1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ======================================================================-====*/
20 #include "clitkSetBackgroundImageFilter.h"
23 #include <itkConnectedComponentImageFilter.h>
24 #include <itkRelabelComponentImageFilter.h>
25 #include <itkBinaryThresholdImageFilter.h>
26 #include <itkPasteImageFilter.h>
28 //--------------------------------------------------------------------
29 template<class ImageType>
30 void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
31 typename ImageType::RegionType region,
32 typename itk::BoundingBox<unsigned long,
33 ImageType::ImageDimension>::Pointer bb) {
34 typedef typename ImageType::IndexType IndexType;
37 for(unsigned int i=0; i<image->GetImageDimension(); i++) {
38 firstIndex[i] = region.GetIndex()[i];
39 lastIndex[i] = region.GetSize()[i];
42 typedef itk::BoundingBox<unsigned long,
43 ImageType::ImageDimension> BBType;
44 typedef typename BBType::PointType PointType;
47 image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
48 image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
50 bb->SetMaximum(lastPoint);
51 bb->SetMinimum(firstPoint);
53 //--------------------------------------------------------------------
56 //--------------------------------------------------------------------
57 template<int Dimension>
58 void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
59 typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
60 typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
62 typedef itk::BoundingBox<unsigned long, Dimension> BBType;
63 typedef typename BBType::PointType PointType;
67 for(unsigned int i=0; i<Dimension; i++) {
68 firstPoint[i] = std::max(bbi1->GetMinimum()[i],
69 bbi2->GetMinimum()[i]);
70 lastPoint[i] = std::min(bbi1->GetMaximum()[i],
71 bbi2->GetMaximum()[i]);
74 bbo->SetMaximum(lastPoint);
75 bbo->SetMinimum(firstPoint);
77 //--------------------------------------------------------------------
80 //--------------------------------------------------------------------
81 template<class ImageType>
82 void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
83 const typename itk::BoundingBox<unsigned long,
84 ImageType::ImageDimension>::Pointer bb,
85 typename ImageType::RegionType & region) {
87 typedef typename ImageType::IndexType IndexType;
88 typedef typename ImageType::PointType PointType;
89 typedef typename ImageType::RegionType RegionType;
90 typedef typename ImageType::SizeType SizeType;
92 // Region starting point
93 IndexType regionStart;
94 PointType start = bb->GetMinimum();
95 image->TransformPhysicalPointToIndex(start, regionStart);
99 PointType maxs = bb->GetMaximum();
100 PointType mins = bb->GetMinimum();
101 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
102 regionSize[i] = floor((maxs[i] - mins[i])/image->GetSpacing()[i]);
106 region.SetIndex(regionStart);
107 region.SetSize(regionSize);
109 //--------------------------------------------------------------------
111 //--------------------------------------------------------------------
112 template<class ImageType, class TMaskImageType>
113 typename ImageType::Pointer
114 clitk::SetBackground(typename ImageType::ConstPointer input,
115 typename TMaskImageType::ConstPointer mask,
116 typename TMaskImageType::PixelType maskBG,
117 typename ImageType::PixelType outValue) {
118 typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> SetBackgroundImageFilterType;
119 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
120 setBackgroundFilter->SetInput(input);
121 setBackgroundFilter->SetInput2(mask);
122 setBackgroundFilter->SetMaskValue(maskBG);
123 setBackgroundFilter->SetOutsideValue(outValue);
124 setBackgroundFilter->Update();
125 return setBackgroundFilter->GetOutput();
127 //--------------------------------------------------------------------
130 //--------------------------------------------------------------------
131 template<class ImageType>
132 int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
133 typename ImageType::PixelType BG,
134 bool isFullyConnected) {
135 // Connected Component label
136 typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
137 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
138 connectFilter->SetInput(input);
139 connectFilter->SetBackgroundValue(BG);
140 connectFilter->SetFullyConnected(isFullyConnected);
141 connectFilter->Update();
144 return connectFilter->GetObjectCount();
146 //--------------------------------------------------------------------
148 //--------------------------------------------------------------------
149 template<class ImageType>
150 typename ImageType::Pointer
151 clitk::Labelize(typename ImageType::Pointer input,
152 typename ImageType::PixelType BG,
153 bool isFullyConnected,
154 int minimalComponentSize) {
155 // Connected Component label
156 typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
157 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
158 connectFilter->SetInput(input);
159 connectFilter->SetBackgroundValue(BG);
160 connectFilter->SetFullyConnected(isFullyConnected);
162 // Sort by size and remove too small area.
