--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ======================================================================-====*/
+
+#ifndef CLITKRELATIVEPOSITIONLIST_H
+#define CLITKRELATIVEPOSITIONLIST_H
+
+// clitk
+#include "clitkSegmentationUtils.h"
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+#include "clitkRelativePosition_ggo.h"
+
+namespace clitk {
+
+ /*--------------------------------------------------------------------
+ Manage a list of RelativePosition operations, to be performed on
+ the same input image, with different objects and parameters.
+ ------------------------------------------------------------------*/
+
+ template <class TImageType>
+ class ITK_EXPORT RelativePositionList:
+ public virtual clitk::FilterBase,
+ public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
+ public itk::ImageToImageFilter<TImageType, TImageType>
+ {
+
+ public:
+ /** Standard class typedefs. */
+ typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
+ typedef RelativePositionList Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(RelativePositionList, ImageToImageFilter);
+
+ /** Some convenient typedefs. */
+ typedef TImageType ImageType;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::RegionType ImageRegionType;
+ typedef typename ImageType::PixelType ImagePixelType;
+ typedef typename ImageType::SizeType ImageSizeType;
+ typedef typename ImageType::IndexType ImageIndexType;
+ typedef typename ImageType::PointType ImagePointType;
+ typedef struct args_info_clitkRelativePosition ArgsInfoType;
+ typedef SliceBySliceRelativePositionFilter<ImageType> SliceRelPosFilterType;
+ typedef AddRelativePositionConstraintToLabelImageFilter<ImageType> RelPosFilterType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+ FILTERBASE_INIT;
+
+ itkGetConstMacro(BackgroundValue, ImagePixelType);
+ itkGetConstMacro(ForegroundValue, ImagePixelType);
+ itkSetMacro(BackgroundValue, ImagePixelType);
+ itkSetMacro(ForegroundValue, ImagePixelType);
+
+ itkSetMacro(InputName, std::string);
+ itkGetConstMacro(InputName, std::string);
+
+ void Read(std::string filename);
+ void SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & options);
+
+ protected:
+ RelativePositionList();
+ virtual ~RelativePositionList() {}
+
+ private:
+ RelativePositionList(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ void GenerateInputRequestedRegion();
+ void GenerateOutputInformation();
+ void GenerateData();
+
+ std::string m_InputName;
+ ImagePixelType m_BackgroundValue;
+ ImagePixelType m_ForegroundValue;
+ typename SliceRelPosFilterType::Pointer mFilter;
+ std::vector<ArgsInfoType> mArgsInfoList;
+ ImagePointer m_working_input;
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#include "clitkRelativePositionList.txx"
+
+#endif
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ======================================================================-====*/
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+clitk::RelativePositionList<TImageType>::
+RelativePositionList() {
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::RelativePositionList<TImageType>::
+Read(std::string filename) {
+ /*
+ The goal here is to read a text file that contains options for the
+ RelativePosition filter. The text file contains options in the
+ same form of the config file of the clitkRelativePosition tool. In
+ this text file, each time a "object" option is found, a new set of
+ options is considered.
+ */
+
+ // Open the file
+ std::ifstream is;
+ openFileForReading(is, filename);
+
+ // Read input -> the structure name that will be used as input
+ // (initial support)
+ skipComment(is);
+ std::string s;
+ is >> s;
+ if (s != "input") {
+ FATAL("while reading RelativePositionList file. This file must start with 'input = '");
+ exit(0);
+ }
+ is >> s;
+ if (s != "=") {
+ FATAL("while reading RelativePositionList file. This file must start with 'input = '");
+ exit(0);
+ }
+ std::string name;
+ is >> name;
+ skipComment(is);
+
+ // Create a temporary filename
+ char n[] = "tmp_clitkRelativePosition_XXXXXX";
+ mkstemp(n); // tmpnam(n);
+ std::string tmpfilename(n);
+
+ // Loop on the file text ; Every time we see a "object" token, we
+ // split the file.
