Merge pull request #464 from fedorov/merged-segments

Add support for merging non-overlapping segments and saving in a single file

CMakeExternals/DCMTK.cmake

@@ -101,6 +101,7 @@ if(NOT DEFINED DCMTK_DIR AND NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
       -DDCMTK_ENABLE_BUILTIN_DICTIONARY:BOOL=ON
       -DDCMTK_ENABLE_PRIVATE_TAGS:BOOL=ON
       -DDCMTK_COMPILE_WIN32_MULTITHREADED_DLL:BOOL=ON
+      -DDCMTK_ENABLE_STL:BOOL=ON
     DEPENDS
       ${${proj}_DEPENDENCIES}
     )

apps/seg/Testing/CMakeLists.txt

@@ -30,6 +30,10 @@ dcmqi_add_test(
     --outputDICOM ${MODULE_TEMP_DIR}/liver.dcm
   )
 
+# Creates a DICOM segmentation file that has 3 segments:
+# - segment for liver (DICOM Segment Number 1)
+# - segment for spine (DICOM Segment Number 2)
+# - segment for heart (DICOM Segment Number 3)
 dcmqi_add_test(
   NAME ${itk2dcm}_makeSEG_multiple_segment_files
   MODULE_NAME ${MODULE_NAME}
@@ -50,6 +54,7 @@ dcmqi_add_test(
       --outputDICOM ${MODULE_TEMP_DIR}/liver_heart_seg_reordered.dcm
     )
 
+
 find_program(DCIODVFY_EXECUTABLE dciodvfy)
 
 if(EXISTS ${DCIODVFY_EXECUTABLE})
@@ -139,6 +144,38 @@ dcmqi_add_test(
       ${itk2dcm}_makeSEG_multiple_segment_files_reordered
     )
 
+  # Reads a DICOM segmentation file that has 3 segments (liver, spine, heart - in this order).
+  # Heart and liver segments overlap.
+  # The goal is to export these segments to NRRD+JSON. Since the liver and heart segments overlap,
+  # one output file will contain 2 segments (liver and spine) and the other will contain only
+  # the heart. This will be reflected in the JSON metadata files with two entries in the outer
+  # array (one for each NRRD file), one with 2 segments (liver,spine) and one with 1 segment (heart).
+  dcmqi_add_test(
+    NAME ${dcm2itk}_makeNRRD_merged_segment_file
+    MODULE_NAME ${MODULE_NAME}
+    COMMAND ${SEM_LAUNCH_COMMAND} $<TARGET_FILE:${dcm2itk}Test>
+      --compare ${BASELINE}/liver_spine_seg.nrrd ${MODULE_TEMP_DIR}/makeNRRD_merged_segment_file-1.nrrd
+      --compare ${BASELINE}/heart_seg.nrrd ${MODULE_TEMP_DIR}/makeNRRD_merged_segment_file-2.nrrd
+      ${dcm2itk}Test
+      --inputDICOM ${MODULE_TEMP_DIR}/liver_heart_seg.dcm
+      --outputDirectory ${MODULE_TEMP_DIR}
+      --prefix makeNRRD_merged_segment_file
+      --mergeSegments
+    TEST_DEPENDS
+      ${itk2dcm}_makeSEG_multiple_segment_files
+  )
+
+  # Compare expected JSON output coming from makeNRRD_merged_segment_file test.
+  dcmqi_add_test(
+    NAME ${dcm2itk}_makeNRRD_merged_segment_file_JSON
+    MODULE_NAME ${MODULE_NAME}
+    COMMAND python ${CMAKE_SOURCE_DIR}/util/comparejson.py
+      ${CMAKE_SOURCE_DIR}/doc/examples/seg-example_multiple_segments_merged.json
+      ${MODULE_TEMP_DIR}/makeNRRD_merged_segment_file-meta.json
+    TEST_DEPENDS
+      ${dcm2itk}_makeNRRD_merged_segment_file
+  )
+
 dcmqi_add_test(
   NAME seg_meta_roundtrip
   MODULE_NAME ${MODULE_NAME}
@@ -160,8 +197,6 @@ dcmqi_add_test(
     ${dcm2itk}_makeNRRD_multiple_segment_files
   )
 
