First version of clitkImage2DicomRTStruct

diff --git a/tests_dav/clitkImage2DicomRTStruct.cxx b/tests_dav/clitkImage2DicomRTStruct.cxx
index d71491ba8d12ea5e6ef26a6f45316a4b8fb44a73..b5916cfca25defe469c6d180c5005d45c2ea0c7f 100644 (file)
--- a/tests_dav/clitkImage2DicomRTStruct.cxx
+++ b/tests_dav/clitkImage2DicomRTStruct.cxx
@@ -21,25 +21,192 @@
 #include "clitkDicomRT_StructureSet.h"
 #include "clitkImage2DicomRTStruct_ggo.h"
 
+#include <vtkGDCMPolyDataReader.h>
+#include <vtkGDCMPolyDataWriter.h>
+#include <vtkRTStructSetProperties.h>
+#include <vtkImageClip.h>
+#include <vtkMarchingSquares.h>
+#include <vtkAppendPolyData.h>
+
 //--------------------------------------------------------------------
 int main(int argc, char * argv[]) {
 
   // Init command line
   GGO(clitkImage2DicomRTStruct, args_info);
 
+  // // Read
+  // DD("read");
+  // vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
+  // reader->SetFileName(args_info.rtstruct_arg);
+  // reader->Update();
+  // DD("reader done");
+  
+  // //======================================
+  // // access to properties
+  // vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+  // DD(p->GetNumberOfStructureSetROIs());
+  // DD(p->GetStructureSetROIName(0));
+  // DD(p->GetStructureSetROINumber(0));  
+  
+
+  // //======================================
+  // // Test read binary image, convert to polydata
+  // typedef float PixelType;
+  // typedef itk::Image<PixelType, 3> ImageType;
+  // ImageType::Pointer input_itk = clitk::readImage<ImageType>(args_info.input_arg, true);
+  // vvImage::Pointer input_vv = vvImageFromITK<3, PixelType>(input_itk);
+  // vtkImageData * input_vtk = input_vv->GetVTKImages()[0];
+  
+  // vtkSmartPointer<vtkImageClip> clipper = vtkSmartPointer<vtkImageClip>::New();
+  // clipper->SetInput(input_vtk);
+  // int* extent = input_vtk->GetExtent();
+  // DDV(extent, 6);
+  // clipper->Delete();
+
+  // uint n = input_vtk->GetDimensions()[2];
+  // DD(n);
+  // std::vector<vtkSmartPointer<vtkPolyData> > contours;
+  // for(uint i=0; i<n; i++) {
+  //   // DD(i);
+  //   // FIXME     vtkDiscreteMarchingCubes INSTEAD
+  //   vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
+  //   squares->SetInput(input_vtk);
+  //   squares->SetImageRange(extent[0], extent[1], extent[2], extent[3], i, i);
+  //   squares->SetValue(1, 1.0);
+  //   squares->Update();
+  //   // DD(squares->GetNumberOfContours());
+    
+  //   vtkSmartPointer<vtkPolyData> m = squares->GetOutput();
+  //   contours.push_back(m);
+  // }
+  // DD("done");
+ 
+  // vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
+  // for(unsigned int i=0; i<n; i++) {
+  //   append->AddInput(contours[i]);
+  // }
+  // append->Update();
+ 
+  // vtkSmartPointer<vtkPolyData> mMesh = vtkSmartPointer<vtkPolyData>::New();
+  // mMesh->DeepCopy(append->GetOutput());
+
+  // // Write vtk
+  // vtkPolyDataWriter * w = vtkPolyDataWriter::New();
+  // w->SetInput(mMesh);
+  // w->SetFileName("toto.vtk");
+  // w->Write();
+  // //======================================
+
+
+  // // Set polydata
+  // vtkPolyData * c =  reader->GetOutput(1); // second one (Oso, not Aorta)
+  // DD(c->GetNumberOfVerts());
+  // DD(c->GetNumberOfLines());
+  // DD(c->GetNumberOfPolys());
+  // DD(c->GetNumberOfStrips());
+  
+
+  // //======================================
+  
+  // DD(p->GetNumberOfContourReferencedFrameOfReferences());
+  // DD(p->GetNumberOfReferencedFrameOfReferences ());
+  // DD(p->GetNumberOfStructureSetROIs ());
+
+  // // Write 
+  // vtkSmartPointer<vtkGDCMPolyDataWriter> writer = vtkGDCMPolyDataWriter::New();
+  // DD(reader->GetNumberOfOutputPorts() );
+  // int numMasks =   reader->GetNumberOfOutputPorts()+1;
+  // DD(numMasks);
+  
+  // writer->SetNumberOfInputPorts( numMasks ); // Add one
+  // // // vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+  // // std::string ref = p->GetReferenceFrameOfReferenceUID();
+  // // const char * algogen = p->GetStructureSetROIGenerationAlgorithm(0);
+  // // DD(ref);
+  // // DD(algogen);
+  // // vtkIdType id = p->GetNumberOfContourReferencedFrameOfReferences();
+  // // p->AddStructureSetROI(id, ref.c_str(), "BIDON", algogen);
+  // // // int n = p->GetNumberOfContourReferencedFrameOfReferences();
+  // // const char * classuid = p->GetContourReferencedFrameOfReferenceClassUID(0, 0);
+  // // const char *instanceuid = p->GetContourReferencedFrameOfReferenceInstanceUID(0, 0);
+  // // DD(classuid);
+  // // DD(instanceuid);
+  // // p->AddContourReferencedFrameOfReference(id, classuid, instanceuid);
+  // // p->AddContourReferencedFrameOfReference(id+1, classuid, instanceuid);
+
+  // // DD(p->GetNumberOfContourReferencedFrameOfReferences());
+  // // DD(p->GetNumberOfReferencedFrameOfReferences ());
+  // // DD(p->GetNumberOfStructureSetROIs ());
+  
+  //   writer->SetFileName("./bidon.dcm");
+  // writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
+
+  // vtkStringArray* roiNames = vtkStringArray::New();
+  // vtkStringArray* roiAlgorithms = vtkStringArray::New();
+  // vtkStringArray* roiTypes = vtkStringArray::New();
+  // roiNames->SetNumberOfValues(numMasks);
+  // roiAlgorithms->SetNumberOfValues(numMasks);
+  // roiTypes->SetNumberOfValues(numMasks);
+
+  // // Add one
+  // int num = reader->GetNumberOfOutputPorts();
+  // DD(num);
+  // // writer->SetInput(0, mMesh); // FIXME first one
+  // vtkPolyData* blank = vtkPolyData::New();
+  // writer->SetInput(0, blank);
+  //   roiNames->InsertValue(0, "blank");
+  //   roiAlgorithms->InsertValue(0, "blank");
+  //   roiTypes->InsertValue(0, "ORGAN");
+
+  // for (int i = 1; i < numMasks; ++i) {
+  //   DD(i);
+  //   writer->SetInput(i, reader->GetOutput(i-1) );
+  //     std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i-1);
+  //   roiNames->InsertValue(i, theString);
+  //   DD(theString);
+  //   theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i-1);
+  //   roiAlgorithms->InsertValue(i, theString);
+  //   theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i-1);
+  //   roiTypes->InsertValue(i, theString);
+  // }
+
+  // vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
+  // // writer->SetRTStructSetProperties(reader->GetRTStructSetProperties());
+  // writer->SetRTStructSetProperties(theProperties);
+  // writer->InitializeRTStructSet("./",
+  //                               reader->GetRTStructSetProperties()->GetStructureSetLabel(),
+  //                               reader->GetRTStructSetProperties()->GetStructureSetName(),
+  //                               roiNames, roiAlgorithms, roiTypes);
+  // writer->SetRTStructSetProperties(theProperties);
+
+  // writer->Write();
+  // DD("write done");
+
+  // DD("end");
+  // writer->Delete();
+  // reader->Delete();    
+  // exit(0); // FIXME stop here (test)
+
   // Read initial 3D image
   typedef float PixelType;
   typedef itk::Image<PixelType, 3> ImageType;
   ImageType::Pointer input = clitk::readImage<ImageType>(args_info.input_arg, true);
 
