From: David Sarrut Date: Fri, 3 Feb 2012 07:13:46 +0000 (+0100) Subject: Moved from repository clitk to clitk.private/tests_dav X-Git-Tag: v1.3.0~104^2~8^2~2 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=a60f638793793247abd4b56acab578a64ddc9d6e;p=clitk.git Moved from repository clitk to clitk.private/tests_dav --- diff --git a/tools/clitkImage2DicomRTStruct.cxx b/tools/clitkImage2DicomRTStruct.cxx deleted file mode 100644 index d71491b..0000000 --- a/tools/clitkImage2DicomRTStruct.cxx +++ /dev/null @@ -1,47 +0,0 @@ -/*========================================================================= - Program: vv http://www.creatis.insa-lyon.fr/rio/vv - Main authors : XX XX XX - - Authors belongs 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 http://www.opensource.org/licenses/bsd-license.php - - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html - - =========================================================================*/ - -#include "clitkImage2DicomRTStructFilter.h" -#include "clitkDicomRT_StructureSet.h" -#include "clitkImage2DicomRTStruct_ggo.h" - -//-------------------------------------------------------------------- -int main(int argc, char * argv[]) { - - // Init command line - GGO(clitkImage2DicomRTStruct, args_info); - - // Read initial 3D image - typedef float PixelType; - typedef itk::Image ImageType; - ImageType::Pointer input = clitk::readImage(args_info.input_arg, true); - - // Create a filter to convert image into dicomRTStruct - clitk::Image2DicomRTStructFilter filter; - filter.SetInput(input); - filter.Update(); - - // Write result - clitk::DicomRT_StructureSet::Pointer s = filter.GetDicomRTStruct(); - // s->Write(args_info.output_arg); - - // This is the end my friend - return 0; -} -//-------------------------------------------------------------------- diff --git a/tools/clitkImage2DicomRTStruct.ggo b/tools/clitkImage2DicomRTStruct.ggo deleted file mode 100644 index 68334b1..0000000 --- a/tools/clitkImage2DicomRTStruct.ggo +++ /dev/null @@ -1,20 +0,0 @@ -# file clitkImage2DicomRTStruct.ggo -package "clitk" -version "Convert (binary) image to DICOM RT Structure Set (contours)" - -option "config" - "Config file" string no -option "verbose" v "Verbose" flag off - -option "input" i "Input image file (binary image" string yes -option "output" o "Output DicomRT filename" string yes - - -# option "image" j "Used to read image info (spacing, origin)" string yes -# option "roi" r "ROI to binarize (if -1 = all roi)" int no default="-1" - -# option "crop" c "Crop binary mask" flag off - -#option "roi" r "ROI to print (ID)" int no -#option "contour" c "contour to print (ID)" int no -#option "offset" o "to display points as image offsets" flag off - diff --git a/tools/clitkLabelImageOverlapMeasure.cxx b/tools/clitkLabelImageOverlapMeasure.cxx deleted file mode 100644 index 9a7b625..0000000 --- a/tools/clitkLabelImageOverlapMeasure.cxx +++ /dev/null @@ -1,46 +0,0 @@ -/*========================================================================= - 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 "clitkIO.h" -#include "clitkLabelImageOverlapMeasure_ggo.h" -#include "clitkLabelImageOverlapMeasureGenericFilter.h" - -//-------------------------------------------------------------------- -int main(int argc, char * argv[]) { - - // Init command line - GGO(clitkLabelImageOverlapMeasure, args_info); - CLITK_INIT; - - // Filter - typedef clitk::LabelImageOverlapMeasureGenericFilter FilterType; - FilterType::Pointer filter = FilterType::New(); - - filter->SetArgsInfo(args_info); - - try { - filter->Update(); - } catch(std::runtime_error e) { - std::cout << e.what() << std::endl; - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -} // This is the end, my friend -//-------------------------------------------------------------------- diff --git a/tools/clitkLabelImageOverlapMeasure.ggo b/tools/clitkLabelImageOverlapMeasure.ggo deleted file mode 100644 index 17c28ed..0000000 --- a/tools/clitkLabelImageOverlapMeasure.ggo +++ /dev/null @@ -1,21 +0,0 @@ -#File clitkLabelImageOverlapMeasure.ggo -package "clitkLabelImageOverlapMeasure" -version "1.0" -purpose "Compute Dice and other coefficients between label images" - -section "General options" -option "config" - "Config file" string no -option "verbose" v "Verbose" flag off -option "imagetypes" - "Display allowed image types" flag off - -section "Input" -option "input1" i "Input mask 1" string yes -option "input2" j "Input mask 2" string