First working version (allow to write rt-struct)

diff --git a/tests_dav/clitkImage2DicomRTStruct.cxx b/tests_dav/clitkImage2DicomRTStruct.cxx
index b5916cfca25defe469c6d180c5005d45c2ea0c7f..264eb05c6bdba56199f07081a43efe8969307a3f 100644 (file)
--- a/tests_dav/clitkImage2DicomRTStruct.cxx
+++ b/tests_dav/clitkImage2DicomRTStruct.cxx
@@ -17,196 +17,31 @@
 
   =========================================================================*/
 
+// clitk
 #include "clitkImage2DicomRTStructFilter.h"
-#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);
+  ImageType::Pointer input = clitk::readImage<ImageType>(args_info.input_arg, args_info.verbose_flag);
 
-  // Create a filter to convert image into dicomRTStruct
+  // Create a filter to convert image into dicomRTStruct and write to disk
   clitk::Image2DicomRTStructFilter<PixelType> filter;
+  filter.SetVerboseFlag(args_info.verbose_flag);
   filter.SetInput(input);
   filter.SetDicomFolder(args_info.dicom_arg);
   filter.SetStructureSetFilename(args_info.rtstruct_arg);
   filter.SetOutputFilename(args_info.output_arg);
+  filter.SetROIName(args_info.roiname_arg, args_info.roitype_arg);
+  filter.SetThresholdValue(args_info.threshold_arg);
   filter.Update();
-  
-  // // 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 3499543b46f752617a016c94dadf149fae62ba39..928d11b5ed4ca205abf494253d62f7a3d6981b45 100644 (file)
--- a/tests_dav/clitkImage2DicomRTStruct.ggo
+++ b/tests_dav/clitkImage2DicomRTStruct.ggo
@@ -1,6 +1,6 @@
 # file clitkImage2DicomRTStruct.ggo
 package "clitk"
-version "Convert (binary) image to DICOM RT Structure Set (contours)"
+version "Add a (binary) image inside a DICOM RT Structure Set (contours)"
 
 option "config"                 - "Config file"                     string     no
 option "verbose"         v "Verbose"                        flag       off
@@ -10,12 +10,7 @@ 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"
-
-# option "crop"                 c "Crop binary mask"            flag off
-
-#option "roi"           r "ROI to print (ID)"           int            no
-#option "contour"       c "contour to print (ID)"       int            no
-#option "offset"                o "to display points as image offsets" flag    off
+option "threshold"       t "Threshold for binary image"                         float   no default = "0.5"
+option "roiname"        - "Name of the roi added into the rt-struct"           string  yes
+option "roitype"        - "Name of the type of roi added into the rt-struct"   string  no default = "ORGAN"