Merge branch 'develop' into feature/dft_background

Pick changes from Martin for the BackgroundConvolution

Author: ayllon

SEImplementation/SEImplementation/CheckImages/CheckImages.h

@@ -76,6 +76,10 @@ class CheckImages : public Configurable {
     m_filtered_image = filtered_image;
   }
 
+  void setThresholdedCheckImage(std::shared_ptr<Image<SeFloat>> thresholded_image) {
+    m_thresholded_image = thresholded_image;
+  }
+
   std::shared_ptr<WriteableImage<SeFloat>> getWriteableCheckImage(std::string id, int width, int height);
   void setCustomCheckImage(std::string id, std::shared_ptr<Image<SeFloat>> image);
 
@@ -117,6 +121,7 @@ class CheckImages : public Configurable {
   std::shared_ptr<DetectionImage> m_detection_image;
   std::shared_ptr<Image<SeFloat>> m_background_image;
   std::shared_ptr<Image<SeFloat>> m_filtered_image;
+  std::shared_ptr<Image<SeFloat>> m_thresholded_image;
   std::shared_ptr<WeightImage> m_variance_image;
   std::shared_ptr<CoordinateSystem> m_coordinate_system;
 
@@ -128,6 +133,7 @@ class CheckImages : public Configurable {
   std::string m_partition_filename;
   std::string m_group_filename;
   std::string m_filtered_filename;
+  std::string m_thresholded_filename;
   std::string m_auto_aperture_filename;
   std::string m_aperture_filename;
   std::string m_moffat_filename;

SEImplementation/SEImplementation/Configuration/CheckImagesConfig.h

@@ -57,6 +57,10 @@ class CheckImagesConfig : public Euclid::Configuration::Configuration {
     return m_filtered_filename;
   }
 
+  const std::string& getThresholdedFilename() const {
+    return m_thresholded_filename;
+  }
+
   const std::string& getAutoApertureFilename() const {
     return m_auto_aperture_filename;
   }
@@ -79,6 +83,7 @@ class CheckImagesConfig : public Euclid::Configuration::Configuration {
   std::string m_partition_filename;
   std::string m_group_filename;
   std::string m_filtered_filename;
+  std::string m_thresholded_filename;
   std::string m_auto_aperture_filename;
   std::string m_aperture_filename;
   std::string m_moffat_filename;

SEImplementation/SEImplementation/Segmentation/BackgroundConvolution.h

@@ -46,26 +46,32 @@ class BgConvolutionImageSource : public ProcessingImageSource<DetectionImage::Pi
         DetectionImage::PixelType conv_weight = 0;
         DetectionImage::PixelType conv_weight_ignoring_threshold = 0;
 
-        for (int cy = 0; cy < m_kernel->getHeight(); cy++) {
-          for (int cx = 0; cx < m_kernel->getWidth(); cx++) {
+        if (m_variance->getValue(ix, iy) < m_threshold) {
 
-            auto x2 = ix + cx - hx;
-            auto y2 = iy + cy - hy;
+          for (int cy = 0; cy < m_kernel->getHeight(); cy++) {
+            for (int cx = 0; cx < m_kernel->getWidth(); cx++) {
 
-            if (x2 >= 0 && x2 < image->getWidth() && y2 >= 0 && y2 < image->getHeight()) {
-              if (m_variance->getValue(x2, y2) < m_threshold) {
-                total += image->getValue(x2, y2) * m_kernel->getValue(cx, cy);
-                conv_weight += m_kernel->getValue(cx, cy);
+              auto x2 = ix + cx - hx;
+              auto y2 = iy + cy - hy;
+
+              if (x2 >= 0 && x2 < image->getWidth() && y2 >= 0 && y2 < image->getHeight()) {
+                if (m_variance->getValue(x2, y2) < m_threshold) {
+                  total += image->getValue(x2, y2) * m_kernel->getValue(cx, cy);
+                  conv_weight += m_kernel->getValue(cx, cy);
+                }
+                total_ignoring_threshold += image->getValue(x2, y2) * m_kernel->getValue(cx, cy);
+                conv_weight_ignoring_threshold += m_kernel->getValue(cx, cy);
+              }
+              if (conv_weight > 0) {
+                tile.getImage()->setValue(ix - x, iy - y, total / conv_weight);
+              } else {
+                tile.getImage()->setValue(ix - x, iy - y, total_ignoring_threshold / conv_weight_ignoring_threshold);
               }
-              total_ignoring_threshold += image->getValue(x2, y2) * m_kernel->getValue(cx, cy);
-              conv_weight_ignoring_threshold += m_kernel->getValue(cx, cy);
             }
           }
         }
-        if (conv_weight > 0) {
-          tile.getImage()->setValue(ix - x, iy - y, total / conv_weight);
-        } else {
-          tile.getImage()->setValue(ix - x, iy - y, total_ignoring_threshold / conv_weight_ignoring_threshold);
+        else {
+          tile.getImage()->setValue(ix - x, iy - y, 0);
         }
       }
     }