yes - -option "label1" l "Label in input1" int no default="1" -option "label2" m "Label in input2" int no default="1" -option "BG" b "Background value" int no default="0" - - - - diff --git a/tools/clitkLabelImageOverlapMeasureGenericFilter.h b/tools/clitkLabelImageOverlapMeasureGenericFilter.h deleted file mode 100644 index a6f8028..0000000 --- a/tools/clitkLabelImageOverlapMeasureGenericFilter.h +++ /dev/null @@ -1,76 +0,0 @@ -/*========================================================================= - 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 CLITKLABELIMAGEOVERLAPMEASUREGENERICFILTER_H -#define CLITKLABELIMAGEOVERLAPMEASUREGENERICFILTER_H - -// clitk -#include "clitkImageToImageGenericFilter.h" -#include "clitkLabelImageOverlapMeasureFilter.h" -#include "clitkBoundingBoxUtils.h" -#include "clitkCropLikeImageFilter.h" - -//-------------------------------------------------------------------- -namespace clitk -{ - - template - class ITK_EXPORT LabelImageOverlapMeasureGenericFilter: - public ImageToImageGenericFilter > - { - public: - //-------------------------------------------------------------------- - LabelImageOverlapMeasureGenericFilter(); - - //-------------------------------------------------------------------- - typedef ImageToImageGenericFilter > Superclass; - typedef LabelImageOverlapMeasureGenericFilter Self; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - //-------------------------------------------------------------------- - itkNewMacro(Self); - itkTypeMacro(LabelImageOverlapMeasureGenericFilter, LightObject); - - //-------------------------------------------------------------------- - void SetArgsInfo(const ArgsInfoType & a); - template - void SetOptionsFromArgsInfoToFilter(FilterType * f) ; - - //-------------------------------------------------------------------- - // Main function called each time the filter is updated - template - void UpdateWithInputImageType(); - - protected: - template void InitializeImageType(); - ArgsInfoType mArgsInfo; - - private: - LabelImageOverlapMeasureGenericFilter(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - - };// end class - //-------------------------------------------------------------------- -} // end namespace clitk - -#ifndef ITK_MANUAL_INSTANTIATION -#include "clitkLabelImageOverlapMeasureGenericFilter.txx" -#endif - -#endif // #define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H diff --git a/tools/clitkLabelImageOverlapMeasureGenericFilter.txx b/tools/clitkLabelImageOverlapMeasureGenericFilter.txx deleted file mode 100644 index bb1b6eb..0000000 --- a/tools/clitkLabelImageOverlapMeasureGenericFilter.txx +++ /dev/null @@ -1,100 +0,0 @@ -/*========================================================================= - 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 - ===========================================================================**/ - -//-------------------------------------------------------------------- -template -clitk::LabelImageOverlapMeasureGenericFilter:: -LabelImageOverlapMeasureGenericFilter(): - ImageToImageGenericFilter("LabelImageOverlapMeasure") -{ - // Default values - cmdline_parser_clitkLabelImageOverlapMeasure_init(&mArgsInfo); - //InitializeImageType<2>(); - InitializeImageType<3>(); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -template -void clitk::LabelImageOverlapMeasureGenericFilter:: -InitializeImageType() -{ - ADD_IMAGE_TYPE(Dim, uchar); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -void clitk::LabelImageOverlapMeasureGenericFilter:: -SetArgsInfo(const ArgsInfoType & a) -{ - mArgsInfo=a; - SetIOVerbose(mArgsInfo.verbose_flag); - if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes(); - if (mArgsInfo.input1_given) AddInputFilename(mArgsInfo.input1_arg); - if (mArgsInfo.input2_given) AddInputFilename(mArgsInfo.input2_arg); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::LabelImageOverlapMeasureGenericFilter:: -SetOptionsFromArgsInfoToFilter(FilterType * f) -{ - f->SetLabel1(mArgsInfo.label1_arg); - f->SetLabel2(mArgsInfo.label2_arg); -} - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::LabelImageOverlapMeasureGenericFilter:: -UpdateWithInputImageType() -{ - // Reading input - typename ImageType::Pointer input1 = this->template GetInput(0); - typename ImageType::Pointer input2 = this->template GetInput(1); - - // Create filter - typedef clitk::LabelImageOverlapMeasureFilter FilterType; - typename FilterType::Pointer filter = FilterType::New(); - - // Set global Options - filter->SetInput(0, input1); - filter->SetInput(1, input2); - SetOptionsFromArgsInfoToFilter(filter); - - // Go ! - filter->Update(); - - // Write/Save results - // typename ImageType::Pointer output = filter->GetOutput(); - // this->template SetNextOutput(output); -} -//-------------------------------------------------------------------- - - diff --git a/tools/clitkRelativePosition.cxx b/tools/clitkRelativePosition.cxx deleted file mode 100644 index 55e0236..0000000 --- a/tools/clitkRelativePosition.cxx +++ /dev/null @@ -1,44 +0,0 @@ -/*========================================================================= - 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 "clitkRelativePosition_ggo.h" -#include "clitkRelativePositionGenericFilter.h" - -//-------------------------------------------------------------------- -int main(int argc, char * argv[]) { - - // Init command line - GGO(clitkRelativePosition, args_info); - CLITK_INIT; - - // Filter - typedef clitk::RelativePositionGenericFilter FilterType; - FilterType::Pointer filter = FilterType::New(); - - filter->SetArgsInfo(args_info); - - try { - filter->Update(); - } catch(std::runtime_error e) { - std::cout << e.what() << std::endl; - } - - return EXIT_SUCCESS; -} // This is the end, my friend -//-------------------------------------------------------------------- diff --git a/tools/clitkRelativePosition.ggo b/tools/clitkRelativePosition.ggo deleted file mode 100644 index bc3f511..0000000 --- a/tools/clitkRelativePosition.ggo +++ /dev/null @@ -1,36 +0,0 @@ -#File clitkRelativePosition.ggo -package "clitkRelativePosition" -version "1.0" -purpose "Constraint a given mask image relatively to another object and an orientation" - -section "General options" -option "config" - "Config file" string no -option "verbose" v "Verbose" flag off -option "verboseStep" - "Verbose each step" flag off -option "writeStep" w "Write image at each step" flag off -option "verboseOptions" - "Display options values" flag off -option "imagetypes" - "Display allowed image types" flag off - -section "Input/Output" -option "input" i "Input mask image filename" string yes -option "object" j "Input mask object filename" string yes -option "output" o "Output image filename" string yes - -section "Main options" -option "orientation" r "L R A P I S (LeftRightAntPostInfSup)" string no multiple default="L" -option "angle1" a "Angle 1 (deg)" double no default="0" -option "angle2" b "Angle 2 (deg)" double no default="0" -option "spacing" s "Resample before (faster) (-1 if not resampling" double default = "-1" no -option "threshold" t "Fuzzy threshold" double no default="0.6" -option "inverse" n "Not flag : inverse of the orientation" flag off -option "doNotRemoveObject" - "if flag is on, do not remove the object" flag off -option "noAutoCrop" c "No auto crop at the end if set" flag off -option "combineWithOr" - "Combine relpos map and support with OR" flag off - -section "Slice by slice processing" -option "sliceBySlice" - "Slice by slice relative position" flag off -option "direction" d "If SbS, indicate the slice direction" int no default="2" -option "uniqueCCL" u "Keep only one CC in each slice" flag off -option "uniqueObjectCCL" - "Keep only one CC in each object slice" flag off - - diff --git a/tools/clitkRelativePositionAnalyzer.cxx b/tools/clitkRelativePositionAnalyzer.cxx deleted file mode 100644 index bb0986d..0000000 --- a/tools/clitkRelativePositionAnalyzer.cxx +++ /dev/null @@ -1,45 +0,0 @@ -/*========================================================================= - 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 "clitkRelativePositionAnalyzer_ggo.h" -#include "clitkRelativePositionAnalyzerGenericFilter.h" - -//-------------------------------------------------------------------- -int main(int argc, char * argv[]) { - - // Init command line - GGO(clitkRelativePositionAnalyzer, args_info); - CLITK_INIT; - - // Filter - typedef clitk::RelativePositionAnalyzerGenericFilter FilterType; - FilterType::Pointer filter = FilterType::New(); - filter->SetArgsInfo(args_info); - - // Go ! - try { - filter->Update(); - } catch(std::runtime_error e) { - std::cout << e.what() << std::endl; - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -} // This is the end, my friend -//-------------------------------------------------------------------- diff --git a/tools/clitkRelativePositionAnalyzer.ggo b/tools/clitkRelativePositionAnalyzer.ggo