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 ======================================================================-====*/
19 #include "clitkLabelImageOverlapMeasureFilter.h"
21 //--------------------------------------------------------------------
22 template <class TImageType>
23 clitk::RelativePositionList<TImageType>::
24 RelativePositionList():
26 clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
27 itk::ImageToImageFilter<TImageType, TImageType>()
29 ComputeOverlapFlagOff();
31 //--------------------------------------------------------------------
34 //--------------------------------------------------------------------
35 template <class TImageType>
37 clitk::RelativePositionList<TImageType>::
38 SetReferenceImageForOverlapMeasure(ImagePointer ref) {
40 ComputeOverlapFlagOn();
42 //--------------------------------------------------------------------
45 //--------------------------------------------------------------------
46 template <class TImageType>
48 clitk::RelativePositionList<TImageType>::
49 Read(std::string filename) {
51 The goal here is to read a text file that contains options for the
52 RelativePosition filter. The text file contains options in the
53 same form of the config file of the clitkRelativePosition tool. In
54 this text file, each time a "object" option is found, a new set of
55 options is considered.
60 openFileForReading(is, filename);
62 // Read input -> the structure name that will be used as input
68 FATAL("while reading RelativePositionList file. This file must start with 'input = '");
73 FATAL("while reading RelativePositionList file. This file must start with 'input = '");
80 // Create a temporary filename
81 char n[] = "tmp_clitkRelativePosition_XXXXXX";
82 mkstemp(n); // tmpnam(n);
83 std::string tmpfilename(n);
85 // Loop on the file text ; Every time we see a "object" token, we
89 std::ostringstream ss;
90 // first part of ss is the last 'object = ' found, stored in s
97 if (s.find("object") != std::string::npos) stop=true;
98 else ss << s << std::endl;
102 std::string text = ss.str();
103 if (text.size() > 10) { // if too small, it is not a list of option
105 openFileForWriting(os, tmpfilename);
107 os << "input = nothing" << std::endl;
108 os << "output = nothing" << std::endl;
111 // Create a struct to store options. I use two step to allow to
112 // fill the args values with de default and then check
113 // automatically the options.
114 ArgsInfoType args_info;
115 std::vector<char> writable(tmpfilename.size() + 1);
116 std::copy(tmpfilename.begin(), tmpfilename.end(), writable.begin());
117 char ** argv = new char*[1];
118 argv[0] = new char[1];
119 struct cmdline_parser_clitkRelativePosition_params params;
121 params.initialize = 1;
122 params.check_required = 0;
123 cmdline_parser_clitkRelativePosition_configfile(&writable[0], &args_info, 1, 1, 1);
124 mArgsInfoList.push_back(args_info);
126 // Delete the temporary file
127 std::remove(tmpfilename.c_str());
131 // Set the main input name
134 //--------------------------------------------------------------------
137 //--------------------------------------------------------------------
138 template <class TImageType>
140 clitk::RelativePositionList<TImageType>::
141 GenerateInputRequestedRegion()
144 itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
145 // Get input pointers and set requested region to common region
146 ImagePointer input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
147 input1->SetRequestedRegion(input1->GetLargestPossibleRegion());
149 //--------------------------------------------------------------------
153 //--------------------------------------------------------------------
154 template <class TImageType>
156 clitk::RelativePositionList<TImageType>::
157 GenerateOutputInformation() {
160 m_working_input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
161 std::string s = GetInputName();
164 if (GetDisplayUsedStructuresOnlyFlag()) {
165 for(uint i=0; i<mArgsInfoList.size(); i++) {
166 // Check if we only want to display structure name
167 AddUsedStructures(s, mArgsInfoList[i].object_arg);
172 // Loop on RelativePositionList of operations
173 for(uint i=0; i<mArgsInfoList.size(); i++) {
175 // clitk::PrintMemory(true, "Start");
176 std::string text = "["+s+"] limits ";
177 if (mArgsInfoList[i].orientation_given) text += std::string(mArgsInfoList[i].orientation_arg[0])+" ";
178 else text = text+"("+toString(mArgsInfoList[i].angle1_arg)+" "+
179 toString(mArgsInfoList[i].angle2_arg)+" "+
180 (mArgsInfoList[i].inverse_flag?"true":"false")+") ";
181 text = text+mArgsInfoList[i].object_arg+" "+toString(mArgsInfoList[i].threshold_arg);
182 if (mArgsInfoList[i].sliceBySlice_flag) {
183 text += " slice by slice";
186 text += " spacing=" + toString(mArgsInfoList[i].spacing_arg);
189 typename RelPosFilterType::Pointer relPosFilter;
191 // Is it slice by slice or 3D ?
