WIP: Use DcmItem in API where possible.

CMakeExternals/DCMTK.cmake

@@ -28,13 +28,13 @@ if(NOT DEFINED DCMTK_DIR AND NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
 
   ExternalProject_SetIfNotDefined(
     ${proj}_GIT_REPOSITORY
-    "${EP_GIT_PROTOCOL}://github.com/commontk/DCMTK.git"
+    "${EP_GIT_PROTOCOL}://github.com/michaelonken/dcmtk.git"
     QUIET
     )
 
   ExternalProject_SetIfNotDefined(
     ${proj}_REVISION_TAG
-    "patched-DCMTK-3.6.6_20210115"
+    "use_dcmitem_instead_of_dcmdataset"
     QUIET
     )
 
@@ -94,11 +94,14 @@ if(NOT DEFINED DCMTK_DIR AND NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
       -DDCMTK_WITH_PNG:BOOL=OFF # see github issue #25
       -DDCMTK_WITH_TIFF:BOOL=OFF  # see github issue #25
       -DDCMTK_WITH_XML:BOOL=OFF  # see github issue #25
-      -DDCMTK_WITH_ICONV:BOOL=OFF  # see github issue #178
+      -DDCMTK_WITH_ICU:BOOL=OFF  # make sure to not include any ICU dependencies
+      -DDCMTK_WITH_ICONV:BOOL=OFF  # make sure to not include any iconv dependencies
       -DDCMTK_WITH_SNDFILE:BOOL=OFF # see github issue #395
       -DDCMTK_FORCE_FPIC_ON_UNIX:BOOL=ON
       -DDCMTK_OVERWRITE_WIN32_COMPILER_FLAGS:BOOL=OFF
-      -DDCMTK_ENABLE_BUILTIN_DICTIONARY:BOOL=ON
+      -DDCMTK_DEFAULT_DICT:STRING=builtin
+      -DDCMTK_ENABLE_CHARSET_CONVERSION:STRING=oficonv
+      -DDCMTK_ENABLE_BUILTIN_OFICONV_DATA:BOOL=ON
       -DDCMTK_ENABLE_PRIVATE_TAGS:BOOL=ON
       -DDCMTK_COMPILE_WIN32_MULTITHREADED_DLL:BOOL=ON
       -DDCMTK_ENABLE_STL:BOOL=ON

CMakeLists.txt

@@ -274,6 +274,7 @@ set(export_targets TRUE)
 if(DCMQI_SUPERBUILD_BINARY_DIR)
   string(FIND ${ITK_DIR}   "${DCMQI_SUPERBUILD_BINARY_DIR}" itk_here)
   string(FIND ${DCMTK_DIR} "${DCMQI_SUPERBUILD_BINARY_DIR}" dcmtk_here)
+  message(STATUS "---------------------------------------- DCMTK DIR: ${DCMTK_DIR} ------------------------------------------")
 
   if(NOT ${itk_here} EQUAL -1 OR NOT ${dcmtk_here} EQUAL -1)
     set(export_targets FALSE)

apps/paramaps/itkimage2paramap.cxx

@@ -45,7 +45,8 @@ int main(int argc, char *argv[])
                         (std::istreambuf_iterator<char>()));
 
   try {
-    DcmDataset* result = dcmqi::ParaMapConverter::itkimage2paramap(parametricMapImage, dcmDatasets, metadata);
+    std::vector<DcmItem*> toItems(dcmDatasets.begin(), dcmDatasets.end());
+    DcmDataset* result = dcmqi::ParaMapConverter::itkimage2paramap(parametricMapImage, toItems, metadata);
 
     if (result == NULL) {
       std::cerr << "ERROR: Conversion failed." << std::endl;

apps/seg/itkimage2segimage.cxx

@@ -120,9 +120,10 @@ int main(int argc, char *argv[])
     }
     segmentations = segmentationsReordered;
   }
-
+  // Copy to DcmItem* vector to use it in itkimage2dcmSegmentation() call
+  std::vector<DcmItem*> dcmItems(dcmDatasets.begin(), dcmDatasets.end());
   try {
-    DcmDataset* result = dcmqi::Itk2DicomConverter::itkimage2dcmSegmentation(dcmDatasets,
+    DcmDataset* result = dcmqi::Itk2DicomConverter::itkimage2dcmSegmentation(dcmItems,
                                                                              segmentations,
                                                                              metadata,
                                                                              skipEmptySlices,

