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()
32 mImageInfoIsSet = false;
36 //--------------------------------------------------------------------
39 //--------------------------------------------------------------------
40 clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter()
44 //--------------------------------------------------------------------
47 //--------------------------------------------------------------------
48 void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi)
52 //--------------------------------------------------------------------
55 //--------------------------------------------------------------------
56 void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b)
60 //--------------------------------------------------------------------
63 //--------------------------------------------------------------------
64 void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s)
69 //--------------------------------------------------------------------
72 //--------------------------------------------------------------------
73 void clitk::DicomRT_ROI_ConvertToImageFilter::SetImageFilename(std::string f)
75 itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
76 if (header->GetNumberOfDimensions() < 3) {
77 std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
80 if (header->GetNumberOfDimensions() > 3) {
81 std::cerr << "Warning dimension > 3 are ignored" << std::endl;
86 for(unsigned int i=0; i<3; i++) {
87 mSpacing[i] = header->GetSpacing(i);
88 mOrigin[i] = header->GetOrigin(i);
89 mSize[i] = header->GetDimensions(i);
91 mImageInfoIsSet = true;
93 //--------------------------------------------------------------------
96 //--------------------------------------------------------------------
97 void clitk::DicomRT_ROI_ConvertToImageFilter::Update()
100 std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
103 if (!mImageInfoIsSet) {
104 std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
110 vtkPolyData * mesh = mROI->GetMesh();
111 DD(mesh->GetNumberOfCells());
114 double *bounds=mesh->GetBounds();
115 // for(int i=0; i<6; i++){
120 std::vector<double> origin;
122 origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
123 origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
124 origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
127 std::vector<double> extend;
129 extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
130 extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
131 extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
133 // If no crop, set initial image size/origin
135 for(int i=0; i<3; i++) {
136 origin[i] = mOrigin[i];
137 extend[i] = mSize[i]-1;
141 // Create new output image
142 mBinaryImage = vtkImageData::New();
143 mBinaryImage->SetScalarTypeToUnsignedChar();
144 mBinaryImage->SetOrigin(&origin[0]);
145 mBinaryImage->SetSpacing(&mSpacing[0]);
146 mBinaryImage->SetExtent(0, extend[0],
149 mBinaryImage->AllocateScalars();
151 // for(int i=0; i<3; i++){
154 // DD(mBinaryImage->GetDimensions()[i]);
156 memset(mBinaryImage->GetScalarPointer(), 0,
157 mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
160 vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
161 extrude->SetInput(mesh);
162 ///We extrude in the -slice_spacing direction to respect the FOCAL convention // ?????????????
163 extrude->SetVector(0, 0, -mSpacing[2]);
166 vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
167 //The following line is extremely important
168 //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
169 sts->SetTolerance(0);
170 sts->SetInformationInput(mBinaryImage);
171 sts->SetInput(extrude->GetOutput());
172 //sts->SetInput(mesh);
174 vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
175 stencil->SetStencil(sts->GetOutput());
176 stencil->SetInput(mBinaryImage);
177 stencil->ReverseStencilOn();
179 mBinaryImage->ShallowCopy(stencil->GetOutput());
182 typedef itk::Image<unsigned char, 3> ImageType;
183 typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
184 ConnectorType::Pointer connector = ConnectorType::New();
185 connector->SetInput(GetOutput());
187 clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
190 //--------------------------------------------------------------------
194 //--------------------------------------------------------------------
195 vtkImageData * clitk::DicomRT_ROI_ConvertToImageFilter::GetOutput()
199 //--------------------------------------------------------------------