v1.0.0-rc.153 (#63)

This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
* jfjoch_broker: Add ROI calculation in non-FPGA workflow
* jfjoch_broker: Fixes to TCP image pusher
* jfjoch_broker: Remove NUMA bindings
* jfjoch_broker: Improvements to indexing
* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results

Reviewed-on: #63

common/PixelMask.cpp

@@ -218,6 +218,55 @@ void PixelMask::LoadUserMask(const DiffractionExperiment& experiment, const std:
                               "Size of input user mask invalid");
 }
 
+void PixelMask::LoadUserMask(const DiffractionExperiment& experiment, const CompressedImage& image) {
+    const size_t width = image.GetWidth();
+    const size_t height = image.GetHeight();
+
+    // The image has to match one of the two layouts handled by the vector
+    // overload below: converted geometry, or raw stacked modules.
+    const bool converted = (width == static_cast<size_t>(experiment.GetXPixelsNumConv()))
+                           && (height == static_cast<size_t>(experiment.GetYPixelsNumConv()));
+    const bool raw = (width == static_cast<size_t>(RAW_MODULE_COLS))
+                     && (height == static_cast<size_t>(RAW_MODULE_LINES * experiment.GetModulesNum()));
+    if (!converted && !raw)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                              "User mask image size doesn't match the detector");
+
+    std::vector<uint8_t> buffer;
+    const uint8_t *bytes = image.GetUncompressedPtr(buffer);
+
+    // A pixel is masked when its value is non-zero. Read each pixel as an
+    // unsigned integer of the matching width - the sign is irrelevant when
+    // comparing against zero.
+    std::vector<uint32_t> mask(width * height);
+    auto binarize = [&](auto sample) {
+        using sample_t = decltype(sample);
+        const auto *typed = reinterpret_cast<const sample_t *>(bytes);
+        for (size_t i = 0; i < mask.size(); i++)
+            mask[i] = (typed[i] != 0) ? 1 : 0;
+    };
+
+    switch (image.GetMode()) {
+        case CompressedImageMode::Uint8:
+        case CompressedImageMode::Int8:
+            binarize(uint8_t{});
+            break;
+        case CompressedImageMode::Uint16:
+        case CompressedImageMode::Int16:
+            binarize(uint16_t{});
+            break;
+        case CompressedImageMode::Uint32:
+        case CompressedImageMode::Int32:
+            binarize(uint32_t{});
+            break;
+        default:
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+                                  "User mask must be an 8-, 16- or 32-bit integer image");
+    }
+
+    LoadUserMask(experiment, mask);
+}
+
 void PixelMask::LoadDECTRISBadPixelMask(const std::vector<uint32_t> &input_mask)  {
     if (input_mask.size() != mask.size())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,