include/dcmqi/ConverterBase.h

@@ -298,8 +298,8 @@ namespace dcmqi {
     }
 
     // AF: I could not quickly figure out how to template this function over image type - suggestions are welcomed!
-    static vector<vector<int> > getSliceMapForSegmentation2DerivationImage(const vector<DcmDataset*> dcmDatasets,
-                                                                                       const ShortImageType::Pointer &labelImage) {
+    static vector<vector<int> > getSliceMapForSegmentation2DerivationImage(const vector<DcmItem*> dcmDatasets,
+                                                                           const ShortImageType::Pointer &labelImage) {
       // Find mapping from the segmentation slice number to the derivation image
       // Assume that orientation of the segmentation is the same as the source series
       unsigned numLabelSlices = labelImage->GetLargestPossibleRegion().GetSize()[2];

include/dcmqi/Dicom2ItkConverter.h

@@ -97,7 +97,7 @@ class Dicom2ItkConverter : public ConverterBase
      *
      * @param segDataset A pointer to the DICOM dataset containing the metadata.
      */
-    void populateMetaInformationFromDICOM(DcmDataset* segDataset);
+    void populateMetaInformationFromDICOM(DcmItem* segDataset);
 
     /**
      * Helper method that uses the OverlapUtil class to retrieve non-overlapping segment

include/dcmqi/Itk2DicomConverter.h

@@ -39,7 +39,7 @@ namespace dcmqi {
     /**
      * @brief Converts itk images data into a DICOM Segmentation object.
      *
-     * @param dcmDatasets A vector of DICOM datasets with the images that the segmentation is based on.
+     * @param dcmDatasets A vector of DICOM items (usually dataset level) with the images that the segmentation is based on.
      * @param segmentations A vector of itk images to be converted.
      * @param metaData A string containing the metadata to be used for the DICOM Segmentation object.
      * @param skipEmptySlices A boolean indicating whether to skip empty slices during the conversion.
@@ -59,7 +59,7 @@ namespace dcmqi {
      *        display.
      * @return A pointer to the resulting DICOM Segmentation object.
      */
-    static DcmDataset* itkimage2dcmSegmentation(vector<DcmDataset*> dcmDatasets,
+    static DcmDataset* itkimage2dcmSegmentation(vector<DcmItem*> dcmDatasets,
                           vector<ShortImageType::Pointer> segmentations,
                           const string &metaData,
                           bool skipEmptySlices=true,
@@ -78,7 +78,7 @@ namespace dcmqi {
      *  @param  segNum2Label mapping from segment number (old) to label ID (new)
      *  @return true if successful, false otherwise
      */
-    static bool mapLabelIDsToSegmentNumbers(DcmDataset* dset, map<Uint16, Uint16> segNum2Label);
+    static bool mapLabelIDsToSegmentNumbers(DcmItem* dset, map<Uint16, Uint16> segNum2Label);
 
     /** Check whether labels (values in given map) are unique and monotonically increasing by 1
      *  @param  segNum2Label mapping from segment number (old) to label ID (new)

include/dcmqi/ParaMapConverter.h

@@ -34,10 +34,10 @@ namespace dcmqi {
   class ParaMapConverter : public ConverterBase {
 
   public:
-    static DcmDataset* itkimage2paramap(const FloatImageType::Pointer &parametricMapImage, vector<DcmDataset*> dcmDatasets,
+    static DcmDataset* itkimage2paramap(const FloatImageType::Pointer &parametricMapImage, vector<DcmItem*> dcmDatasets,
                                         const string &metaData);
 
-    static pair <FloatImageType::Pointer, string> paramap2itkimage(DcmDataset *pmapDataset);
+    static pair <FloatImageType::Pointer, string> paramap2itkimage(DcmDataset *pmapDataset); //TODO: Check
   protected:
     static OFCondition addFrame(DPMParametricMapIOD &map, const FloatImageType::Pointer &parametricMapImage,
                                 const JSONParametricMapMetaInformationHandler &metaInfo, const unsigned long frameNo, OFVector<FGBase*> perFrameGroups);

libsrc/CMakeLists.txt

@@ -73,7 +73,7 @@ set(_dcmtk_includes)
 if(TARGET DCMTK::DCMTK)
   set(_dcmtk_libs DCMTK::DCMTK)
 else()
-  set(_dcmtk_libs ${DCMTK_LIBRARIES})
+  set(_dcmtk_libs DCMTK::DCMTK)
   set(_dcmtk_includes ${DCMTK_INCLUDE_DIRS})
 endif()
 

libsrc/Dicom2ItkConverter.cpp

@@ -253,7 +253,7 @@ itk::SmartPointer<ShortImageType> Dicom2ItkConverter::nextResult()
 