192 if (mArgsInfoList[i].sliceBySlice_flag) {
193 typename SliceRelPosFilterType::Pointer f = SliceRelPosFilterType::New();
195 SetFilterOptions(relPosFilter, mArgsInfoList[i]);
197 // Set SbS specific options
198 f->SetUniqueConnectedComponentBySliceFlag(mArgsInfoList[i].uniqueCCL_flag);
199 f->SetObjectCCLSelectionFlag(mArgsInfoList[i].uniqueObjectCCL_flag);
200 f->IgnoreEmptySliceObjectFlagOn();
201 //f->SetObjectCCLSelectionDimension(0);
202 //f->SetObjectCCLSelectionDirection(-1);
203 //f->SetAutoCropFlag(false);
205 if (mArgsInfoList[i].verboseOptions_flag) f->PrintOptions();
208 relPosFilter = clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::New();
209 SetFilterOptions(relPosFilter, mArgsInfoList[i]);
211 if (mArgsInfoList[i].verboseOptions_flag) relPosFilter->PrintOptions();
215 relPosFilter->SetInput(m_working_input);
218 relPosFilter->Update();
219 m_working_input = relPosFilter->GetOutput();
220 StopCurrentStep<ImageType>(m_working_input);
222 // Compute overlap with reference if needed
223 if (GetComputeOverlapFlag()) {
224 typedef clitk::LabelImageOverlapMeasureFilter<ImageType> FilterType;
225 typename FilterType::Pointer filter = FilterType::New();
226 filter->SetInput(0, m_working_input);
227 filter->SetInput(1, m_reference);
233 //--------------------------------------------------------------------
236 //--------------------------------------------------------------------
237 template <class TImageType>
239 clitk::RelativePositionList<TImageType>::
242 // Final Step -> set output
243 this->GraftOutput(m_working_input);
245 //--------------------------------------------------------------------
248 //--------------------------------------------------------------------
249 template <class TImageType>
251 clitk::RelativePositionList<TImageType>::
252 SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & options) {
254 if (options.orientation_given > 1) {
255 clitkExceptionMacro("Error in the RelPos options. I need a single --orientation (for the moment)."
256 << " Current options are for obj = '" << options.object_arg
257 << "', threshold = " << options.threshold_arg << std::endl);
260 ImagePointer object = GetAFDB()->template GetImage<ImageType>(options.object_arg);
261 filter->SetInputObject(object);
262 filter->WriteStepFlagOff();
263 filter->SetVerboseImageSizeFlag(GetVerboseImageSizeFlag());
264 filter->SetFuzzyThreshold(options.threshold_arg);
265 filter->SetInverseOrientationFlag(options.inverse_flag); // MUST BE BEFORE AddOrientationTypeString
267 if (options.orientation_given == 1) {
268 for(uint i=0; i<options.orientation_given; i++)
269 filter->AddOrientationTypeString(options.orientation_arg[i]);
272 if (options.angle1_given && options.angle2_given) {
273 filter->AddAnglesInDeg(options.angle1_arg, options.angle2_arg);
276 clitkExceptionMacro("Error in the RelPos options. I need --orientation or (--angle1 and --angle2)."
277 << " Current options are for obj = '" << options.object_arg
278 << "', threshold = " << options.threshold_arg << std::endl);
281 filter->SetIntermediateSpacing(options.spacing_arg);
282 if (options.spacing_arg == -1) filter->IntermediateSpacingFlagOff();
283 else filter->IntermediateSpacingFlagOn();
284 filter->SetVerboseStepFlag(options.verboseStep_flag);
285 filter->SetAutoCropFlag(!options.noAutoCrop_flag);
287 //--------------------------------------------------------------------