--- /dev/null
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+
+#MARK_AS_ADVANCED( FORCE CMAKE_BACKWARDS_COMPATIBILITY )
+
+# for CMake 2.6 corrected behaviour (see "cmake --help-policy CMP0003")
+IF(COMMAND cmake_policy AND ${CMAKE_MAJOR_VERSION} EQUAL 2 AND ${CMAKE_MINOR_VERSION} GREATER 4)
+ CMAKE_POLICY(SET CMP0003 NEW)
+ CMAKE_POLICY(SET CMP0005 NEW)
+ CMAKE_POLICY(SET CMP0011 NEW)
+ENDIF(COMMAND cmake_policy AND ${CMAKE_MAJOR_VERSION} EQUAL 2 AND ${CMAKE_MINOR_VERSION} GREATER 4)
+
+CMAKE_POLICY(SET CMP0048 NEW)
+
+#foreach(p
+# CMP0025 # CMake 3.0
+# CMP0042 # CMake 3.0
+# CMP0054 # CMake 3.1
+# CMP0056 # CMake 3.2
+# CMP0058 # CMake 3.3
+# )
+# if(POLICY ${p})
+# cmake_policy(SET ${p} NEW)
+# endif()
+#endforeach()
+
+# The project version
+SET(PROJECT_VERSION_MAJOR 1)
+SET(PROJECT_VERSION_MINOR 1)
+SET(PROJECT_VERSION_PATCH 0)
+
+SET(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}")
+
+SET(STMS_VERSION_MAJOR 1)
+SET(STMS_VERSION_MINOR 1)
+SET(STMS_VERSION_PATCH 0)
+
+SET(STMS_VERSION "${STMS_VERSION_MAJOR}.${STMS_VERSION_MINOR}.${STMS_VERSION_PATCH}")
+SET(STMS_VERSION_DATE "25/03/2015")
+
+
+
+#project(STMS)
+project(STMS
+ VERSION
+ LANGUAGES C CXX)
+
+# Mode Release
+OPTION(CMAKE_BUILD_TYPE "Debug Release" Release)
+
+# Mode debug
+#OPTION(CMAKE_BUILD_TYPE "Debug Release" Debug)
+
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=gnu++11 -Wall -fopenmp -Ofast" CACHE STRING " Flags for compile" FORCE)
+
+FIND_PACKAGE(ITK REQUIRED)
+INCLUDE(${ITK_USE_FILE})
+
+IF("${PROJECT_BINARY_DIR}" STREQUAL "${PROJECT_SOURCE_DIR}")
+ MESSAGE(FATAL_ERROR "Building in the source tree is not allowed !! Quit; remove the file 'CMakeCache.txt' and the folder 'CMakeFiles' and build outside the sources")
+ENDIF("${PROJECT_BINARY_DIR}" STREQUAL "${PROJECT_SOURCE_DIR}")
+
+SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+OPTION(BUILD_SHARED_LIBRARIES "OFF to obtain Static execatables" OFF)
+#SET(CMAKE_EXE_LINKER_FLAGS "-static")
+
+
+INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/Lib/PrePostProcessing)
+INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/Lib/SpatioTemporalMeanShift)
+
+add_subdirectory(Lib)
+add_subdirectory(Src)
+
+
+
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+ experimentPath : Absolute path to the folder containing all the experiment data
+ imageExtension : Extension of the image files. There is no default value, has to be specified.
+ commonRoot : The beginning of the image file names has to be the same. The images should be noted "commonRoot"+"timePoint"+"imageExtension"
+
+ ### listInput ###
+ inputFolder : Folder containing the input image sequence
+ numberOfTimePoints : Number of time points in the sequence. The time points should be comprised between 1 and numberOfTimePoints.
+ maskImage : Specify a mask image if you want to process STMS only with the mask pixel values. It has to be stored in the "Mask" folder and to be a binary image (0/1). Set tu null if no mask.
+
+ ### listOutput ###
+ outputFolder : Folder containing the output image sequence
+ commonRoot : The beginning of the image file names has to be the same. The images will be saved as "commonRoot"+"timePoint"+"scaleParameters"+"imageExtension"
+-->
+
+<STMS_ProcessInfo
+ experimentPath="/run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/Images/"
+ imageExtension=".nii.gz" >
+<!--
+ <listInput
+ inputFolder="G1/"
+ commonRoot="ROI_"
+ maskImage="Mask"
+ />
+-->
+
+ <listInput
+ inputFolder="G1/"
+ commonRoot="ROI_"
+ maskImage="null"
+ />
+
+ <listOutput
+ outputFolder="G1_Outputs/"
+ commonRoot="G1_STMS_"
+ />
+</STMS_ProcessInfo>
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+ experimentPath : Absolute path to the folder containing all the experiment data
+ imageExtension : Extension of the image files. There is no default value, has to be specified.
+ commonRoot : The beginning of the image file names has to be the same. The images should be noted "commonRoot"+"timePoint"+"imageExtension"
+
+ ### listInput ###
+ inputFolder : Folder containing the input image sequence
+ maskImage : Specify a mask image if you want to process STMS only with the mask pixel values. It has to be stored in the "Mask" folder and to be a binary image (0/1). Set tu null if no mask.
+
+ ### listOutput ###
+ outputFolder : Folder containing the output image sequence
+ commonRoot : The beginning of the image file names has to be the same. The images will be saved as "commonRoot"+"timePoint"+"scaleParameters"+"imageExtension"
+-->
+
+<STMS_ProcessInfo
+ experimentPath="/run/media/mure/HDD/Recherche/These/Repositories/Mure/Dev/Cpp/itkSTMS/Data/Images/"
+ imageExtension=".nii.gz" >
+
+ <listInput
+ inputFolder="P1_NiiPerf/"
+ commonRoot="Perf_"
+ maskImage="null"
+ />
+
+ <listOutput
+ outputFolder="P1_NiiPerf-out/"
+ commonRoot="P1-Perf_"
+ />
+</STMS_ProcessInfo>
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+ experimentPath : Absolute path to the folder containing all the experiment data
+ imageExtension : Extension of the image files. There is no default value, has to be specified.
+ commonRoot : The beginning of the image file names has to be the same. The images should be noted "commonRoot"+"timePoint"+"imageExtension"
+
+ ### listInput ###
+ inputFolder : Folder containing the input image sequence
+ numberOfTimePoints : Number of time points in the sequence. The time points should be comprised between 1 and numberOfTimePoints.
+ maskImage : Specify a mask image if you want to process STMS only with the mask pixel values. It has to be stored in the "Mask" folder and to be a binary image (0/1). Set tu null if no mask.
+
+ ### listOutput ###
+ outputFolder : Folder containing the output image sequence
+ commonRoot : The beginning of the image file names has to be the same. The images will be saved as "commonRoot"+"timePoint"+"scaleParameters"+"imageExtension"
+-->
+
+<STMS_ProcessInfo
+ experimentPath="/run/media/mure/HDD/Recherche/These/Repositories/Mure/Dev/Cpp/itkSTMS/Data/Images/"
+ imageExtension=".nii.gz" >
+
+ <listInput
+ inputFolder="Simu/"
+ commonRoot="Simu"
+ maskImage="null"
+ />
+
+ <listOutput
+ outputFolder="Simu_Outputs/"
+ commonRoot="Simu_STMS_"
+ />
+</STMS_ProcessInfo>
--- /dev/null
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+ experimentPath : Absolute path to the folder containing all the experiment data
+ imageExtension : Extension of the image files. There is no default value, has to be specified.
+ commonRoot : The beginning of the image file names has to be the same. The images should be noted "commonRoot"+"timePoint"+"imageExtension"
+
+ ### listInput ###
+ inputFolder : Folder containing the input image sequence
+ numberOfTimePoints : Number of time points in the sequence. The time points should be comprised between 1 and numberOfTimePoints.
+ maskImage : Specify a mask image if you want to process STMS only with the mask pixel values. It has to be stored in the "Mask" folder and to be a binary image (0/1). Set tu null if no mask.
+
+ ### listOutput ###
+ outputFolder : Folder containing the output image sequence
+ commonRoot : The beginning of the image file names has to be the same. The images will be saved as "commonRoot"+"timePoint"+"scaleParameters"+"imageExtension"
+-->
+
+<STMS_ProcessInfo
+ experimentPath="../../itkSTMS/Data/Images/"
+ imageExtension=".nii.gz" >
+
+ <listInput
+ inputFolder="Simu/"
+ commonRoot="Simu"
+ maskImage="null"
+ />
+
+ <listOutput
+ outputFolder="Simu_Outputs/"
+ commonRoot="Simu_STMS_"
+ />
+</STMS_ProcessInfo>
--- /dev/null
+SUBDIRS(SpatioTemporalMeanShift)
+SUBDIRS(PrePostProcessing)
--- /dev/null
+#----------------------------------------------------------------------------
+# USER! : SET THE NAME OF YOUR LIBRARY
+# (Replace 'MyLib' by your own library name)
+
+#############################
+SET ( LIBRARY_NAME PrePostProcessing )
+#############################
+
+#----------------------------------------------------------------------------
+
+#----------------------------------------------------------------------------
+# CREATES A USER OPTION IN CMAKE
+OPTION ( BUILD_${LIBRARY_NAME} "Build ${LIBRARY_NAME} library ?" ON)
+#----------------------------------------------------------------------------
+
+#----------------------------------------------------------------------------
+IF ( BUILD_${LIBRARY_NAME} )
+#----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # BUILD LIBRARY
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # LIBRARY HEADERS (TO BE INSTALLED)
+ # EITHER LIST ALL .h, *.txx IN CURRENT DIR USING NEXT LINE:
+
+ FILE(GLOB ${LIBRARY_NAME}_HEADERS "*.h" "*.txx" "*.hxx")
+
+ # OR MANUALLY LIST YOUR HEADERS WITH NEXT COMMAND
+ # SET ( ${LIBRARY_NAME}_HEADERS
+ #
+ # )
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # LIBRARY SOURCES (TO BE COMPILED)
+ # EITHER LIST ALL .cxx, *.cpp, *.cc IN CURRENT DIR USING NEXT LINE:
+
+ FILE(GLOB ${LIBRARY_NAME}_SOURCES *.cxx *.cpp *.cc ${${LIBRARY_NAME}_HEADERS})
+
+ # OR MANUALLY LIST YOUR FILES WITH NEXT COMMAND (WITHOUT EXTENSION)
+ # SET ( ${LIBRARY_NAME}_SOURCES
+ #
+ # )
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # LIBRARY DEPENDENCIES (LIBRARIES TO LINK WITH)
+ #
+ # USER! : Uncomment the Libraries you need
+ #
+ SET ( ${LIBRARY_NAME}_LINK_LIBRARIES
+ # ${crea_LIBRARIES}
+ # ${WXWIDGETS_LIBRARIES}
+ # ${KWWidgets_LIBRARIES}
+ # ${VTK_LIBRARIES}
+ # ${ITK_LIBRARIES}
+ # ${GDCM_LIBRARIES}
+ # ${BOOST_LIBRARIES}
+
+ # If this library must link against other libraries
+ # USER! : Add here any extra Library you need
+
+ )
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # MACRO WHICH DOES ALL THE JOB : BUILD AND INSTALL
+
+ # USER! : The default is to create a Dynamic Library.
