Merge pull request #495 from QIICR/merge-beyond-nrrd

allow saving merged segments to all formats

Author: fedorov

.github/workflows/cmake-macos.yml

@@ -24,7 +24,7 @@ jobs:
         fetch-tags: true     
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.7.14'
+        python-version: '3.10.11'
 
     # Install build tools (cmake and ninja) as well as jsondiff
     - name: "Install jsondiff"
@@ -119,4 +119,4 @@ jobs:
         --prerelease-packages ${{ github.workspace }}/dcmqi-build/dcmqi-build/dcmqi-*-mac-*.tar.gz \
         --prerelease-packages-clear-pattern "dcmqi-*-mac-*" \
         --prerelease-packages-keep-pattern "*<COMMIT_DATE>-<COMMIT_SHORT_SHA>*" \
-        --exit-success-if-missing-token --token ${{ secrets.GA_TOKEN }}
+        --exit-success-if-missing-token --token ${{ secrets.GA_TOKEN }}

apps/seg/segimage2itkimage.cxx

@@ -25,11 +25,6 @@ int main(int argc, char *argv[])
     dcmtk::log4cplus::BasicConfigurator::doConfigure();
   }
 
-  if (mergeSegments && outputType != "nrrd") {
-    std::cerr << "ERROR: mergeSegments option is only supported when output format is NRRD!" << std::endl;
-    return EXIT_FAILURE;
-  }
-
   if(helper::isUndefinedOrPathDoesNotExist(inputSEGFileName, "Input DICOM file")
      || helper::isUndefinedOrPathDoesNotExist(outputDirName, "Output directory"))
     return EXIT_FAILURE;

apps/seg/segimage2itkimage.xml

@@ -72,7 +72,7 @@
       <channel>input</channel>
       <longflag>mergeSegments</longflag>
       <default>false</default>
-      <description>Save all segments into a single file. When segments are non-overlapping, output is a single 3D file. If overlapping, single 4D following conventions of 3D Slicer segmentations format. Only supported when the output is NRRD for now.</description>
+      <description>Save all segments into a single file. When segments are non-overlapping, output is a single 3D file. If overlapping segments are identified, multiple 3D files will be created each containing non-overlapping segments. Metadata JSON files will be created for each such 3D file.</description>
     </boolean>
 
   </parameters>