ENH: a different shot at refactoring

include/dcmqi/Helper.h

@@ -19,7 +19,6 @@
 
 using namespace std;
 
-
 namespace dcmqi {
 
 
@@ -50,6 +49,9 @@ namespace dcmqi {
     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);
   };
 
 }

include/dcmqi/ImageVolume.h

@@ -15,7 +15,11 @@ 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
+  // 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
@@ -47,7 +51,11 @@ namespace dcmqi {
   protected:
     int initializeDirections(FGInterface &);
     int initializeExtent(FGInterface &);
-    bool getDeclaredSpacing(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:
 

include/dcmqi/ImageVolumeGeometry.h

@@ -0,0 +1,47 @@
+//
+// Created by Andrey Fedorov on 3/11/17.
+//
+
+#ifndef DCMQI_IMAGEVOLUMEGEOMETRY_H
+#define DCMQI_IMAGEVOLUMEGEOMETRY_H
+
+
+#include <vnl/vnl_vector.h>
+#include <itkVector.h>
+#include <itkSize.h>
+#include <itkImage.h>
+
+class ImageVolumeGeometry {
+
+  friend class MultiframeObject;
+  friend class ParametricMapObject;
+
+public:
+  typedef itk::Vector<double,3> DoubleVectorType;
+  typedef itk::Size<3> SizeType;
+
+  //  implementation of the image volume geometry
+  // NB: duplicated from MultiframeObject!
+  typedef unsigned char DummyPixelType;
+  typedef itk::Image<DummyPixelType, 3> DummyImageType;
+  typedef DummyImageType::PointType PointType;
+  typedef DummyImageType::DirectionType DirectionType;
+
+  ImageVolumeGeometry();
+
+  int setSpacing(DoubleVectorType);
+  int setOrigin(PointType);
+  int setExtent(SizeType);
+  int setDirections(DirectionType);
+
+protected:
+  // use vnl_vector to simplify support of vector calculations
+  vnl_vector<double> rowDirection, columnDirection, sliceDirection;
+  vnl_vector<double> origin;
+  vnl_vector<unsigned> extent;
+  vnl_vector<double> spacing;
+
+};
+
+
+#endif //DCMQI_IMAGEVOLUMEGEOMETRY_H

include/dcmqi/JSONSegmentationMetaInformationHandler.h

@@ -47,6 +47,7 @@ namespace dcmqi {
     void readSegmentAttributes();
 
     Json::Value createAndGetSegmentAttributes();
+
   };
 
 }

include/dcmqi/MultiframeConverter.h

@@ -44,9 +44,12 @@ namespace dcmqi {
 
   class MultiframeConverter {
   public:
-    virtual int convert();
+    //virtual int convert();
+    MultiframeConverter(){
+    };
+
+
 
-  protected:
     static IODGeneralEquipmentModule::EquipmentInfo getEquipmentInfo();
     static IODEnhGeneralEquipmentModule::EquipmentInfo getEnhEquipmentInfo();
     static ContentIdentificationMacro createContentIdentificationInformation(JSONMetaInformationHandlerBase &metaInfo);

