QIICR · fedorov · Mar 10, 2017 · Mar 11, 2017 · Mar 14, 2017 · Mar 16, 2017
diff --git a/.gitignore b/.gitignore
@@ -35,3 +35,5 @@ CMakeLists.txt.user*
 __pycache__/
 *.py[cod]
 *$py.class
+
+node_modules
diff --git a/README.md b/README.md
@@ -1,7 +1,4 @@
-
-[![OpenHub](https://www.openhub.net/p/dcmqi/widgets/project_thin_badge.gif)](https://www.openhub.net/p/dcmqi) [![codecov](https://codecov.io/gh/QIICR/dcmqi/branch/master/graph/badge.svg)](https://codecov.io/gh/QIICR/dcmqi) [![Join the chat at https://gitter.im/QIICR/dcmqi](https://badges.gitter.im/QIICR/dcmqi.svg)](https://gitter.im/QIICR/dcmqi?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
-
-
+[![OpenHub](https://www.openhub.net/p/dcmqi/widgets/project_thin_badge.gif)](https://www.openhub.net/p/dcmqi) [![codecov](https://codecov.io/gh/QIICR/dcmqi/branch/master/graph/badge.svg)](https://codecov.io/gh/QIICR/dcmqi) [![Join the chat at https://gitter.im/QIICR/dcmqi](https://badges.gitter.im/QIICR/dcmqi.svg)](https://gitter.im/QIICR/dcmqi?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) 
 
 | Docker | [![](https://images.microbadger.com/badges/version/qiicr/dcmqi:v1.0.5.svg)](https://microbadger.com/images/qiicr/dcmqi:v1.0.5) | [![](https://images.microbadger.com/badges/version/qiicr/dcmqi.svg)](https://microbadger.com/images/qiicr/dcmqi) |
 |--------|--------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------|

diff --git a/apps/paramaps/itkimage2paramap.cxx b/apps/paramaps/itkimage2paramap.cxx
@@ -3,7 +3,7 @@
 
 // DCMQI includes
 #undef HAVE_SSTREAM // Avoid redefinition warning
-#include "dcmqi/ParaMapConverter.h"
+#include "dcmqi/ParametricMapConverter.h"
 #include "dcmqi/internal/VersionConfigure.h"
 
 
@@ -44,7 +44,7 @@ int main(int argc, char *argv[])
   std::string metadata( (std::istreambuf_iterator<char>(metainfoStream) ),
                         (std::istreambuf_iterator<char>()));
 
-  DcmDataset* result = dcmqi::ParaMapConverter::itkimage2paramap(parametricMapImage, dcmDatasets, metadata);
+  DcmDataset* result = dcmqi::itkimage2paramapReplacement(parametricMapImage, dcmDatasets, metadata);
 
   if (result == NULL) {
     return EXIT_FAILURE;

diff --git a/apps/paramaps/paramap2itkimage.cxx b/apps/paramaps/paramap2itkimage.cxx
@@ -3,7 +3,7 @@
 
 // DCMQI includes
 #undef HAVE_SSTREAM // Avoid redefinition warning
-#include "dcmqi/ParaMapConverter.h"
+#include "dcmqi/ParametricMapConverter.h"
 #include "dcmqi/internal/VersionConfigure.h"
 
 
@@ -25,7 +25,7 @@ int main(int argc, char *argv[])
   CHECK_COND(sliceFF.loadFile(inputFileName.c_str()));
   DcmDataset* dataset = sliceFF.getDataset();
 
-  pair <FloatImageType::Pointer, string> result =  dcmqi::ParaMapConverter::paramap2itkimage(dataset);
+  pair <FloatImageType::Pointer, string> result =  dcmqi::paramap2itkimageReplacement(dataset);
 
   string fileExtension = helper::getFileExtensionFromType(outputType);
 

diff --git a/apps/seg/itkimage2segimage.cxx b/apps/seg/itkimage2segimage.cxx
@@ -3,7 +3,7 @@
 
 // DCMQI includes
 #undef HAVE_SSTREAM // Avoid redefinition warning
-#include "dcmqi/ImageSEGConverter.h"
+#include "dcmqi/SegmentationImageConverter.h"
 #include "dcmqi/internal/VersionConfigure.h"
 
 typedef dcmqi::Helper helper;
@@ -91,7 +91,7 @@ int main(int argc, char *argv[])
     segmentations = segmentationsReordered;
   }
 
-  DcmDataset* result = dcmqi::ImageSEGConverter::itkimage2dcmSegmentation(dcmDatasets, segmentations, metadata, skipEmptySlices);
+  DcmDataset* result = dcmqi::SegmentationImageConverter::itkimage2dcmSegmentation(dcmDatasets, segmentations, metadata, skipEmptySlices);
 
   if (result == NULL){
     return EXIT_FAILURE;

diff --git a/apps/seg/segimage2itkimage.cxx b/apps/seg/segimage2itkimage.cxx
@@ -3,7 +3,7 @@
 
