X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkImage2DicomRTStructFilter.txx;h=1b241a99824a233a094058f1b8196d09c4e99772;hb=f4ee750a005c1406848ffdfd85a0ebcbe824bca6;hp=cc90104216d6ca2ef9d37f77e92156bf47c4fe9f;hpb=2b5b3e906ee95519169e9b6d4bb2da9d2e00d8b3;p=clitk.git

diff --git a/common/clitkImage2DicomRTStructFilter.txx b/common/clitkImage2DicomRTStructFilter.txx
index cc90104..1b241a9 100644
--- a/common/clitkImage2DicomRTStructFilter.txx
+++ b/common/clitkImage2DicomRTStructFilter.txx
@@ -57,7 +57,10 @@
 template<class PixelType>
 clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
 {
-  DD("Image2DicomRTStructFilter Const");
+  m_StructureSetFilename = "";
+  m_DicomFolder = "";
+  m_OutputFilename = "default-output.dcm";
+  m_ThresholdValue = 0.5;
 }
 //--------------------------------------------------------------------
 
@@ -66,7 +69,17 @@ clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
 template<class PixelType>
 clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
 {
-  DD("Image2DicomRTStructFilter Destructor");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class PixelType>
+void
+clitk::Image2DicomRTStructFilter<PixelType>::SetROIName(std::string name, std::string type)
+{
+  m_ROIName = name;
+  m_ROIType = type;
 }
 //--------------------------------------------------------------------
 
@@ -75,27 +88,33 @@ clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
 template<class PixelType>
 void clitk::Image2DicomRTStructFilter<PixelType>::Update() 
 {
-  DD("Image2DicomRTStructFilter::GenerateData");
+  // Check this is a RT-Struct
+  gdcm::Reader gdcm_reader;
+  gdcm_reader.SetFileName(m_StructureSetFilename.c_str());
+  if (!gdcm_reader.Read()) {
+    clitkExceptionMacro("Error could not open the file '" << m_StructureSetFilename << std::endl);
+  }
+  gdcm::MediaStorage ms;
+  ms.SetFromFile(gdcm_reader.GetFile());
+  if (ms != gdcm::MediaStorage::RTStructureSetStorage) {
+    clitkExceptionMacro("File '" << m_StructureSetFilename << "' is not a DICOM-RT-Struct file." << std::endl);
+  }
 
   // Read rt struct
   vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
   reader->SetFileName(m_StructureSetFilename.c_str());
-  reader->Update();
-  DD("reader done");
+  reader->Update();  
 
   // Get properties
   vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
-  DD(p->GetNumberOfStructureSetROIs());
-  DD(p->GetStructureSetROIName(0));
-  DD(p->GetStructureSetROINumber(0));  
+  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
-  DD(numMasks);
-  
-  // numMasks = 3; //FIXME temporary
-
   writer->SetNumberOfInputPorts(numMasks);    
   writer->SetFileName(m_OutputFilename.c_str());
   writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
@@ -108,41 +127,37 @@ void clitk::Image2DicomRTStructFilter<PixelType>::Update()
   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);
-  DD("Update");
   convert->Update();
-  DD("here");
-  DD("end update");
   vtkPolyData* mesh = convert->GetOutputMesh();
-  DD(mesh->GetNumberOfVerts());
-  DD(mesh->GetNumberOfLines());
-  DD(mesh->GetNumberOfPolys());
-  DD(mesh->GetNumberOfStrips());
-
-  // Add on (FIXME) to replace with binary image
-  // vtkPolyData* blank = vtkPolyData::New();
-  // writer->SetInput(0, blank);
-  writer->SetInput(0, mesh);
-  roiNames->InsertValue(0, "blank");
-  roiAlgorithms->InsertValue(0, "blank");
-  roiTypes->InsertValue(0, "ORGAN");
-
-  for (unsigned int i = 1; i < numMasks; ++i) {
-    // DD(i);
-    writer->SetInput(i, reader->GetOutput(i-1));
-    std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i-1);
+  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-1);
+    theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
     roiAlgorithms->InsertValue(i, theString);
-    theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i-1);
+    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
+  //  Visu DEBUG
   vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
   cubeMapper->SetInput( mesh );
   cubeMapper->SetScalarRange(0,7);
@@ -167,80 +182,25 @@ void clitk::Image2DicomRTStructFilter<PixelType>::Update()
   renWin->Render();
   iren->Start();
   */
-  
-
   // End visu
 
-
+  // Write (need to read dicom for slice id)
   vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
-  DD(p->GetStudyInstanceUID());
   writer->SetRTStructSetProperties(theProperties);
-  /*writer->InitializeRTStructSet2(p,"./",
-                                 reader->GetRTStructSetProperties()->GetStructureSetLabel(),
-                                 reader->GetRTStructSetProperties()->GetStructureSetName(),
-                                 roiNames, roiAlgorithms, roiTypes);*/  
+  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);
-  
-  DD("after init");
+                                roiNames, roiAlgorithms, roiTypes);  
   writer->Write();
-  DD("write done");
-
   reader->Delete();
   roiNames->Delete();
   roiTypes->Delete();
-  //theProperties->Delete();
   roiAlgorithms->Delete();
-  //blank->Delete();
   writer->Delete();
-  
-  ////////////////////
-  
-
-  /*
-
-  // DicomRTStruct
-  DD(m_StructureSet->GetName());
-  clitk::DicomRT_ROI * roi = m_StructureSet->GetROIFromROINumber(1); // Aorta
-  DD(roi->GetName());
-  DD(roi->GetROINumber());
-
-
-  // Get 
-  
-
-
-
-  // Add an image to the roi
-  vvImage::Pointer im = vvImageFromITK<3, PixelType>(m_Input);
-  roi->SetImage(im);
-
-  // Get one contour
-  DD("Compute Mesh");
-  roi->ComputeContoursFromImage(); // FIXME do the set mesh for the moment (to change)
-  // roi->ComputeMeshFromContour();
-  vtkSmartPointer<vtkPolyData> mesh = roi->GetMesh();
-  DD("done");
-  
-  // Change the mesh (shift by 10);
-  // const vtkSmartPointer<vtkPoints> & points = mesh->GetPoints();
-  // for(uint i=0; i<mesh->GetNumberOfVerts (); i++) {
-  //   DD(i);
-  //   double * p = points->GetPoint(i);
-  //   p[0] += 30;
-  //   points->SetPoint(i, p);
-  // }
-  roi->SetName("TOTO");
-  roi->SetDicomUptodateFlag(true); // indicate that dicom info must be updated from the mesh.
-    
-  // Convert to dicom ?
-  DD("TODO");
-  
-  // Write
-  structset->Write("toto.dcm");
-  */
 }
 //--------------------------------------------------------------------