+ # if you need to create a static library
+ # comment out the following line :
+
+ #CREA_ADD_LIBRARY( ${LIBRARY_NAME} )
+
+ # and uncomment the 2 lines hereafter:
+
+ ADD_LIBRARY(${LIBRARY_NAME} STATIC ${${LIBRARY_NAME}_SOURCES})
+ TARGET_LINK_LIBRARIES(${LIBRARY_NAME} ${${LIBRARY_NAME}_LINK_LIBRARIES} )
+ SET_TARGET_PROPERTIES(${LIBRARY_NAME} PROPERTIES LINKER_LANGUAGE C)
+
+ #
+ #----------------------------------------------------------------------------
+
+ #---------------------------------------------------------------------------
+ENDIF ( BUILD_${LIBRARY_NAME} )
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ArgumentsAnalysis.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+
+#ifndef itkSTMS_ArgumentsAnalysis_H
+#define itkSTMS_ArgumentsAnalysis_H
+
+#include <getopt.h>
+#include <string>
+
+namespace itkSTMS
+{
+ static struct option long_options[] =
+ {
+ {"expDescription", required_argument, 0, 'd'},
+ {"imageDimension", required_argument, 0, 'i'},
+ {"numTimePoints", required_argument, 0, 'n'},
+ {"startTimePoint", required_argument, 0, 's'},
+ {"xScale", required_argument, 0, 'x'},
+ {"yScale", required_argument, 0, 'y'},
+ {"zScale", required_argument, 0, 'z'},
+ {"rScale", required_argument, 0, 'r'},
+ {"epsilon", required_argument, 0, 'e'},
+ {"maxIt", required_argument, 0, 'm'},
+ {"merge", no_argument , 0, 'g'},
+ {"help", no_argument , 0, 'h'},
+ {0, 0, 0, 0}
+ };
+
+ struct ParamsAnalysisOutputType
+ {
+ std::string expDescription;
+ float spScales[3];
+ float rScale;
+ float epsilon;
+ unsigned int maxIt;
+ unsigned int dim;
+ unsigned int numTimePoints;
+ unsigned int startTimePoint;
+ bool merge;
+ std::string help;
+ bool isOk;
+ };
+
+
+ class itkSTMS_ArgumentsAnalysis{
+
+ public:
+ itkSTMS_ArgumentsAnalysis(int argc, char **argv);
+ void Update();
+ void ParametersDisplay();
+ void ParametersAnalysisInfo();
+ void CheckProvidedParameters();
+ inline ParamsAnalysisOutputType* GetSTMSParams(){ return &readParams; }
+
+ private:
+ ParamsAnalysisOutputType readParams;
+ int argc;
+ char **argv;
+
+ };
+} // end of namespace itkSTMS
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_ArgumentsAnalysis.hxx"
+#endif
+
+#endif // itkSTMS_ArgumentsAnalysis_H
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ArgumentsAnalysis.hxx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ArgumentsAnalysis_HXX
+#define itkSTMS_ArgumentsAnalysis_HXX
+
+#include <iomanip>
+#include <string>
+#include "itkSTMS_ArgumentsAnalysis.h"
+
+namespace itkSTMS
+{
+itkSTMS_ArgumentsAnalysis::itkSTMS_ArgumentsAnalysis(int argc, char **argv)
+{
+ readParams.expDescription = "";
+ readParams.numTimePoints = 0;
+ readParams.startTimePoint = 1;
+ readParams.epsilon = 0.01;
+ readParams.maxIt = 100 ;
+ readParams.spScales[0] = 1.0;
+ readParams.spScales[1] = 1.0;
+ readParams.spScales[2] = 1.0;
+ readParams.rScale = 1.0;
+ readParams.dim = 3;
+ readParams.merge = false;
+ readParams.help = "";
+ readParams.isOk = false;
+
+ this->argc = argc;
+ this->argv = argv;
+}
+
+void itkSTMS_ArgumentsAnalysis::ParametersDisplay()
+{
+ std::cout << std::endl <<
+ std::setw(29) << std::left << "Experiment description" << ": " << readParams.expDescription << std::endl;
+ std::cout << std::setw(29) << std::left << "Image dimension" << ": " << readParams.dim << std::endl;
+ std::cout << std::setw(29) << std::left << "Number of time-points" << ": " << readParams.numTimePoints << std::endl;
+ std::cout << std::setw(29) << std::left << "Staring time point" << ": " << readParams.startTimePoint << std::endl;
+ std::cout << std::setw(29) << std::left << "X scale" << ": " << readParams.spScales[0] << std::endl;
+ std::cout << std::setw(29) << std::left << "Y scale" << ": " << readParams.spScales[1] << std::endl;
+ std::cout << std::setw(29) << std::left << "Z scale" << ": " << readParams.spScales[2] << std::endl;
+ std::cout << std::setw(29) << std::left << "Range scale" << ": " << readParams.rScale << std::endl;
+ std::cout << std::setw(29) << std::left << "Epsilon" << ": " << readParams.epsilon << std::endl;
+ std::cout << std::setw(29) << std::left << "Maximum number of iterations" << ": " << readParams.maxIt << std::endl;
+ std::cout << std::setw(29) << std::left << "Samples merging" << ": " << readParams.merge << std::endl << std::endl;
+}
+
+void itkSTMS_ArgumentsAnalysis::ParametersAnalysisInfo()
+{
+ std::cout << std::endl <<
+ std::setw(17) << std::left << "--expDescription" << ": Path to the XML file used to generate the image sequence." << std::endl;
+ std::cout << std::setw(17) << std::left << "--imageDimension" << ": Number of spatial components. (Default 3)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--numTimePoints" << ": Number of time-points." << std::endl;
+ std::cout << std::setw(17) << std::left << "--startTimePoint" << ": Starting time point (default is 0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--xScale" << ": Spatial scale used for the x axis. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--yScale" << ": Spatial scale used for the z axis. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--zScale" << ": Spatial scale used for the z axis. Optional when using 2D images. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--rScale" << ": Range scale used to set the tolerance on the infinity norm. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--epsilon" << ": Stopping criteria of the STM-S procedure. Minimum global displacement of the samples. (Default 0.01)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--maxIt" << ": Maximum number of iterations of the STM-S procedure. (Default 100)" << std::endl << std::endl;
+ std::cout << std::setw(17) << std::left << "--merge" << ": Specify if the samples are merged during the STMS procedure. No merging by default, no argument is needed after --merge." << std::endl << std::endl;
+ std::cout << std::setw(17) << std::left << "--help" << ": Usage help" << std::endl << std::endl;
+}
+
+
+void itkSTMS_ArgumentsAnalysis::CheckProvidedParameters(){
+
+ if( readParams.expDescription != "")
+ readParams.isOk = true;
+}
+
+void itkSTMS_ArgumentsAnalysis::Update()
+{
+ int c;
+ bool first_it = true;
+ while (1)
+ {
+ /* getopt_long stores the option index here. */
+ int option_index = 0;
+
+ c = getopt_long (argc, argv, "d:i::n:x::y::z::r::e::m::g::h::s::",
+ long_options, &option_index);
+
+ std::string str;
+
+ switch (c)
+ {
+ case 'd':
+ readParams.expDescription = std::string(optarg);
+ break;
+
+ case 'i':
+ str = std::string(optarg);
+ readParams.dim = (unsigned int)std::stoi( str );
+ break;
+
+ case 'n':
+ str = std::string(optarg);
+ readParams.numTimePoints = (unsigned int)std::stoi( str );
+ break;
+
+ case 's':
+ str = std::string(optarg);
+ readParams.startTimePoint = (unsigned int)std::stoi( str );
+ break;
+
+ case 'x':
+ str = std::string(optarg);
+ readParams.spScales[0] = std::stof( str );
+ break;
+
+ case 'y':
+ str = std::string(optarg);
+ readParams.spScales[1] = std::stof( str );
+ break;
+
+ case 'z':
+ str = std::string(optarg);
+ readParams.spScales[2] = std::stof( str );
+ break;
+
+ case 'r':
+ str = std::string(optarg);
+ readParams.rScale = std::stof( str );
+ break;
+
+ case 'e':
+ str = std::string(optarg);
+ readParams.epsilon = std::stof( str );
+ break;
+
+ case 'm':
+ str = std::string(optarg);
+ readParams.maxIt = (unsigned int)std::stoi( str );
+ break;
+
+ case 'g':
+ readParams.merge = true;
+ break;
+
+ case 'h':
+ std::cout << std::endl << "Usage help:";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_SUCCESS );
+ break;
+
+ case '?':
+ std::cout << std::endl << "Usage help:";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_FAILURE );
+ break;
+ }
+
+ if( (c==-1) & first_it )
+ {
+ std::cout << std::endl << "Usage help:";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_SUCCESS );
+ }
+
+ first_it = false;
+
+ /* Detect the end of the options. */
+ if ( (c==-1) & !first_it )
+ {
+ break;
+ }
+ }
+
+ CheckProvidedParameters();
+ if( readParams.isOk )
+ {
+ ParametersDisplay();
+ }
+ else
+ {
+ std::cout << std::endl << "All required parameters are not provided";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_FAILURE );
+ }
+}
+
+} // end of namespace itkSTMS
+#endif // itkSTMS_ArgumentsAnalysis_HXX
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ArgumentsAnalysis_Spine.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ArgumentsAnalysisSpine_H
+#define itkSTMS_ArgumentsAnalysisSpine_H
+
+#include <getopt.h>
+#include <string>
+#include <list>
+
+namespace itkSTMS_Spine
+{
+ static struct option long_options[] =
+ {
+ {"image", required_argument, 0, 'd'},
+ {"mask", required_argument, 0, 'l'},
+ {"outFolder", required_argument, 0, 'o'},
+ {"imageDimension", required_argument, 0, 'i'},
+ {"imageExtension", required_argument, 0, 'q'},
+ {"xScale", required_argument, 0, 'x'},
+ {"yScale", required_argument, 0, 'y'},
+ {"zScale", required_argument, 0, 'z'},
+ {"rScale", required_argument, 0, 'r'},
+ {"epsilon", required_argument, 0, 'e'},
+ {"maxIt", required_argument, 0, 'm'},
+ {"merge", no_argument , 0, 'g'},
+ {"help", no_argument , 0, 'h'},
+ {0, 0, 0, 0}
+ };
+
+ struct ParamsAnalysisOutputType
+ {
+ std::list<std::string> images;
+ std::string mask;
+ std::string outFolder;
+ float spScales[3];
+ float rScale;
+ float epsilon;
+ unsigned int maxIt;
+ unsigned int dim;
+ unsigned int numTimePoints;
+ bool merge;
+ std::string imageExtension;
+
+ std::string help;
+ bool isOk;
+ };
+
+
+ class itkSTMS_ArgumentsAnalysis{
+
+ public:
+ itkSTMS_ArgumentsAnalysis(int argc, char **argv);
+ void Update();
+ void ParametersDisplay();
+ void ParametersAnalysisInfo();
+ void CheckProvidedParameters();
+ inline ParamsAnalysisOutputType* GetSTMSParams(){ return &readParams; }
+
+ private:
+ ParamsAnalysisOutputType readParams;
+ int argc;
+ char **argv;
+
+ };
+} // end of namespace itkSTMS
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_ArgumentsAnalysis_Spine.hxx"
+#endif
+
+#endif // itkSTMS_ArgumentsAnalysisSpine_H
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ArgumentsAnalysis_Spine.hxx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ArgumentsAnalysisSpine_HXX
+#define itkSTMS_ArgumentsAnalysisSpine_HXX
+
+#include<iostream>
+#include <iomanip>
+#include<string>
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+
+namespace itkSTMS_Spine
+{
+itkSTMS_ArgumentsAnalysis::itkSTMS_ArgumentsAnalysis(int argc, char **argv)
+{
+ readParams.numTimePoints = 0;
+ readParams.epsilon = 0.01;
+ readParams.maxIt = 100 ;
+ readParams.spScales[0] = 1.0;
+ readParams.spScales[1] = 1.0;
+ readParams.spScales[2] = 1.0;
+ readParams.rScale = 1.0;
+ readParams.dim = 3;
+ readParams.merge = false;
+ readParams.help = "";
+ readParams.mask = "";
+ readParams.outFolder = "";
+ readParams.isOk = false;
+ readParams.imageExtension = ".nii.gz";
+
+ this->argc = argc;
+ this->argv = argv;
+}
+
+void itkSTMS_ArgumentsAnalysis::ParametersDisplay()
+{
+ std::cout << std::endl <<
+ std::setw(29) << std::left << "Image dimension" << ": " << readParams.dim << std::endl;
+ std::cout << std::setw(29) << std::left << "Mask image" << ": " << readParams.mask << std::endl;
+ std::cout << std::setw(29) << std::left << "Output folder" << ": " << readParams.outFolder << std::endl;
+ std::cout << std::setw(29) << std::left << "Nb of time-points" << ": " << readParams.numTimePoints << std::endl;
+ std::cout << std::setw(29) << std::left << "X scale" << ": " << readParams.spScales[0] << std::endl;