+ while (is) {
+ bool stop=false;
+ std::ostringstream ss;
+ // first part of ss is the last 'object = ' found, stored in s
+ ss << s << std::endl;
+ while (!stop) {
+ skipComment(is);
+ if (!is) stop = true;
+ else {
+ std::getline(is, s);
+ // DD(s);
+ if (s.find("object") != std::string::npos) stop=true;
+ else ss << s << std::endl;
+ if (!is) stop = true;
+ }
+ }
+ std::string text = ss.str();
+ if (text.size() > 10) { // if too small, it is not a list of option
+ std::ofstream os;
+ openFileForWriting(os, tmpfilename);
+ os << text;
+ os.close();
+
+ // Create a struct to store options
+ ArgsInfoType args_info;
+ args_info.input_given = 1;
+ args_info.input_arg = new char[1];
+ args_info.output_given = 1;
+ args_info.output_arg = new char[1];
+ std::vector<char> writable(tmpfilename.size() + 1);
+ std::copy(tmpfilename.begin(), tmpfilename.end(), writable.begin());
+ cmdline_parser_clitkRelativePosition_configfile(&writable[0], &args_info, 1, 1, 0);
+
+ // Store the args
+ mArgsInfoList.push_back(args_info);
+
+ // Delete the temporary file
+ std::remove(tmpfilename.c_str());
+ }
+ }
+
+ // Set the main input name
+ SetInputName(name);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::RelativePositionList<TImageType>::
+GenerateInputRequestedRegion()
+{
+ // Call default
+ itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
+ // Get input pointers and set requested region to common region
+ ImagePointer input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ input1->SetRequestedRegion(input1->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::RelativePositionList<TImageType>::
+GenerateOutputInformation() {
+
+ // Get input
+ m_working_input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+
+ // Loop on RelativePositionList of operations
+ std::string s = GetInputName();
+ for(uint i=0; i<mArgsInfoList.size(); i++) {
+ std::string text = "["+s+"] limits "+
+ mArgsInfoList[i].orientation_arg[0]+" "+
+ mArgsInfoList[i].object_arg+" "+
+ toString(mArgsInfoList[i].threshold_arg);
+ if (mArgsInfoList[i].sliceBySlice_flag) {
+ text += " slice by slice";
+ }
+ else text += " 3D";
+
+ StartNewStep(text);
+ typename RelPosFilterType::Pointer relPosFilter;
+
+ // DD(mArgsInfoList[i].sliceBySlice_flag);
+ if (mArgsInfoList[i].sliceBySlice_flag) {
+ relPosFilter = SliceRelPosFilterType::New();
+ dynamic_cast<SliceRelPosFilterType*>(&*relPosFilter)->SetDirection(2);
+ }
+ else {
+ relPosFilter = clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::New();
+ }
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetVerboseImageSizeFlag(GetVerboseImageSizeFlag());
+ relPosFilter->SetInput(m_working_input);
+ SetFilterOptions(relPosFilter, mArgsInfoList[i]);
+ //relPosFilter->PrintOptions();
+ relPosFilter->Update();
+ m_working_input = relPosFilter->GetOutput();
+ StopCurrentStep<ImageType>(m_working_input);
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::RelativePositionList<TImageType>::
+GenerateData()
+{
+ // Final Step -> set output
+ this->GraftOutput(m_working_input);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::RelativePositionList<TImageType>::
+SetFilterOptions(typename RelPosFilterType::Pointer filter,
+ ArgsInfoType & options) {
+
+ if (options.orientation_given != 1) {
+ DD("ERRROR DEBUG TODO no more than 1 orientation yet");
+ exit(0);
+ }
+
+ ImagePointer object = GetAFDB()->template GetImage<ImageType>(options.object_arg);
+ filter->SetInputObject(object);
+ filter->SetFuzzyThreshold(options.threshold_arg);
+ filter->SetInverseOrientationFlag(options.inverse_flag); // MUST BE BEFORE AddOrientationTypeString
+ for(uint i=0; i<options.orientation_given; i++)
+ filter->AddOrientationTypeString(options.orientation_arg[i]);
+ filter->SetIntermediateSpacing(options.spacing_arg);
+ if (options.spacing_arg == -1) filter->IntermediateSpacingFlagOff();
+ filter->IntermediateSpacingFlagOn();
+
+ if (options.sliceBySlice_flag) {
+ SliceRelPosFilterType * f = dynamic_cast<SliceRelPosFilterType*>(&*filter);
+ f->SetUniqueConnectedComponentBySliceFlag(options.uniqueCCL_flag);
+ f->SetObjectCCLSelectionFlag(options.uniqueObjectCCL_flag);
+ f->IgnoreEmptySliceObjectFlagOn();
+ //filter->SetObjectCCLSelectionDimension(0);
+ //filter->SetObjectCCLSelectionDirection(-1);
+ //filter->SetAutoCropFlag(false);
+ }
+ filter->SetAutoCropFlag(!options.noAutoCrop_flag);
+}
+//--------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
+
+#ifndef CLITKSTRUCTURESEXTRACTIONFILTER_H
+#define CLITKSTRUCTURESEXTRACTIONFILTER_H
+
+// clitk
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+#include "clitkFilterBase.h"
+#include "clitkRelativePositionList.h"
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ /*
+ - Convenient class to add some capabilities to a filter :
+ FilterBase, FilterWithAnatomicalFeatureDatabaseManagement and
+ RelativePositionList
+ */