 // -------------------------------------------------------------------------------------
 
-void Dicom2ItkConverter::populateMetaInformationFromDICOM(DcmDataset* segDataset)
+void Dicom2ItkConverter::populateMetaInformationFromDICOM(DcmItem* segDataset)
 {
     OFString creatorName, sessionID, timePointID, seriesDescription, seriesNumber, instanceNumber, bodyPartExamined,
         coordinatingCenter;

libsrc/Itk2DicomConverter.cpp

@@ -25,11 +25,11 @@ namespace dcmqi {
 
   // -------------------------------------------------------------------------------------
 
-  DcmDataset* Itk2DicomConverter::itkimage2dcmSegmentation(vector<DcmDataset*> dcmDatasets,
-                                                          vector<ShortImageType::Pointer> segmentations,
-                                                          const string &metaData,
-                                                          bool skipEmptySlices,
-                                                          bool useLabelIDAsSegmentNumber) {
+  DcmDataset* Itk2DicomConverter::itkimage2dcmSegmentation(vector<DcmItem*> dcmDatasets,
+                                                           vector<ShortImageType::Pointer> segmentations,
+                                                           const string &metaData,
+                                                           bool skipEmptySlices,
+                                                           bool useLabelIDAsSegmentNumber) {
 
     ShortImageType::SizeType inputSize = segmentations[0]->GetBufferedRegion().GetSize();
 
@@ -359,7 +359,7 @@ namespace dcmqi {
                 frameData[framePixelCnt] = 0;
             }
 
-            OFVector<DcmDataset*> siVector;
+            OFVector<DcmItem*> siVector;
             for(size_t derImageInstanceNum=0;
                 derImageInstanceNum<slice2derimg[sliceNumber].size();
                 derImageInstanceNum++){
@@ -503,7 +503,7 @@ namespace dcmqi {
   }
 
 
-  bool Itk2DicomConverter::mapLabelIDsToSegmentNumbers(DcmDataset* dset, map<Uint16,Uint16> segNum2Label)
+  bool Itk2DicomConverter::mapLabelIDsToSegmentNumbers(DcmItem* dset, map<Uint16,Uint16> segNum2Label)
   {
     cout << "Mapping Label IDs to Segment Numbers" << endl;
     DcmSequenceOfItems* seq = NULL;

libsrc/ParaMapConverter.cpp

@@ -26,7 +26,7 @@ using namespace std;
 
 namespace dcmqi {
 
-  DcmDataset* ParaMapConverter::itkimage2paramap(const FloatImageType::Pointer &parametricMapImage, vector<DcmDataset*> dcmDatasets,
+  DcmDataset* ParaMapConverter::itkimage2paramap(const FloatImageType::Pointer &parametricMapImage, vector<DcmItem*> dcmDatasets,
                                          const string &metaData) {
 
     MinMaxCalculatorType::Pointer calculator = MinMaxCalculatorType::New();
@@ -67,7 +67,7 @@ namespace dcmqi {
 
     DPMParametricMapIOD* pMapDoc = OFget<DPMParametricMapIOD>(&obj);
 
-    DcmDataset* srcDataset = NULL;
+    DcmItem* srcDataset = NULL;
     if(dcmDatasets.size()){
       srcDataset = dcmDatasets[0];
     }
@@ -296,7 +296,7 @@ namespace dcmqi {
 
     for (unsigned long sliceNumber = 0; result.good() && (sliceNumber < inputSize[2]); sliceNumber++) {
 
-      OFVector<DcmDataset*> siVector;
+      OFVector<DcmItem*> siVector;
       for(size_t derImageInstanceNum=0;
           derImageInstanceNum<slice2derimg[sliceNumber].size();
           derImageInstanceNum++){