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>

image_analysis/CMakeLists.txt

@@ -4,7 +4,9 @@ ADD_LIBRARY(JFJochImageAnalysis STATIC
         MXAnalysisAfterFPGA.h
         MXAnalysisAfterFPGA.cpp
         SpotAnalyze.cpp
-        SpotAnalyze.h)
+        SpotAnalyze.h
+        dark_mask_analysis/DarkMaskAnalysis.cpp
+        dark_mask_analysis/DarkMaskAnalysis.h)
 
 FIND_PACKAGE(Eigen3 3.4 REQUIRED NO_MODULE)  # provides Eigen3::Eigen
 

image_analysis/dark_mask_analysis/DarkMaskAnalysis.cpp

@@ -0,0 +1,58 @@
+// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "DarkMaskAnalysis.h"
+#include "../../common/JFJochException.h"
+
+DarkMaskAnalysis::DarkMaskAnalysis(const DarkMaskSettings &settings, size_t det_size)
+    : max_allowed_value(settings.GetMaxCounts()),
+      max_frames_with_signal(settings.GetMaxFramesWithCounts()),
+      mask(det_size, 0) {}
+
+template<class T>
+void DarkMaskAnalysis::check(const T *ptr) {
+    std::unique_lock ul(m);
+    for (int i = 0; i < mask.size(); i++) {
+        auto v64 = static_cast<int64_t>(ptr[i]);
+        if (v64 > max_allowed_value)
+            mask[i]++;
+    }
+}
+
+void DarkMaskAnalysis::AnalyzeImage(const DataMessage &data, std::vector<uint8_t> buffer) {
+    if (data.image.GetWidth() * data.image.GetHeight() != mask.size())
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Invalid size of input image");
+
+    auto ptr = data.image.GetUncompressedPtr(buffer);
+
+    switch (data.image.GetMode()) {
+        case CompressedImageMode::Int8:
+            check(reinterpret_cast<const int8_t *>(ptr));
+            break;
+        case CompressedImageMode::Uint8:
+            check(reinterpret_cast<const uint8_t *>(ptr));
+            break;
+        case CompressedImageMode::Int16:
+            check(reinterpret_cast<const int16_t *>(ptr));
+            break;
+        case CompressedImageMode::Uint16:
+            check(reinterpret_cast<const uint16_t *>(ptr));
+            break;
+        case CompressedImageMode::Int32:
+            check(reinterpret_cast<const int32_t *>(ptr));
+            break;
+        case CompressedImageMode::Uint32:
+            check(reinterpret_cast<const uint32_t *>(ptr));
+            break;
+        default:
+            throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "RGB/float image mode not supported");
+    }
+}
+
+std::vector<uint32_t> DarkMaskAnalysis::GetMask() const {
+    std::unique_lock ul(m);
+    std::vector<uint32_t> tmp(mask.size(), 0);
+    for (int i = 0; i < mask.size(); i++)
+        tmp[i] = (mask[i] > max_frames_with_signal) ? 1 : 0;
+    return tmp;
+}

image_analysis/dark_mask_analysis/DarkMaskAnalysis.h

@@ -0,0 +1,30 @@
+// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#ifndef JFJOCH_DARKMASKANALYSIS_H
+#define JFJOCH_DARKMASKANALYSIS_H
+
+#include <cstdint>
+#include <vector>
+#include <mutex>
+#include "../common/CompressedImage.h"
+#include "../common/PixelMask.h"
+#include "../common/DiffractionExperiment.h"
+
+class DarkMaskAnalysis {
+    mutable std::mutex m;
+
+    const int64_t max_allowed_value;
+    const int64_t max_frames_with_signal;
+
+    std::vector<uint32_t> mask;
+
+    template <class T> void check(const T *ptr);
+public:
+    DarkMaskAnalysis(const DarkMaskSettings& settings, size_t det_size);
+    void AnalyzeImage(const DataMessage &msg, std::vector<uint8_t> buffer);
+    std::vector<uint32_t> GetMask() const;
+};
+
+
+#endif //JFJOCH_MASKDARKANALYSIS_H