jfjoch_writer: Save grid scan geometry explicitly (not in NXmx :(, as NXmx is too confusing)

reader/JFJochHDF5Reader.cpp

@@ -5,6 +5,7 @@
 #include "spdlog/fmt/fmt.h"
 #include "../image_analysis/bragg_integration/CalcISigma.h"
 #include "../image_analysis/spot_finding/SpotUtils.h"
+#include "../common/GridScanSettings.h"
 
 std::vector<hsize_t> GetDimension(HDF5Object& object, const std::string& path) {
     const auto dim = object.GetDimension(path);
@@ -234,8 +235,18 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
         dataset->experiment.ImportInstrumentMetadata(metadata);
 
         if (master_file->Exists("/entry/sample/transformations")) {
-            auto omega = ReadAxis(master_file.get(), "omega");
-            dataset->experiment.Goniometer(omega);
+            if (master_file->Exists("/entry/sample/transformations/omega")) {
+                auto omega = ReadAxis(master_file.get(), "omega");
+                dataset->experiment.Goniometer(omega);
+            } else if (master_file->Exists("/entry/sample/grid_scan")) {
+                dataset->experiment.GridScan(GridScanSettings(
+                    master_file->GetInt("/entry/sample/grid_scan/n_fast"),
+                    master_file->GetFloat("/entry/sample/grid_scan/step_x") * 1e6f,
+                    master_file->GetFloat("/entry/sample/grid_scan/step_y") * 1e6f,
+                    master_file->GetOptBool("/entry/sample/grid_scan/snake_scan").value_or(false),
+                    master_file->GetOptBool("/entry/sample/grid_scan/vertical_scan").value_or(false)
+                    ));
+            }
         }
 
         auto tmp = master_file->ReadOptVector<float>("/entry/sample/unit_cell");

tests/JFJochReaderTest.cpp

@@ -271,6 +271,7 @@ TEST_CASE("JFJochReader_Goniometer", "[HDF5][Full]") {
         reader.ReadFile("test17_master.h5");
         auto dataset = reader.GetDataset();
 
+        REQUIRE(!dataset->experiment.GetGridScan().has_value());
         REQUIRE(dataset->experiment.GetGoniometer().has_value());
 
         CHECK(dataset->experiment.GetGoniometer()->GetStart_deg() == 95.0);
@@ -285,6 +286,58 @@ TEST_CASE("JFJochReader_Goniometer", "[HDF5][Full]") {
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
+TEST_CASE("JFJochReader_GridScan", "[HDF5][Full]") {
+    DiffractionExperiment x(DetJF(1));
+
+    x.FilePrefix("test_reader_grid_scan").ImagesPerTrigger(950).OverwriteExistingFiles(true);
+    x.BeamX_pxl(100).BeamY_pxl(200).DetectorDistance_mm(150)
+            .IncidentEnergy_keV(WVL_1A_IN_KEV).PixelSigned(false).BitDepthImage(16)
+            .FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
+    x.GridScan(GridScanSettings(25, -7.5, 8.0, true, true));
+
+    RegisterHDF5Filter();
+
+    std::vector<uint16_t> image(x.GetPixelsNum(), 0);
+    {
+        StartMessage start_message;
+        x.FillMessage(start_message);
+
+        FileWriter file_set(start_message);
+
+        DataMessage message{};
+        for (int i = 0; i < 5; i++) {
+            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+            message.number = 0;
+
+            REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+        }
+
+        EndMessage end_message;
+        end_message.max_image_number = 4;
+        file_set.WriteHDF5(end_message);
+
+        file_set.Finalize();
+    }
+    {
+        JFJochHDF5Reader reader;
+        reader.ReadFile("test_reader_grid_scan_master.h5");
+        auto dataset = reader.GetDataset();
+
+
+        REQUIRE(!dataset->experiment.GetGoniometer().has_value());
+        REQUIRE(dataset->experiment.GetGridScan().has_value());
+
+        CHECK(dataset->experiment.GetGridScan()->IsSnakeScan());
+        CHECK(dataset->experiment.GetGridScan()->IsVerticalScan());
+        CHECK(dataset->experiment.GetGridScan()->GetNFast() == 25);
+        CHECK(dataset->experiment.GetGridScan()->GetGridStepX_um() == Catch::Approx(-7.5));
+        CHECK(dataset->experiment.GetGridScan()->GetGridStepY_um() == Catch::Approx(8.0));
+    }
+    remove("test_reader_grid_scan_master.h5");
+
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
 TEST_CASE("JFJochReader_DataI16", "[HDF5][Full]") {
     DiffractionExperiment x(DetJF(1));
 

writer/HDF5NXmx.cpp

@@ -586,6 +586,15 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
             depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_z";
         }
     } else if (start.grid_scan.has_value()) {
+        HDF5Group grid_scan_group(group, "grid_scan");
+        grid_scan_group.NXClass("NXcollection");
+
+        SaveScalar(grid_scan_group, "snake_scan", start.grid_scan->IsSnakeScan());
+        SaveScalar(grid_scan_group, "vertical_scan", start.grid_scan->IsVerticalScan());
+        SaveScalar(grid_scan_group, "n_fast", start.grid_scan->GetNFast());
+        SaveScalar(grid_scan_group, "step_x", start.grid_scan->GetGridStepX_um() * 1e-6)->Units("m");
+        SaveScalar(grid_scan_group, "step_y", start.grid_scan->GetGridStepY_um() * 1e-6)->Units("m");
+
         HDF5Group transformations(group, "transformations");
         transformations.NXClass("NXtransformations");
         hdf5_file->HardLink("/entry/sample/transformations","/entry/sample/goniometer");