deleted file mode 100644 index cf0feb1..0000000 --- a/tools/clitkRelativePositionAnalyzer.ggo +++ /dev/null @@ -1,31 +0,0 @@ -#File clitkRelativePositionAnalyzer.ggo -package "clitkRelativePositionAnalyzer" -version "1.0" -purpose "Analyze relative position of a target according to structures" - -section "General options" -option "config" - "Config file" string no -option "verbose" v "Verbose" flag off -option "imagetypes" - "Display allowed image types" flag off - -section "Input/Output" -option "support" i "Input mask support" string yes -option "object" j "Input mask object" string yes -option "target" t "Input mask target" string yes -option "output" o "Output image " string yes - -section "Options for building the relative positions" -option "bins" - "Number of histo bins for fuzzy map" int default="100" no -option "tol" - "Target area loss tolerance (|0-1])" double default="0.01" no - -option "angle1" a "Angle 1 (deg)" double no default="0" -option "angle2" b "Angle 2 (deg)" double no default="0" -option "inverse" n "Not flag : inverse of the orientation" flag off - - -section "Compute some statistic on afdb" -option "afdb" - "Input Anatomical Feature DB" string no multiple -option "afdb_path" - "Path to search image in afdb" string no multiple -option "station" - "Station name" string no - - diff --git a/tools/clitkRelativePositionAnalyzerGenericFilter.h b/tools/clitkRelativePositionAnalyzerGenericFilter.h deleted file mode 100644 index fc5f67e..0000000 --- a/tools/clitkRelativePositionAnalyzerGenericFilter.h +++ /dev/null @@ -1,77 +0,0 @@ -/*========================================================================= - 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 CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H -#define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H - -// clitk -#include "clitkIO.h" -#include "clitkImageToImageGenericFilter.h" -#include "clitkRelativePositionAnalyzerFilter.h" -#include "clitkSliceBySliceRelativePositionFilter.h" - -//-------------------------------------------------------------------- -namespace clitk -{ - - template - class ITK_EXPORT RelativePositionAnalyzerGenericFilter: - public ImageToImageGenericFilter > - { - public: - //-------------------------------------------------------------------- - RelativePositionAnalyzerGenericFilter(); - ~RelativePositionAnalyzerGenericFilter() {} - - //-------------------------------------------------------------------- - typedef ImageToImageGenericFilter > Superclass; - typedef RelativePositionAnalyzerGenericFilter Self; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - //-------------------------------------------------------------------- - itkNewMacro(Self); - itkTypeMacro(RelativePositionAnalyzerGenericFilter, LightObject); - - //-------------------------------------------------------------------- - void SetArgsInfo(const ArgsInfoType & a); - template - void SetOptionsFromArgsInfoToFilter(FilterType * f) ; - - //-------------------------------------------------------------------- - // Main function called each time the filter is updated - template - void UpdateWithInputImageType(); - - protected: - template void InitializeImageType(); - ArgsInfoType mArgsInfo; - - private: - RelativePositionAnalyzerGenericFilter(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - - };// end class - //-------------------------------------------------------------------- -} // end namespace clitk - -#ifndef ITK_MANUAL_INSTANTIATION -#include "clitkRelativePositionAnalyzerGenericFilter.txx" -#endif - -#endif // #define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H diff --git a/tools/clitkRelativePositionAnalyzerGenericFilter.txx b/tools/clitkRelativePositionAnalyzerGenericFilter.txx deleted file mode 100644 index 5074504..0000000 --- a/tools/clitkRelativePositionAnalyzerGenericFilter.txx +++ /dev/null @@ -1,110 +0,0 @@ -/*========================================================================= - 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 - ===========================================================================**/ - -//-------------------------------------------------------------------- -template -clitk::RelativePositionAnalyzerGenericFilter:: -RelativePositionAnalyzerGenericFilter(): - ImageToImageGenericFilter("RelativePositionAnalyzer") -{ - // Default values - cmdline_parser_clitkRelativePositionAnalyzer_init(&mArgsInfo); - InitializeImageType<3>(); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionAnalyzerGenericFilter:: -InitializeImageType() -{ - ADD_IMAGE_TYPE(Dim, uchar); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -void clitk::RelativePositionAnalyzerGenericFilter:: -SetArgsInfo(const ArgsInfoType & a) -{ - mArgsInfo=a; - SetIOVerbose(mArgsInfo.verbose_flag); - if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes(); - if (mArgsInfo.support_given) AddInputFilename(mArgsInfo.support_arg); - if (mArgsInfo.object_given) AddInputFilename(mArgsInfo.object_arg); - if (mArgsInfo.target_given) AddInputFilename(mArgsInfo.target_arg); - if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionAnalyzerGenericFilter:: -SetOptionsFromArgsInfoToFilter(FilterType * f) -{ - f->SetNumberOfBins(mArgsInfo.bins_arg); - f->SetAreaLossTolerance(mArgsInfo.tol_arg); - clitk::RelativePositionDirectionType d; - if (mArgsInfo.angle1_given) d.angle1 = clitk::deg2rad(mArgsInfo.angle1_arg); - if (mArgsInfo.angle2_given) d.angle2 = clitk::deg2rad(mArgsInfo.angle2_arg); - if (mArgsInfo.inverse_given) d.notFlag = clitk::deg2rad(mArgsInfo.inverse_flag); - f->SetDirection(d); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionAnalyzerGenericFilter:: -UpdateWithInputImageType() -{ - // Create filter - typedef clitk::RelativePositionAnalyzerFilter FilterType; - typename FilterType::Pointer filter = FilterType::New(); - - // Reading input - typename ImageType::Pointer support = this->template GetInput(0); - typename ImageType::Pointer object = this->template GetInput(1); - typename ImageType::Pointer target = this->template GetInput(2); - filter->SetInputSupport(support); - filter->SetInputObject(object); - filter->SetInputTarget(target); - - // Set global Options - SetOptionsFromArgsInfoToFilter(filter); - - // Go ! - filter->Update(); - - // Display output - filter->GetInfo().Println(); - filter->GetInfoReverse().Println(); -} -//-------------------------------------------------------------------- - - diff --git a/tools/clitkRelativePositionDataBaseAnalyzer.cxx b/tools/clitkRelativePositionDataBaseAnalyzer.cxx deleted file mode 100644 index b74cec4..0000000 --- a/tools/clitkRelativePositionDataBaseAnalyzer.cxx +++ /dev/null @@ -1,48 +0,0 @@ -/*========================================================================= - 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 "clitkRelativePositionDataBaseAnalyzer_ggo.h" -#include "clitkIO.h" -#include "clitkRelativePositionDataBaseAnalyzerFilter.h" - -//-------------------------------------------------------------------- -int main(int argc, char * argv[]) { - - // Init command line - GGO(clitkRelativePositionDataBaseAnalyzer, args_info); - CLITK_INIT; - - // Filter - typedef clitk::RelativePositionDataBaseAnalyzerFilter FilterType; - FilterType filter; - filter.SetDatabaseFilename(args_info.db_arg); - filter.SetStationName(args_info.station_arg); - // filter.SetStationName(args_info.object_arg);//FIXME - filter.SetOutputFilename(args_info.output_arg); - - try { - filter.Update(); - } catch(std::runtime_error e) { - std::cout << e.what() << std::endl; - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -} // This is the end, my friend -//-------------------------------------------------------------------- diff --git a/tools/clitkRelativePositionDataBaseAnalyzer.ggo b/tools/clitkRelativePositionDataBaseAnalyzer.ggo deleted file mode 100644 index 0da0bcd..0000000 --- a/tools/clitkRelativePositionDataBaseAnalyzer.ggo +++ /dev/null @@ -1,14 +0,0 @@ -#File clitkRelativePositionDataBaseAnalyzer.ggo -package "clitkRelativePositionDataBaseAnalyzer" -version "1.0" -purpose "Analyze a DB of relative positions for several patient and structures" - -section "General options" -option "config" - "Config file" string no -option "verbose" v "Verbose" flag off - -section "Input/Output" -option "db" i "Input database of RelPost" string yes -option "station" s "Studied station name" string yes -option "object" - "Studied object/struct name" string no -option "output" o "Output rpl file" string yes diff --git a/tools/clitkRelativePositionDataBaseBuilder.cxx b/tools/clitkRelativePositionDataBaseBuilder.cxx deleted file mode 100644 index 4c8db03..0000000 --- a/tools/clitkRelativePositionDataBaseBuilder.cxx +++ /dev/null @@ -1,52 +0,0 @@ -/*========================================================================= - 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 "clitkRelativePositionDataBaseBuilder_ggo.h" -#include "clitkRelativePositionDataBaseBuilderGenericFilter.h" - -//-------------------------------------------------------------------- -int main(int argc, char * argv[]) { - - // Init command line - GGO(clitkRelativePositionDataBaseBuilder, args_info); - CLITK_INIT; - - // Filter - typedef clitk::RelativePositionDataBaseBuilderGenericFilter FilterType; - FilterType::Pointer filter = FilterType::New(); - - // Set options - filter->SetArgsInfo(args_info); - - // Add an input to determine the type of image - NewAFDB(afdb, args_info.afdb_arg); - std::string f = afdb->GetTagValue(args_info.supportName_arg); - f = std::string(args_info.afdb_path_arg)+"/"+f; - filter->AddInputFilename(f); - - try { - filter->Update(); - } catch(std::runtime_error e) { - std::cout << e.what() << std::endl; - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -} // This is the end, my friend -//-------------------------------------------------------------------- diff --git a/tools/clitkRelativePositionDataBaseBuilder.ggo b/tools/clitkRelativePositionDataBaseBuilder.ggo deleted file mode 100644 index c71c462..0000000 --- a/tools/clitkRelativePositionDataBaseBuilder.ggo +++ /dev/null @@ -1,25 +0,0 @@ -#File clitkRelativePositionDataBaseBuilder.ggo -package "clitkRelativePositionDataBaseBuilder" -version "1.0" -purpose "Analyze relative position of a target according to structures" - -section "General options" -option "config" - "Config file" string no -option "verbose" v "Verbose" flag off -option "imagetypes" - "Display allowed image types" flag off - -section "Input/Output" -option "afdb" a "Input Anatomical Feature DB" string yes -option "afdb_path" - "Path to search image in afdb" string no - -option "supportName" i "Input mask support name in afdb" string yes -option "targetName" t "Input mask target name in afdb" string yes -option "objectName" j "Input mask object name in afdb" string yes multiple - -option "output" o "Output image " string yes - -section "Options for building the relative positions" -option "bins" b "Number of histo bins for fuzzy map" int default="100" no -option "nb" n "Number of angles to test" int default="4" no -option "tol" - "Target area loss tolerance (|0-1])" double default="0.01" no - diff --git a/tools/clitkRelativePositionDataBaseBuilderGenericFilter.h b/tools/clitkRelativePositionDataBaseBuilderGenericFilter.h deleted file mode 100644 index bf88269..0000000 --- a/tools/clitkRelativePositionDataBaseBuilderGenericFilter.h +++ /dev/null @@ -1,76 +0,0 @@ -/*========================================================================= - 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 CLITKRelativePositionDataBaseBuilderGENERICFILTER_H -#define CLITKRelativePositionDataBaseBuilderGENERICFILTER_H - -// clitk -#include "clitkIO.h" -#include "clitkImageToImageGenericFilter.h" -#include "clitkRelativePositionDataBaseBuilderFilter.h" -#include "clitkSliceBySliceRelativePositionFilter.h" - -//-------------------------------------------------------------------- -namespace clitk -{ - - template - class ITK_EXPORT RelativePositionDataBaseBuilderGenericFilter: - public ImageToImageGenericFilter > - { - public: - //-------------------------------------------------------------------- - RelativePositionDataBaseBuilderGenericFilter(); - - //-------------------------------------------------------------------- - typedef ImageToImageGenericFilter > Superclass; - typedef RelativePositionDataBaseBuilderGenericFilter Self; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - //-------------------------------------------------------------------- - itkNewMacro(Self); - itkTypeMacro(RelativePositionDataBaseBuilderGenericFilter, LightObject); - - //-------------------------------------------------------------------- - void SetArgsInfo(const ArgsInfoType & a); - template - void SetOptionsFromArgsInfoToFilter(FilterType * f) ; - - //-------------------------------------------------------------------- - // Main function called each time the filter is updated - template - void UpdateWithInputImageType(); - - protected: - template void InitializeImageType(); - ArgsInfoType mArgsInfo; - - private: - RelativePositionDataBaseBuilderGenericFilter(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - - };// end class - //-------------------------------------------------------------------- -} // end namespace clitk - -#ifndef ITK_MANUAL_INSTANTIATION -#include "clitkRelativePositionDataBaseBuilderGenericFilter.txx" -#endif - -#endif // #define CLITKRelativePositionDataBaseBuilderGENERICFILTER_H diff --git a/tools/clitkRelativePositionDataBaseBuilderGenericFilter.txx b/tools/clitkRelativePositionDataBaseBuilderGenericFilter.txx deleted file mode 100644 index a6bba29..0000000 --- a/tools/clitkRelativePositionDataBaseBuilderGenericFilter.txx +++ /dev/null @@ -1,101 +0,0 @@ -/*========================================================================= - 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 - ===========================================================================**/ - -//-------------------------------------------------------------------- -template -clitk::RelativePositionDataBaseBuilderGenericFilter:: -RelativePositionDataBaseBuilderGenericFilter(): - ImageToImageGenericFilter("RelativePositionDataBaseBuilder") -{ - // Default values - cmdline_parser_clitkRelativePositionDataBaseBuilder_init(&mArgsInfo); - InitializeImageType<3>(); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionDataBaseBuilderGenericFilter:: -InitializeImageType() -{ - ADD_IMAGE_TYPE(Dim, uchar); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -void clitk::RelativePositionDataBaseBuilderGenericFilter:: -SetArgsInfo(const ArgsInfoType & a) -{ - mArgsInfo=a; - SetIOVerbose(mArgsInfo.verbose_flag); - if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes(); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionDataBaseBuilderGenericFilter:: -SetOptionsFromArgsInfoToFilter(FilterType * f) -{ - f->SetAFDBFilename(mArgsInfo.afdb_arg); - f->SetAFDBPath(mArgsInfo.afdb_path_arg); - f->SetNumberOfBins(mArgsInfo.bins_arg); - f->SetNumberOfAngles(mArgsInfo.nb_arg); - f->SetAreaLossTolerance(mArgsInfo.tol_arg); - f->SetSupportName(mArgsInfo.supportName_arg); - f->SetTargetName(mArgsInfo.targetName_arg); - for(unsigned int i=0; iAddObjectName(mArgsInfo.objectName_arg[i]); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionDataBaseBuilderGenericFilter:: -UpdateWithInputImageType() -{ - // Create filter - typedef clitk::RelativePositionDataBaseBuilderFilter FilterType; - typename FilterType::Pointer filter = FilterType::New(); - - // Set global Options - SetOptionsFromArgsInfoToFilter(filter); - - // Go ! - filter->Update(); - - // Write/Save results - // typename ImageType::Pointer output = filter->GetOutput(); - //this->template SetNextOutput(output); - -} -//-------------------------------------------------------------------- - - diff --git a/tools/clitkRelativePositionGenericFilter.h b/tools/clitkRelativePositionGenericFilter.h deleted file mode 100644 index bb9ec6f..0000000 --- a/tools/clitkRelativePositionGenericFilter.h +++ /dev/null @@ -1,76 +0,0 @@ -/*========================================================================= - 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 CLITKRELATIVEPOSITIONGENERICFILTER_H -#define CLITKRELATIVEPOSITIONGENERICFILTER_H - -// clitk -#include "clitkIO.h" -#include "clitkImageToImageGenericFilter.h" -#include "clitkAddRelativePositionConstraintToLabelImageFilter.h" -#include "clitkSliceBySliceRelativePositionFilter.h" - -//-------------------------------------------------------------------- -namespace clitk -{ - - template - class ITK_EXPORT RelativePositionGenericFilter: - public ImageToImageGenericFilter > - { - public: - //-------------------------------------------------------------------- - RelativePositionGenericFilter(); - - //-------------------------------------------------------------------- - typedef ImageToImageGenericFilter > Superclass; - typedef RelativePositionGenericFilter Self; - typedef itk::SmartPointer Pointer; - typedef itk::SmartPointer ConstPointer; - - //-------------------------------------------------------------------- - itkNewMacro(Self); - itkTypeMacro(RelativePositionGenericFilter, LightObject); - - //-------------------------------------------------------------------- - void SetArgsInfo(const ArgsInfoType & a); - template - void SetOptionsFromArgsInfoToFilter(FilterType * f) ; - - //-------------------------------------------------------------------- - // Main function called each time the filter is updated - template - void UpdateWithInputImageType(); - - protected: - template void InitializeImageType(); - ArgsInfoType mArgsInfo; - - private: - RelativePositionGenericFilter(const Self&); //purposely not implemented - void operator=(const Self&); //purposely not implemented - - };// end class - //-------------------------------------------------------------------- -} // end