+ std::cout << std::setw(29) << std::left << "Y scale" << ": " << readParams.spScales[1] << std::endl;
+ std::cout << std::setw(29) << std::left << "Z scale" << ": " << readParams.spScales[2] << std::endl;
+ std::cout << std::setw(29) << std::left << "Range scale" << ": " << readParams.rScale << std::endl;
+ std::cout << std::setw(29) << std::left << "Epsilon" << ": " << readParams.epsilon << std::endl;
+ std::cout << std::setw(29) << std::left << "Maximum number of iterations" << ": " << readParams.maxIt << std::endl;
+ std::cout << std::setw(29) << std::left << "Images extension" << ": " << readParams.imageExtension << std::endl;
+ std::cout << std::setw(29) << std::left << "Samples merging" << ": " << readParams.merge << std::endl << std::endl;
+}
+
+void itkSTMS_ArgumentsAnalysis::ParametersAnalysisInfo()
+{
+ std::cout << std::endl <<
+ std::setw(17) << std::left << "--image " << ": Path to an image of the sequence." << std::endl;
+ std::cout << std::setw(17) << std::left << "--mask" << ": Binary mask image (optional)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--outFolder" << ": Output images folder" << std::endl;
+ std::cout << std::setw(17) << std::left << "--imageDimension" << ": Number of spatial components. (Default 3)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--imageExtension" << ": Extension of the images. (Default .nii.gz)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--xScale" << ": Spatial scale used for the x axis. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--yScale" << ": Spatial scale used for the z axis. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--zScale" << ": Spatial scale used for the z axis. Optional when using 2D images. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--rScale" << ": Range scale used to set the tolerance on the infinity norm. (Default 1.0)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--epsilon" << ": Stopping criteria of the STM-S procedure. Minimum global displacement of the samples. (Default 0.01)" << std::endl;
+ std::cout << std::setw(17) << std::left << "--maxIt" << ": Maximum number of iterations of the STM-S procedure. (Default 100)" << std::endl << std::endl;
+ std::cout << std::setw(17) << std::left << "--merge" << ": Specify if the samples are merged during the STMS procedure. No merging by default, no argument is needed after --merge." << std::endl << std::endl;
+ std::cout << std::setw(17) << std::left << "--help" << ": Usage help" << std::endl << std::endl;
+}
+
+
+void itkSTMS_ArgumentsAnalysis::CheckProvidedParameters(){
+
+ if( !readParams.images.empty() & !readParams.outFolder.empty())
+ readParams.isOk = true;
+}
+
+void itkSTMS_ArgumentsAnalysis::Update()
+{
+ int c;
+ bool first_it = true;
+ while (1)
+ {
+ /* getopt_long stores the option index here. */
+ int option_index = 0;
+
+ c = getopt_long (argc, argv, "d:l::o:i::x::y::z::r::e::m::g::h::q::",
+ long_options, &option_index);
+
+ std::string str;
+
+ switch (c)
+ {
+ case 'd':
+ readParams.images.push_back( std::string(optarg) );
+ break;
+
+ case 'q':
+ readParams.imageExtension = std::string(optarg);
+ break;
+
+ case 'l':
+ readParams.mask = std::string(optarg);
+ break;
+
+ case 'o':
+ readParams.outFolder = std::string(optarg);
+ break;
+
+ case 'i':
+ str = std::string(optarg);
+ readParams.dim = (unsigned int)std::stoi( str );
+ break;
+
+ case 'x':
+ str = std::string(optarg);
+ readParams.spScales[0] = std::stof( str );
+ break;
+
+ case 'y':
+ str = std::string(optarg);
+ readParams.spScales[1] = std::stof( str );
+ break;
+
+ case 'z':
+ str = std::string(optarg);
+ readParams.spScales[2] = std::stof( str );
+ break;
+
+ case 'r':
+ str = std::string(optarg);
+ readParams.rScale = std::stof( str );
+ break;
+
+ case 'e':
+ str = std::string(optarg);
+ readParams.epsilon = std::stof( str );
+ break;
+
+ case 'm':
+ str = std::string(optarg);
+ readParams.maxIt = (unsigned int)std::stoi( str );
+ break;
+
+ case 'g':
+ readParams.merge = true;
+ break;
+
+ case 'h':
+ std::cout << std::endl << "Usage help:";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_SUCCESS );
+ break;
+
+ case '?':
+ std::cout << std::endl << "Usage help:";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_FAILURE );
+ break;
+ }
+
+ if( (c==-1) & first_it )
+ {
+ std::cout << std::endl << "Usage help:";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_SUCCESS );
+ }
+
+ first_it = false;
+
+ /* Detect the end of the options. */
+ if ( (c==-1) & !first_it )
+ {
+ break;
+ }
+ }
+
+ CheckProvidedParameters();
+ if( readParams.isOk )
+ {
+ readParams.numTimePoints = (unsigned int)readParams.images.size();
+ ParametersDisplay();
+ }
+ else
+ {
+ std::cout << std::endl << "All required parameters are not provided";
+ ParametersAnalysisInfo();
+ std::exit( EXIT_FAILURE );
+ }
+}
+
+} // end of namespace itkSTMS
+#endif // itkSTMS_ArgumentsAnalysisSpine_HXX
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ImageSequenceToTemporalSet.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ImageSequenceToTemporalSet_h
+#define itkSTMS_ImageSequenceToTemporalSet_h
+
+#include <string>
+#include <vector>
+//#include <array>
+
+#include "itkImage.h"
+#include "itkSTMS_XMLFileParser.h"
+#include "itkSTMS_ArgumentsAnalysis.h"
+#include "itkImageFileReader.h"
+#include "itkImageRegionConstIteratorWithIndex.h"
+#include "itkMinimumMaximumImageCalculator.h"
+
+#ifndef STMS_NUMBERING_FORM_ONE
+#define STMS_NUMBERING_FORM_ONE "1"
+#endif
+
+namespace itkSTMS
+{
+ template < class ImageType, class MaskImageType >
+ class itkSTMS_ImageSequenceToTemporalSet
+ {
+
+ public:
+ // Reader typedefs
+ typedef itk::ImageFileReader< ImageType > ReaderType;
+ typedef typename ReaderType::Pointer ReaderPointer;
+ typedef itk::ImageFileReader< MaskImageType > MaskReaderType;
+ typedef typename MaskReaderType::Pointer MaskReaderPointer;
+
+ // Mask processing typedefs
+ typedef itk::MinimumMaximumImageCalculator< MaskImageType >
+ MinMaxCalculatorType;
+ typedef typename MinMaxCalculatorType::Pointer MinMaxCalculatorPointer;
+
+ // Iterator typedefs
+ typedef itk::ImageRegionConstIteratorWithIndex< ImageType > IteratorType;
+ typedef itk::ImageRegionConstIteratorWithIndex< MaskImageType > MaskIteratorType;
+
+ // Sample set typedefs
+ typedef unsigned int IndexType;
+ typedef float SpatialType;
+ typedef typename ImageType::PixelType PixelType;
+
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::SizeType SizeType;
+
+ typedef std::vector< SpatialType > SpatialVectorType;
+ typedef std::vector< PixelType > RangeVectorType;
+
+ typedef std::vector< IndexType > IndexSampleSetType;
+ typedef std::vector< SpatialVectorType > SpatialSampleSetType;
+ typedef std::vector< RangeVectorType > RangeSampleSetType;
+
+ // Mask image typedefs
+ typedef typename MaskImageType::PixelType MaskPixelType;
+ typedef typename MaskImageType::Pointer MaskImagePointer;
+ typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
+
+ // Methods
+ itkSTMS_ImageSequenceToTemporalSet( itkSTMS::ParamsAnalysisOutputType* stmsParameters );
+ inline ~itkSTMS_ImageSequenceToTemporalSet(){ delete xmlParser; }
+
+ void GenerateDataSets();
+
+ inline IndexSampleSetType* GetIndexSet (){ return &indexSet; }
+ inline IndexSampleSetType* GetClassSet (){ return &classSet; }
+ inline IndexSampleSetType* GetMergingSet(){ return &mergingSet; }
+ inline IndexSampleSetType* GetWeightsSet(){ return &weightsSet; }
+ inline SpatialSampleSetType* GetSpatialSet(){ return &spatialSet; }
+ inline RangeSampleSetType* GetRangeSet (){ return &rangeSet; }
+
+ inline itkSTMS::ParserOutputType* GetExperimentDescription(){ return expDescription; }
+
+ private:
+ // Attributes
+ itkSTMS::itkSTMS_XMLFileParser* xmlParser;
+ itkSTMS::ParserOutputType* expDescription;
+ itkSTMS::ParamsAnalysisOutputType* stmsParameters;
+
+ IndexSampleSetType indexSet,
+ classSet,
+ mergingSet,
+ weightsSet;
+ SpatialSampleSetType spatialSet;
+ RangeSampleSetType rangeSet;
+
+ MaskPixelType maskValue;
+ MaskImagePointer mask;
+ MaskReaderPointer mReader;
+ MinMaxCalculatorPointer MinMaxCalculator;
+ std::string maskPath;
+ MaskIteratorType mIt;
+
+ }; // end of class itkSTMS_ImageSequenceToTemporalSet
+} // end of namespace itkstms
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_ImageSequenceToTemporalSet.txx"
+#endif
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ImageSequenceToTemporalSet.txx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ImageSequenceToTemporalSet_txx
+#define itkSTMS_ImageSequenceToTemporalSet_txx
+
+#include <string>
+#include "itkSTMS_ImageSequenceToTemporalSet.h"
+#include "itkSTMS_XMLFileParser.h"
+#include "itkSTMS_ArgumentsAnalysis.h"
+#include "itkFancyString.h"
+
+
+namespace itkSTMS
+{
+
+template < class ImageType, class MaskImageType >
+itkSTMS_ImageSequenceToTemporalSet < ImageType, MaskImageType >
+::itkSTMS_ImageSequenceToTemporalSet( ParamsAnalysisOutputType* stmsParameters )
+{
+ // Get experiments parameters given by the user
+ this->stmsParameters = stmsParameters;
+
+ // XML file parsing
+ xmlParser = new itkSTMS::itkSTMS_XMLFileParser();
+ xmlParser->SetFileName( this->stmsParameters->expDescription );
+ xmlParser->Update();
+
+ expDescription = xmlParser->GetXMLParams();
+
+ // If a mask image is specified ==> instanciation of a mask iterator (region with the highest value in the mask)
+ if( expDescription->maskImage != "null" )
+ {
+ mask = MaskImageType::New();
+ mReader = MaskReaderType::New();
+ MinMaxCalculator = MinMaxCalculatorType::New();
+
+ maskPath = expDescription->experimentPath+expDescription->inputFolder+expDescription->maskImage+expDescription->imageExtension;
+ mReader->SetFileName( maskPath );
+ mReader->Update();
+ mask = mReader->GetOutput();
+
+ MinMaxCalculator->SetImage( mask );
+ MinMaxCalculator->ComputeMaximum();
+ maskValue = (MaskPixelType)MinMaxCalculator->GetMaximum();
+
+ mIt = MaskIteratorType( mask, mask->GetLargestPossibleRegion() ); //->GetBufferedRegion() );
+ }
+}
+
+
+template < class ImageType, class MaskImageType >
+void
+itkSTMS_ImageSequenceToTemporalSet< ImageType, MaskImageType >
+::GenerateDataSets()
+{
+ bool first = true;
+ std::string str;
+ IndexType idx;
+
+ // Preprocessing of the whole image sequence // stmsParameters->startTimePoint
+ for( unsigned int i=1 ; i<=stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1 ; ++i )
+ {
+ idx = 0;
+
+ char buffer[6];
+ int n = 0;
+
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 6 ) n=sprintf (buffer, "%05d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 5 ) n=sprintf (buffer, "%04d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 4 ) n=sprintf (buffer, "%03d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 3 ) n=sprintf (buffer, "%02d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 2 ) n=sprintf (buffer, "%01d", i + stmsParameters->startTimePoint - 1);
+
+ std::string imagePath = expDescription->experimentPath+expDescription->inputFolder+expDescription->inputCommonRoot+buffer+expDescription->imageExtension;
+
+ ImagePointer image
+ = ImageType::New();
+ ReaderPointer reader
+ = itk::ImageFileReader< ImageType >::New();
+
+ reader->SetFileName( imagePath );
+ reader->Update();
+ image = reader->GetOutput();
+
+ IteratorType it( image, image->GetLargestPossibleRegion() );
+ SizeType Size = image->GetLargestPossibleRegion().GetSize();
+
+ // If there is no mask image specified, all the pixels are extracted
+ if( expDescription->maskImage == "null" )
+ {
+ // Only the range values have to be extracted at each time-point. The others need to be extracted just one time.