 // DCMQI includes
 #undef HAVE_SSTREAM // Avoid redefinition warning
-#include "dcmqi/ImageSEGConverter.h"
+#include "dcmqi/SegmentationImageConverter.h"
 #include "dcmqi/internal/VersionConfigure.h"
 
 
@@ -24,7 +24,7 @@ int main(int argc, char *argv[])
   CHECK_COND(sliceFF.loadFile(inputSEGFileName.c_str()));
   DcmDataset* dataset = sliceFF.getDataset();
 
-  pair <map<unsigned,ShortImageType::Pointer>, string> result =  dcmqi::ImageSEGConverter::dcmSegmentation2itkimage(dataset);
+  pair <map<unsigned,ShortImageType::Pointer>, string> result =  dcmqi::dcmSegmentation2itkimageReplacement(dataset);
 
   string outputPrefix = prefix.empty() ? "" : prefix + "-";
 

diff --git a/doc/examples/pm-example-float.json b/doc/examples/pm-example-float.json
@@ -22,8 +22,8 @@
     "CodeMeaning": "m2/s"
   },
   "MeasurementMethodCode": {
-    "CodeValue": "DWMPxxxx10",
-    "CodingSchemeDesignator": "99QIICR",
+    "CodeValue": "113290",
+    "CodingSchemeDesignator": "DCM",
     "CodeMeaning": "Mono-exponential diffusion model"
   },
   "SourceImageDiffusionBValues": ["0","1400"],

diff --git a/doc/examples/pm-example.json b/doc/examples/pm-example.json
@@ -22,8 +22,8 @@
     "CodeMeaning": "um2/s"
   },
   "MeasurementMethodCode": {
-    "CodeValue": "DWMPxxxx10",
-    "CodingSchemeDesignator": "99QIICR",
+    "CodeValue": "113290",
+    "CodingSchemeDesignator": "DCM",
     "CodeMeaning": "Mono-exponential diffusion model"
   },
   "SourceImageDiffusionBValues": ["0","1400"],

diff --git a/include/dcmqi/DICOMFrame.h b/include/dcmqi/DICOMFrame.h
@@ -0,0 +1,104 @@
+//
+// Created by Andrey Fedorov on 3/9/17.
+//
+
+#ifndef DCMQI_DICOMFRAME_H
+#define DCMQI_DICOMFRAME_H
+
+#include <dcmtk/dcmdata/dcdatset.h>
+#include <dcmtk/dcmdata/dctk.h>
+#include "ImageVolumeGeometry.h"
+#include "Exceptions.h"
+
+namespace dcmqi {
+
+  // Describe input/output frames for the purposes of sorting and associating with the
+  // slices of the ITK volume
+  class DICOMFrame {
+  public:
+    // distinguish between the frames from the legacy data and enhanced multiframe objects
+    enum {
+      LegacyInstanceFrame = 0,
+      EnhancedInstanceFrame
+    };
+
+    DICOMFrame(DcmDataset *dataset, int number=0) :
+        frameNumber(number),
+        frameDataset(dataset) {
+
+      Uint32 numFrames;
+      if(dataset->findAndGetUint32(DCM_NumberOfFrames, numFrames).good()){
+        frameType = EnhancedInstanceFrame;
+        if(!number){
+          std::cerr << "ERROR: DICOMFrame object for an enhanced frame is initialized with frame 0!" << std::endl;
+        }
+      } else {
+        frameType = LegacyInstanceFrame;
+        initializeFrameGeometryFromLegacyInstance();
+      }
+
+      OFString seriesUIDOF, instanceUIDOF, classUIDOF;
+      if(dataset->findAndGetOFString(DCM_SeriesInstanceUID, seriesUIDOF).good()){
+        seriesUID = seriesUIDOF.c_str();
+      }
+      if(dataset->findAndGetOFString(DCM_SOPInstanceUID, instanceUIDOF).good()){
+        instanceUID = instanceUIDOF.c_str();
+      }
+      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
+    };
+
+    vnl_vector<double> getFrameIPP(){
+      return frameIPP;
+    };
+
+    string getSeriesUID() const {
+      return seriesUID;
+    }
+
+    string getInstanceUID() const{
+      return instanceUID;
+    }
+
+    string getClassUID() const {
+      return classUID;
+    }
+
+    DcmDataset* getDataset() const {
+      return frameDataset;
+    }
+
+  private:
+
+    int initializeFrameGeometryFromLegacyInstance();
+    int initializeFrameGeometryFromEnhancedInstance();
+
+    int frameType;
+    DcmDataset *frameDataset;
+    int frameNumber;
+    vnl_vector<double> frameIPP;
+
+    string seriesUID, instanceUID, classUID;
+
+    ImageVolumeGeometry frameGeometry;
+
+  };
+
+  struct DICOMFrame_compare {
+    bool operator() (const DICOMFrame& lhs, const DICOMFrame& rhs) const{
+      std::stringstream s1,s2;
+      s1 << lhs.getInstanceUID();
+      s2 << rhs.getInstanceUID();
+      return (s1.str() < s2.str()) && (lhs.getFrameNumber() < rhs.getFrameNumber());
+    }
+  };
+
+}
+
+#endif //DCMQI_DICOMFRAME_H
diff --git a/include/dcmqi/Helper.h b/include/dcmqi/Helper.h
@@ -17,8 +17,9 @@
 // DCMQI includes
 #include "dcmqi/Exceptions.h"
 