+ //--------------------------------------------------------------------
+ template <class TImageType>
+ class StructuresExtractionFilter:
+ public virtual FilterBase,
+ public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
+ public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
+ {
+ public:
+ // Standard class typedefs
+ typedef StructuresExtractionFilter Self;
+ typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ // Run-time type information (and related methods)
+ itkTypeMacro(StructuresExtractionFilter, ImageToImageFilter);
+
+ /** Some convenient typedefs. */
+ typedef TImageType ImageType;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::RegionType ImageRegionType;
+ typedef typename ImageType::PixelType ImagePixelType;
+ typedef typename ImageType::SizeType ImageSizeType;
+ typedef typename ImageType::IndexType ImageIndexType;
+ typedef typename ImageType::PointType ImagePointType;
+
+ typedef uchar MaskImagePixelType;
+ typedef itk::Image<MaskImagePixelType, 3> MaskImageType;
+ typedef typename MaskImageType::Pointer MaskImagePointer;
+ typedef typename MaskImageType::RegionType MaskImageRegionType;
+ typedef typename MaskImageType::SizeType MaskImageSizeType;
+ typedef typename MaskImageType::IndexType MaskImageIndexType;
+ typedef typename MaskImageType::PointType MaskImagePointType;
+
+ typedef itk::Image<MaskImagePixelType, 2> MaskSliceType;
+ typedef typename MaskSliceType::Pointer MaskSlicePointer;
+ typedef typename MaskSliceType::PointType MaskSlicePointType;
+ typedef typename MaskSliceType::RegionType MaskSliceRegionType;
+ typedef typename MaskSliceType::SizeType MaskSliceSizeType;
+ typedef typename MaskSliceType::IndexType MaskSliceIndexType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+ FILTERBASE_INIT;
+
+ itkGetConstMacro(BackgroundValue, MaskImagePixelType);
+ itkGetConstMacro(ForegroundValue, MaskImagePixelType);
+ itkSetMacro(BackgroundValue, MaskImagePixelType);
+ itkSetMacro(ForegroundValue, MaskImagePixelType);
+
+ // RelativePositionList management
+ void AddRelativePositionListFilename(std::string s);
+ MaskImagePointer ApplyRelativePositionList(std::string name, MaskImageType * input);
+
+ protected:
+ StructuresExtractionFilter();
+ virtual ~StructuresExtractionFilter() {}
+
+ virtual void GenerateData() {}
+
+ MaskImagePixelType m_BackgroundValue;
+ MaskImagePixelType m_ForegroundValue;
+
+ // RelativePositionList
+ std::vector<std::string> mListOfRelativePositionListFilename;
+ typedef clitk::RelativePositionList<MaskImageType> RelPosListType;
+ typedef typename RelPosListType::Pointer RelPosListPointer;
+ std::map<std::string, RelPosListPointer> mMapOfRelativePositionList;
+
+ private:
+ StructuresExtractionFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#include "clitkStructuresExtractionFilter.txx"
+
+#endif // CLITKSTRUCTURESEXTRACTIONFILTER_H
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
+
+// clitk
+#include "clitkStructuresExtractionFilter.h"
+
+//--------------------------------------------------------------------
+template <class TImageType>
+clitk::StructuresExtractionFilter<TImageType>::
+StructuresExtractionFilter():
+ clitk::FilterBase(),
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+ itk::ImageToImageFilter<TImageType, MaskImageType>()
+{
+ SetBackgroundValue(0);
+ SetForegroundValue(1);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::StructuresExtractionFilter<TImageType>::
+AddRelativePositionListFilename(std::string s) {
+ mListOfRelativePositionListFilename.push_back(s);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+typename clitk::StructuresExtractionFilter<TImageType>::MaskImagePointer
+clitk::StructuresExtractionFilter<TImageType>::
+ApplyRelativePositionList(std::string name, MaskImageType * input)
+{
+ // Create all RelativePositionList
+ for(int i=0; i<mListOfRelativePositionListFilename.size(); i++) {
+ RelPosListPointer rpl = RelPosListType::New();
+ rpl->SetAFDB(GetAFDB());
+ rpl->Read(mListOfRelativePositionListFilename[i]);
+ std::string s = rpl->GetInputName();
+ mMapOfRelativePositionList[s] = rpl;
+ }
+
+ RelPosListPointer relpos;
+ if (mMapOfRelativePositionList.find(name) == mMapOfRelativePositionList.end()) {
+ std::cerr << "Warning: I do not find '" << name << "' in the RelativePositionList." << std::endl;
+ //DD("Not find !"); // do nothing
+ }
+ else {
+ relpos = mMapOfRelativePositionList[name];
+ relpos->SetVerboseStepFlag(GetVerboseStepFlag());
+ relpos->SetCurrentStepBaseId(GetCurrentStepBaseId());
+ relpos->SetCurrentStepId(GetCurrentStepId());
+ relpos->SetCurrentStepNumber(GetCurrentStepNumber());
+ relpos->SetWriteStepFlag(GetWriteStepFlag());
+ relpos->SetInput(input);
+ relpos->Update();
+ input = relpos->GetOutput();
+ }
+ SetCurrentStepNumber(relpos->GetCurrentStepNumber());
+ return input;
+}
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff