NXmx::Facility(const StartMessage &start) {
     SaveScalar(*hdf5_file, "/entry/source/name", start.source_name)
             ->Attr("short_name", start.source_name_short);
 
+    if (!start.source_type.empty())
+        SaveScalar(*hdf5_file, "/entry/source/type", start.source_type);
+
     HDF5Group(*hdf5_file, "/entry/instrument").NXClass("NXinstrument");
     SaveScalar(*hdf5_file, "/entry/instrument/name", start.instrument_name)
             ->Attr("short_name", start.instrument_name_short);
@@ -223,17 +228,17 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
         group.SaveVector("unit_cell", v);
     }
 
-    if ((end.max_image_number > 0) && (start.omega.increment != 0.0f)) {
-        group.SaveScalar("depends_on", "/entry/sample/transformations/omega");
+    if ((end.max_image_number > 0) && start.goniometer) {
+        group.SaveScalar("depends_on", "/entry/sample/transformations/" + start.goniometer->name);
         HDF5Group transformations(group, "transformations");
         transformations.NXClass("NXtransformations");
 
         std::vector<double> angle_container(end.max_image_number);
         for (int32_t i = 0; i < end.max_image_number; i++)
-            angle_container[i] = start.omega.start + i * start.omega.increment;
-        std::vector<double> axis = {start.omega.axis[0], start.omega.axis[1], start.omega.axis[2]};
+            angle_container[i] = start.goniometer->start + i * start.goniometer->increment;
+        std::vector<double> axis = {start.rotation_axis[0], start.rotation_axis[1], start.rotation_axis[2]};
 
-        SaveVector(transformations, "omega", angle_container)->
+        SaveVector(transformations, start.goniometer->name, angle_container)->
                 Transformation("deg", ".", "", "", "rotation", axis, {0,0,0}, "");
     } else
         group.SaveScalar("depends_on", ".");

writer/HDF5Sum.cpp

@@ -1,91 +0,0 @@
-// Copyright (2019-2023) Paul Scherrer Institute
-
-#include <iostream>
-
-#include "../compression/JFJochCompressor.h"
-#include "HDF5Objects.h"
-#include "HDF5DataFile.h"
-
-int main(int argc, char **argv) {
-    RegisterHDF5Filter();
-
-    if (argc != 4) {
-        std::cerr << "Usage: ./HDF5Sum <HDF5 input file> <HDF5 output file> <summation factor>" << std::endl;
-        exit(EXIT_FAILURE);
-    }
-    char *pEnd = nullptr;
-    size_t summation_factor = std::strtol(argv[3], &pEnd, 10);
-
-    if (summation_factor <= 1) {
-        std::cerr << "Summation factor must be at least 2" << std::endl;
-        exit(EXIT_FAILURE);
-    }
-
-    try {
-        HDF5ReadOnlyFile data_in(argv[1]);
-        HDF5DataSet dataset_in(data_in, "/entry/data/data");
-        HDF5DataSpace file_space_in(dataset_in);
-
-        if (file_space_in.GetNumOfDimensions() != 3) {
-            std::cerr << "Doesn't look like JF data file" << std::endl;
-            exit(EXIT_FAILURE);
-        }
-
-        hsize_t nimages_in = file_space_in.GetDimensions()[0];
-        hsize_t height = file_space_in.GetDimensions()[1];
-        hsize_t width = file_space_in.GetDimensions()[2];
-
-        if (nimages_in < summation_factor) {
-            std::cerr << "Summation factor doesn't make sense (must be less or equal than images in the input file)" << std::endl;
-            exit(EXIT_FAILURE);
-        }
-        hsize_t nimages_out = nimages_in / summation_factor;
-
-        std::cout << "Summing dataset of " << nimages_in << " to " << nimages_out << " images" << std::endl;
-
-        HDF5DataFile dataFile(std::string(argv[2]), std::vector<float>(), nimages_out, 1);
-
-        std::vector<hsize_t> dim = {summation_factor, height, width};
-
-        constexpr const int32_t underload_sum = INT32_MIN;
-        constexpr const int32_t overload_sum = INT32_MAX;
-
-        JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
-        std::vector<uint8_t> output(bshuf_compress_lz4_bound(height*width, 4, 4096) + 12);
-
-        for (int i = 0; i < nimages_out; i++) {
-            std::vector<hsize_t> start = {summation_factor * i,0,0};
-            std::vector<int16_t> image_in(summation_factor * height*width);
-            dataset_in.ReadVector(image_in, start, dim);
-
-            std::vector<int32_t> image_out(height*width, 0);
-            for (int j = 0; j < summation_factor; j++) {
-                for (int pxl = 0; pxl < width * height; pxl++) {
-                    int16_t tmp = image_in[j * width * height + pxl];
-                    if ((tmp < INT16_MIN + 4) || (image_out[pxl] == underload_sum))
-                        image_out[pxl] = underload_sum;
-                    else if ((tmp > INT16_MAX - 4) || (image_out[pxl] == overload_sum))
-                        image_out[pxl] = overload_sum;
-                    else image_out[pxl] += tmp;
-                }
-            }
-
-            auto image_size = compressor.Compress(output.data(), image_out);
-            DataMessage message;
-            message.image.data = output.data();
-            message.image.size = image_size;
-            message.image.pixel_depth_bytes = 4;
-            message.image.pixel_is_signed = true;
-            message.image.xpixel = width;
-            message.image.ypixel = height;
-            message.image.algorithm = CompressionAlgorithm::BSHUF_LZ4;
-            message.number = i;
-
-            dataFile.Write(message, i);
-        }
-    } catch (const JFJochException &e) {
-        std::cerr << "Error: " << e.what() << std::endl;
-        exit(EXIT_FAILURE);
-    }
-    exit(EXIT_SUCCESS);
-}