--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+ - BSD http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#include "clitkDicomRT_ROI_ConvertToImageFilter.h"
+#include "clitkDicomRT_StructureSet.h"
+#include "clitkDicomRTStruct2BinaryImage_ggo.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkDicomRTStruct2BinaryImage, args_info);
+
+ // Read and display information
+ clitk::DicomRT_StructureSet s;
+ s.Read(args_info.input_arg);
+ // s.Print(std::cout);
+
+ // New filter to convert to binary image
+ clitk::DicomRT_ROI_ConvertToImageFilter filter;
+ filter.SetCropMaskEnabled(args_info.crop_flag);
+ filter.SetImageFilename(args_info.image_arg); // Used to get spacing + origin
+ if (args_info.roi_arg != -1) {
+ filter.SetROI(s.GetROI(args_info.roi_arg));
+ filter.SetOutputImageFilename(args_info.output_arg);
+ filter.Update();
+ }
+ else {
+ for(unsigned int i=0; i<s.GetListOfROI().size(); i++) {
+ std::string name = s.GetListOfROI()[i]->GetName();
+ int num = s.GetListOfROI()[i]->GetROINumber();
+ filter.SetROI(s.GetListOfROI()[i]);
+ name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
+ std::string n = std::string(args_info.output_arg).append
+ (clitk::toString(num)).append
+ ("_").append
+ (name).append
+ (".mhd");
+ if (args_info.verbose_flag) {
+ std::cout << i << " " << s.GetListOfROI()[i]->GetName() << " num=" << num << " : " << n << std::endl;
+ }
+ filter.SetOutputImageFilename(n);
+ filter.Update();
+ }
+ }
+
+ // This is the end my friend
+ return 0;
+}
--- /dev/null
+# file clitkDicomRTStruct2BinaryImage.ggo
+Package "clitk"
+version "Convert DICOM RT Structure Set (contours) to binary image"
+
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+option "input" i "Input Dicom file" 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 "output" o "Output image filename" string yes
+
+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
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+ - BSD http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#include "clitkDicomRT_StructureSet.h"
+#include "clitkDicomRTStructInfo_ggo.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkDicomRTStructInfo, args_info);
+
+ // Read and display information
+ clitk::DicomRT_StructureSet s;
+ s.Read(args_info.input_arg);
+ s.Print(std::cout);
+
+ // This is the end my friend
+ return 0;
+}
--- /dev/null
+# file clitkDicomRTStructInfo.ggo
+Package "clitk"
+version "Read and print DICOM RT Structure set file (contours)"
+
+option "config" - "Config file" string no
+option "input" i "Input Dicom file" string yes
+
+#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
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+ - BSD http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#include "clitkDicomRT_ROI.h"
+#include <vtkSmartPointer.h>
+#include <vtkAppendPolyData.h>
+
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI::DicomRT_ROI() {
+ mName = "NoName";
+ mNumber = -1;
+ mColor.resize(3);
+ mColor[0] = mColor[1] = mColor[2] = 0;
+ mMeshIsUpToDate = false;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI::~DicomRT_ROI() {
+
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+int clitk::DicomRT_ROI::GetROINumber() const {
+ return mNumber;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+const std::string & clitk::DicomRT_ROI::GetName() const {
+ return mName;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+const std::vector<double> & clitk::DicomRT_ROI::GetDisplayColor() const {
+ return mColor;
+}
+//--------------------------------------------------------------------
+
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::Print(std::ostream & os) const {
+ os << "ROI " << mNumber << "\t" << mName
+ << "\t(" << mColor[0] << " " << mColor[1] << " " << mColor[2] << ")"
+ << "\t Contours = " << mListOfContours.size() << std::endl;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item) {
