v1.0.0-rc.96 (#1)

This is an UNSTABLE release.

* Fixes in CI pipeline
* jfjoch_broker: Remove PNG preview, no dependency on libpng
* jfjoch_writer: Fix UTC timestamp being generated wrong (mix between milli- and microseconds)
* jfjoch_viewer: Show data collection time in dataset tooltip
* jfjoch_viewer: Allow to choose the calibrant (presets for LaB6 and silver behenate)
* jfjoch_viewer: Auto foreground value
* Use external libjpeg-turbo and libtiff: simpler build stack, these are built and linked statically in automated Docker builds
* Remove OpenBLAS dependency

Reviewed-on: #1
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>

reader/JFJochReaderImage.cpp

@@ -75,6 +75,8 @@ void JFJochReaderImage::ProcessInputImage(const void *data, size_t npixel, int64
 
     size_t good_pixel = 0;
 
+    valid_pixel.reserve(image.size());
+
     for (int i = 0; i < npixel; i++) {
         int32_t val;
         if (img_ptr[i] <= INT32_MAX)
@@ -100,9 +102,27 @@ void JFJochReaderImage::ProcessInputImage(const void *data, size_t npixel, int64
         } else {
             good_pixel++;
             image[i] = val;
-            valid_pixel.emplace(val, i);
+            valid_pixel.emplace_back(std::make_pair(val, i));
         }
     }
+    // Sort based on the first element only
+    std::sort(valid_pixel.begin(), valid_pixel.end(),
+        [](const auto& a, const auto& b) {return a.first < b.first;});
+
+    CalcAutoContrast();
+}
+
+
+void JFJochReaderImage::CalcAutoContrast() {
+    if (valid_pixel.empty())
+        auto_foreground = 10;
+    else {
+        auto it = valid_pixel.crbegin();
+        const auto index = static_cast<size_t>(valid_pixel.size() * auto_foreground_range);
+        std::advance(it, std::max<size_t>(1ULL, index) - 1);
+
+        auto_foreground =  std::max(1, it->first);
+    }
 }
 
 const DataMessage &JFJochReaderImage::ImageData() const {
@@ -125,7 +145,7 @@ const std::unordered_set<int64_t> &JFJochReaderImage::ErrorPixels() const {
     return error_pixel;
 }
 
-const std::map<int32_t, int32_t> &JFJochReaderImage::ValidPixels() const {
+const std::vector<std::pair<int32_t, int32_t>> &JFJochReaderImage::ValidPixels() const {
     return valid_pixel;
 }
 
@@ -149,7 +169,7 @@ void JFJochReaderImage::AddImage(const JFJochReaderImage &other) {
     error_pixel.clear();
     saturated_pixel.clear();
     valid_pixel.clear();
-
+    valid_pixel.reserve(image.size());
     for (int i = 0; i < image.size(); i++) {
         if (image[i] == GAP_PXL_VALUE || other.image[i] == GAP_PXL_VALUE)
             image[i] = GAP_PXL_VALUE;
@@ -169,10 +189,16 @@ void JFJochReaderImage::AddImage(const JFJochReaderImage &other) {
                 saturated_pixel.emplace(i);
             } else {
                 image[i] = static_cast<int32_t>(sum);
-                valid_pixel.emplace(sum, i);
+                valid_pixel.emplace_back(std::make_pair(sum, i));
             }
         }
     }
+
+    // Sort based on the first element only
+    std::sort(valid_pixel.begin(), valid_pixel.end(),
+        [](const auto& a, const auto& b) { return a.first < b.first; });
+
+    CalcAutoContrast();
 }
 
 void JFJochReaderImage::CalcROI(const ROIElement *input) {
@@ -247,3 +273,7 @@ std::shared_ptr<JFJochReaderDataset> JFJochReaderImage::CreateMutableDataset() {
     dataset = new_dataset;
     return new_dataset;
 }
+
+int32_t JFJochReaderImage::GetAutoContrastValue() const {
+   return auto_foreground;
+}