From b3f649f6e833485a45e94f99bd78d1dce03b3852 Mon Sep 17 00:00:00 2001
From: delmon <delmon>
Date: Mon, 4 Apr 2011 15:40:44 +0000
Subject: [PATCH] Mathieu Malaterre : - From gdcm 1.x to gdcm 2.0 - Upgrade
 RT_Contour

---
 common/clitkDicomRT_Contour.cxx | 60 +++++++++++++++++++++++++++++++
 common/clitkDicomRT_Contour.h   |  1 +
 common/clitkDicomRT_ROI.cxx     | 64 +++++++++++++++++++++++++++++++++
 common/clitkDicomRT_ROI.h       |  1 +
 4 files changed, 126 insertions(+)

diff --git a/common/clitkDicomRT_Contour.cxx b/common/clitkDicomRT_Contour.cxx
index 9f63dac..e39928a 100644
--- a/common/clitkDicomRT_Contour.cxx
+++ b/common/clitkDicomRT_Contour.cxx
@@ -20,6 +20,11 @@
 #include "clitkDicomRT_Contour.h"
 #include <vtkCellArray.h>
 
+#if GDCM_MAJOR_VERSION == 2
+#include "gdcmAttribute.h"
+#include "gdcmItem.h"
+#endif
+
 //--------------------------------------------------------------------
 clitk::DicomRT_Contour::DicomRT_Contour()
 {
@@ -49,6 +54,61 @@ void clitk::DicomRT_Contour::Print(std::ostream & os) const
 
 //--------------------------------------------------------------------
 #if GDCM_MAJOR_VERSION == 2
+bool clitk::DicomRT_Contour::Read(gdcm::Item const & item)
+{
+  const gdcm::DataSet& nestedds2 = item.GetNestedDataSet();
+
+  // Contour type [Contour Geometric Type]
+  gdcm::Attribute<0x3006,0x0042> contgeotype;
+  contgeotype.SetFromDataSet( nestedds2 );
+
+  if (contgeotype.GetValue() != "CLOSED_PLANAR " && contgeotype.GetValue() != "POINT ") { ///WARNING to the space after the name ...
+    //std::cerr << "Skip this contour : type=" << mType << std::endl;
+    return false;
+  }
+  if (contgeotype.GetValue() == "POINT ") {
+    std::cerr << "Warning: POINT type not fully supported. (don't use GetMesh() with this!)"
+      << std::endl;
+  }
+
+  gdcm::Attribute<0x3006,0x0046> numcontpoints;
+  numcontpoints.SetFromDataSet( nestedds2 );
+  // Number of points [Number of Contour Points]
+  mNbOfPoints = numcontpoints.GetValue();
+  // DD(mNbOfPoints);
+
+  gdcm::Attribute<0x3006,0x0050> at;
+  gdcm::Tag tcontourdata(0x3006,0x0050);
+  const gdcm::DataElement & contourdata = nestedds2.GetDataElement( tcontourdata );
+  at.SetFromDataElement( contourdata );
+  const double* points = at.GetValues();
+  unsigned int npts = at.GetNumberOfValues() / 3;
+
+  assert(at.GetNumberOfValues() == static_cast<unsigned int>(mNbOfPoints)*3);
+
+  // Organize values
+  mData = vtkSmartPointer<vtkPoints>::New();
+  mData->SetDataTypeToDouble();
+  mData->SetNumberOfPoints(mNbOfPoints);
+  for(unsigned int i=0; i<mNbOfPoints; i++) {
+    double p[3];
+    p[0] = points[i*3];
+    p[1] = points[i*3+1];
+    p[2] = points[i*3+2];
+    mData->SetPoint(i, p);
+    if (mZ == -1) mZ = p[2];
+    if (p[2] != mZ) {
+      DD(i);
+      DD(p[2]);
+      DD(mZ);
+      std::cout << "ERROR ! contour not in the same slice" << std::endl;
+      assert(p[2] == mZ);
+    }
+  }
+
+  return true;
+
+}
 #else
 bool clitk::DicomRT_Contour::Read(gdcm::SQItem * item)
 {
diff --git a/common/clitkDicomRT_Contour.h b/common/clitkDicomRT_Contour.h
index 53a1875..abf069f 100644
--- a/common/clitkDicomRT_Contour.h
+++ b/common/clitkDicomRT_Contour.h
@@ -43,6 +43,7 @@ public:
 
   void Print(std::ostream & os = std::cout) const;
 #if GDCM_MAJOR_VERSION == 2
+  bool Read(gdcm::Item const & item);
 #else
   bool Read(gdcm::SQItem * item);
 #endif
diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index 67e5341..cd8af0c 100644
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -21,6 +21,11 @@
 #include <vtkSmartPointer.h>
 #include <vtkAppendPolyData.h>
 
+#if GDCM_MAJOR_VERSION == 2
+#include "gdcmAttribute.h"
+#include "gdcmItem.h"
+#endif
+
 //--------------------------------------------------------------------
 clitk::DicomRT_ROI::DicomRT_ROI()
 {
@@ -130,6 +135,65 @@ double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const
 
 //--------------------------------------------------------------------
 #if GDCM_MAJOR_VERSION == 2
+void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item const & item)
+{
+  const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+
+  gdcm::Attribute<0x3006,0x0084> referencedroinumber;
+  referencedroinumber.SetFromDataSet( nestedds );
+  // Change number if needed
+
+  // TODO
+
+  // ROI number [Referenced ROI Number]
+  mNumber = referencedroinumber.GetValue();
+
+  // Retrieve ROI Name
+  mName = rois[mNumber];
+
+  // ROI Color [ROI Display Color]
+  gdcm::Attribute<0x3006,0x002a> color = {};
+  color.SetFromDataSet( nestedds );
+  assert( color.GetNumberOfValues() == 3 );
+  mColor[0] = color.GetValue(0);
+  mColor[1] = color.GetValue(1);
+  mColor[2] = color.GetValue(2);
+
+  // Read contours [Contour Sequence]
+  gdcm::Tag tcsq(0x3006,0x0040);
+  if( !nestedds.FindDataElement( tcsq ) )
+    {
+    }
+  const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
+  if( !sqi2 || !sqi2->GetNumberOfItems() )
+    {
+    }
+  unsigned int nitems = sqi2->GetNumberOfItems();
+
+  bool contour_processed=false;
+  bool delta_computed=false;
+  double last_z=0;
+  for(unsigned int i = 0; i < nitems; ++i)
+    {
+    const gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
+    DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+    bool b = c->Read(j);
+    if (b) {
+      mListOfContours.push_back(c);
+      if (contour_processed) {
+        double delta=c->GetZ() - last_z;
+        if (delta_computed)
+          assert(mZDelta == delta);
+        else
+          mZDelta = delta;
+      } else
+        contour_processed=true;
+      last_z=c->GetZ();
+    }
+  }
+
+}
 #else
 void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
 {
diff --git a/common/clitkDicomRT_ROI.h b/common/clitkDicomRT_ROI.h
index 8a24b47..b6cc676 100644
--- a/common/clitkDicomRT_ROI.h
+++ b/common/clitkDicomRT_ROI.h
@@ -36,6 +36,7 @@ public:
 
   void Print(std::ostream & os = std::cout) const;
 #if GDCM_MAJOR_VERSION == 2
+  void Read(std::map<int, std::string> & rois, gdcm::Item const & item);
 #else
   void Read(std::map<int, std::string> & rois, gdcm::SQItem * item);
 #endif
-- 
2.46.1