1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
3 Main authors : XX XX XX
6 - University of LYON http://www.universite-lyon.fr/
7 - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
8 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
10 This software is distributed WITHOUT ANY WARRANTY; without even
11 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
12 PURPOSE. See the copyright notices for more information.
14 It is distributed under dual licence
15 - BSD http://www.opensource.org/licenses/bsd-license.php
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
18 =========================================================================*/
20 #include "clitkDicomRT_ROI_ConvertToImageFilter.h"
21 #include <vtkPolyDataToImageStencil.h>
22 #include <vtkSmartPointer.h>
23 #include <vtkImageStencil.h>
24 #include <vtkLinearExtrusionFilter.h>
25 #include <itkVTKImageToImageFilter.h>
26 #include "clitkImageCommon.h"
28 //--------------------------------------------------------------------
29 clitk::DicomRT_ROI_ConvertToImageFilter::DicomRT_ROI_ConvertToImageFilter() {
31 mImageInfoIsSet = false;
35 //--------------------------------------------------------------------
38 //--------------------------------------------------------------------
39 clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter() {
42 //--------------------------------------------------------------------
45 //--------------------------------------------------------------------
46 void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi) {
49 //--------------------------------------------------------------------
52 //--------------------------------------------------------------------
53 void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b) {
56 //--------------------------------------------------------------------
59 //--------------------------------------------------------------------
60 void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s) {
64 //--------------------------------------------------------------------
67 //--------------------------------------------------------------------
68 void clitk::DicomRT_ROI_ConvertToImageFilter::SetImageFilename(std::string f) {
69 itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
70 if (header->GetNumberOfDimensions() < 3) {
71 std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
74 if (header->GetNumberOfDimensions() > 3) {
75 std::cerr << "Warning dimension > 3 are ignored" << std::endl;
80 for(unsigned int i=0; i<3; i++) {
81 mSpacing[i] = header->GetSpacing(i);
82 mOrigin[i] = header->GetOrigin(i);
83 mSize[i] = header->GetDimensions(i);
85 mImageInfoIsSet = true;
87 //--------------------------------------------------------------------
90 //--------------------------------------------------------------------
91 void clitk::DicomRT_ROI_ConvertToImageFilter::Update() {
93 std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
96 if (!mImageInfoIsSet) {
97 std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
103 vtkPolyData * mesh = mROI->GetMesh();
104 // DD(mesh->GetNumberOfCells());
107 double *bounds=mesh->GetBounds();
108 // for(int i=0; i<6; i++){
113 std::vector<double> origin;
115 origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
116 origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
117 origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
120 std::vector<double> extend;
122 extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
123 extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
124 extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
126 // If no crop, set initial image size/origin
128 for(int i=0; i<3; i++) {
129 origin[i] = mOrigin[i];
130 extend[i] = mSize[i]-1;
134 // Create new output image
135 mBinaryImage = vtkImageData::New();
136 mBinaryImage->SetScalarTypeToUnsignedChar();
137 mBinaryImage->SetOrigin(&origin[0]);
138 mBinaryImage->SetSpacing(&mSpacing[0]);
139 mBinaryImage->SetExtent(0, extend[0],
142 mBinaryImage->AllocateScalars();
144 // for(int i=0; i<3; i++){
147 // DD(mBinaryImage->GetDimensions()[i]);
149 memset(mBinaryImage->GetScalarPointer(), 0,
150 mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
153 vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
154 extrude->SetInput(mesh);
155 ///We extrude in the -slice_spacing direction to respect the FOCAL convention // ?????????????
156 extrude->SetVector(0, 0, -mSpacing[2]);
159 vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
160 //The following line is extremely important
161 //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
162 sts->SetTolerance(0);
163 sts->SetInformationInput(mBinaryImage);
164 sts->SetInput(extrude->GetOutput());
165 //sts->SetInput(mesh);
167 vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
168 stencil->SetStencil(sts->GetOutput());
169 stencil->SetInput(mBinaryImage);
170 stencil->ReverseStencilOn();
172 mBinaryImage->ShallowCopy(stencil->GetOutput());
175 typedef itk::Image<unsigned char, 3> ImageType;
176 typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
177 ConnectorType::Pointer connector = ConnectorType::New();
178 connector->SetInput(GetOutput());
180 clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
183 //--------------------------------------------------------------------
187 //--------------------------------------------------------------------
188 vtkImageData * clitk::DicomRT_ROI_ConvertToImageFilter::GetOutput() {
191 //--------------------------------------------------------------------