include/dcmqi/MultiframeObject.h

@@ -0,0 +1,131 @@
+//
+// Created by Andrey Fedorov on 3/11/17.
+//
+
+#ifndef DCMQI_MULTIFRAMEOBJECT_H
+#define DCMQI_MULTIFRAMEOBJECT_H
+
+
+#include <dcmtk/dcmfg/fgpixmsr.h>
+#include <dcmtk/dcmfg/fgplanor.h>
+#include <dcmtk/dcmfg/fgplanpo.h>
+#include <dcmtk/dcmfg/fgfracon.h>
+#include <dcmtk/dcmfg/fgderimg.h>
+#include <dcmtk/dcmiod/modfloatingpointimagepixel.h>
+
+#include <itkImage.h>
+#include <json/json.h>
+
+#include <vector>
+#include <dcmtk/dcmiod/modequipment.h>
+#include <dcmtk/dcmiod/modenhequipment.h>
+#include <dcmtk/dcmiod/modmultiframedimension.h>
+
+#include "dcmqi/Exceptions.h"
+#include "dcmqi/ImageVolumeGeometry.h"
+
+using namespace std;
+/*
+ * Class to support conversion between DICOM and ITK representations
+ * of multiframe objects
+ *
+ *
+ */
+class MultiframeObject {
+
+public:
+
+  // initialization from DICOM is always from the dataset(s)
+  //  that encode DICOM representation, optionally augmented by the
+  //  derivation datasets that potentially can be helpful in some
+  //  situations.
+  int initializeFromDICOM(std::vector<DcmDataset*> sourceDataset);
+  int initializeFromDICOM(std::vector<DcmDataset*> sourceDatasets,
+                          std::vector<DcmDataset*> derivationDatasets);
+
+  // initialization from ITK will be specific to the derived types,
+  //  although there will be some common initialization of the metadata
+
+  // Output is always a single DcmDataset, since this is a multiframe
+  //  object
+  DcmDataset* getDcmDataset() const;
+  Json::Value getMetaDataJson() const;
+
+  // get ITK representation will be specific to the derived classes,
+  //  since the type of the ITK image and the number of ITK images is
+  //  different between PM and SEG
+
+protected:
+
+  // Helpers to convert to dummy image type to support common
+  //  implementation of the image volume geometry
+  typedef unsigned char DummyPixelType;
+  typedef itk::Image<DummyPixelType, 3> DummyImageType;
+  typedef DummyImageType::PointType PointType;
+  typedef DummyImageType::DirectionType DirectionType;
+
+  int initializeMetaDataFromString(const std::string&);
+  // what this function does depends on whether we are coming from
+  //  DICOM or from ITK. No parameters, since all it does is exchange
+  //  between DICOM and MetaData
+  int initializeEquipmentInfo();
+  int initializeContentIdentification();
+
+  // from ITK
+  int initializeVolumeGeometryFromITK(DummyImageType::Pointer);
+
+  virtual int initializeCompositeContext();
+  virtual bool metaDataIsComplete();
+
+  // List of tags, and FGs they belong to, for initializing dimensions module
+  int initializeDimensions(IODMultiframeDimensionModule&, std::vector<std::pair<DcmTag, DcmTag> >);
+
+  // constants to describe original representation of the data being converted
+  enum {
+    DICOM_REPR = 0,
+    ITK_REPR
+  };
+  int sourceRepresentationType;
+
+  // TODO: abstract this into a different class, which would help with:
+  //  - checking for presence of attributes
+  //  - handling of defaults (in the future, initialized from the schema?)
+  //  - simplifying common access patterns (access to the Code tuples)
+  Json::Value metaDataJson;
+
+  // Multiframe DICOM object representation
+  DcmDataset* dcmRepresentation;
+
+  ImageVolumeGeometry volumeGeometry;
+
+  // DcmDataset(s) that hold the original representation of the
+  //  object, when the sourceRepresentationType == DICOM_REPR
+  OFVector<DcmDataset*> sourceDcmDatasets;
+
+  // Common components present in the derived classes
+  // TODO: check whether both PM and SEG use Enh module or not, refactor based on that
+  IODEnhGeneralEquipmentModule::EquipmentInfo equipmentInfoModule;
+  ContentIdentificationMacro contentIdentificationMacro;
+  IODMultiframeDimensionModule dimensionsModule;
+
+  // DcmDataset(s) that were used to derive the object
+  //  Probably will only be populated when sourceRepresentationType == ITK_REPR
+  // Purpose of those:
+  //  1) initialize derivation derivationImageFG (ITK->)
+  //  2) initialize CommonInstanceReferenceModule (ITK->)
+  //  3) initialize common attributes (ITK->)
+  OFVector<DcmDataset*> derivationDcmDatasets;
+
+  // Functional groups common to all MF objects:
+  //  - Shared
+  FGPixelMeasures pixelMeasuresFG;
+  FGPlaneOrientationPatient planeOrientationPatientFG;
+  //  - Per-frame
+  OFVector<FGPlanePosPatient> planePosPatientFGList;
+  OFVector<FGFrameContent> frameContentFGList;
+  OFVector<FGDerivationImage> derivationImageFGList;
+
+};
+
+
+#endif //DCMQI_MULTIFRAMEOBJECT_H

include/dcmqi/ParametricMapConverter.h

@@ -50,7 +50,7 @@ namespace dcmqi {
                                  const string &metaData);
     static pair <FloatImageType::Pointer, string> paramap2itkimage(DcmDataset *pmapDataset);
 
-    // do the conversion
+    // given one representation, generate the parallel one
     int convert();
 
     // get the result
@@ -75,6 +75,7 @@ namespace dcmqi {
     // these are the items we will need in the process of conversion
     vector<DcmDataset*> referencedDatasets;
     string metaData;
+
   };
 
