Add gdcm dependencies

[clitk.git] / common / clitkImage2DicomRTStructFilter.txx

diff --git a/common/clitkImage2DicomRTStructFilter.txx b/common/clitkImage2DicomRTStructFilter.txx
index b4e921269a1ff0dc7d874176a9c5b967ac711502..051211b6d0d325fa882875b86fc02f861035f8b3 100644 (file)
--- a/common/clitkImage2DicomRTStructFilter.txx
+++ b/common/clitkImage2DicomRTStructFilter.txx
@@ -23,7 +23,9 @@
 
 // clitk
 #include "clitkImage2DicomRTStructFilter.h"
+#include "clitkBinaryImageToMeshFilter.h"
 #include "clitkImageCommon.h"
+#include "vvFromITK.h"
 
 // vtk
 #include <vtkPolyDataToImageStencil.h>
@@ -32,14 +34,33 @@
 #include <vtkLinearExtrusionFilter.h>
 #include <vtkMetaImageWriter.h>
 #include <vtkImageData.h>
+
+// FIXME to remove
+#include "vtkPolyDataMapper.h"
+#include "vtkPolyDataMapper2D.h"
+#include "vtkRenderWindowInteractor.h"
+#include "vtkPolyDataReader.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderer.h"
+#include "vtkCamera.h"
+#include "vtkProperty.h"
+#include "vtkProperty2D.h"
+
+// itk
 #include <itkImage.h>
 #include <itkVTKImageToImageFilter.h>
 
+// gdcm
+#include <vtkGDCMPolyDataWriter.h>
+
 //--------------------------------------------------------------------
 template<class PixelType>
 clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
 {
-  DD("Image2DicomRTStructFilter Const");
+  m_StructureSetFilename = "";
+  m_DicomFolder = "";
+  m_OutputFilename = "default-output.dcm";
+  m_ThresholdValue = 0.5;
 }
 //--------------------------------------------------------------------
 
@@ -48,18 +69,126 @@ clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
 template<class PixelType>
 clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
 {
-  DD("Image2DicomRTStructFilter Destructor");
 }
 //--------------------------------------------------------------------
 
 
 //--------------------------------------------------------------------
 template<class PixelType>
-void clitk::Image2DicomRTStructFilter<PixelType>::Update() 
+void
+clitk::Image2DicomRTStructFilter<PixelType>::SetROIName(std::string name, std::string type)
 {
-  DD("Image2DicomRTStructFilter::Update");
+  m_ROIName = name;
+  m_ROIType = type;
+}
+//--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+template<class PixelType>
+void clitk::Image2DicomRTStructFilter<PixelType>::Update() 
+{
+  // Read rt struct
+  vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
+  reader->SetFileName(m_StructureSetFilename.c_str());
+  reader->Update();
+
+  // Get properties
+  vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+  if (GetVerboseFlag()) {
+    std::cout << "Number of structures in the dicom-rt-struct : " 
+              << p->GetNumberOfStructureSetROIs() << std::endl;
+  }
+  
+  // Init writer
+  vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
+  int numMasks = reader->GetNumberOfOutputPorts() + 1;//add one more
+  writer->SetNumberOfInputPorts(numMasks);    
+  writer->SetFileName(m_OutputFilename.c_str());
+  writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
+
+  // List of already present rois
+  vtkStringArray* roiNames = vtkStringArray::New();
+  vtkStringArray* roiAlgorithms = vtkStringArray::New();
+  vtkStringArray* roiTypes = vtkStringArray::New();
+  roiNames->SetNumberOfValues(numMasks);
+  roiAlgorithms->SetNumberOfValues(numMasks);
+  roiTypes->SetNumberOfValues(numMasks);
+  
+  // Convert the image into a mesh
+  typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
+  typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
+  convert->SetThresholdValue(m_ThresholdValue);
+  convert->SetInput(m_Input);
+  convert->Update();
+  vtkPolyData* mesh = convert->GetOutputMesh();
+  if (GetVerboseFlag()) {
+    std::cout << "Mesh has " << mesh->GetNumberOfLines() << " lines." << std::endl;
+  }
+
+  // Copy previous contours
+  for (unsigned int i = 0; i < numMasks-1; ++i) {
+    writer->SetInput(i, reader->GetOutput(i));
+    std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
+    roiNames->InsertValue(i, theString);
+    theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
+    roiAlgorithms->InsertValue(i, theString);
+    theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i);
+    roiTypes->InsertValue(i, theString);
+  }  
+
+  // Add new one
+  int last = numMasks-1;
+  writer->SetInput(last, mesh);
+  roiNames->InsertValue(last, m_ROIName);
+  roiAlgorithms->InsertValue(last, "CLITK_CREATED");
+  roiTypes->InsertValue(last, m_ROIType);
+
+  /*
+  //  Visu DEBUG
+  vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
+  cubeMapper->SetInput( mesh );
+  cubeMapper->SetScalarRange(0,7);
+  vtkActor *cubeActor = vtkActor::New();
+  cubeActor->SetMapper(cubeMapper);
+  vtkProperty * property = cubeActor->GetProperty();
+  property->SetRepresentationToWireframe();
+
+  vtkRenderer *renderer = vtkRenderer::New();
+  vtkRenderWindow *renWin = vtkRenderWindow::New();
+  renWin->AddRenderer(renderer);
+
+  vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
+  iren->SetRenderWindow(renWin);
+
+  renderer->AddActor(cubeActor);
+  renderer->ResetCamera();
+  renderer->SetBackground(1,1,1);
+
+  renWin->SetSize(300,300);
+
+  renWin->Render();
+  iren->Start();
+  */
+  // End visu
+
+  // Write (need to read dicom for slice id)
+  vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
+  writer->SetRTStructSetProperties(theProperties);
+  if (GetVerboseFlag()) {
+    std::cout << "Looking for dicom info, study instance "
+              << p->GetStudyInstanceUID() << std::endl;
+  }
+  writer->InitializeRTStructSet(m_DicomFolder,
+                                reader->GetRTStructSetProperties()->GetStructureSetLabel(),
+                                reader->GetRTStructSetProperties()->GetStructureSetName(),
+                                roiNames, roiAlgorithms, roiTypes);  
+  writer->Write();
+  reader->Delete();
+  roiNames->Delete();
+  roiTypes->Delete();
+  roiAlgorithms->Delete();
+  writer->Delete();
 }
 //--------------------------------------------------------------------