163 typedef itk::RelabelComponentImageFilter<ImageType, ImageType> RelabelFilterType;
164 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
165 relabelFilter->InPlaceOn();
166 relabelFilter->SetInput(connectFilter->GetOutput());
167 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
168 relabelFilter->Update();
171 return relabelFilter->GetOutput();
173 //--------------------------------------------------------------------
176 //--------------------------------------------------------------------
177 template<class ImageType>
178 typename ImageType::Pointer
179 clitk::RemoveLabels(typename ImageType::Pointer input,
180 typename ImageType::PixelType BG,
181 std::vector<typename ImageType::PixelType> & labelsToRemove) {
182 typename ImageType::Pointer working_image = input;
183 for (unsigned int i=0; i <labelsToRemove.size(); i++) {
184 typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
185 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
186 setBackgroundFilter->SetInput(input);
187 setBackgroundFilter->SetInput2(input);
188 setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
189 setBackgroundFilter->SetOutsideValue(BG);
190 setBackgroundFilter->Update();
191 working_image = setBackgroundFilter->GetOutput();
193 return working_image;
195 //--------------------------------------------------------------------
198 //--------------------------------------------------------------------
199 template<class ImageType>
200 typename ImageType::Pointer
201 clitk::KeepLabels(typename ImageType::Pointer input,
202 typename ImageType::PixelType BG,
203 typename ImageType::PixelType FG,
204 typename ImageType::PixelType firstKeep,
205 typename ImageType::PixelType lastKeep,
207 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
208 typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
209 binarizeFilter->SetInput(input);
210 binarizeFilter->SetLowerThreshold(firstKeep);
211 if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
212 binarizeFilter->SetInsideValue(FG);
213 binarizeFilter->SetOutsideValue(BG);
214 binarizeFilter->Update();
215 return binarizeFilter->GetOutput();
217 //--------------------------------------------------------------------
220 //--------------------------------------------------------------------
221 template<class ImageType>
222 typename ImageType::Pointer
223 clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
224 typename ImageType::PixelType BG,
225 typename ImageType::PixelType FG,
226 bool isFullyConnected,
227 int minimalComponentSize,
228 LabelizeParameters<typename ImageType::PixelType> * param)
230 typename ImageType::Pointer working_image;
231 working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
232 working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
233 working_image = KeepLabels<ImageType>(working_image,
235 param->GetFirstKeep(),
236 param->GetLastKeep(),
237 param->GetUseLastKeep());
238 return working_image;
240 //--------------------------------------------------------------------
243 //--------------------------------------------------------------------
244 template<class ImageType>
245 typename ImageType::Pointer
246 clitk::EnlargeImageLike(typename ImageType::Pointer input,
247 typename ImageType::Pointer like,
248 typename ImageType::PixelType backgroundValue)
250 if (!HaveSameSpacing<ImageType, ImageType>(input, like)) {
251 FATAL("Images must have the same spacing");
254 typename ImageType::Pointer output = ImageType::New();
255 typename ImageType::SizeType size;
256 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
257 size[i] = lrint((like->GetLargestPossibleRegion().GetSize()[i]*like->GetSpacing()[i])/
258 (double)like->GetSpacing()[i]);
261 typename ImageType::RegionType region;
262 region.SetSize(size);
263 output->SetRegions(region);
264 output->SetSpacing(like->GetSpacing());
265 output->SetOrigin(like->GetOrigin());
267 output->FillBuffer(backgroundValue);
268 typedef itk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
269 typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
270 typename PasteFilterType::InputImageIndexType index;
271 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
272 index[i] = lrint((input->GetOrigin()[i] - like->GetOrigin()[i])/(double)input->GetSpacing()[i]);
275 pasteFilter->SetSourceImage(input);
276 pasteFilter->SetDestinationImage(output);
277 pasteFilter->SetDestinationIndex(index);
278 pasteFilter->SetSourceRegion(input->GetLargestPossibleRegion());
279 pasteFilter->Update();
280 return pasteFilter->GetOutput();
282 //--------------------------------------------------------------------