+
+ // ROI number [Referenced ROI Number]
+ mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str());
+
+ // Retrieve ROI Name
+ mName = rois[mNumber];
+
+ // ROI Color [ROI Display Color]
+ mColor = clitk::parse_string<double>(item->GetEntryValue(0x3006,0x002a),'\\');
+
+ // Read contours [Contour Sequence]
+ gdcm::SeqEntry * contours=item->GetSeqEntry(0x3006,0x0040);
+ for(gdcm::SQItem* j=contours->GetFirstSQItem();j!=0;j=contours->GetNextSQItem()) {
+ DicomRT_Contour * c = new DicomRT_Contour;
+ bool b = c->Read(j);
+ if (b) mListOfContours.push_back(c);
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vtkPolyData * clitk::DicomRT_ROI::GetMesh() {
+ if (!mMeshIsUpToDate) {
+ ComputeMesh();
+ }
+ return mMesh;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::ComputeMesh() {
+ vtkAppendPolyData * append = vtkAppendPolyData::New();
+ for(unsigned int i=0; i<mListOfContours.size(); i++) {
+ append->AddInput(mListOfContours[i]->GetMesh());
+ }
+ append->Update();
+ mMesh = append->GetOutput();
+ mMeshIsUpToDate = true;
+}
+//--------------------------------------------------------------------
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+ - BSD http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#ifndef CLITKDICOMRT_ROI_H
+#define CLITKDICOMRT_ROI_H
+
+#include "clitkDicomRT_Contour.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ class DicomRT_ROI {
+
+ public:
+ DicomRT_ROI();
+ ~DicomRT_ROI();
+
+ void Print(std::ostream & os = std::cout) const;
+ void Read(std::map<int, std::string> & rois, gdcm::SQItem * item);
+
+ int GetROINumber() const;
+ const std::string & GetName() const;
+ const std::vector<double> & GetDisplayColor() const;
+ vtkPolyData * GetMesh();
+
+ protected:
+ void ComputeMesh();
+ std::string mName;
+ int mNumber;
+ std::vector<double> mColor;
+ std::vector<DicomRT_Contour*> mListOfContours;
+ vtkPolyData * mMesh;
+ bool mMeshIsUpToDate;
+ };
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+#endif // CLITKDICOMRT_ROI_H
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+ - BSD http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#include "clitkDicomRT_ROI_ConvertToImageFilter.h"
+#include <vtkPolyDataToImageStencil.h>
+#include <vtkSmartPointer.h>
+#include <vtkImageStencil.h>
+#include <vtkLinearExtrusionFilter.h>
+#include <itkVTKImageToImageFilter.h>
+#include "clitkImageCommon.h"
+
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI_ConvertToImageFilter::DicomRT_ROI_ConvertToImageFilter() {
+ mROI = NULL;
+ mImageInfoIsSet = false;
+ mWriteOutput = false;
+ mCropMask = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter() {
+
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi) {
+ mROI = roi;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b) {
+ mCropMask = b;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s) {
+ mOutputFilename = s;
+ mWriteOutput = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::SetImageFilename(std::string f) {
+ itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
+ if (header->GetNumberOfDimensions() < 3) {
+ std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
+ exit(0);
+ }
+ if (header->GetNumberOfDimensions() > 3) {
+ std::cerr << "Warning dimension > 3 are ignored" << std::endl;
+ }
+ mSpacing.resize(3);
+ mOrigin.resize(3);
+ mSize.resize(3);
+ for(unsigned int i=0; i<3; i++) {
+ mSpacing[i] = header->GetSpacing(i);
+ mOrigin[i] = header->GetOrigin(i);
+ mSize[i] = header->GetDimensions(i);
+ }
+ mImageInfoIsSet = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI_ConvertToImageFilter::Update() {
+ if (!mROI) {
+ std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
+ exit(0);
+ }
+ if (!mImageInfoIsSet) {
+ std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
+ exit(0);
+ }
+ // DD("Update");
+
+ // Get Mesh