+ if( first )
+ {
+ // Containers initialisation
+ unsigned int numSamples = (unsigned int)Size[0];
+
+ for( unsigned int j=1 ; j<stmsParameters->dim ; ++j )
+ numSamples *= (unsigned int)Size[j];
+
+ indexSet = IndexSampleSetType( numSamples, 0 );
+ classSet = IndexSampleSetType( numSamples, 0 );
+ mergingSet = IndexSampleSetType( numSamples, 0 );
+ weightsSet = IndexSampleSetType( numSamples, 1 );
+ spatialSet = SpatialSampleSetType( numSamples, SpatialVectorType(stmsParameters->dim, 0));
+ rangeSet = RangeSampleSetType ( numSamples, RangeVectorType(stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1, 0) );
+ }
+
+ // Samples extraction
+ it.GoToBegin();
+ while( !it.IsAtEnd() ){
+ if( first ){
+ indexSet[idx] = idx;
+ classSet[idx] = idx+1;
+
+ for( unsigned int j=0 ; j<stmsParameters->dim ; ++j )
+ spatialSet[idx][j] = (SpatialType)( it.GetIndex()[j]/stmsParameters->spScales[j] );
+ }
+
+ rangeSet[idx++][i-1] = (PixelType)(it.Get()/stmsParameters->rScale);
+ ++it;
+ }
+
+ if( first )
+ first = false;
+ }
+ // If a mask is specified, just the characteristics of the pixels equal to maskValue in the mask image are extracted
+ else
+ {
+ // In this case the number of samples is not known in advance
+ if( first )
+ {
+ indexSet = IndexSampleSetType();
+ classSet = IndexSampleSetType();
+ mergingSet = IndexSampleSetType();
+ weightsSet = IndexSampleSetType();
+ spatialSet = SpatialSampleSetType();
+ rangeSet = RangeSampleSetType();
+
+ indexSet.reserve ( Size[0]*Size[1] );
+ classSet.reserve ( Size[0]*Size[1] );
+ mergingSet.reserve( Size[0]*Size[1] );
+ weightsSet.reserve( Size[0]*Size[1] );
+ spatialSet.reserve( Size[0]*Size[1] );
+ rangeSet.reserve ( Size[0]*Size[1] );
+ }
+
+ // Samples extraction
+ mIt.GoToBegin();
+ it.GoToBegin();
+ while( !mIt.IsAtEnd() )
+ {
+ if(mIt.Get() == maskValue)
+ {
+ if( first )
+ {
+ SpatialVectorType spComp = SpatialVectorType(stmsParameters->dim, 0);
+ for( unsigned int j=0 ; j<stmsParameters->dim ; ++j )
+ spComp[j] = (SpatialType)( it.GetIndex()[j]/stmsParameters->spScales[j] );
+
+ indexSet.push_back ( idx );
+ classSet.push_back ( ++idx );
+ mergingSet.push_back( 0 );
+ weightsSet.push_back( 1 );
+ spatialSet.push_back( spComp );
+ rangeSet.push_back( RangeVectorType(stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1, (PixelType)(it.Get()/stmsParameters->rScale)) );
+ }
+ else
+ rangeSet[idx++][i-1] = (PixelType)(it.Get()/stmsParameters->rScale);
+ }
+
+ ++mIt;
+ ++it;
+ }
+
+ if( first )
+ first = false;
+ }
+ }
+}
+
+} // end of namespace itkSTMS
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ImageSequenceToTemporalSet_Spine.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ImageSequenceToTemporalSetSpine_h
+#define itkSTMS_ImageSequenceToTemporalSetSpine_h
+
+#include <string>
+#include <vector>
+//#include <array>
+
+#include "itkImage.h"
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+#include "itkImageFileReader.h"
+#include "itkImageRegionConstIteratorWithIndex.h"
+#include "itkMinimumMaximumImageCalculator.h"
+
+namespace itkSTMS_Spine
+{
+ template < class ImageType, class MaskImageType >
+ class itkSTMS_ImageSequenceToTemporalSet
+ {
+
+ public:
+ // Reader typedefs
+ typedef itk::ImageFileReader< ImageType > ReaderType;
+ typedef typename ReaderType::Pointer ReaderPointer;
+ typedef itk::ImageFileReader< MaskImageType > MaskReaderType;
+ typedef typename MaskReaderType::Pointer MaskReaderPointer;
+
+ // Mask processing typedefs
+ typedef itk::MinimumMaximumImageCalculator< MaskImageType >
+ MinMaxCalculatorType;
+ typedef typename MinMaxCalculatorType::Pointer MinMaxCalculatorPointer;
+
+ // Iterator typedefs
+ typedef itk::ImageRegionConstIteratorWithIndex< ImageType > IteratorType;
+ typedef itk::ImageRegionConstIteratorWithIndex< MaskImageType > MaskIteratorType;
+
+ // Sample set typedefs
+ typedef unsigned int IndexType;
+ typedef float SpatialType;
+ typedef typename ImageType::PixelType PixelType;
+
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::SizeType SizeType;
+
+ typedef std::vector< SpatialType > SpatialVectorType;
+ typedef std::vector< PixelType > RangeVectorType;
+
+ typedef std::vector< IndexType > IndexSampleSetType;
+ typedef std::vector< SpatialVectorType > SpatialSampleSetType;
+ typedef std::vector< RangeVectorType > RangeSampleSetType;
+
+ // Mask image typedefs
+ typedef typename MaskImageType::PixelType MaskPixelType;
+ typedef typename MaskImageType::Pointer MaskImagePointer;
+ typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
+
+ // Methods
+ itkSTMS_ImageSequenceToTemporalSet( itkSTMS_Spine::ParamsAnalysisOutputType* stmsParameters );
+
+ void GenerateDataSets();
+
+ inline IndexSampleSetType* GetIndexSet (){ return &indexSet; }
+ inline IndexSampleSetType* GetClassSet (){ return &classSet; }
+ inline IndexSampleSetType* GetMergingSet(){ return &mergingSet; }
+ inline IndexSampleSetType* GetWeightsSet(){ return &weightsSet; }
+ inline SpatialSampleSetType* GetSpatialSet(){ return &spatialSet; }
+ inline RangeSampleSetType* GetRangeSet (){ return &rangeSet; }
+
+ private:
+ // Attributes
+ itkSTMS_Spine::ParamsAnalysisOutputType* stmsParameters;
+
+ IndexSampleSetType indexSet,
+ classSet,
+ mergingSet,
+ weightsSet;
+ SpatialSampleSetType spatialSet;
+ RangeSampleSetType rangeSet;
+
+ MaskPixelType maskValue;
+ MaskImagePointer mask;
+ MaskReaderPointer mReader;
+ MinMaxCalculatorPointer MinMaxCalculator;
+ MaskIteratorType mIt;
+
+ }; // end of class itkSTMS_ImageSequenceToTemporalSet
+} // end of namespace itkstms
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_ImageSequenceToTemporalSet_Spine.txx"
+#endif
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_ImageSequenceToTemporalSet_Spine.txx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_ImageSequenceToTemporalSetSpine_txx
+#define itkSTMS_ImageSequenceToTemporalSetSpine_txx
+
+#include <string>
+#include "itkSTMS_ImageSequenceToTemporalSet_Spine.h"
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+
+
+namespace itkSTMS_Spine
+{
+
+template < class ImageType, class MaskImageType >
+itkSTMS_ImageSequenceToTemporalSet < ImageType, MaskImageType >
+::itkSTMS_ImageSequenceToTemporalSet( ParamsAnalysisOutputType* stmsParameters )
+{
+ // Get experiments parameters given by the user
+ this->stmsParameters = stmsParameters;
+
+ // If a mask image is specified ==> instanciation of a mask iterator (region with the highest value in the mask)
+ if( !this->stmsParameters->mask.empty() )
+ {
+ mask = MaskImageType::New();
+ mReader = MaskReaderType::New();
+ MinMaxCalculator = MinMaxCalculatorType::New();
+
+ mReader->SetFileName( this->stmsParameters->mask );
+ mReader->Update();
+ mask = mReader->GetOutput();
+
+ MinMaxCalculator->SetImage( mask );
+ MinMaxCalculator->ComputeMaximum();
+ maskValue = (MaskPixelType)MinMaxCalculator->GetMaximum();
+
+ mIt = MaskIteratorType( mask, mask->GetLargestPossibleRegion() ); //->GetBufferedRegion() );
+ }
+}
+
+
+template < class ImageType, class MaskImageType >
+void
+itkSTMS_ImageSequenceToTemporalSet< ImageType, MaskImageType >
+::GenerateDataSets()
+{
+ bool first = true;
+ std::string str;
+ IndexType idx, i;
+
+ // Preprocessing of the whole image sequence
+ i=1;
+ for (std::list<std::string>::iterator it_images = stmsParameters->images.begin(); it_images != stmsParameters->images.end(); ++it_images)
+ {
+ idx = 0;
+
+ ImagePointer image
+ = ImageType::New();
+ ReaderPointer reader
+ = itk::ImageFileReader< ImageType >::New();
+
+ reader->SetFileName( *it_images );
+ reader->Update();
+ image = reader->GetOutput();
+
+ IteratorType it( image, image->GetLargestPossibleRegion() );
+ SizeType Size = image->GetLargestPossibleRegion().GetSize();
+
+ // If there is no mask image specified, all the pixels are extracted
+ if( stmsParameters->mask.empty() )
+ {
+ // Only the range values have to be extracted at each time-point. The others need to be extracted just one time.