namespace clitk - -#ifndef ITK_MANUAL_INSTANTIATION -#include "clitkRelativePositionGenericFilter.txx" -#endif - -#endif // #define CLITKRELATIVEPOSITIONGENERICFILTER_H diff --git a/tools/clitkRelativePositionGenericFilter.txx b/tools/clitkRelativePositionGenericFilter.txx deleted file mode 100644 index 8af353a..0000000 --- a/tools/clitkRelativePositionGenericFilter.txx +++ /dev/null @@ -1,160 +0,0 @@ -/*========================================================================= - 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 - ===========================================================================**/ - -#include "clitkImageCommon.h" - -//-------------------------------------------------------------------- -template -clitk::RelativePositionGenericFilter:: -RelativePositionGenericFilter(): - ImageToImageGenericFilter("RelativePosition") -{ - // Default values - cmdline_parser_clitkRelativePosition_init(&mArgsInfo); - InitializeImageType<3>(); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionGenericFilter:: -InitializeImageType() -{ - ADD_IMAGE_TYPE(Dim, uchar); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template -void clitk::RelativePositionGenericFilter:: -SetArgsInfo(const ArgsInfoType & a) -{ - mArgsInfo=a; - SetIOVerbose(mArgsInfo.verbose_flag); - if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes(); - if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg); - if (mArgsInfo.object_given) AddInputFilename(mArgsInfo.object_arg); - if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionGenericFilter:: -SetOptionsFromArgsInfoToFilter(FilterType * f) -{ - f->SetVerboseOptionFlag(mArgsInfo.verboseOptions_flag); - f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag); - f->SetWriteStepFlag(mArgsInfo.writeStep_flag); - - // Must be set before AddOrientationTypeString - f->SetInverseOrientationFlag(mArgsInfo.inverse_flag); - - for(uint i=0; iAddOrientationTypeString(mArgsInfo.orientation_arg[i]); - } - - if (mArgsInfo.spacing_given) { - f->IntermediateSpacingFlagOn(); - f->SetIntermediateSpacing(mArgsInfo.spacing_arg); - } - else { - f->IntermediateSpacingFlagOff(); - } - - f->SetFuzzyThreshold(mArgsInfo.threshold_arg); - f->SetRemoveObjectFlag(!mArgsInfo.doNotRemoveObject_flag); - f->SetAutoCropFlag(!mArgsInfo.noAutoCrop_flag); - f->SetCombineWithOrFlag(mArgsInfo.combineWithOr_flag); -} - -//-------------------------------------------------------------------- -// Update with the number of dimensions and the pixeltype -//-------------------------------------------------------------------- -template -template -void clitk::RelativePositionGenericFilter:: -UpdateWithInputImageType() -{ - // Reading input - typename ImageType::Pointer input = this->template GetInput(0); - typename ImageType::Pointer object = this->template GetInput(1); - - if (mArgsInfo.sliceBySlice_flag) { - // Create filter - typedef clitk::SliceBySliceRelativePositionFilter FilterType; - typename FilterType::Pointer filter = FilterType::New(); - - // Set the filter (needed for example for threaded monitoring) - this->SetFilterBase(filter); - - // Set global Options - filter->SetInput(input); - filter->SetInputObject(object); - SetOptionsFromArgsInfoToFilter(filter); - - // Set options only for SliceBySliceRelativePositionFilter - filter->SetDirection(mArgsInfo.direction_arg); - filter->SetUniqueConnectedComponentBySliceFlag(mArgsInfo.uniqueCCL_flag); - if (mArgsInfo.uniqueObjectCCL_flag) { - filter->UseTheLargestObjectCCLFlagOn(); - } - else { - filter->UseTheLargestObjectCCLFlagOff(); - } - - // Go ! - filter->Update(); - - // Write/Save results - typename ImageType::Pointer output = filter->GetOutput(); - this->template SetNextOutput(output); - } - else { - // Create filter - typedef clitk::AddRelativePositionConstraintToLabelImageFilter FilterType; - typename FilterType::Pointer filter = FilterType::New(); - - // Set the filter (needed for example for threaded monitoring) - this->SetFilterBase(filter); - - // Set global Options - filter->SetInput(input); - filter->SetInputObject(object); - if (mArgsInfo.angle1_given && mArgsInfo.angle2_given) - filter->AddAnglesInDeg(mArgsInfo.angle1_arg, mArgsInfo.angle2_arg); - SetOptionsFromArgsInfoToFilter(filter); - - // Go ! - filter->Update(); - - // Write/Save results - typename ImageType::Pointer output = filter->GetOutput(); - this->template SetNextOutput(output); - } -} -//-------------------------------------------------------------------- - -