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 "clitkDicomRTStruct2ImageFilter.h"
25 #include "clitkImageCommon.h"
28 #include <vtkVersion.h>
29 #include <vtkPolyDataToImageStencil.h>
30 #include <vtkSmartPointer.h>
31 #include <vtkImageStencil.h>
32 #include <vtkLinearExtrusionFilter.h>
33 #include <vtkMetaImageWriter.h>
36 //--------------------------------------------------------------------
37 clitk::DicomRTStruct2ImageFilter::DicomRTStruct2ImageFilter()
43 //--------------------------------------------------------------------
46 //--------------------------------------------------------------------
47 clitk::DicomRTStruct2ImageFilter::~DicomRTStruct2ImageFilter()
51 //--------------------------------------------------------------------
54 //--------------------------------------------------------------------
55 bool clitk::DicomRTStruct2ImageFilter::ImageInfoIsSet() const
57 return mSize.size() && mSpacing.size() && mOrigin.size();
59 //--------------------------------------------------------------------
62 //--------------------------------------------------------------------
63 void clitk::DicomRTStruct2ImageFilter::SetWriteOutputFlag(bool b)
67 //--------------------------------------------------------------------
70 //--------------------------------------------------------------------
71 void clitk::DicomRTStruct2ImageFilter::SetROI(clitk::DicomRT_ROI * roi)
75 //--------------------------------------------------------------------
78 //--------------------------------------------------------------------
79 void clitk::DicomRTStruct2ImageFilter::SetCropMaskEnabled(bool b)
83 //--------------------------------------------------------------------
86 //--------------------------------------------------------------------
87 void clitk::DicomRTStruct2ImageFilter::SetOutputImageFilename(std::string s)
92 //--------------------------------------------------------------------
95 //--------------------------------------------------------------------
96 void clitk::DicomRTStruct2ImageFilter::SetImage(vvImage::Pointer image)
98 if (image->GetNumberOfDimensions() != 3) {
99 std::cerr << "Error. Please provide a 3D image." << std::endl;
105 for(unsigned int i=0; i<3; i++) {
106 mSpacing[i] = image->GetSpacing()[i];
107 mOrigin[i] = image->GetOrigin()[i];
108 mSize[i] = image->GetSize()[i];
111 //--------------------------------------------------------------------
114 //--------------------------------------------------------------------
115 void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
117 itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
118 if (header->GetNumberOfDimensions() < 3) {
119 std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
122 if (header->GetNumberOfDimensions() > 3) {
123 std::cerr << "Warning dimension > 3 are ignored" << std::endl;
128 for(unsigned int i=0; i<3; i++) {
129 mSpacing[i] = header->GetSpacing(i);
130 mOrigin[i] = header->GetOrigin(i);
131 mSize[i] = header->GetDimensions(i);
134 //--------------------------------------------------------------------
137 //--------------------------------------------------------------------
138 void clitk::DicomRTStruct2ImageFilter::SetOutputOrigin(const double* origin)
140 std::copy(origin,origin+3,std::back_inserter(mOrigin));
142 //--------------------------------------------------------------------
145 //--------------------------------------------------------------------
146 void clitk::DicomRTStruct2ImageFilter::SetOutputSpacing(const double* spacing)
148 std::copy(spacing,spacing+3,std::back_inserter(mSpacing));
150 //--------------------------------------------------------------------
153 //--------------------------------------------------------------------
154 void clitk::DicomRTStruct2ImageFilter::SetOutputSize(const unsigned long* size)
156 std::copy(size,size+3,std::back_inserter(mSize));
158 //--------------------------------------------------------------------
161 //--------------------------------------------------------------------
162 void clitk::DicomRTStruct2ImageFilter::Update()
165 std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
168 if (!ImageInfoIsSet()) {
169 std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
174 vtkPolyData * mesh = mROI->GetMesh();
177 double *bounds=mesh->GetBounds();
180 std::vector<double> origin;
182 origin[0] = floor((bounds[0]-mOrigin[0])/mSpacing[0]-2)*mSpacing[0]+mOrigin[0];
183 origin[1] = floor((bounds[2]-mOrigin[1])/mSpacing[1]-2)*mSpacing[1]+mOrigin[1];
184 origin[2] = floor((bounds[4]-mOrigin[2])/mSpacing[2]-2)*mSpacing[2]+mOrigin[2];
187 std::vector<double> extend;
189 extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
190 extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
191 extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
193 // If no crop, set initial image size/origin
195 for(int i=0; i<3; i++) {
196 origin[i] = mOrigin[i];
197 extend[i] = mSize[i]-1;
201 // Create new output image
202 mBinaryImage = vtkSmartPointer<vtkImageData>::New();
203 #if VTK_MAJOR_VERSION <= 5
204 mBinaryImage->SetScalarTypeToUnsignedChar();
206 mBinaryImage->SetOrigin(&origin[0]);
207 mBinaryImage->SetSpacing(&mSpacing[0]);
208 mBinaryImage->SetExtent(0, extend[0],
211 #if VTK_MAJOR_VERSION <= 5
212 mBinaryImage->AllocateScalars();
214 mBinaryImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
217 memset(mBinaryImage->GetScalarPointer(), 0,
218 mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
221 vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
222 #if VTK_MAJOR_VERSION <= 5
223 extrude->SetInput(mesh);
225 extrude->SetInputData(mesh);
227 ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
228 extrude->SetVector(0, 0, -mSpacing[2]);
231 vtkSmartPointer<vtkPolyDataToImageStencil> sts=vtkSmartPointer<vtkPolyDataToImageStencil>::New();
232 //The following line is extremely important
233 //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
234 sts->SetTolerance(0);
235 sts->SetInformationInput(mBinaryImage);
236 #if VTK_MAJOR_VERSION <= 5
237 sts->SetInput(extrude->GetOutput());
239 sts->SetInputConnection(extrude->GetOutputPort(0));
241 //sts->SetInput(mesh);
243 vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
244 #if VTK_MAJOR_VERSION <= 5
245 stencil->SetStencil(sts->GetOutput());
247 stencil->SetStencilConnection(sts->GetOutputPort(0));
249 #if VTK_MAJOR_VERSION <= 5
250 stencil->SetInput(mBinaryImage);
252 stencil->SetInputData(mBinaryImage);
254 stencil->ReverseStencilOn();
258 vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
259 w->SetInput(stencil->GetOutput());
260 w->SetFileName("binary2.mhd");
264 mBinaryImage->ShallowCopy(stencil->GetOutput());
267 typedef itk::Image<unsigned char, 3> ImageType;
268 typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
269 ConnectorType::Pointer connector = ConnectorType::New();
270 connector->SetInput(GetOutput());
272 clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
275 //--------------------------------------------------------------------
279 //--------------------------------------------------------------------
280 vtkImageData * clitk::DicomRTStruct2ImageFilter::GetOutput()
282 assert(mBinaryImage);
285 //--------------------------------------------------------------------