+ if( first )
+ {
+ // Containers initialisation
+ unsigned int numSamples = (unsigned int)Size[0];
+
+ for( unsigned int j=1 ; j<stmsParameters->dim ; ++j )
+ numSamples *= (unsigned int)Size[j];
+
+ indexSet = IndexSampleSetType( numSamples, 0 );
+ classSet = IndexSampleSetType( numSamples, 0 );
+ mergingSet = IndexSampleSetType( numSamples, 0 );
+ weightsSet = IndexSampleSetType( numSamples, 1 );
+ spatialSet = SpatialSampleSetType( numSamples, SpatialVectorType(stmsParameters->dim, 0));
+ rangeSet = RangeSampleSetType ( numSamples, RangeVectorType(stmsParameters->numTimePoints, 0) );
+ }
+
+ // Samples extraction
+ it.GoToBegin();
+ while( !it.IsAtEnd() ){
+ if( first ){
+ indexSet[idx] = idx;
+ classSet[idx] = idx+1;
+
+ for( unsigned int j=0 ; j<stmsParameters->dim ; ++j )
+ spatialSet[idx][j] = (SpatialType)( it.GetIndex()[j]/stmsParameters->spScales[j] );
+ }
+
+ rangeSet[idx++][i-1] = (PixelType)(it.Get()/stmsParameters->rScale);
+ ++it;
+ }
+
+ if( first )
+ first = false;
+ }
+ // If a mask is specified, just the characteristics of the pixels equal to maskValue in the mask image are extracted
+ else
+ {
+ // In this case the number of samples is not known in advance
+ if( first )
+ {
+ indexSet = IndexSampleSetType();
+ classSet = IndexSampleSetType();
+ mergingSet = IndexSampleSetType();
+ weightsSet = IndexSampleSetType();
+ spatialSet = SpatialSampleSetType();
+ rangeSet = RangeSampleSetType();
+
+ indexSet.reserve ( Size[0]*Size[1] );
+ classSet.reserve ( Size[0]*Size[1] );
+ mergingSet.reserve( Size[0]*Size[1] );
+ weightsSet.reserve( Size[0]*Size[1] );
+ spatialSet.reserve( Size[0]*Size[1] );
+ rangeSet.reserve ( Size[0]*Size[1] );
+ }
+
+ // Samples extraction
+ mIt.GoToBegin();
+ it.GoToBegin();
+ while( !mIt.IsAtEnd() )
+ {
+ if(mIt.Get() == maskValue)
+ {
+ if( first )
+ {
+ SpatialVectorType spComp = SpatialVectorType(stmsParameters->dim, 0);
+ for( unsigned int j=0 ; j<stmsParameters->dim ; ++j )
+ spComp[j] = (SpatialType)( it.GetIndex()[j]/stmsParameters->spScales[j] );
+
+ indexSet.push_back ( idx );
+ classSet.push_back ( ++idx );
+ mergingSet.push_back( 0 );
+ weightsSet.push_back( 1 );
+ spatialSet.push_back( spComp );
+ rangeSet.push_back( RangeVectorType(stmsParameters->numTimePoints, (PixelType)(it.Get()/stmsParameters->rScale)) );
+ }
+ else
+ rangeSet[idx++][i-1] = (PixelType)(it.Get()/stmsParameters->rScale);
+ }
+
+ ++mIt;
+ ++it;
+ }
+
+ if( first )
+ first = false;
+ }
+
+ ++i;
+ }
+}
+
+} // end of namespace itkSTMS
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_TemporalSetToImageSequence.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_TemporalSetToImageSequence_h
+#define itkSTMS_TemporalSetToImageSequence_h
+
+#include <string>
+#include <vector>
+#include <math.h>
+
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImageRegionIteratorWithIndex.h"
+
+
+#ifndef STMS_NUMBERING_FORM_ONE
+#define STMS_NUMBERING_FORM_ONE "1"
+#endif
+
+namespace itkSTMS
+{
+ template < class ImageType, class ClassImageType >
+ class itkSTMS_TemporalSetToImageSequence
+ {
+ public:
+ // Reader and writer typedefs
+ typedef itk::ImageFileReader< ImageType > ReaderType;
+ typedef typename ReaderType::Pointer ReaderPointer;
+ typedef itk::ImageFileWriter< ImageType > WriterType;
+ typedef typename WriterType::Pointer WriterPointer;
+ typedef itk::ImageFileWriter< ClassImageType > ClassWriterType;
+ typedef typename ClassWriterType::Pointer ClassWriterPointer;
+
+ // Sample set typedefs
+ typedef unsigned int IndexType;
+ typedef float SpatialType;
+ typedef typename ImageType::PixelType PixelType;
+
+ typedef std::vector< SpatialType > SpatialVectorType;
+ typedef std::vector< PixelType > RangeVectorType;
+
+ typedef std::vector< IndexType > IndexSampleSetType;
+ typedef std::vector< SpatialVectorType > SpatialSampleSetType;
+ typedef std::vector< RangeVectorType > RangeSampleSetType;
+
+ // Image typedefs
+ typedef typename ImageType::IndexType SpatialIndexType;
+ typedef typename ImageType::RegionType RegionType;
+
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::SizeType SizeType;
+
+ typedef typename ClassImageType::Pointer ClassImagePointer;
+ typedef typename ClassImageType::RegionType ClassRegionType;
+
+
+ // Methods
+ itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl,
+ SpatialSampleSetType* sp,
+ RangeSampleSetType* ra,
+ itkSTMS::ParamsAnalysisOutputType* params,
+ itkSTMS::ParserOutputType* desc );
+
+ void GenerateImageSequence();
+
+ private:
+ // Attributes
+ itkSTMS::ParserOutputType* expDescription;
+ itkSTMS::ParamsAnalysisOutputType* stmsParameters;
+
+ IndexSampleSetType* classSet;
+ SpatialSampleSetType* spatialSet;
+ RangeSampleSetType* rangeSet;
+
+ }; // end of class itkSTMS_TemporalSetToImageSequence
+} // end of namespace itkstms
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_TemporalSetToImageSequence.txx"
+#endif
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_TemporalSetToImageSequence.txx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_TemporalSetToImageSequence_txx
+#define itkSTMS_TemporalSetToImageSequence_txx
+
+#include "itkSTMS_TemporalSetToImageSequence.h"
+#include "itkSTMS_XMLFileParser.h"
+#include "itkSTMS_ArgumentsAnalysis.h"
+
+namespace itkSTMS
+{
+
+template < class ImageType, class ClassImageType >
+itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
+::itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl, SpatialSampleSetType* sp, RangeSampleSetType* ra,
+ itkSTMS::ParamsAnalysisOutputType* params, itkSTMS::ParserOutputType* desc )
+{
+ this->stmsParameters = params;
+ this->expDescription = desc;
+
+ this->classSet = cl;
+ this->spatialSet = sp;
+ this->rangeSet = ra;
+}
+
+
+template < class ImageType, class ClassImageType >
+void
+itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
+::GenerateImageSequence()
+{
+ bool first = true;
+
+ // Output images allocation
+ ImagePointer image
+ = ImageType::New();
+ ReaderPointer reader
+ = ReaderType::New();
+
+ std::string imagePath = expDescription->experimentPath+expDescription->inputFolder+expDescription->inputCommonRoot+STMS_NUMBERING_FORM_ONE+expDescription->imageExtension;
+
+ reader->SetFileName( imagePath );
+ reader->Update();
+ image = reader->GetOutput();
+
+ SpatialIndexType start, outIndex, classIndex;
+ start.Fill(0);
+
+ RegionType region;
+ region.SetSize( image->GetBufferedRegion().GetSize());
+ region.SetIndex(start);
+
+ ClassRegionType classRegion;
+ classRegion.SetSize( image->GetBufferedRegion().GetSize());
+ classRegion.SetIndex( start );
+
+
+ std::string outputPath, classPath;
+
+ ClassImagePointer classImage
+ = ClassImageType::New();
+
+ classImage->SetRegions( classRegion );
+ classImage->Allocate();
+ classImage->FillBuffer( 15.0 );
+
+
+ classPath = expDescription->experimentPath+expDescription->outputFolder+
+ expDescription->outputCommonRoot+
+ "_Class_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
+ "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
+ "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
+ "_R-"+std::to_string(stmsParameters->rScale)+"_"+
+ expDescription->outputImageExtension;
+
+ ClassWriterPointer classWriter
+ = ClassWriterType::New();
+ classWriter->SetFileName( classPath );
+
+ // Filetered image sequence and class image saving
+ for( unsigned int i=1 ; i<=stmsParameters->numTimePoints - stmsParameters->startTimePoint + 1; ++i ){
+
+ char buffer[6];
+ int n;
+
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 6 ) n=sprintf (buffer, "%05d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 5 ) n=sprintf (buffer, "%04d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 4 ) n=sprintf (buffer, "%03d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 3 ) n=sprintf (buffer, "%02d", i + stmsParameters->startTimePoint - 1);
+ if( sizeof(STMS_NUMBERING_FORM_ONE) == 2 ) n=sprintf (buffer, "%01d", i + stmsParameters->startTimePoint - 1);
+
+ outputPath = expDescription->experimentPath+expDescription->outputFolder+
+ expDescription->outputCommonRoot+
+ "_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
+ "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
+ "_Z-"+std::to_string((unsigned int)stmsParameters->spScales[2])+
+ "_R-"+std::to_string(stmsParameters->rScale)+"_"+
+ buffer+expDescription->outputImageExtension;
+
+ ImagePointer outImage
+ = ImageType::New();
+
+ outImage->SetRegions( region );
+ outImage->Allocate();
+ outImage->FillBuffer( 15.0 );
+
+ WriterPointer writer
+ = WriterType::New();
+ writer->SetFileName( outputPath );
+
+ //#pragma omp parrallel for ...
+ for(unsigned int j=0 ; j<classSet->size() ; ++j)
+ {
+ for( unsigned int k=0 ; k<stmsParameters->dim ; ++k)
+ {
+ outIndex[k] = (IndexType)( round(spatialSet->at(j)[k]*stmsParameters->spScales[k]) );
+
+ if( first )
+ classIndex[k] = outIndex[k];
+ }
+
+ outImage->SetPixel( outIndex, rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale );
+
+ if( first )
+ classImage->SetPixel(classIndex, classSet->at(j));
+ }
+
+ writer->SetInput( outImage );
+ writer->Update();
+
+ if( first )
+ {
+ classWriter->SetInput( classImage );
+ classWriter->Update();
+ first = false;
+ }
+ }
+}
+
+} // end of namespace itkSTMS
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_TemporalSetToImageSequence_Spine.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_TemporalSetToImageSequenceSpine_h
+#define itkSTMS_TemporalSetToImageSequenceSpine_h
+
+#include <string>
+#include <vector>
+#include <math.h>
+
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImageRegionIteratorWithIndex.h"
+
+namespace itkSTMS_Spine
+{
+ template < class ImageType, class ClassImageType >
+ class itkSTMS_TemporalSetToImageSequence
+ {
+ public:
+ // Reader and writer typedefs
+ typedef itk::ImageFileReader< ImageType > ReaderType;
+ typedef typename ReaderType::Pointer ReaderPointer;
+ typedef itk::ImageFileWriter< ImageType > WriterType;
+ typedef typename WriterType::Pointer WriterPointer;
+ typedef itk::ImageFileWriter< ClassImageType > ClassWriterType;
+ typedef typename ClassWriterType::Pointer ClassWriterPointer;
+
+ // Sample set typedefs
+ typedef unsigned int IndexType;
+ typedef float SpatialType;
+ typedef typename ImageType::PixelType PixelType;
+
+ typedef std::vector< SpatialType > SpatialVectorType;
+ typedef std::vector< PixelType > RangeVectorType;
+
+ typedef std::vector< IndexType > IndexSampleSetType;
+ typedef std::vector< SpatialVectorType > SpatialSampleSetType;
+ typedef std::vector< RangeVectorType > RangeSampleSetType;
+
+ // Image typedefs
+ typedef typename ImageType::IndexType SpatialIndexType;
+ typedef typename ImageType::RegionType RegionType;
+
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::SizeType SizeType;
+
+ typedef typename ClassImageType::Pointer ClassImagePointer;
+ typedef typename ClassImageType::RegionType ClassRegionType;
+
+
+ // Methods
+ itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl,
+ SpatialSampleSetType* sp,
+ RangeSampleSetType* ra,
+ itkSTMS_Spine::ParamsAnalysisOutputType* params );
+
+ void GenerateImageSequence();
+
+ private:
+ // Attributes
+ itkSTMS_Spine::ParamsAnalysisOutputType* stmsParameters;
+
+ IndexSampleSetType* classSet;
+ SpatialSampleSetType* spatialSet;
+ RangeSampleSetType* rangeSet;
+
+ }; // end of class itkSTMS_TemporalSetToImageSequence
+} // end of namespace itkstms
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_TemporalSetToImageSequence_Spine.txx"
+#endif
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_TemporalSetToImageSequence_Spine.txx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_TemporalSetToImageSequenceSpine_txx
+#define itkSTMS_TemporalSetToImageSequenceSpine_txx
+
+#include "itkSTMS_TemporalSetToImageSequence_Spine.h"
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+
+namespace itkSTMS_Spine
+{
+
+template < class ImageType, class ClassImageType >
+itkSTMS_TemporalSetToImageSequence < ImageType, ClassImageType >
+::itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl, SpatialSampleSetType* sp, RangeSampleSetType* ra,
+ itkSTMS_Spine::ParamsAnalysisOutputType* params)
+{
+ this->stmsParameters = params;
+ this->classSet = cl;
+ this->spatialSet = sp;
+ this->rangeSet = ra;
+}
+
+
+template < class ImageType, class ClassImageType >
+void
+itkSTMS_TemporalSetToImageSequence< ImageType, ClassImageType >
+::GenerateImageSequence()
+{
+ bool first = true;
+
+ // Output images allocation
+ ImagePointer image
+ = ImageType::New();
+ ReaderPointer reader
+ = ReaderType::New();
+
+ reader->SetFileName( *stmsParameters->images.begin() );
+ reader->Update();
+ image = reader->GetOutput();
+
+ SpatialIndexType start, outIndex, classIndex;
+ start.Fill(0);
+
+ RegionType region;
+ region.SetSize( image->GetBufferedRegion().GetSize());
+ region.SetIndex(start);
+
+ ClassRegionType classRegion;
+ classRegion.SetSize( image->GetBufferedRegion().GetSize());
+ classRegion.SetIndex( start );
+
+
+ std::string outputPath, classPath;
+
+ ClassImagePointer classImage
+ = ClassImageType::New();
+
+ classImage->SetRegions( classRegion );
+ classImage->Allocate();
+ classImage->FillBuffer( 15.0 );
+
+
+ // Filetered image sequence and class image saving
+ // for( unsigned int i=1 ; i<=stmsParameters->numTimePoints ; ++i )
+ // {
+ unsigned int i=1;
+ for (std::list<std::string>::iterator it_images = stmsParameters->images.begin(); it_images != stmsParameters->images.end(); ++it_images)
+ {
+ outputPath = stmsParameters->outFolder+ it_images->substr( it_images->find_last_of("/"), it_images->length()-stmsParameters->imageExtension.length()-it_images->find_last_of("/") ) +
+ "_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
+ "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
+ "_Z-"+std::to_string(stmsParameters->spScales[2])+
+ "_R-"+std::to_string(stmsParameters->rScale)+"_"+
+ std::to_string(i)+stmsParameters->imageExtension;
+
+ ImagePointer outImage
+ = ImageType::New();
+
+ outImage->SetRegions( region );
+ outImage->Allocate();
+ outImage->FillBuffer( 15.0 );
+
+ WriterPointer writer
+ = WriterType::New();
+ writer->SetFileName( outputPath );
+
+ //#pragma omp parrallel for ...