 }

include/dcmqi/ParametricMapObject.h

@@ -0,0 +1,62 @@
+//
+// Created by Andrey Fedorov on 3/11/17.
+//
+
+#ifndef DCMQI_PARAMETRICMAPOBJECT_H
+#define DCMQI_PARAMETRICMAPOBJECT_H
+
+
+#include <dcmtk/dcmfg/fgframeanatomy.h>
+#include <dcmtk/dcmfg/fgidentpixeltransform.h>
+#include <dcmtk/dcmfg/fgparametricmapframetype.h>
+#include <dcmtk/dcmfg/fgrealworldvaluemapping.h>
+#include <dcmtk/dcmpmap/dpmparametricmapiod.h>
+#include <itkCastImageFilter.h>
+
+#include "MultiframeObject.h"
+
+/*
+ *
+ */
+class ParametricMapObject : public MultiframeObject {
+public:
+  typedef IODFloatingPointImagePixelModule::value_type Float32PixelType;
+  typedef itk::Image<Float32PixelType, 3> Float32ITKImageType;
+
+  // metadata is mandatory, since not all of the attributes can be present
+  //  in the derivation DcmDataset(s)
+  int initializeFromITK(Float32ITKImageType::Pointer, const string&);
+  // metadata is mandatory, optionally, derivation DcmDataset(s) can
+  //  help
+  int initializeFromITK(Float32ITKImageType::Pointer, const string&,
+                        std::vector<DcmDataset*>);
+
+  int updateMetaDataFromDICOM(std::vector<DcmDataset*>);
+
+protected:
+  typedef itk::CastImageFilter<Float32ITKImageType,DummyImageType>
+      Float32ToDummyCasterType;
+
+  int initializeVolumeGeometry();
+  int createParametricMap();
+  int initializeDimensionsModule();
+  int initializeCompositeContext();
+
+  // Functional groups initialization
+
+  // Functional groups specific to PM:
+  //  - Shared
+  FGFrameAnatomy frameAnatomyFG;
+  FGIdentityPixelValueTransformation identityPixelValueTransformationFG;
+  FGParametricMapFrameType parametricMapFrameTypeFG;
+  FGRealWorldValueMapping rwvmFG;
+
+  // Data containers specific to this object
+  Float32ITKImageType::Pointer itkImage;
+
+private:
+  DPMParametricMapIOD* parametricMap;
+};
+
+
+#endif //DCMQI_PARAMETRICMAPOBJECT_H

include/dcmqi/SegmentationImageObject.h

@@ -0,0 +1,16 @@
+//
+// Created by Andrey Fedorov on 3/11/17.
+//
+
+#ifndef DCMQI_SEGMENTATIONIMAGEOBJECT_H
+#define DCMQI_SEGMENTATIONIMAGEOBJECT_H
+
+
+#include "MultiframeObject.h"
+
+class SegmentationImageObject : public MultiframeObject {
+
+};
+
+
+#endif //DCMQI_SEGMENTATIONIMAGEOBJECT_H

libsrc/CMakeLists.txt

@@ -1,7 +1,6 @@
 
 #-----------------------------------------------------------------------------
-set(ADDITIONAL_SRCS DICOMFrame.cpp ../include/dcmqi/DICOMFrame.h ImageVolume.cpp ../include/dcmqi/ImageVolume.h SegmentVolume.cpp ../include/dcmqi/SegmentVolume.h)
->>>>>>> WIP: refactoring of the multiframe conversion implementation
+set(ADDITIONAL_SRCS DICOMFrame.cpp ../include/dcmqi/DICOMFrame.h ImageVolume.cpp ../include/dcmqi/ImageVolume.h SegmentVolume.cpp ../include/dcmqi/SegmentVolume.h MultiframeObject.cpp ../include/dcmqi/MultiframeObject.h ParametricMapObject.cpp ../include/dcmqi/ParametricMapObject.h SegmentationImageObject.cpp ../include/dcmqi/SegmentationImageObject.h ImageVolumeGeometry.cpp ../include/dcmqi/ImageVolumeGeometry.h)
 
 if(DCMQI_BUILTIN_JSONCPP)
   list(APPEND ADDITIONAL_SRCS

libsrc/Helper.cpp

@@ -1,5 +1,6 @@
 
 // DCMQI includes
+#include <dcmqi/QIICRUIDs.h>
 #include "dcmqi/Helper.h"
 
 namespace dcmqi {
@@ -340,5 +341,15 @@ namespace dcmqi {
     return new CodeSequenceMacro(code.c_str(), designator.c_str(), meaning.c_str());
   }
 
+  OFString Helper::generateUID() {
+    char charUID[128];
+    dcmGenerateUniqueIdentifier(charUID, QIICR_UID_ROOT);
+    return OFString(charUID);
+  }
 
+  OFString Helper::getTagAsOFString(DcmDataset* dcm, DcmTagKey tag) {
+    OFString value;
+    CHECK_COND(dcm->findAndGetOFString(tag, value));
+    return value;
+  }
 }