Merge pull request #568 from astrorama/develop

Release 0.21

Author: marcschefer

.github/workflows/main.yml

@@ -82,6 +82,7 @@ jobs:
 # Run tests #
 #############
   litmus-test:
+    if: ${{ always() }}
     needs: [ build, get_fedora_releases ]
     runs-on: ubuntu-latest
     strategy:

.jenkinsFile

@@ -0,0 +1,3 @@
+#!groovy
+@Library('integration-library@release-9') _
+pipelineElements(artifactId:"SourceXtractorPlusPlus", groupId:"EL", component:'eden.3.0')

CMakeLists.txt

@@ -6,4 +6,4 @@ find_package(ElementsProject)
 #---------------------------------------------------------------
 
 # Declare project name and version
-elements_project(SourceXtractorPlusPlus 0.19.2 USE Alexandria 2.28.2 DESCRIPTION "SourceXtractor++, the next generation SExtractor")
+elements_project(SourceXtractorPlusPlus 0.21 USE Alexandria 2.31.0 DESCRIPTION "SourceXtractor++, the next generation SExtractor")

README.md

@@ -17,13 +17,13 @@ Documentation: https://astrorama.github.io/SourceXtractorPlusPlus/
 SourceXtractor++ is available on [Anaconda Cloud for Linux and MacOSX](https://anaconda.org/astrorama/sourcextractor)
 
 ```bash
-conda install -c conda-forge -c astrorama sourcextractor==0.19
+conda install -c conda-forge -c astrorama sourcextractor==0.19.2
  ```
 
 We would recommend, however, to install it into its own environment.
 
 ```bash
-conda create -n sourcex -c astrorama -c conda-forge sourcextractor==0.19
+conda create -n sourcex -c astrorama -c conda-forge sourcextractor==0.19.2
 conda activate sourcex
  ```
 
@@ -97,7 +97,7 @@ join the group (if a google account is at hand) or to ask us to add you as a mem
 While we are working on several refereed papers describing SourceXtractor++ and its software architecture, the software package can be referenced with two ADASS conference proceedings:
 
 - [Bertin, E.; Schefer, M. ; Apostolakos, N. ; Álvarez-Ayllón, A.; Dubath, P. ; Kümmel, M.: 2020ASPC..527..461B](https://ui.adsabs.harvard.edu/abs/2020ASPC..527..461B/abstract)
-- [Kümmel, M. ; Bertin, E.; Schefer, M. ; Apostolakos, N. ; Álvarez-Ayllón, A.; Dubath, P.: 2020ASPC..527...29K](https://ui.adsabs.harvard.edu/abs/2020ASPC..527...29K/abstract) 
+- [Kümmel, M.; Álvarez-Ayllón, A.; Bertin, E.; Dubath, P.; Gavazzi, R.; Hartley, W.; Schefer, M.: 2022arXiv221202428K](https://ui.adsabs.harvard.edu/abs/2022arXiv221202428K/abstract) 
 
 Resources for the SourceXtractor++ development are in most part provided by funding from the [Euclid satellite project](https://www.euclid-ec.org/) via the various national agencies.
 For Euclid Consortium papers it is sufficient to point to the [SourceXtractor++ webpage](https://github.com/astrorama/SourceXtractorPlusPlus) and add

SEFramework/SEFramework/Pipeline/Segmentation.h

@@ -87,7 +87,9 @@ class Segmentation::LabellingListener {
     m_detection_frame(detection_frame) {}
 
   void publishSource(std::unique_ptr<SourceInterface> source) const {
-    source->setProperty<DetectionFrame>(m_detection_frame);
+    if (m_detection_frame) {
+      source->setProperty<DetectionFrame>(m_detection_frame);
+    }
     m_segmentation.sendSource(std::move(source));
   }
 

SEFramework/SEFramework/Psf/VariablePsfStack.h

@@ -103,8 +103,8 @@ class VariablePsfStack final : public Psf {
   std::vector<SeFloat> m_dec_values;
   std::vector<SeFloat> m_x_values;
   std::vector<SeFloat> m_y_values;
-  std::vector<int>     m_gridx_values;
-  std::vector<int>     m_gridy_values;
+  std::vector<double>  m_gridx_values;
+  std::vector<double>  m_gridy_values;
 
   std::vector<std::string> m_components = {"X_IMAGE", "Y_IMAGE"};
 

SEFramework/src/lib/CoordinateSystem/WCS.cpp

@@ -253,9 +253,12 @@ ImageCoordinate WCS::worldToImage(WorldCoordinate world_coordinate) const {
 
   int status = 0;
   int ret_val = wcss2p(&wcs_copy, 1, 1, wc_array, &phi, &theta, ic_array, pc_array, &status);
-  wcsRaiseOnTransformError(&wcs_copy, ret_val);
+  if (ret_val != WCSERR_SUCCESS) {
+    logger.warn() << "Bad worldToImage from RA/Dec: " << wc_array[0] << "/" << wc_array[1];
+    pc_array[0] = -std::numeric_limits<double>::infinity();
+    pc_array[1] = -std::numeric_limits<double>::infinity();
+  }
   wcsfree(&wcs_copy);
-
   return ImageCoordinate(pc_array[0] - 1, pc_array[1] - 1); // -1 as fits standard coordinates start at 1
 }
 

SEFramework/src/lib/FITS/FitsFile.cpp

@@ -36,10 +36,14 @@
 #include <boost/regex.hpp>
 
 #include "ElementsKernel/Exception.h"
+#include "ElementsKernel/Logging.h"
+
 #include "SEFramework/FITS/FitsFile.h"
 
 namespace SourceXtractor {
 
+static Elements::Logging logger = Elements::Logging::getLogger("FitsFile");
+
 /**
  * Cast a string to a C++ type depending on the format of the content.
  * - if only digits are present, it will be casted to int64_t
@@ -69,7 +73,8 @@ static typename MetadataEntry::value_t valueAutoCast(const std::string& value) {
   // We used to use boost::io::quoted here, but it seems that starting with 1.73 it
   // does not work well when the escape code and the delimiter are the same
   std::string unquoted;
-  bool        escape = false;
+  bool escape = false;
+
   unquoted.reserve(value.size());
   for (auto i = value.begin(); i != value.end(); ++i) {
     if (*i == '\'' && !escape) {
@@ -264,7 +269,7 @@ void FitsFile::loadHeadFile() {
     return;
   }
 
-  auto          hdu_iter = m_image_hdus.begin();
+  auto hdu_iter = m_image_hdus.begin();
   std::ifstream file;
 
   // open the file and check
@@ -273,6 +278,11 @@ void FitsFile::loadHeadFile() {
     throw Elements::Exception() << "Cannot load ascii header file: " << head_filename;
   }
 
+  logger.info() << "Loading .head file: " << head_filename << " for fits: " << m_path;
+
+  int headers_nb = 0;
+  int hdu_nb = 0;
+  bool is_new_hdu = true;
   while (file.good() && hdu_iter != m_image_hdus.end()) {
     int current_hdu = *hdu_iter;
 
@@ -287,6 +297,7 @@ void FitsFile::loadHeadFile() {
 
     if (boost::to_upper_copy(line) == "END") {
       current_hdu = *(++hdu_iter);
+      is_new_hdu = true;
     } else {
       static boost::regex regex("([^=]{1,8})=([^\\/]*)(\\/ (.*))?");
       boost::smatch       sub_matches;
@@ -298,10 +309,17 @@ void FitsFile::loadHeadFile() {
         boost::trim(value);
         boost::trim(comment);
         m_headers.at(current_hdu - 1)[keyword] = MetadataEntry{valueAutoCast(value), {{"comment", comment}}};
-        ;
+        headers_nb++;
+        if (is_new_hdu) {
+          hdu_nb++;
+          is_new_hdu = false;
+        }
       }
     }
   }
+  if (headers_nb > 0) {
+    logger.info() << "Headers overriden: " << headers_nb << " in " << hdu_nb << " hdu(s)";
+  }
 }
 
 std::vector<int> FitsFile::getDimensions(int hdu) const {

SEFramework/src/lib/FITS/FitsImageSource.cpp

@@ -330,7 +330,7 @@ const std::map<std::string, MetadataEntry>& FitsImageSource::getMetadata() const
 }
 
 void FitsImageSource::setMetadata(const std::string& key, const MetadataEntry& value) {
-  auto acc  = m_handler->getAccessor<FitsFile>();
+  auto acc  = m_handler->getAccessor<FitsFile>(FileHandler::kWrite);
   auto fptr = acc->m_fd.getFitsFilePtr();
   switchHdu(fptr, m_hdu_number);
 

SEFramework/src/lib/Pipeline/Segmentation.cpp

@@ -29,7 +29,7 @@ Segmentation::Segmentation(std::shared_ptr<DetectionImageFrame::ImageFilter> ima
 }
 
 void Segmentation::processFrame(std::shared_ptr<DetectionImageFrame> frame) const {
-  if (m_filter_image_processing != nullptr) {
+  if (m_filter_image_processing != nullptr && frame != nullptr) {
     frame->setFilter(m_filter_image_processing);
   }