+ for(unsigned int j=0 ; j<classSet->size() ; ++j)
+ {
+ for( unsigned int k=0 ; k<stmsParameters->dim ; ++k)
+ {
+ outIndex[k] = (IndexType)( round(spatialSet->at(j)[k]*stmsParameters->spScales[k]) );
+
+ if( first )
+ classIndex[k] = outIndex[k];
+ }
+
+ outImage->SetPixel( outIndex, rangeSet->at( classSet->at(j)-1 )[i-1]*stmsParameters->rScale );
+
+ if( first )
+ classImage->SetPixel(classIndex, classSet->at(j));
+ }
+
+ writer->SetInput( outImage );
+ writer->Update();
+
+ if( first )
+ {
+ classPath = stmsParameters->outFolder +
+ it_images->substr( it_images->find_last_of("/"), it_images->length()-stmsParameters->imageExtension.length()-it_images->find_last_of("/") ) +
+ "_Class_X-"+std::to_string((unsigned int)stmsParameters->spScales[0])+
+ "_Y-"+std::to_string((unsigned int)stmsParameters->spScales[1])+
+ "_Z-"+std::to_string(stmsParameters->spScales[2])+
+ "_R-"+std::to_string(stmsParameters->rScale)+"_"+
+ stmsParameters->imageExtension;
+
+ ClassWriterPointer classWriter
+ = ClassWriterType::New();
+ classWriter->SetFileName( classPath );
+
+ classWriter->SetInput( classImage );
+ classWriter->Update();
+ first = false;
+ }
+
+ ++i;
+ }
+}
+
+} // end of namespace itkSTMS
+
+#endif
--- /dev/null
+/*
+ #
+ # File : itkSTMS_XMLFileParser.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_XMLFileParser_H
+#define itkSTMS_XMLFileParser_H
+
+#include <string>
+#include "itkDOMNodeXMLReader.h"
+#include "itkFancyString.h"
+
+namespace itkSTMS
+{
+ struct ParserOutputType{
+ std::string experimentPath;
+ std::string imageExtension;
+ std::string outputImageExtension;
+ std::string inputCommonRoot;
+ std::string inputFolder;
+ std::string maskImage;
+ std::string outputFolder;
+ std::string outputCommonRoot;
+ };
+
+
+ class itkSTMS_XMLFileParser{
+ public:
+ typedef itk::DOMNodeXMLReader InputType;
+ typedef typename InputType::Pointer InputPointer;
+ typedef typename itk::DOMNode::Pointer NodePointer;
+
+ itkSTMS_XMLFileParser();
+ void Update();
+
+ inline void SetFileName(std::string fileName){ this->fileName = fileName; }
+ inline std::string GetFileName(){ return( this->fileName ); }
+ inline ParserOutputType* GetXMLParams(){ return( &xmlParams ); }
+
+ private:
+ ParserOutputType xmlParams;
+ InputPointer parser;
+ std::string fileName;
+ NodePointer DomObject, listInput, listOutput;
+ };
+} // end of namespace itkSTMS
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_XMLFileParser.hxx"
+#endif
+
+#endif // itkSTMS_XMLFileParser_H
--- /dev/null
+/*
+ #
+ # File : itkSTMS_XMLFileParser.hxx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_XMLFileParser_HXX
+#define itkSTMS_XMLFileParser_HXX
+
+#include "itkSTMS_XMLFileParser.h"
+
+namespace itkSTMS
+{
+itkSTMS_XMLFileParser::itkSTMS_XMLFileParser()
+{
+ xmlParams.experimentPath = "";
+ xmlParams.imageExtension = "";
+ xmlParams.outputImageExtension = "";
+ xmlParams.inputCommonRoot = "";
+ xmlParams.inputFolder = "";
+ xmlParams.maskImage = "";
+ xmlParams.outputFolder = "";
+ xmlParams.outputCommonRoot = "";
+}
+
+
+void itkSTMS_XMLFileParser::Update()
+{
+ parser = InputType::New();
+ parser->SetFileName( this->fileName );
+ parser->Update();
+
+ DomObject = parser->GetOutput();
+ if ( DomObject->GetName() != "STMS_ProcessInfo" )
+ {
+ std::cout << std::endl << std::endl << "Unrecognized input XML document! STMS_ProcessInfo expected" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ // Read common parameters
+ xmlParams.experimentPath = DomObject->GetAttribute( "experimentPath" );
+ if ( xmlParams.experimentPath == "" )
+ {
+ std::cout << std::endl << std::endl << "experimentPath not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ xmlParams.imageExtension = DomObject->GetAttribute( "imageExtension" );
+ if ( xmlParams.imageExtension == "" )
+ {
+ std::cout << std::endl << std::endl << "imageExtension not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ xmlParams.outputImageExtension = DomObject->GetAttribute( "outputImageExtension" );
+ if ( xmlParams.outputImageExtension == "" )
+ {
+ std::cout << std::endl << std::endl << "outputImageExtension not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ // Read input parameters
+ listInput = DomObject->GetChild( "listInput" );
+ xmlParams.inputFolder = listInput->GetAttribute( "inputFolder" );
+ if ( xmlParams.inputFolder == "" )
+ {
+ std::cout << std::endl << std::endl << "inputFolder not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ xmlParams.inputCommonRoot = listInput->GetAttribute( "commonRoot" );
+ if ( xmlParams.inputCommonRoot == "" )
+ {
+ std::cout << std::endl << std::endl << "inputCommonRoot not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ xmlParams.maskImage = listInput->GetAttribute( "maskImage" );
+ if ( xmlParams.maskImage == "" )
+ {
+ std::cout << std::endl << std::endl << "maskImage not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ // Read output parameters
+ listOutput = DomObject->GetChild( "listOutput" );
+ xmlParams.outputFolder = listOutput->GetAttribute( "outputFolder" );
+ if ( xmlParams.outputFolder == "" )
+ {
+ std::cout << std::endl << std::endl << "outputFolder not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+
+ xmlParams.outputCommonRoot = listOutput->GetAttribute( "commonRoot" );
+ if ( xmlParams.outputCommonRoot == "" )
+ {
+ std::cout << std::endl << std::endl << "outputCommonRoot not found" << std::endl << std::endl;
+ std::exit( EXIT_FAILURE );
+ }
+}
+} // end of namespace itkSTMS
+#endif // itkSTMS_XMLFileParser_HXX
--- /dev/null
+#----------------------------------------------------------------------------
+# USER! : SET THE NAME OF YOUR LIBRARY
+# (Replace 'MyLib' by your own library name)
+
+#############################
+SET ( LIBRARY_NAME SpatioTemporalMeanShift )
+#############################
+
+#----------------------------------------------------------------------------
+
+#----------------------------------------------------------------------------
+# CREATES A USER OPTION IN CMAKE
+OPTION ( BUILD_${LIBRARY_NAME} "Build ${LIBRARY_NAME} library ?" ON)
+#----------------------------------------------------------------------------
+
+#----------------------------------------------------------------------------
+IF ( BUILD_${LIBRARY_NAME} )
+#----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # BUILD LIBRARY
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # LIBRARY HEADERS (TO BE INSTALLED)
+ # EITHER LIST ALL .h, *.txx IN CURRENT DIR USING NEXT LINE:
+
+ FILE(GLOB ${LIBRARY_NAME}_HEADERS "*.h" "*.txx")
+
+ # OR MANUALLY LIST YOUR HEADERS WITH NEXT COMMAND
+ # SET ( ${LIBRARY_NAME}_HEADERS
+ #
+ # )
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # LIBRARY SOURCES (TO BE COMPILED)
+ # EITHER LIST ALL .cxx, *.cpp, *.cc IN CURRENT DIR USING NEXT LINE:
+
+ FILE(GLOB ${LIBRARY_NAME}_SOURCES *.cxx *.cpp *.cc ${${LIBRARY_NAME}_HEADERS})
+
+ # OR MANUALLY LIST YOUR FILES WITH NEXT COMMAND (WITHOUT EXTENSION)
+ # SET ( ${LIBRARY_NAME}_SOURCES
+ #
+ # )
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # LIBRARY DEPENDENCIES (LIBRARIES TO LINK WITH)
+ #
+ # USER! : Uncomment the Libraries you need
+ #
+ SET ( ${LIBRARY_NAME}_LINK_LIBRARIES
+ # ${crea_LIBRARIES}
+ # ${WXWIDGETS_LIBRARIES}
+ # ${KWWidgets_LIBRARIES}
+ # ${VTK_LIBRARIES}
+ # ${ITK_LIBRARIES}
+ # ${GDCM_LIBRARIES}
+ # ${BOOST_LIBRARIES}
+
+ # If this library must link against other libraries
+ # USER! : Add here any extra Library you need
+
+ )
+ #----------------------------------------------------------------------------
+
+ #----------------------------------------------------------------------------
+ # MACRO WHICH DOES ALL THE JOB : BUILD AND INSTALL
+
+ # USER! : The default is to create a Dynamic Library.
+ # if you need to create a static library
+ # comment out the following line :
+
+ #CREA_ADD_LIBRARY( ${LIBRARY_NAME} )
+
+ # and uncomment the 2 lines hereafter:
+
+ ADD_LIBRARY(${LIBRARY_NAME} STATIC ${${LIBRARY_NAME}_SOURCES})
+ TARGET_LINK_LIBRARIES(${LIBRARY_NAME} ${${LIBRARY_NAME}_LINK_LIBRARIES} )
+ SET_TARGET_PROPERTIES(${LIBRARY_NAME} PROPERTIES LINKER_LANGUAGE C)
+
+ #
+ #----------------------------------------------------------------------------
+
+ #---------------------------------------------------------------------------
+ENDIF ( BUILD_${LIBRARY_NAME} )
--- /dev/null
+/*
+ #
+ # File : itkSTMS_BlurringSTMS.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_BlurringSTMS_H
+#define itkSTMS_BlurringSTMS_H
+
+#include "itkSTMS_ArgumentsAnalysis.h"
+#include "itkSTMS_ImageSequenceToTemporalSet.h"
+#include "itkImageFileReader.h"
+
+#ifndef STMS_NUMBERING_FORM_ONE
+#define STMS_NUMBERING_FORM_ONE "1"
+#endif
+
+namespace itkSTMS
+{
+ template < class IndexType, class SpatialType, class PixelType, class ImageType>
+ class itkSTMS_BlurringSTMS
+ {
+ public:
+
+ typedef itkSTMS::ParamsAnalysisOutputType ParametersType;
+
+ // Sample set typedefs
+ typedef std::vector< SpatialType > SpatialVectorType;
+ typedef std::vector< PixelType > RangeVectorType;
+
+ typedef std::vector< IndexType > IndexSampleSetType;
+ typedef std::vector< SpatialVectorType > SpatialSampleSetType;
+ typedef std::vector< RangeVectorType > RangeSampleSetType;
+
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef itk::ImageFileReader<ImageType> ReaderType;
+ typedef typename ReaderType::Pointer ReaderPointer;
+
+ // Image typedefs
+ typedef typename ImageType::IndexType ImageIndexType;
+ typedef std::vector<ImageIndexType> ImageIndexSetType;
+
+ // Methods
+ itkSTMS_BlurringSTMS( IndexSampleSetType* idx,
+ IndexSampleSetType* cla,
+ IndexSampleSetType* wei,
+ SpatialSampleSetType* sp,
+ RangeSampleSetType* ra,
+ ParametersType* params,
+ ParserOutputType* desc );
+
+ inline ~itkSTMS_BlurringSTMS(){ delete classSetMemory;
+ delete spatialSetMemory; }
+
+ inline IndexSampleSetType* GetIndexSet (){ return indexSet; }
+ inline IndexSampleSetType* GetClassSet (){ return classSet; }
+ inline IndexSampleSetType* GetWeightsSet (){ return weightsSet; }
+ inline SpatialSampleSetType* GetSpatialSet (){ return spatialSet; }
+ inline RangeSampleSetType* GetRangeSet (){ return rangeSet; }
+ inline IndexSampleSetType* GetClassMemory (){ return classSetMemory; }
+ inline SpatialSampleSetType* GetSpatialMemory (){ return spatialSetMemory; }
+
+ void GenerateData();
+ void NoMergeSTMSFiltering();
+ void ClassificationNoMergeSTMSFiltering();
+ void MergeSTMSFiltering();
+ void MergeSamples();
+ void FinalMerging();
+
+ template<class T> void VectorDistance(float &dist, std::vector< T > &a, std::vector< T > &b);
+ void InfiniteNorm (bool &dist, RangeVectorType &a, RangeVectorType &b);
+ void MergeInfiniteNorm(bool &dist, RangeVectorType &a, RangeVectorType &b);
+
+ template<class T> void VectorWeightedMean(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w);
+ template<class T> void VectorWeightedAcc(std::vector<T> &a, std::vector<T> &b, unsigned int &b_w);
+ template<class T> void VectorWeightedAcc(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w);
+ template<class T> void VectorMul(std::vector<T> &a, unsigned int &coeff);
+ template<class T> void VectorDiv(std::vector<T> &a, unsigned int &coeff);
+ template<class T> void VectorAcc(std::vector<T> &a, std::vector<T> &b);
+
+ private:
+ // Attributes
+ float mergeFactor;
+
+ ParametersType* stmsParams;
+ ParserOutputType* expDescription;
+
+ IndexSampleSetType* classSetMemory;
+ SpatialSampleSetType* spatialSetMemory;
+ IndexSampleSetType* indexSet;
+ IndexSampleSetType* classSet;
+ IndexSampleSetType* weightsSet;
+ SpatialSampleSetType* spatialSet;
+ RangeSampleSetType * rangeSet;
+ };
+
+} // end of namespace itkSTMS
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_BlurringSTMS.txx"
+#endif
+
+#endif // itkSTMS_BlurringSTMS_H
--- /dev/null
+/*
+ #
+ # File : itkSTMS_BlurringSTMS.txx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_BlurringSTMS_TXX
+#define itkSTMS_BlurringSTMS_TXX
+
+#include <random>
+#include <algorithm>
+#include <iterator>
+#include "itkSTMS_BlurringSTMS.h"
+#include "itkSTMS_XMLFileParser.h"
+
+
+double gettime()
+{
+ struct timespec timestamp;
+
+ clock_gettime(CLOCK_REALTIME, ×tamp);
+ return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
+}
+
+
+namespace itkSTMS
+{
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::itkSTMS_BlurringSTMS( IndexSampleSetType* idx, IndexSampleSetType* cla, IndexSampleSetType* wei,
+ SpatialSampleSetType* sp, RangeSampleSetType* ra, ParametersType* params, ParserOutputType* desc)
+{
+ this->indexSet = idx;
+ this->classSet = cla;
+ this->weightsSet = wei;
+ this->spatialSet = sp;
+ this->rangeSet = ra;
+
+ this->classSetMemory = new IndexSampleSetType ( *this->classSet );
+ this->spatialSetMemory = new SpatialSampleSetType( *this->spatialSet );
+
+ this->stmsParams = params;
+ this->expDescription = desc;
+
+ this->mergeFactor = 1000;
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::GenerateData()
+{
+ double dtime;
+
+ if( !stmsParams->merge )
+ {
+ std::cout<< std::endl<<"No merge Filtering!"<<std::endl<<"numSamples: "<< indexSet->size() <<std::endl<< std::endl;
+ NoMergeSTMSFiltering();
+
+ dtime=gettime();
+ ClassificationNoMergeSTMSFiltering();
+ dtime = gettime()-dtime;
+ std::cout<< std::endl<<"Classif: " << dtime/1000 << " s" <<std::endl;
+ FinalMerging();
+ }
+ else
+ {
+ std::cout<<std::endl<<"Merge Filtering!"<<std::endl<<"numSamples: "<< indexSet->size() <<std::endl<< std::endl;
+ MergeSTMSFiltering();
+ FinalMerging();
+ // ClassificationNoMergeSTMSFiltering();
+ }
+}
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::ClassificationNoMergeSTMSFiltering()
+{
+
+ IndexSampleSetType* newClassSet
+ = new IndexSampleSetType();
+ newClassSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newWeightsSet
+ = new IndexSampleSetType();
+ newWeightsSet->reserve( indexSet->size() );
+
+ IndexSampleSetType* newIndexSet
+ = new IndexSampleSetType();
+ newIndexSet->reserve ( indexSet->size() );
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType();
+
+ newSpatialSet->reserve( indexSet->size() );
+
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType();
+ newRangeSet->reserve ( indexSet->size() );
+
+
+ newClassSet->push_back ( 1 );
+ newWeightsSet->push_back( 1 );
+ newIndexSet->push_back ( indexSet->at(0) );
+ newSpatialSet->push_back( spatialSet->at(0) );
+ newRangeSet->push_back ( rangeSet->at(0) );
+ classSetMemory->at( indexSet->at(0) ) = newClassSet->at(0);
+
+
+ unsigned int k;
+ bool newC;
+ float spDist;
+ bool raNorm;
+
+ for(unsigned int i=1 ; i<indexSet->size() ; ++i)
+ {
+ newC = true;
+ k=0;
+
+ while( (k<newClassSet->size()) && newC )
+ {
+ VectorDistance( spDist, newSpatialSet->at(k), spatialSet->at(i) );
+ if( spDist<=1 )
+ {
+ InfiniteNorm( raNorm, newRangeSet->at(k), rangeSet->at(i) );
+ if( raNorm )
+ {
+ VectorWeightedMean( newSpatialSet->at(k), newWeightsSet->at(k), spatialSet->at(i), weightsSet->at(i) );
+ VectorWeightedMean( newRangeSet->at(k) , newWeightsSet->at(k), rangeSet->at(i) , weightsSet->at(i) );
+
+ classSetMemory->at( indexSet->at(i) ) = newClassSet->at(k);
+ newC = false;
+ }
+ else
+ ++k;
+ }
+ else
+ ++k;
+ }
+
+ if( newC )
+ {
+ newClassSet->push_back( (IndexType)newClassSet->back()+1 );
+ newWeightsSet->push_back( 1 );
+ newIndexSet->push_back ( indexSet->at(i) );
+ newSpatialSet->push_back( spatialSet->at(i) );
+ newRangeSet->push_back ( rangeSet->at(i) );
+ classSetMemory->at( indexSet->at(i) ) = newClassSet->back();
+ }
+ }
+
+ classSet->swap ( *newClassSet );
+ weightsSet->swap( *newWeightsSet );
+ indexSet->swap ( *newIndexSet );
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+
+ delete newClassSet;
+ delete newWeightsSet;
+ delete newIndexSet;
+ delete newSpatialSet;
+ delete newRangeSet;
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::NoMergeSTMSFiltering()
+{
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType( indexSet->size(), SpatialVectorType(stmsParams->dim, 0) );
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType( indexSet->size(), RangeVectorType(stmsParams->numTimePoints, 0) );
+
+ float globalEvolution = INFINITY;
+ float epsilon = (stmsParams->epsilon)*(stmsParams->epsilon);
+ float spDist, raDist;
+ bool raNorm;
+ unsigned int iter = 0;
+
+ double dtime;
+ while( (globalEvolution>epsilon) & (iter<stmsParams->maxIt) )
+ {
+ dtime=gettime();
+ globalEvolution = 0.0;
+
+ #pragma omp parallel for reduction(+:globalEvolution) private(spDist, raDist, raNorm)
+ for(unsigned int i=0 ; i<indexSet->size() ; ++i)
+ {
+ unsigned int count = 0;
+ SpatialVectorType tmpSpatial( stmsParams->dim, 0 );
+ RangeVectorType tmpRange ( stmsParams->numTimePoints, 0 );
+
+ for(unsigned int j=0 ; j<indexSet->size() ; ++j)
+ {
+ VectorDistance( spDist, spatialSet->at(i), spatialSet->at(j));
+
+ if( spDist<=1 )
+ {
+ InfiniteNorm(raNorm, rangeSet->at(i), rangeSet->at(j));
+
+ if( raNorm )
+ {
+ VectorAcc( tmpSpatial, spatialSet->at(j) );
+ VectorAcc( tmpRange , rangeSet->at(j) );
+
+ ++count;
+ }
+ }
+ }
+
+ if( count>1 )
+ {
+ VectorDiv( tmpSpatial, count );
+ VectorDiv( tmpRange , count );
+ }
+
+ VectorDistance(spDist, spatialSet->at(i), tmpSpatial);
+ VectorDistance(raDist, rangeSet->at(i), tmpRange);
+
+ globalEvolution += (spDist+raDist);
+
+ #pragma omp critical
+ {
+ newSpatialSet->at(i) = tmpSpatial;
+ newRangeSet->at(i) = tmpRange;
+ }
+ }
+
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+
+ ++iter;
+ dtime = gettime()-dtime;
+ std::cout<< "Iter: " << iter <<" "<< dtime/1000 << " s" <<" GE: "<< globalEvolution <<std::endl;
+ }
+
+ delete newSpatialSet;
+ delete newRangeSet;
+}
+
+
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::MergeSTMSFiltering()
+{
+
+ float globalEvolution = INFINITY;
+ float epsilon = (stmsParams->epsilon)*(stmsParams->epsilon);
