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://www.centreleonberard.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 =========================================================================*/
24 #include "clitkDicomRT_ROI_ConvertToImageFilter.h"
25 #include "clitkImageCommon.h"
28 #include <vtkPolyDataToImageStencil.h>
29 #include <vtkSmartPointer.h>
30 #include <vtkImageStencil.h>
31 #include <vtkLinearExtrusionFilter.h>
32 #include <vtkMetaImageWriter.h>
35 //--------------------------------------------------------------------
36 clitk::DicomRT_ROI_ConvertToImageFilter::DicomRT_ROI_ConvertToImageFilter()
42 //--------------------------------------------------------------------
45 //--------------------------------------------------------------------
46 clitk::DicomRT_ROI_ConvertToImageFilter::~DicomRT_ROI_ConvertToImageFilter()
50 //--------------------------------------------------------------------
52 bool clitk::DicomRT_ROI_ConvertToImageFilter::ImageInfoIsSet() const
54 return mSize.size() && mSpacing.size() && mOrigin.size();
57 //--------------------------------------------------------------------
58 void clitk::DicomRT_ROI_ConvertToImageFilter::SetROI(clitk::DicomRT_ROI * roi)
62 //--------------------------------------------------------------------
65 //--------------------------------------------------------------------
66 void clitk::DicomRT_ROI_ConvertToImageFilter::SetCropMaskEnabled(bool b)
70 //--------------------------------------------------------------------
73 //--------------------------------------------------------------------
74 void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputImageFilename(std::string s)
79 //--------------------------------------------------------------------
82 //--------------------------------------------------------------------
83 void clitk::DicomRT_ROI_ConvertToImageFilter::SetImageFilename(std::string f)
85 itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
86 if (header->GetNumberOfDimensions() < 3) {
87 std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
90 if (header->GetNumberOfDimensions() > 3) {
91 std::cerr << "Warning dimension > 3 are ignored" << std::endl;
96 for(unsigned int i=0; i<3; i++) {
97 mSpacing[i] = header->GetSpacing(i);
98 mOrigin[i] = header->GetOrigin(i);
99 mSize[i] = header->GetDimensions(i);
102 //--------------------------------------------------------------------
104 void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputOrigin(const double* origin)
106 std::copy(origin,origin+3,std::back_inserter(mOrigin));
108 //--------------------------------------------------------------------
109 void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputSpacing(const double* spacing)
111 std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
113 //--------------------------------------------------------------------
114 void clitk::DicomRT_ROI_ConvertToImageFilter::SetOutputSize(const unsigned long* size)
116 std::copy(size,size+3,std::back_inserter(mSize));
119 //--------------------------------------------------------------------
120 void clitk::DicomRT_ROI_ConvertToImageFilter::Update()
123 std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
126 if (!ImageInfoIsSet()) {
127 std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
132 vtkPolyData * mesh = mROI->GetMesh();
135 double *bounds=mesh->GetBounds();
136 // for(int i=0; i<6; i++){
141 std::vector<double> origin;
143 origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
144 origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
145 origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
148 std::vector<double> extend;
150 extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
151 extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
152 extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
154 // If no crop, set initial image size/origin
156 for(int i=0; i<3; i++) {
157 origin[i] = mOrigin[i];
158 extend[i] = mSize[i]-1;
162 // Create new output image
163 mBinaryImage = vtkSmartPointer<vtkImageData>::New();
164 mBinaryImage->SetScalarTypeToUnsignedChar();
165 mBinaryImage->SetOrigin(&origin[0]);
166 mBinaryImage->SetSpacing(&mSpacing[0]);
167 mBinaryImage->SetExtent(0, extend[0],
170 mBinaryImage->AllocateScalars();
172 // for(int i=0; i<3; i++){
175 // DD(mBinaryImage->GetDimensions()[i]);
177 memset(mBinaryImage->GetScalarPointer(), 0,
178 mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
181 vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
182 extrude->SetInput(mesh);
183 ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
184 extrude->SetVector(0, 0, -mSpacing[2]);
187 vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
188 //The following line is extremely important
189 //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
190 sts->SetTolerance(0);
191 sts->SetInformationInput(mBinaryImage);
192 sts->SetInput(extrude->GetOutput());
193 //sts->SetInput(mesh);
195 vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
196 stencil->SetStencil(sts->GetOutput());
197 stencil->SetInput(mBinaryImage);
198 stencil->ReverseStencilOn();
202 vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
203 w->SetInput(stencil->GetOutput());
204 w->SetFileName("binary2.mhd");
208 mBinaryImage->ShallowCopy(stencil->GetOutput());
211 typedef itk::Image<unsigned char, 3> ImageType;
212 typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
213 ConnectorType::Pointer connector = ConnectorType::New();
214 connector->SetInput(GetOutput());
216 clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
219 //--------------------------------------------------------------------
223 //--------------------------------------------------------------------
224 vtkImageData * clitk::DicomRT_ROI_ConvertToImageFilter::GetOutput()
226 assert(mBinaryImage);
229 //--------------------------------------------------------------------