-
-
 set(TEST_SEG_SIZES 24x38x3 23x38x3)
 
 foreach(seg_size ${TEST_SEG_SIZES})

apps/seg/itkimage2segimage.cxx

@@ -1,9 +1,9 @@
 // CLP includes
+#include "dcmqi/Itk2DicomConverter.h"
 #include "itkimage2segimageCLP.h"
 
 // DCMQI includes
 #undef HAVE_SSTREAM // Avoid redefinition warning
-#include "dcmqi/ImageSEGConverter.h"
 #include "dcmqi/internal/VersionConfigure.h"
 
 // DCMTK includes
@@ -122,7 +122,7 @@ int main(int argc, char *argv[])
   }
 
   try {
-    DcmDataset* result = dcmqi::ImageSEGConverter::itkimage2dcmSegmentation(dcmDatasets, segmentations, metadata, skipEmptySlices);
+    DcmDataset* result = dcmqi::Itk2DicomConverter::itkimage2dcmSegmentation(dcmDatasets, segmentations, metadata, skipEmptySlices);
 
     if (result == NULL){
       std::cerr << "ERROR: Conversion failed." << std::endl;

apps/seg/segimage2itkimage.cxx

@@ -1,15 +1,17 @@
 // CLP includes
 #include "segimage2itkimageCLP.h"
+#include <itkSmartPointer.h>
 
 // DCMQI includes
 #undef HAVE_SSTREAM // Avoid redefinition warning
-#include "dcmqi/ImageSEGConverter.h"
+#include "dcmqi/Dicom2ItkConverter.h"
 #include "dcmqi/internal/VersionConfigure.h"
 
 // DCMTK includes
 #include <dcmtk/oflog/configrt.h>
 
 typedef dcmqi::Helper helper;
+typedef itk::ImageFileWriter<ShortImageType> WriterType;
 
 
 int main(int argc, char *argv[])
@@ -23,6 +25,11 @@ 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;
@@ -34,31 +41,47 @@ int main(int argc, char *argv[])
   DcmDataset* dataset = sliceFF.getDataset();
 
   try {
-    pair <map<unsigned,ShortImageType::Pointer>, string> result =  dcmqi::ImageSEGConverter::dcmSegmentation2itkimage(dataset);
+    dcmqi::Dicom2ItkConverter converter;
+    std::string metaInfo;
+    OFCondition result  =  converter.dcmSegmentation2itkimage(dataset, metaInfo, mergeSegments);
+    if (result.bad())
+    {
+      std::cerr << "ERROR: Failed to convert DICOM SEG to ITK image: " << result.text() << std::endl;
+      return EXIT_FAILURE;
+    }
 
     string outputPrefix = prefix.empty() ? "" : prefix + "-";
 
     string fileExtension = dcmqi::Helper::getFileExtensionFromType(outputType);
-
-    for(map<unsigned,ShortImageType::Pointer>::const_iterator sI=result.first.begin();sI!=result.first.end();++sI){
-      typedef itk::ImageFileWriter<ShortImageType> WriterType;
+    itk::SmartPointer<ShortImageType> itkImage = converter.begin();
+    size_t fileIndex = 1;
+    while (itkImage)
+    {
       stringstream imageFileNameSStream;
-
-      imageFileNameSStream << outputDirName << "/" << outputPrefix << sI->first << fileExtension;
-
-      WriterType::Pointer writer = WriterType::New();
-      writer->SetFileName(imageFileNameSStream.str().c_str());
-      writer->SetInput(sI->second);
-      writer->SetUseCompression(1);
-      writer->Update();
+      cout << "Writing itk image to " << outputDirName << "/" << outputPrefix << fileIndex << fileExtension;
+      imageFileNameSStream << outputDirName << "/" << outputPrefix << fileIndex << fileExtension;
+
+      try {
+        WriterType::Pointer writer = WriterType::New();
+        writer->SetFileName(imageFileNameSStream.str().c_str());
+        writer->SetInput(itkImage);
+        writer->SetUseCompression(1);
+        writer->Update();
+        cout << " ... done" << endl;
+      } catch (itk::ExceptionObject & error) {
+        std::cerr << "fatal ITK error: " << error << std::endl;
+        return EXIT_FAILURE;
+      }
+      itkImage = converter.next();
+      fileIndex++;
     }
 
     stringstream jsonOutput;
     jsonOutput << outputDirName << "/" << outputPrefix << "meta.json";
 
     ofstream outputFile;
     outputFile.open(jsonOutput.str().c_str());
-    outputFile << result.second;
+    outputFile << metaInfo;
     outputFile.close();
 
     return EXIT_SUCCESS;

apps/seg/segimage2itkimage.xml

@@ -66,6 +66,15 @@
       <description>Display more verbose output, useful for troubleshooting.</description>
     </boolean>
 
+    <boolean>
+      <name>mergeSegments</name>
+      <label>Merge segments</label>
+      <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>
+    </boolean>
+
   </parameters>
 
 </executable>

doc/examples/seg-example_multiple_segments_merged.json

@@ -0,0 +1,68 @@
+{
+   "BodyPartExamined" : "",
+   "ClinicalTrialCoordinatingCenterName" : "BWH",
+   "ClinicalTrialSeriesID" : "Session1",
+   "ClinicalTrialTimePointID" : "1",
+   "ContentCreatorName" : "Doe^John",
+   "InstanceNumber" : "1",
+   "SeriesDescription" : "Segmentation",
+   "SeriesNumber" : "300",
+   "segmentAttributes" : [
+      [
+         {
+            "SegmentAlgorithmName" : "SlicerEditor",
+            "SegmentAlgorithmType" : "SEMIAUTOMATIC",
+            "SegmentDescription" : "Liver Segmentation",
+            "SegmentLabel" : "Liver",
+            "SegmentedPropertyCategoryCodeSequence" : {
+               "CodeMeaning" : "Tissue",
+               "CodeValue" : "85756007",
+               "CodingSchemeDesignator" : "SCT"
+            },
+            "SegmentedPropertyTypeCodeSequence" : {
+               "CodeMeaning" : "Liver",
+               "CodeValue" : "10200004",
+               "CodingSchemeDesignator" : "SCT"
+            },
+            "labelID" : 1,
+            "recommendedDisplayRGBValue" : [ 220, 129, 101 ]
+         },
+         {
+            "SegmentAlgorithmType" : "MANUAL",
+            "SegmentDescription" : "Anatomical Structure",
+            "SegmentLabel" : "Thoracic spine",
+            "SegmentedPropertyCategoryCodeSequence" : {
+               "CodeMeaning" : "Anatomical Structure",
+               "CodeValue" : "123037004",
+               "CodingSchemeDesignator" : "SCT"
+            },
+            "SegmentedPropertyTypeCodeSequence" : {
+               "CodeMeaning" : "Thoracic spine",
+               "CodeValue" : "122495006",
+               "CodingSchemeDesignator" : "SCT"
+            },
+            "labelID" : 2,
+            "recommendedDisplayRGBValue" : [ 226, 202, 134 ]
+         }
+      ],
+      [
+         {
+            "SegmentAlgorithmType" : "MANUAL",
+            "SegmentDescription" : "Anatomical Structure",
+            "SegmentLabel" : "Heart",
+            "SegmentedPropertyCategoryCodeSequence" : {
+               "CodeMeaning" : "Anatomical Structure",
+               "CodeValue" : "123037004",
+               "CodingSchemeDesignator" : "SCT"
+            },
+            "SegmentedPropertyTypeCodeSequence" : {
+               "CodeMeaning" : "Heart",
+               "CodeValue" : "80891009",
+               "CodingSchemeDesignator" : "SCT"
+            },
+            "labelID" : 3,
+            "recommendedDisplayRGBValue" : [ 206, 110, 84 ]
+         }
+      ]
+   ]
+}

docker/Makefile

@@ -44,17 +44,19 @@ prereq.build_dicom3tools: prereq.pull_dockcross
 	&& ( $(TMP)/dockcross make -j$(grep -c processor /proc/cpuinfo) World > /dev/null 2>&1 )\
 	|| echo "Reusing "
 
-# Download and install "ajv" 
+# Download and install "ajv"
 prereq.install_npm_packages: prereq.pull_dockcross
 	mkdir -p $(ROOT_DIR)/$(BUILD_DIR)
+	echo "Root dir: $(ROOT_DIR)"
+	echo "Build dir: $(BUILD_DIR)"
 	# If needed, download node
 	cd $(ROOT_DIR)/$(BUILD_DIR) && \
-	[ ! -e node-v6.9.5-linux-x64 ] && \
-  wget --no-check-certificate https://nodejs.org/dist/v6.9.5/node-v6.9.5-linux-x64.tar.xz && \
-	tar xf node-v6.9.5-linux-x64.tar.xz || true
+	[ ! -e node-v12.19.1-linux-x64 ] && \
+  wget --no-check-certificate https://nodejs.org/dist/v12.19.1/node-v12.19.1-linux-x64.tar.xz && \
+	tar xf node-v12.19.1-linux-x64.tar.xz || true
 	# Install tools required to run DCMQI "doc" tests
 	cd $(ROOT_DIR) && \
-	$(TMP)/dockcross bash -c "export PATH=/work/build/node-v6.9.5-linux-x64/bin:$$PATH && sudo npm install ajv-cli@3.3.0 -g"
+	$(TMP)/dockcross bash -c "export PATH=/work/build/node-v12.19.1-linux-x64/bin:$$PATH && sudo npm install ajv-cli@3.3.0 -g"
 
 # Configure, build and package
 dcmqi.generate_package: prereq.pull_dockcross

include/dcmqi/ConverterBase.h

@@ -37,7 +37,9 @@
 using namespace std;
 
 typedef short ShortPixelType;
+typedef unsigned char CharPixelType;
 typedef itk::Image<ShortPixelType, 3> ShortImageType;
+typedef itk::Image<CharPixelType, 3> CharImageType;
 typedef itk::ImageFileReader<ShortImageType> ShortReaderType;
 
 namespace dcmqi {
@@ -219,6 +221,21 @@ namespace dcmqi {
         sort(originDistances.begin(), originDistances.end());
 
         sliceSpacing = fabs(originDistances[0]-originDistances[1]);
+        if (sliceSpacing == 0)
+        {
+          cout << "Slice spacing is zero, trying to get/use it from DICOM file instead" << endl;
+          // Get Slice Spacing as defined in Pixel Measures FG
+          OFBool isPerFrame;
+          FGPixelMeasures *pixelMeasures = OFstatic_cast(FGPixelMeasures*,
+                                                         fgInterface.get(0, DcmFGTypes::EFG_PIXELMEASURES, isPerFrame));
+          if(!pixelMeasures){
+            cerr << "Canont get Slice Spacing, Pixel Measures FG is missing!" << endl;
+            return EXIT_FAILURE;
+          }
+          if(pixelMeasures->getSpacingBetweenSlices(sliceSpacing,0).good()){
+            cout << "Using Slice Spacing (from DICOM file): " << sliceSpacing << endl;
+          }
+        }
 
         // for(size_t i=1;i<originDistances.size(); i++){
           // float dist1 = fabs(originDistances[i-1]-originDistances[i]);
@@ -232,7 +249,6 @@ namespace dcmqi {
             if(it->second>1)
               overlappingFramesCnt++;
         }
-
         cout << "Total frames with unique IPP: " << originDistances.size() << endl;
         cout << "Total overlapping frames: " << overlappingFramesCnt << endl;
       }
@@ -244,6 +260,9 @@ namespace dcmqi {
         sliceSpacing = 1.0;
       }
       cout << "Origin: " << imageOrigin << endl;
+      cout << "Slice extent: " << sliceExtent << endl;
+      cout << "Slice spacing: " << sliceSpacing << endl;
+
 
       return 0;
     }