v1.0.0-rc.97

This is an UNSTABLE release and not recommended for production use (please use rc.96 instead).

* jfjoch_broker: For DECTRIS detectors add dark data collection during initialization for bad pixel mask
* jfjoch_broker: Refactor of calibration logic for more clear code (likely to introduce problems)
* jfjoch_viewer: Add option to handle user pixel mask (experimental)
* jfjoch_viewer: More options for ROI
* jfjoch_viewer: Add window to display calibration

Reviewed-on: #2
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>

tests/JFJochReaderTest.cpp

@@ -69,12 +69,82 @@ TEST_CASE("JFJochReader_MasterFile", "[HDF5][Full]") {
         REQUIRE(dataset->experiment.GetUnitCell().has_value());
         CHECK(dataset->experiment.GetUnitCell()->b == 20.0);
         CHECK(dataset->experiment.GetUnitCell()->beta == 101.0);
+        CHECK(dataset->calibration_data.empty());
     }
     remove("test08_master.h5");
 
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
+TEST_CASE("JFJochReader_MasterFile_Calibration", "[HDF5][Full]") {
+    DiffractionExperiment x(DetJF(1));
+
+    x.FilePrefix("test_reader_calibration").ImagesPerTrigger(1).OverwriteExistingFiles(true);
+    RegisterHDF5Filter();
+
+    std::vector<uint16_t> calib_1(200*300, 10);
+    std::vector<int32_t> calib_2(100*400, 55);
+    std::vector<float> calib_f(100*400, 1234.56f);
+    {
+        StartMessage start_message;
+        x.FillMessage(start_message);
+
+        CompressedImage calibration_01(calib_1, 200, 300);
+        CompressedImage calibration_02(calib_2, 100, 400);
+        CompressedImage calibration_f(calib_f, 100, 400);
+        calibration_01.Channel("c1");
+        calibration_02.Channel("c2");
+        calibration_f.Channel("cf");
+
+        EndMessage end_message;
+        end_message.max_image_number = 0;
+        std::unique_ptr<NXmx> master = std::make_unique<NXmx>(start_message);
+        master->WriteCalibration(calibration_01);
+        master->WriteCalibration(calibration_02);
+        master->WriteCalibration(calibration_f);
+        master->Finalize(end_message);
+        master.reset();
+    }
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("test_reader_calibration_master.h5"));
+        auto dataset = reader.GetDataset();
+        REQUIRE(dataset->calibration_data.size() == 3);
+        CHECK(dataset->calibration_data[0] == "c1");
+        CHECK(dataset->calibration_data[1] == "c2");
+        CHECK(dataset->calibration_data[2] == "cf");
+
+        std::vector<uint8_t> buffer;
+        std::vector<uint8_t> buff_2;
+        REQUIRE_THROWS(reader.ReadCalibration(buffer, "c3"));
+        CompressedImage test;
+        REQUIRE_NOTHROW(test = reader.ReadCalibration(buffer, "c1"));
+        CHECK(test.GetByteDepth() == 2);
+        CHECK(test.GetHeight() == 200);
+        CHECK(test.GetWidth() == 300);
+        CHECK(test.GetMode() == CompressedImageMode::Uint16);
+        CHECK(reinterpret_cast<const uint16_t *>(test.GetUncompressedPtr(buff_2))[76] == 10);
+
+        REQUIRE_NOTHROW(test = reader.ReadCalibration(buffer, "c2"));
+        CHECK(test.GetByteDepth() == 4);
+        CHECK(test.GetHeight() == 100);
+        CHECK(test.GetWidth() == 400);
+        CHECK(test.GetMode() == CompressedImageMode::Int32);
+        CHECK(reinterpret_cast<const int32_t *>(test.GetUncompressedPtr(buff_2))[76] == 55);
+
+        REQUIRE_NOTHROW(test = reader.ReadCalibration(buffer, "cf"));
+        CHECK(test.GetByteDepth() == 4);
+        CHECK(test.GetHeight() == 100);
+        CHECK(test.GetWidth() == 400);
+        CHECK(test.GetMode() == CompressedImageMode::Float32);
+        CHECK(reinterpret_cast<const float *>(test.GetUncompressedPtr(buff_2))[76] == Catch::Approx(1234.56f));
+    }
+    remove("test_reader_calibration_master.h5");
+
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+
 TEST_CASE("JFJochReader_DefaultExperiment", "[HDF5][Full]") {
     DiffractionExperiment x(DetJF(1));