Release 1.0 (#603)

* Update CMakeLists.txt

Bump develop version number

* Update README.md

Update version in conda instructions

* fix use of deprecated function

* also update functions in frame config

* fix for a bug in quadtree causing moffat grouping crash

* Update main.yml to use v4 action

* Update Alexandria 2.31.4 (#599)

* Update Alexandria 2.31.4

To fix building on Fedora 41

* Add dnf to dependencies.txt

* Restrict model fitting window to a disk (#596)

* test: restrict fitting area to a disk

* revert change in residual block

* you can't fix stupid

* fitting window with checkimage WIP

* Fix python configuration problem

* Implement all window types

* fix code factor problem

* wip: add extra parameter to store x and y source size

* add configuration for width and height of sources in no detect mode

* minor style fixes

* Added rotated ellipse

* added ellipse_scale config option, fixed windows on the borders

* Allow disabling PSF renormalization in model fitting (#597)

* psf renormalization on/off option WIP

* DownSampledImagePsf renormalization

* propagate renormalization configuration from MeasurementImage

* remove unsued include, fix warnings in MoffatModelFitting

* propagate config for and fix DownsampledPsf

* Allows a reference image to be provided to provide the reference coordinate system (#598)

* Fix PixelCentroid error with no detect mode (#602)

* update version to 1.0

Author: marcschefer

.github/workflows/dependencies.txt

@@ -3,6 +3,7 @@ $PYTHON-numpy
 $PYTHON-pytest
 $PYTHON-sphinx
 $PYTHON-setuptools
+$PYTHON-dnf
 CCfits-devel
 blas-devel
 $BOOST-$PYTHON-devel

.github/workflows/main.yml

@@ -62,7 +62,7 @@ jobs:
         id: build
         uses: astrorama/actions/[email protected]
       - name: Upload RPM to GitHub
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.os-type }}${{ matrix.os-version }}
           path: ${{ steps.build.outputs.rpm-dir }}/*.rpm
@@ -93,21 +93,21 @@ jobs:
     container: ${{ matrix.os-type }}:${{ matrix.os-version }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install dependencies
         uses: astrorama/actions/setup-dependencies@v3
         with:
           dependency-list: .github/workflows/test-dependencies.txt
       - name: Download RPM
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: ${{ matrix.os-type }}${{ matrix.os-version }}
       - name: Install SourceXtractor++
         run: yum install -y SourceXtractorPlusPlus*.x86_64.rpm
       - name: Run tests
         run: ./.github/workflows/run-litmus.sh
       - name: Upload reports and logs
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.os-type }}${{ matrix.os-version }}-test-results
           path: /tmp/sourcex/

CMakeLists.txt

@@ -6,4 +6,4 @@ find_package(ElementsProject)
 #---------------------------------------------------------------
 
 # Declare project name and version
-elements_project(SourceXtractorPlusPlus 0.22 USE Alexandria 2.31.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")
+elements_project(SourceXtractorPlusPlus 1.0 USE Alexandria 2.31.4 DESCRIPTION "SourceXtractor++, the next generation SExtractor")

SEImplementation/SEImplementation/CheckImages/CheckImages.h

@@ -117,6 +117,8 @@ class CheckImages : public Configurable {
 
   std::shared_ptr<WriteableImage<MeasurementImage::PixelType>> getModelFittingImage(unsigned int frame_number);
 
+  std::shared_ptr<WriteableImage<int>> getFittingWindowImage(unsigned int frame_number);
+
   std::shared_ptr<WriteableImage<MeasurementImage::PixelType>> getPsfImage(unsigned int frame_number);
 
   std::shared_ptr<WriteableImage<float>> getMLDetectionImage(unsigned int plane_number, size_t index);
@@ -186,6 +188,7 @@ class CheckImages : public Configurable {
   std::map<unsigned int, std::shared_ptr<WriteableImage<int>>> m_measurement_aperture_images;
   std::map<unsigned int, std::shared_ptr<WriteableImage<int>>> m_measurement_auto_aperture_images;
   std::map<unsigned int, std::shared_ptr<WriteableImage<MeasurementImage::PixelType>>> m_check_image_model_fitting, m_check_image_psf;
+  std::map<unsigned int, std::shared_ptr<WriteableImage<int>>> m_check_image_fitting_window;
   std::vector<std::map<unsigned int, std::shared_ptr<WriteableImage<float>>>> m_check_image_ml_detection;
 