+ vtkPolyData * mesh = mROI->GetMesh();
+ // DD(mesh->GetNumberOfCells());
+
+ // Get bounds
+ double *bounds=mesh->GetBounds();
+ // for(int i=0; i<6; i++){
+// DD(bounds[i]);
+// }
+
+ // Compute origin
+ std::vector<double> origin;
+ origin.resize(3);
+ origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
+ origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
+ origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
+
+ // Compute extend
+ std::vector<double> extend;
+ extend.resize(3);
+ extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
+ extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
+ extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
+
+ // If no crop, set initial image size/origin
+ if (!mCropMask) {
+ for(int i=0; i<3; i++) {
+ origin[i] = mOrigin[i];
+ extend[i] = mSize[i]-1;
+ }
+ }
+
+ // Create new output image
+ mBinaryImage = vtkImageData::New();
+ mBinaryImage->SetScalarTypeToUnsignedChar();
+ mBinaryImage->SetOrigin(&origin[0]);
+ mBinaryImage->SetSpacing(&mSpacing[0]);
+ mBinaryImage->SetExtent(0, extend[0],
+ 0, extend[1],
+ 0, extend[2]);
+ mBinaryImage->AllocateScalars();
+
+ // for(int i=0; i<3; i++){
+ // DD(origin[i]);
+ // DD(extend[i]);
+ // DD(mBinaryImage->GetDimensions()[i]);
+ // }
+ memset(mBinaryImage->GetScalarPointer(), 0,
+ mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
+
+ // Extrude
+ vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
+ extrude->SetInput(mesh);
+ ///We extrude in the -slice_spacing direction to respect the FOCAL convention // ?????????????
+ extrude->SetVector(0, 0, -mSpacing[2]);
+
+ // Binarization
+ vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
+ //The following line is extremely important
+ //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
+ sts->SetTolerance(0);
+ sts->SetInformationInput(mBinaryImage);
+ sts->SetInput(extrude->GetOutput());
+ //sts->SetInput(mesh);
+
+ vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
+ stencil->SetStencil(sts->GetOutput());
+ stencil->SetInput(mBinaryImage);
+ stencil->ReverseStencilOn();
+ stencil->Update();
+ mBinaryImage->ShallowCopy(stencil->GetOutput());
+
+ if (mWriteOutput) {
+ typedef itk::Image<unsigned char, 3> ImageType;
+ typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
+ ConnectorType::Pointer connector = ConnectorType::New();
+ connector->SetInput(GetOutput());
+ connector->Update();
+ clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
+ }
+}
+//--------------------------------------------------------------------
+
+
+
+//--------------------------------------------------------------------
+vtkImageData * clitk::DicomRT_ROI_ConvertToImageFilter::GetOutput() {
+ return mBinaryImage;
+}
+//--------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+ - BSD http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+#ifndef CLITKDICOMRT_ROI_CONVERTTOIMAGEFILTER_H
+#define CLITKDICOMRT_ROI_CONVERTTOIMAGEFILTER_H
+
+#include "clitkDicomRT_ROI.h"
+#include "clitkImageCommon.h"
+#include <vtkImageData.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ class DicomRT_ROI_ConvertToImageFilter {
+
+ public:
+ DicomRT_ROI_ConvertToImageFilter();
+ ~DicomRT_ROI_ConvertToImageFilter();
+
+ void SetROI(clitk::DicomRT_ROI * roi);
+ void SetImageFilename(std::string s);
+ void SetOutputImageFilename(std::string s);
+ void Update();
+ vtkImageData * GetOutput();
+ void SetCropMaskEnabled(bool b);
+
+ protected:
+ bool mImageInfoIsSet;
+ bool mWriteOutput;
+ bool mCropMask;
+ std::string mOutputFilename;
+ std::vector<double> mSpacing;
+ std::vector<double> mOrigin;
+ std::vector<int> mSize;
+ clitk::DicomRT_ROI * mROI;
+ vtkImageData * mBinaryImage;
+ };
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+#endif // CLITKDICOMRT_ROI_CONVERTTOIMAGEFILTER_H
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff