merge develop

Author: marcschefer

.github/workflows/main.yml

@@ -56,14 +56,14 @@ jobs:
         uses: actions/checkout@v3
       - name: Get package name and version
         id: package-version
-        uses: astrorama/actions/elements-project@v3.3
+        uses: astrorama/actions/elements-project@v3.4
       - name: Install dependencies
-        uses: astrorama/actions/setup-dependencies@v3.3
+        uses: astrorama/actions/setup-dependencies@v3.4
         with:
           dependency-list: .github/workflows/dependencies.txt
       - name: Build
         id: build
-        uses: astrorama/actions/elements-build-rpm@v3.3
+        uses: astrorama/actions/elements-build-rpm@v3.4
       - name: Upload RPM to GitHub
         uses: actions/upload-artifact@v2
         with:
@@ -72,7 +72,7 @@ jobs:
           retention-days: 1
       - name: Upload RPM to repository
         if: ${{ github.repository_owner == 'astrorama' }}
-        uses: astrorama/actions/upload-rpm@v3.3
+        uses: astrorama/actions/upload-rpm@v3.4
         env:
           REPOSITORY_USER: ${{ secrets.REPOSITORY_USER }}
           REPOSITORY_PASSWORD: ${{ secrets.REPOSITORY_PASSWORD }}

CMakeLists.txt

@@ -6,4 +6,4 @@ find_package(ElementsProject)
 #---------------------------------------------------------------
 
 # Declare project name and version
-elements_project(SourceXtractorPlusPlus 0.19 USE Alexandria 2.28 DESCRIPTION "SourceXtractor++, the next generation SExtractor")
+elements_project(SourceXtractorPlusPlus 0.20 USE Alexandria 2.28 DESCRIPTION "SourceXtractor++, the next generation SExtractor")

README.md

@@ -17,23 +17,25 @@ 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
+conda install -c conda-forge -c astrorama sourcextractor==0.19
  ```
 
 We would recommend, however, to install it into its own environment.
 
 ```bash
-conda create -n sourcex -c astrorama -c conda-forge sourcextractor
+conda create -n sourcex -c astrorama -c conda-forge sourcextractor==0.19
 conda activate sourcex
  ```
 
 **Note:** If you want the development version to test a future functionality or bugfix, it can also be done with conda:
 
 ```bash
-conda create -n sourcex-dev -c astrorama/label/develop -c astrorama -c conda-forge sourcextractor
+conda create -n sourcex-dev -c astrorama/label/develop -c astrorama -c conda-forge sourcextractor=x.xx
 conda activate sourcex-dev
 ```
 
+We recommend always using an explicit version number as there is no guarantee that `conda` will install the latest version otherwise.
+
 ## Fedora / CentOS
 
 SourceXtractor++ is shipped directly in Fedora and CentOS. It can be installed simply as follows:
@@ -76,11 +78,16 @@ And install with
 dnf install SourceXtractorPlusPlus
 ```
 
+## Test Data Set
+
+A test data set covering various data reduction scenarios is available [here](https://cloud.physik.lmu.de/index.php/s/3K4KemBsw5y9yqd).
+I contains the input data, all relevant configuration files, the SourceXtractor++ commands and the expected output results for a reference.
+
 ## Discussion group for SourceXtractor++ users
 
-In order to facilitaet an active disucssion among SourceXtractor++ users we have created
+In order to facilitate an active discussion among SourceXtractor++ users we have created
 a [users group](https://groups.google.com/g/sourcextractor_plusplus). We encourage all users to directly
-join the group (if a google account is at hand) or to ask us to add you as member
+join the group (if a google account is at hand) or to ask us to add you as a member
 (open an issue on the [github page](https://astrorama.github.io/SourceXtractorPlusPlus/).
 
 

SEFramework/src/lib/FITS/FitsFile.cpp

@@ -126,7 +126,10 @@ void FitsFile::open() {
       m_fits_ptr.reset(ptr);
     }
     if (status != 0) {
-      throw Elements::Exception() << "Can't open FITS file: " << m_path << " status: " << status;
+      char error_message[32];
+      fits_get_errstatus(status, error_message);
+      throw Elements::Exception()
+          << "Can't open FITS file: " << m_path << " status: " << status << " = " << error_message;
     }
   }
   assert(ptr->Fptr->open_count == 1);
@@ -144,7 +147,10 @@ void FitsFile::refresh() {
 
   fits_open_image(&ptr, m_path.native().c_str(), m_is_writeable ? READWRITE : READONLY, &status);
   if (status != 0) {
-    throw Elements::Exception() << "Can't close and reopen FITS file: " << m_path << " status: " << status;
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
+    throw Elements::Exception()
+        << "Can't close and reopen FITS file: " << m_path << " status: " << status << " = " << error_message;
   }
   assert(ptr->Fptr->open_count == 1);
   m_fits_ptr.reset(ptr);
@@ -165,7 +171,10 @@ void FitsFile::loadInfo() {
   m_image_hdus.clear();
   int number_of_hdus = 0;
   if (fits_get_num_hdus(ptr, &number_of_hdus, &status) < 0) {
-    throw Elements::Exception() << "Can't get the number of HDUs in FITS file: " << m_path;
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
+    throw Elements::Exception() << "Can't get the number of HDUs in FITS file: " << m_path
+        << " status: " << status << " = " << error_message;
   }
   m_headers.clear();
   m_headers.resize(number_of_hdus);
@@ -175,7 +184,10 @@ void FitsFile::loadInfo() {
   for (int hdu_number = 1; hdu_number <= number_of_hdus; ++hdu_number) {
     fits_movabs_hdu(ptr, hdu_number, &hdu_type, &status);
     if (status != 0) {
-      throw Elements::Exception() << "Can't switch HDUs while opening: " << m_path;
+      char error_message[32];
+      fits_get_errstatus(status, error_message);
+      throw Elements::Exception() << "Can't switch HDUs while opening: " << m_path
+          << " status: " << status << " = " << error_message;
     }
 
     if (hdu_type == IMAGE_HDU) {
@@ -309,8 +321,11 @@ std::vector<int> FitsFile::getDimensions(int hdu) const {
 
   fits_get_img_param(m_fits_ptr.get(), 3, &bitpix, &naxis, naxes, &status);
   if (status != 0 || (naxis != 2 && naxis != 3)) {
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
     throw Elements::Exception()
-        << "Can't find 2D image or data cube in FITS file: " << m_path << "[" << hdu << "]";
+        << "Can't find 2D image or data cube in FITS file: " << m_path << "[" << hdu << "]"
+        << " status: " << status << " = " << error_message;
   }
 
   std::vector<int> dims;

SEFramework/src/lib/FITS/FitsImageSource.cpp

@@ -96,8 +96,11 @@ FitsImageSource::FitsImageSource(const std::string& filename, int hdu_number,
 
   fits_get_img_param(fptr, 2, &bitpix, &naxis, naxes, &status);
   if (status != 0 || (naxis != 2 && naxis != 3)) {
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
     throw Elements::Exception()
-        << "Can't find 2D image or data cube in FITS file: " << filename << "[" << m_hdu_number << "]";
+        << "Can't find 2D image or data cube in FITS file: " << filename << "[" << m_hdu_number << "]"
+        << " status: " << status << " = " << error_message;
   }
 
   m_width = naxes[0];
@@ -139,15 +142,21 @@ FitsImageSource::FitsImageSource(const std::string& filename, int width, int hei
     if (empty_primary &&  acc->m_fd.getImageHdus().empty()) {
       fits_create_img(fptr, FLOAT_IMG, 0, nullptr, &status);
       if (status != 0) {
-        throw Elements::Exception() << "Can't create empty hdu: " << filename << " status: " << status;
+        char error_message[32];
+        fits_get_errstatus(status, error_message);
+        throw Elements::Exception() << "Can't create empty hdu: " << filename
+            << " status: " << status << " = " << error_message;
       }
     }
 
     long naxes[2] = {width, height};
     fits_create_img(fptr, getImageType(), 2, naxes, &status);
 
     if (fits_get_hdu_num(fptr, &m_hdu_number) < 0) {
-      throw Elements::Exception() << "Can't get the active HDU from the FITS file: " << filename << " status: " << status;
+      char error_message[32];
+      fits_get_errstatus(status, error_message);
+      throw Elements::Exception() << "Can't get the active HDU from the FITS file: " << filename
+          << " status: " << status << " = " << error_message;
     }
 
     int hdutype = 0;
@@ -164,9 +173,10 @@ FitsImageSource::FitsImageSource(const std::string& filename, int width, int hei
 
         fits_update_card(fptr, padded_key.str().c_str(), str.c_str(), &status);
         if (status != 0) {
-          char err_txt[31];
-          fits_get_errstatus(status, err_txt);
-          throw Elements::Exception() << "Couldn't write the WCS headers (" << err_txt << "): " << str << " status: " << status;
+          char error_message[32];
+          fits_get_errstatus(status, error_message);
+          throw Elements::Exception() << "Couldn't write the WCS headers: " << filename
+              << " status: " << status << " = " << error_message;
         }
       }
     }
@@ -178,7 +188,10 @@ FitsImageSource::FitsImageSource(const std::string& filename, int width, int hei
     }
 
     if (status != 0) {
-      throw Elements::Exception() << "Couldn't allocate space for new FITS file: " << filename << " status: " << status;
+      char error_message[32];
+      fits_get_errstatus(status, error_message);
+      throw Elements::Exception() << "Couldn't allocate space for new FITS file: " << filename
+          << " status: " << status << " = " << error_message;
     }
 
     acc->m_fd.refresh(); // make sure changes to the file structure are taken into account
@@ -209,7 +222,10 @@ std::shared_ptr<ImageTile> FitsImageSource::getImageTile(int x, int y, int width
   fits_read_subset(fptr, getDataType(), first_pixel, last_pixel, increment,
                    nullptr, tile->getDataPtr(), nullptr, &status);
   if (status != 0) {
-    throw Elements::Exception() << "Error reading image tile from FITS file.";
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
+    throw Elements::Exception() << "Error reading image tile from FITS file."
+      << " status: " << status << " = " << error_message;
   }
 
   return tile;
@@ -231,7 +247,10 @@ void FitsImageSource::saveTile(ImageTile& tile) {
 
   fits_write_subset(fptr, getDataType(), first_pixel, last_pixel, tile.getDataPtr(), &status);
   if (status != 0) {
-    throw Elements::Exception() << "Error saving image tile to FITS file.";
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
+    throw Elements::Exception() << "Error saving image tile to FITS file."
+        << " status: " << status << " = " << error_message;
   }
   fits_flush_buffer(fptr, 0, &status);
 }
@@ -243,8 +262,10 @@ void FitsImageSource::switchHdu(fitsfile *fptr, int hdu_number) const {
   fits_movabs_hdu(fptr, hdu_number, &hdu_type, &status);
 
   if (status != 0) {
-    throw Elements::Exception() << "Could not switch to HDU # " << hdu_number << " in file "
-                                << m_filename;
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
+    throw Elements::Exception() << "Could not switch to HDU # " << hdu_number << " in file " << m_filename
+        << " status: " << status << " = " << error_message;
   }
   if (hdu_type != IMAGE_HDU) {
     throw Elements::Exception() << "Trying to access non-image HDU in file " << m_filename;
@@ -324,9 +345,10 @@ void FitsImageSource::setMetadata(const std::string& key, const MetadataEntry& v
   fits_update_card(fptr, padded_key.str().c_str(), str.c_str(), &status);
 
   if (status != 0) {
-    char err_txt[31];
-    fits_get_errstatus(status, err_txt);
-    throw Elements::Exception() << "Couldn't write the metadata (" << err_txt << "): " << str;
+    char error_message[32];
+    fits_get_errstatus(status, error_message);
+    throw Elements::Exception() << "Couldn't write the metadata: " << str
+      << " status: " << status << " = " << error_message;
   }
 
   // update the metadata

SEImplementation/src/lib/Configuration/DetectionImageConfig.cpp

@@ -97,7 +97,7 @@ void DetectionImageConfig::initialize(const UserValues& args) {
           continue;
         } else {
           if (m_extensions.size() == 0) {
-            throw Elements::Exception() << "Can't find 2D image in FITS file: " << m_detection_image_path;
+            throw;
           }
           break;
         }

SEImplementation/src/lib/Configuration/WeightImageConfig.cpp

@@ -156,7 +156,7 @@ void WeightImageConfig::initialize(const UserValues& args) {
             continue;
           } else {
             if (m_weight_images.size() == 0) {
-              throw Elements::Exception() << "Can't find 2D image in FITS file: " << weight_image_filename;
+              throw;
             }
             break;
           }