-using namespace std;
+#include <json/json.h>
 
+using namespace std;
 
 namespace dcmqi {
 
@@ -60,10 +61,21 @@ namespace dcmqi {
 
     static CodeSequenceMacro stringToCodeSequenceMacro(string str);
     static DSRCodedEntryValue stringToDSRCodedEntryValue(string str);
+    static string codeSequenceMacroToString(CodeSequenceMacro);
+
+    static CodeSequenceMacro jsonToCodeSequenceMacro(Json::Value);
 
     static void checkValidityOfFirstSrcImage(DcmSegmentation *segdoc);
 
     static CodeSequenceMacro* createNewCodeSequence(const string& code, const string& designator, const string& meaning);
+
+    static OFString generateUID();
+    static OFString getTagAsOFString(DcmDataset*, DcmTagKey);
+
+    static string getCodeSequenceValue(CodeSequenceMacro &codeSequence);
+    static string getCodeSequenceDesignator(CodeSequenceMacro &codeSequence);
+    static string getCodeSequenceMeaning(CodeSequenceMacro &codeSequence);
+    static Json::Value codeSequence2Json(CodeSequenceMacro &codeSequence);
   };
 
 }

diff --git a/include/dcmqi/ImageVolume.h b/include/dcmqi/ImageVolume.h
@@ -0,0 +1,74 @@
+//
+// Created by Andrey Fedorov on 3/9/17.
+//
+
+#ifndef DCMQI_IMAGEVOLUME_H
+#define DCMQI_IMAGEVOLUME_H
+
+#include <vnl/vnl_vector.h>
+#include <dcmtk/dcmfg/fginterface.h>
+#include <dcmtk/dcmiod/modfloatingpointimagepixel.h>
+
+#include <itkImage.h>
+
+namespace dcmqi {
+
+  // Maintain properties of the image volume
+  // Attributes ara parallel to those of itkImageData, but limited to what we need for the task of conversion,
+  // and the class is not templated over the pixel type, since we may not know the pixel type
+  // at the time class is instantiated.
+  //
+  // Initially, limit implementation and support to just Float32 used by the original PM converter.
+
+  class ImageVolume {
+  public:
+    // pixel types that are relevant for the types of objects we want to support
+    enum {
+      FLOAT32 = 0, // PM
+      FLOAT64,     // PM
+      UINT16       // PM or SEG
+    };
+
+    typedef IODFloatingPointImagePixelModule::value_type Float32PixelType;
+    typedef itk::Image<Float32PixelType, 3> Float32ITKImageType;
+
+    ImageVolume(){
+      rowDirection.set_size(3);
+      columnDirection.set_size(3);
+      sliceDirection.set_size(3);
+      origin.set_size(3);
+      spacing.set_size(3);
+      pixelData = NULL;
+    }
+
+    // while going from DICOM PM/SEG, we get volume information from FGInterface
+    int initializeFromDICOM(FGInterface&);
+    int initializeFromITK(Float32ITKImageType::Pointer);
+
+    // TODO - inherited class? or separate segments before passing to this one?
+    // int initializeFromSegment(FGInterface&, unsigned);
+
+  protected:
+    int initializeDirections(FGInterface &);
+    int initializeExtent(FGInterface &);
+    bool getDeclaredSliceSpacing(FGInterface&);
+    bool getCalculatedSliceSpacing();
+
+    int setDirections(vnl_vector<double> rowDirection, vnl_vector<double> columnDirection, vnl_vector<double> sliceDirection);
+    int setOrigin(vnl_vector<double>);
+
+  private:
+
+    // use vnl_vector to simplify support of vector calculations
+    vnl_vector<double> rowDirection, columnDirection, sliceDirection;
+    vnl_vector<double> origin;
+    unsigned sliceExtent;
+    vnl_vector<double> spacing;
+    void* pixelData;
+    int pixelDataType;
+  };
+
+};
+
+
+#endif //DCMQI_IMAGEVOLUME_H