   std::vector<std::shared_ptr<DetectionImage>> m_detection_images;
@@ -202,6 +205,7 @@ class CheckImages : public Configurable {
   std::vector<std::shared_ptr<CoordinateSystem>> m_coordinate_systems;
 
   boost::filesystem::path m_model_fitting_image_filename;
+  boost::filesystem::path m_fitting_window_image_filename;
   boost::filesystem::path m_residual_filename;
   boost::filesystem::path m_background_filename;
   boost::filesystem::path m_variance_filename;

SEImplementation/SEImplementation/Configuration/CheckImagesConfig.h

@@ -45,6 +45,10 @@ class CheckImagesConfig : public Euclid::Configuration::Configuration {
     return m_model_fitting_filename;
   }
 
+  const std::string& getFittingWindowImageFilename() const {
+    return m_fitting_window_filename;
+  }
+
   const std::string& getModelFittingResidualFilename() const {
     return m_model_fitting_residual_filename;
   }
@@ -112,6 +116,7 @@ class CheckImagesConfig : public Euclid::Configuration::Configuration {
 private:
 
   std::string m_model_fitting_filename;
+  std::string m_fitting_window_filename;
   std::string m_model_fitting_residual_filename;
   std::string m_background_filename;
   std::string m_variance_filename;

SEImplementation/SEImplementation/Configuration/DetectionImageConfig.h

@@ -54,6 +54,7 @@ class DetectionImageConfig : public Euclid::Configuration::Configuration {
 
   std::shared_ptr<DetectionImage> getDetectionImage(size_t index = 0) const;
   std::shared_ptr<CoordinateSystem> getCoordinateSystem(size_t index = 0) const;
+  bool isReferenceImage() const { return m_is_reference_image; }
 
   double getGain(size_t index = 0) const { return m_extensions.at(index).m_gain; }
   double getSaturation(size_t index = 0) const { return m_extensions.at(index).m_saturation; }
@@ -69,7 +70,11 @@ class DetectionImageConfig : public Euclid::Configuration::Configuration {
   }
 
   size_t getExtensionsNb() const {
-    return m_extensions.size();
+    if (m_is_reference_image) {
+      return 0;
+    } else {
+      return m_extensions.size();
+    }
   }
 
 private:
@@ -89,6 +94,7 @@ class DetectionImageConfig : public Euclid::Configuration::Configuration {
 
   std::vector<DetectionImageExtension> m_extensions;
 
+  bool m_is_reference_image {false};
 }; /* End of DetectionImageConfig class */
 
 } /* namespace SourceXtractor */

SEImplementation/SEImplementation/Configuration/MeasurementImageConfig.h

@@ -65,6 +65,8 @@ class MeasurementImageConfig : public Euclid::Configuration::Configuration {
     bool m_is_data_cube;
     int m_image_layer;
     int m_weight_layer;
+
+    bool m_psf_renormalize;
   };
 
   explicit MeasurementImageConfig(long manager_id);

SEImplementation/SEImplementation/Configuration/ModelFittingConfig.h

@@ -23,10 +23,14 @@
 #define _SEIMPLEMENTATION_CONFIGURATION_MODELFITTINGCONFIG_H
 
 #include <vector>
+
 #include <SEImplementation/Plugin/FlexibleModelFitting/FlexibleModelFittingParameter.h>
 #include <SEImplementation/Plugin/FlexibleModelFitting/FlexibleModelFittingModel.h>
 #include <SEImplementation/Plugin/FlexibleModelFitting/FlexibleModelFittingFrame.h>
 #include <SEImplementation/Plugin/FlexibleModelFitting/FlexibleModelFittingPrior.h>
+
+#include <SEImplementation/Plugin/FlexibleModelFitting/FlexibleModelFittingIterativeTask.h>
+
 #include <Configuration/Configuration.h>
 
 namespace SourceXtractor {
@@ -60,6 +64,8 @@ class ModelFittingConfig : public Euclid::Configuration::Configuration {
   int getMetaIterations() const { return m_meta_iterations; }
   double getDeblendFactor() const { return m_deblend_factor; }
   double getMetaIterationStop() const { return m_meta_iteration_stop; }
+  FlexibleModelFittingIterativeTask::WindowType getWindowType() const { return m_window_type; }
+  double getEllipseScale() const { return m_ellipse_scale; }
 