SEImplementation/SEImplementation/Segmentation/Lutz.h

@@ -8,6 +8,8 @@
 #ifndef _SEIMPLEMENTATION_SEGMENTATION_LUTZ_H_
 #define _SEIMPLEMENTATION_SEGMENTATION_LUTZ_H_
 
+#include "ElementsKernel/Logging.h"
+
 #include "SEFramework/Source/SourceFactory.h"
 #include "SEFramework/Task/TaskProvider.h"
 #include "SEFramework/Source/SourceWithOnDemandProperties.h"

SEImplementation/src/lib/CheckImages/CheckImages.cpp

@@ -55,6 +55,7 @@ void CheckImages::configure(Euclid::Configuration::ConfigManager& manager) {
   m_partition_filename = config.getPartitionFilename();
   m_group_filename = config.getGroupFilename();
   m_filtered_filename = config.getFilteredFilename();
+  m_thresholded_filename = config.getThresholdedFilename();
   m_auto_aperture_filename = config.getAutoApertureFilename();
   m_aperture_filename = config.getApertureFilename();
   m_moffat_filename = config.getMoffatFilename();
@@ -169,6 +170,11 @@ void CheckImages::saveImages() {
     FitsWriter::writeFile(*m_filtered_image, m_filtered_filename, m_coordinate_system);
   }
 
+  // if possible, save the thresholded image
+  if (m_thresholded_image != nullptr && m_thresholded_filename != "") {
+    FitsWriter::writeFile(*m_thresholded_image, m_thresholded_filename, m_coordinate_system);
+  }
+
   // if possible, create and save the residual image
   if (m_check_image_model_fitting != nullptr && m_residual_filename != "") {
     auto residual_image = SubtractImage<SeFloat>::create(m_detection_image, m_check_image_model_fitting);

SEImplementation/src/lib/Configuration/CheckImagesConfig.cpp

@@ -24,6 +24,7 @@ static const std::string CHECK_SEGMENTATION { "check-image-segmentation" };
 static const std::string CHECK_PARTITION { "check-image-partition" };
 static const std::string CHECK_GROUPING { "check-image-grouping" };
 static const std::string CHECK_FILTERED { "check-image-filtered" };
+static const std::string CHECK_THRESHOLDED { "check-image-thresholded" };
 static const std::string CHECK_AUTO_APERTURE { "check-image-auto-aperture" };
 static const std::string CHECK_APERTURE { "check-image-aperture" };
 static const std::string CHECK_MOFFAT { "check-image-moffat" };
@@ -49,6 +50,8 @@ std::map<std::string, Configuration::OptionDescriptionList> CheckImagesConfig::g
         "Path to save the grouping check image"},
       {CHECK_FILTERED.c_str(), po::value<std::string>()->default_value(""),
         "Path to save the filtered check image"},
+      {CHECK_THRESHOLDED.c_str(), po::value<std::string>()->default_value(""),
+        "Path to save the thresholded check image"},
       {CHECK_AUTO_APERTURE.c_str(), po::value<std::string>()->default_value(""),
         "Path to save the auto aperture check image"},
       {CHECK_APERTURE.c_str(), po::value<std::string>()->default_value(""),
@@ -67,6 +70,7 @@ void CheckImagesConfig::initialize(const UserValues& args) {
   m_partition_filename = args.find(CHECK_PARTITION)->second.as<std::string>();
   m_group_filename = args.find(CHECK_GROUPING)->second.as<std::string>();
   m_filtered_filename = args.find(CHECK_FILTERED)->second.as<std::string>();
+  m_thresholded_filename = args.find(CHECK_THRESHOLDED)->second.as<std::string>();
   m_auto_aperture_filename = args.find(CHECK_AUTO_APERTURE)->second.as<std::string>();
   m_aperture_filename = args.find(CHECK_APERTURE)->second.as<std::string>();
   m_moffat_filename = args.find(CHECK_MOFFAT)->second.as<std::string>();

SEMain/src/program/SExtractor.cpp

@@ -311,7 +311,7 @@ class SEMain : public Elements::Program {
         << " RMS: " << sqrt(detection_frame->getVarianceMap()->getValue(0,0))
         << " threshold: "  << detection_frame->getDetectionThreshold();
 
-    CheckImages::getInstance().setFilteredCheckImage(detection_frame->getFilteredImage());
+    //CheckImages::getInstance().setFilteredCheckImage(detection_frame->getFilteredImage());
 
     // Perform measurements (multi-threaded part)
     measurement->startThreads();
@@ -326,6 +326,7 @@ class SEMain : public Elements::Program {
     measurement->waitForThreads();
 
     CheckImages::getInstance().setFilteredCheckImage(detection_frame->getFilteredImage());
+    CheckImages::getInstance().setThresholdedCheckImage(detection_frame->getThresholdedImage());
     CheckImages::getInstance().saveImages();
     TileManager::getInstance()->flush();
     size_t n_writen_rows = output->flush();