ENH: fixing issues identified by tests

QIICR · Jun 22, 2017 · 3baebf7 · 3baebf7
1 parent ae7ff4c
commit 3baebf7
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Showing 8 changed files with 44 additions and 12 deletions.
diff --git a/apps/paramaps/itkimage2paramap.cxx b/apps/paramaps/itkimage2paramap.cxx
@@ -38,7 +38,7 @@ int main(int argc, char *argv[])
   std::string metadata( (std::istreambuf_iterator<char>(metainfoStream) ),
                         (std::istreambuf_iterator<char>()));
 
-  DcmDataset* result = dcmqi::ParametricMapConverter::itkimage2paramap(parametricMapImage, dcmDatasets, metadata);
+  DcmDataset* result = dcmqi::itkimage2paramapReplacement(parametricMapImage, dcmDatasets, metadata);
 
   if (result == NULL) {
     return EXIT_FAILURE;

diff --git a/include/dcmqi/DICOMFrame.h b/include/dcmqi/DICOMFrame.h
@@ -47,23 +47,26 @@ namespace dcmqi {
       if(dataset->findAndGetOFString(DCM_SOPClassUID, classUIDOF).good()){
         classUID = classUIDOF.c_str();
       }
+
+    };
+
+    int getFrameNumber() const {
+      return frameNumber; // 0 for legacy datasets, 1 or above for enhanced objects
     };
 
-    int getFrameNumber() const; // 0 for legacy datasets, 1 or above for enhanced objects
-    OFString getInstanceUID() const;
     vnl_vector<double> getFrameIPP(){
       return frameIPP;
     };
 
-    string getSeriesUID(){
+    string getSeriesUID() const {
       return seriesUID;
     }
 
-    string getInstanceUID(){
+    string getInstanceUID() const{
       return instanceUID;
     }
 
-    string getClassUID(){
+    string getClassUID() const {
       return classUID;
     }
 

diff --git a/include/dcmqi/MultiframeObject.h b/include/dcmqi/MultiframeObject.h
@@ -78,7 +78,7 @@ class MultiframeObject {
   int initializeVolumeGeometryFromITK(DummyImageType::Pointer);
 
   // initialize attributes of the composite context that are common for all multiframe objects
-  virtual int initializeCompositeContext();
+  //virtual int initializeCompositeContext();
   // check whether all of the attributes required for initialization of the object are present in the
   //   input metadata
   virtual bool metaDataIsComplete();
@@ -113,8 +113,12 @@ class MultiframeObject {
   Json::Value metaDataJson;
 
   // Multiframe DICOM object representation
+  // probably not needed, since need object-specific DCMTK class in
+  // derived classes
   DcmDataset* dcmRepresentation;
 
+  // probably not needed at this level, since for SEG each segment will
+  // have separate geometry definition
   ImageVolumeGeometry volumeGeometry;
 
   // DcmDataset(s) that hold the original representation of the

diff --git a/include/dcmqi/ParametricMapObject.h b/include/dcmqi/ParametricMapObject.h
@@ -33,6 +33,10 @@ class ParametricMapObject : public MultiframeObject {
 
   int updateMetaDataFromDICOM(std::vector<DcmDataset*>);
 
+  DPMParametricMapIOD* getDICOMRepresentation(){
+    return parametricMap;
+  };
+
 protected:
   typedef itk::CastImageFilter<Float32ITKImageType,DummyImageType>
       Float32ToDummyCasterType;

diff --git a/libsrc/DICOMFrame.cpp b/libsrc/DICOMFrame.cpp
@@ -7,6 +7,7 @@
 namespace dcmqi {
   int DICOMFrame::initializeFrameGeometryFromLegacyInstance() {
     OFString ippStr;
+    frameIPP.set_size(3);
     for(int j=0;j<3;j++){
       CHECK_COND(frameDataset->findAndGetOFString(DCM_ImagePositionPatient, ippStr, j));
       frameIPP[j] = atof(ippStr.c_str());

diff --git a/libsrc/MultiframeObject.cpp b/libsrc/MultiframeObject.cpp
@@ -18,16 +18,22 @@ int MultiframeObject::initializeMetaDataFromString(const std::string &metaDataSt
 
 int MultiframeObject::initializeEquipmentInfo() {
   if(sourceRepresentationType == ITK_REPR){
+    equipmentInfoModule = IODEnhGeneralEquipmentModule::EquipmentInfo(QIICR_MANUFACTURER, QIICR_DEVICE_SERIAL_NUMBER,
+                                                                      QIICR_MANUFACTURER_MODEL_NAME, QIICR_SOFTWARE_VERSIONS);
+    /*
     equipmentInfoModule.m_Manufacturer = QIICR_MANUFACTURER;
     equipmentInfoModule.m_DeviceSerialNumber = QIICR_DEVICE_SERIAL_NUMBER;
     equipmentInfoModule.m_ManufacturerModelName = QIICR_MANUFACTURER_MODEL_NAME;
     equipmentInfoModule.m_SoftwareVersions = QIICR_SOFTWARE_VERSIONS;
+    */
+
   } else { // DICOM_REPR
   }
   return EXIT_SUCCESS;
 }
 
 int MultiframeObject::initializeContentIdentification() {
+
   if(sourceRepresentationType == ITK_REPR){
     CHECK_COND(contentIdentificationMacro.setContentCreatorName("dcmqi"));
     if(metaDataJson.isMember("ContentDescription")){
@@ -40,6 +46,12 @@ int MultiframeObject::initializeContentIdentification() {
     } else {
       CHECK_COND(contentIdentificationMacro.setContentLabel("DCMQI"));
     }
+    if(metaDataJson.isMember("InstanceNumber")){
+      CHECK_COND(contentIdentificationMacro.setInstanceNumber(metaDataJson["InstanceNumber"].asCString()));
+    } else {
+      CHECK_COND(contentIdentificationMacro.setInstanceNumber("1"));
+    }
+    CHECK_COND(contentIdentificationMacro.check())
     return EXIT_SUCCESS;
   } else { // DICOM_REPR
   }

diff --git a/libsrc/ParametricMapConverter.cpp b/libsrc/ParametricMapConverter.cpp
@@ -6,18 +6,22 @@
 // DCMQI includes
 #include "dcmqi/ParametricMapConverter.h"
 #include "dcmqi/SegmentationImageConverter.h"
+#include "dcmqi/ParametricMapObject.h"
 
 using namespace std;
 
 namespace dcmqi {
 
   DcmDataset* itkimage2paramapReplacement(const FloatImageType::Pointer &parametricMapImage, vector<DcmDataset*> dcmDatasets,
                                          const string &metaData) {
-    /*
-    ParametricMapConverter pmConverter(parametricMapImage, dcmDatasets, metaData);
-    pmConverter.convert();
+    ParametricMapObject pm;
+    pm.initializeFromITK(parametricMapImage, metaData, dcmDatasets);
+
+    DPMParametricMapIOD* pmap = pm.getDICOMRepresentation();
+
+    DcmDataset* output = new DcmDataset();
+    CHECK_COND(pmap->writeDataset(*output));
 
-    return convert.getDataset(); */
     return NULL;
   }
 

diff --git a/libsrc/ParametricMapObject.cpp b/libsrc/ParametricMapObject.cpp
@@ -26,6 +26,8 @@ int ParametricMapObject::initializeFromITK(Float32ITKImageType::Pointer inputIma
   // NB: the sequence of steps initializing different components of the object parallels that
   //  in the original converter function. It probably makes sense to revisit the sequence
   //  of these steps. It does not necessarily need to happen in this order.
+  initializeEquipmentInfo();
+  initializeContentIdentification();
 
   // TODO: consider creating parametric map object after all FGs are initialized instead
   createParametricMap();
@@ -101,8 +103,10 @@ int ParametricMapObject::createParametricMap() {
 
                                                                     DPMTypes::CQ_RESEARCH);
   // TODO: look into the following, check with @che85 on the purpose of this line!
-  if (OFCondition* pCondition = OFget<OFCondition>(&obj))
+  if (OFCondition* pCondition = OFget<OFCondition>(&obj)) {
+    std::cerr << "Failed to create parametric map object!" << std::endl;
     return EXIT_FAILURE;
+  }
 
   parametricMap = OFget<DPMParametricMapIOD>(&obj);