 private:
   std::string m_least_squares_engine;
@@ -69,6 +75,9 @@ class ModelFittingConfig : public Euclid::Configuration::Configuration {
   int m_meta_iterations { 3 };
   double m_deblend_factor { 1.0 };
   double m_meta_iteration_stop { 0.0001 };
+  FlexibleModelFittingIterativeTask::WindowType m_window_type
+      { FlexibleModelFittingIterativeTask::WindowType::RECTANGLE };
+  double m_ellipse_scale { 3.0 };
 
   std::map<int, std::shared_ptr<FlexibleModelFittingParameter>> m_parameters;
   std::map<int, std::shared_ptr<FlexibleModelFittingModel>> m_models;

SEImplementation/SEImplementation/Image/DownSampledImagePsf.h

@@ -41,11 +41,13 @@ namespace SourceXtractor {
 class DownSampledImagePsf {
 public:
 
-  DownSampledImagePsf(double pixel_scale, std::shared_ptr<VectorImage<SeFloat>> image, double down_scaling=1.0);
+  DownSampledImagePsf(double pixel_scale, std::shared_ptr<VectorImage<SeFloat>> image,
+      double down_scaling=1.0, bool normalize_psf = true);
 
   virtual ~DownSampledImagePsf() = default;
 
   double getPixelScale() const;
+
   std::size_t getSize() const;
   std::shared_ptr<VectorImage<SourceXtractor::SeFloat>> getScaledKernel(SeFloat scale) const;
   void convolve(std::shared_ptr<WriteableImage<float>> image) const;
@@ -57,6 +59,7 @@ class DownSampledImagePsf {
 private:
   double m_down_scaling;
   std::shared_ptr<ImagePsf> m_psf;
+  bool m_normalize_psf { true };
 };
 
 } // end of SourceXtractor

SEImplementation/SEImplementation/Plugin/AssocMode/AssocMode.h

@@ -40,13 +40,15 @@ class AssocMode : public Property {
    */
   virtual ~AssocMode() = default;
 
-  AssocMode() : m_has_assoc(false), m_assoc_data(std::vector<size_t>({0})), m_ref_frame_pixel_radius(1), m_group_id(0) {
+  AssocMode() : m_has_assoc(false), m_assoc_data(std::vector<size_t>({0})),
+      m_ref_frame_pixel_width(1), m_ref_frame_pixel_height(1), m_group_id(0) {
   }
 
   AssocMode(bool has_assoc, const std::vector<double>& assoc_data,
-      double ref_frame_pixel_radius=0.0, unsigned int group_id=0) :
+      double ref_frame_pixel_width=0.0, double ref_frame_pixel_height=0.0, unsigned int group_id=0) :
       m_has_assoc(has_assoc), m_assoc_data(std::vector<size_t>({assoc_data.size()})),
-      m_ref_frame_pixel_radius(ref_frame_pixel_radius), m_group_id(group_id) {
+      m_ref_frame_pixel_width(ref_frame_pixel_width), m_ref_frame_pixel_height(ref_frame_pixel_height),
+      m_group_id(group_id) {
     for (size_t i=0; i<assoc_data.size(); i++) {
       m_assoc_data.at(i) = assoc_data[i];
     }
@@ -60,8 +62,12 @@ class AssocMode : public Property {
     return m_assoc_data;
   }
 
-  double getRefFramePixelRadius() const {
-    return m_ref_frame_pixel_radius;
+  double getRefFramePixelWidth() const {
+    return m_ref_frame_pixel_width;
+  }
+
+  double getRefFramePixelHeight() const {
+    return m_ref_frame_pixel_height;
   }
 
   unsigned int getGroupId() const {
@@ -72,7 +78,9 @@ class AssocMode : public Property {
   bool m_has_assoc;
 
   NdArray<SeFloat> m_assoc_data;
-  double m_ref_frame_pixel_radius;
+  //double m_ref_frame_pixel_radius;
+  double m_ref_frame_pixel_width;
+  double m_ref_frame_pixel_height;
   unsigned int m_group_id;
 };