+  // // Read initial RT Struct
+  // clitk::DicomRT_StructureSet::Pointer structset = clitk::DicomRT_StructureSet::New();
+  // structset->Read(args_info.rtstruct_arg);
+
   // Create a filter to convert image into dicomRTStruct
   clitk::Image2DicomRTStructFilter<PixelType> filter;
   filter.SetInput(input);
+  filter.SetDicomFolder(args_info.dicom_arg);
+  filter.SetStructureSetFilename(args_info.rtstruct_arg);
+  filter.SetOutputFilename(args_info.output_arg);
   filter.Update();
   
-  // Write result
-  clitk::DicomRT_StructureSet::Pointer s = filter.GetDicomRTStruct();
-  //  s->Write(args_info.output_arg);
+  // // Write result
+  // clitk::DicomRT_StructureSet::Pointer s = filter.GetDicomRTStruct();
+  // s->Write(args_info.output_arg);
 
   // This is the end my friend 
   return 0;

diff --git a/tests_dav/clitkImage2DicomRTStruct.ggo b/tests_dav/clitkImage2DicomRTStruct.ggo
index 68334b1f9f0a2449142d47db91da8fce25f51511..3499543b46f752617a016c94dadf149fae62ba39 100644 (file)
--- a/tests_dav/clitkImage2DicomRTStruct.ggo
+++ b/tests_dav/clitkImage2DicomRTStruct.ggo
@@ -5,9 +5,10 @@ version "Convert (binary) image to DICOM RT Structure Set (contours)"
 option "config"                 - "Config file"                     string     no
 option "verbose"         v "Verbose"                        flag       off
 
-option "input"          i "Input image file (binary image"  string     yes
-option "output"                 o "Output DicomRT filename"         string     yes
-
+option "input"          i "Input image file (binary image) to be converted into contours"  string      yes
+option "rtstruct"       r "Input rt struct"                  string    yes
+option "dicom"          d "Input folder where the initial dicom ct is"                 string  yes
+option "output"                 o "Output DicomRT filename"          string    yes
 
 # option "image"                j "Used to read image info (spacing, origin)"    string        yes
 # option "roi"          r "ROI to binarize (if -1 = all roi)"            int    no default="-1"