+ float spDist, raDist;
+ bool raNorm, mergeNorm;
+ unsigned int iter = 0;
+ unsigned int merging;
+
+ double dtime;
+ while( (globalEvolution>epsilon) & (iter<stmsParams->maxIt) )
+ {
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType( *spatialSet );
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType ( *rangeSet );
+
+ dtime=gettime();
+ globalEvolution = 0.0;
+ merging = 0;
+
+ #pragma omp parallel for reduction(+:globalEvolution, merging) private(spDist, raDist, raNorm, mergeNorm)
+ for(unsigned int i=0 ; i<indexSet->size() ; ++i)
+ {
+ unsigned int weight = 0;
+ bool merge = false;
+ SpatialVectorType tmpSpatial( stmsParams->dim, 0 );
+ RangeVectorType tmpRange ( stmsParams->numTimePoints, 0 );
+
+ for(unsigned int j=0 ; j<indexSet->size() ; ++j)
+ {
+ VectorDistance( spDist, spatialSet->at(i), spatialSet->at(j));
+
+ if( spDist<=1 )
+ {
+ InfiniteNorm(raNorm, rangeSet->at(i), rangeSet->at(j));
+
+ if( raNorm )
+ {
+ VectorWeightedAcc(tmpSpatial, spatialSet->at(j), weightsSet->at(j));
+ VectorWeightedAcc(tmpRange , rangeSet->at(j) , weightsSet->at(j));
+
+ weight += weightsSet->at(j);
+
+ MergeInfiniteNorm(mergeNorm, rangeSet->at(i), rangeSet->at(j));
+ if( (spDist <= (1/mergeFactor)) && mergeNorm )
+ merge = true;
+ }
+ }
+ }
+
+ if(weight > weightsSet->at(i))
+ {
+ if( merge )
+ merging += 1;
+ else
+ merge = 0;
+ }
+ else
+ merge = 0;
+
+
+ VectorDiv( tmpSpatial, weight );
+ VectorDiv( tmpRange , weight );
+
+ #pragma omp critical
+ {
+ newSpatialSet->at(i) = tmpSpatial;
+ newRangeSet->at(i) = tmpRange;
+ }
+
+ VectorDistance(spDist, spatialSet->at(i), tmpSpatial);
+ VectorDistance(raDist, rangeSet->at(i), tmpRange);
+
+ globalEvolution += (spDist+raDist);
+ }
+
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+
+ delete newSpatialSet;
+ delete newRangeSet;
+
+ if(merging > 0)
+ MergeSamples();
+
+ ++iter;
+ dtime = gettime()-dtime;
+ std::cout<< "Iter: " << iter <<" "<< dtime/1000 << " s" <<" GE: "<< globalEvolution << " numSamples: "<< classSet->size() <<std::endl;
+ }
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::MergeSamples()
+{
+
+ IndexSampleSetType* newClassSet
+ = new IndexSampleSetType();
+ newClassSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newWeightsSet
+ = new IndexSampleSetType();
+ newWeightsSet->reserve( indexSet->size() );
+
+ IndexSampleSetType* newIndexSet
+ = new IndexSampleSetType();
+ newIndexSet->reserve ( indexSet->size() );
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType();
+
+ newSpatialSet->reserve( indexSet->size() );
+
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType();
+ newRangeSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newClassSetMemory
+ = new IndexSampleSetType( *classSetMemory );
+
+ IndexSampleSetType* indexes
+ = new IndexSampleSetType( *classSet );
+
+ std::random_device rd;
+ std::mt19937 g(rd());
+
+ std::shuffle(indexes->begin(), indexes->end(), g);
+
+
+ newClassSet->push_back ( 1 );
+ newWeightsSet->push_back( weightsSet->at( indexes->at(0)-1 ) );
+ newIndexSet->push_back ( indexSet->at ( indexes->at(0)-1 ) );
+ newSpatialSet->push_back( spatialSet->at( indexes->at(0)-1 ) );
+ newRangeSet->push_back ( rangeSet->at ( indexes->at(0)-1 ) );
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(indexes->at(0)-1))
+ newClassSetMemory->at(l) = 1;
+ }
+
+ unsigned int k;
+ bool newC;
+ float spDist;
+ bool raNorm;
+ unsigned int i;
+
+ for(unsigned int m=1 ; m<indexes->size() ; ++m)
+ {
+ i = indexes->at(m)-1;
+
+ newC = true;
+ k=0;
+
+ while( (k<newClassSet->size()) && newC )
+ {
+ VectorDistance( spDist, newSpatialSet->at(k), spatialSet->at(i) );
+ MergeInfiniteNorm( raNorm, newRangeSet->at(k), rangeSet->at(i) );
+ if( (spDist<=1/mergeFactor)&&raNorm )
+ {
+ VectorWeightedAcc( newSpatialSet->at(k), newWeightsSet->at(k), spatialSet->at(i), weightsSet->at(i) );
+ VectorWeightedAcc( newRangeSet->at(k) , newWeightsSet->at(k), rangeSet->at(i) , weightsSet->at(i) );
+
+ newWeightsSet->at(k) += weightsSet->at(i);
+
+ VectorDiv(newSpatialSet->at(k), newWeightsSet->at(k));
+ VectorDiv(newRangeSet->at(k), newWeightsSet->at(k));
+
+ for(unsigned int l=0 ; l<classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->at(k);
+ }
+
+ newC = false;
+ }
+ else
+ ++k;
+ }
+
+ if( newC )
+ {
+ newClassSet->push_back( newClassSet->back()+1 );
+ newWeightsSet->push_back( weightsSet->at(i) );
+ newIndexSet->push_back ( indexSet->at(i) );
+ newSpatialSet->push_back( spatialSet->at(i) );
+ newRangeSet->push_back ( rangeSet->at(i) );
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->back();
+ }
+ }
+ }
+
+ classSet->swap ( *newClassSet );
+ weightsSet->swap( *newWeightsSet );
+ indexSet->swap ( *newIndexSet );
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+ classSetMemory->swap ( *newClassSetMemory );
+
+ delete newClassSet;
+ delete newWeightsSet;
+ delete newIndexSet;
+ delete newSpatialSet;
+ delete newRangeSet;
+ delete newClassSetMemory;
+ delete indexes;
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::FinalMerging()
+{
+ unsigned int size = INFINITY;
+ std::string imagePath = expDescription->experimentPath+expDescription->inputFolder+expDescription->inputCommonRoot+STMS_NUMBERING_FORM_ONE+expDescription->imageExtension;
+
+ while(size > classSet->size()){
+ IndexSampleSetType* newClassSet
+ = new IndexSampleSetType();
+ newClassSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newWeightsSet
+ = new IndexSampleSetType();
+ newWeightsSet->reserve( indexSet->size() );
+
+ IndexSampleSetType* newIndexSet
+ = new IndexSampleSetType();
+ newIndexSet->reserve ( indexSet->size() );
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType();
+
+ newSpatialSet->reserve( indexSet->size() );
+
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType();
+ newRangeSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newClassSetMemory
+ = new IndexSampleSetType( *classSetMemory );
+
+ newClassSet->push_back ( 1 );
+ newWeightsSet->push_back( 1 );
+ newIndexSet->push_back ( indexSet->at(0) );
+ newSpatialSet->push_back( spatialSet->at(0) );
+ newRangeSet->push_back ( rangeSet->at(0) );
+
+ unsigned int k;
+ bool newC;
+ bool raNorm;
+
+ for(unsigned int i=1 ; i<classSet->size() ; ++i)
+ {
+ newC = true;
+ k=0;
+
+ while( (k<newClassSet->size()) && newC )
+ {
+ InfiniteNorm( raNorm, newRangeSet->at(k), rangeSet->at(i) );
+ if( raNorm ){
+
+ ReaderPointer reader = ReaderType::New();
+ ImagePointer image = ImageType::New();
+
+ reader->SetFileName( imagePath );
+ reader->Update();
+ image = reader->GetOutput();
+ image->FillBuffer( 0 );
+
+ ImageIndexSetType* refClass = new ImageIndexSetType();
+ ImageIndexSetType* candClass = new ImageIndexSetType();
+ refClass->reserve( classSet->size()/2 );
+ candClass->reserve( classSet->size()/2 );
+
+
+ for(unsigned int m=0 ; m<newClassSetMemory->size() ; ++m)
+ {
+ ImageIndexType idx;
+ if(newClassSetMemory->at(m) == classSet->at(i)){
+
+ #pragma omp simd
+ for(unsigned int n=0 ; n<stmsParams->dim ; ++n)
+ idx[n] = spatialSetMemory->at(m)[n]*stmsParams->spScales[n];
+
+ candClass->push_back( idx );
+ image->SetPixel(candClass->back(), 1);
+ }
+ else
+ {
+ if(newClassSetMemory->at(m) == newClassSet->at(k)){
+
+ #pragma omp simd
+ for(unsigned int n=0 ; n<stmsParams->dim ; ++n)
+ idx[n] = spatialSetMemory->at(m)[n]*stmsParams->spScales[n];
+
+ refClass->push_back( idx );
+ image->SetPixel(refClass->back(), 2);
+ }
+ }
+ }
+
+ bool connex = false;
+ if(stmsParams->dim == 2)
+ {
+ if(refClass->size() < candClass->size())
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<refClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ idx[0] = refClass->at(m)[0]+x;
+ idx[1] = refClass->at(m)[1]+y;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0)
+ {
+ if(image->GetPixel(idx) == 2)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+ else
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<candClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ idx[0] = candClass->at(m)[0]+x;
+ idx[1] = candClass->at(m)[1]+y;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0)
+ {
+ if(image->GetPixel(idx) == 1)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+
+ }
+ else
+ {
+ if(refClass->size() < candClass->size())
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<refClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ for(int z=-1 ; z<=1 ; ++z)
+ {
+ idx[0] = refClass->at(m)[0]+x;
+ idx[1] = refClass->at(m)[1]+y;
+ idx[2] = refClass->at(m)[2]+z;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0 && idx[2]<image->GetBufferedRegion().GetSize()[2] && idx[2]>0)
+ {
+ if(image->GetPixel(idx) == 2)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ z = 2;
+ }
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+ else
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<candClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ for(int z=-1 ; z<=1 ; ++z)
+ {
+ idx[0] = candClass->at(m)[0]+x;
+ idx[1] = candClass->at(m)[1]+y;
+ idx[2] = candClass->at(m)[2]+z;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0 && idx[2]<image->GetBufferedRegion().GetSize()[2] && idx[2]>0)
+ {
+ if(image->GetPixel(idx) == 1)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ z = 2;
+ }
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+ }
+
+ if( connex )
+ {
+
+ VectorWeightedAcc( newSpatialSet->at(k), newWeightsSet->at(k), spatialSet->at(i), weightsSet->at(i) );
+ VectorWeightedAcc( newRangeSet->at(k) , newWeightsSet->at(k), rangeSet->at(i) , weightsSet->at(i) );
+
+ newWeightsSet->at(k) += weightsSet->at(i);
+
+ VectorDiv(newSpatialSet->at(k), newWeightsSet->at(k));
+ VectorDiv(newRangeSet->at(k), newWeightsSet->at(k));
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->at(k);
+ }
+
+ newC = false;
+ }
+ else
+ ++k;
+
+ delete refClass;
+ delete candClass;
+ }
+ else
+ ++k;
+ }
+
+ if( newC )
+ {
+ newClassSet->push_back( newClassSet->back()+1 );
+ newWeightsSet->push_back( weightsSet->at(i) );
+ newIndexSet->push_back ( indexSet->at(i) );
+ newSpatialSet->push_back( spatialSet->at(i) );
+ newRangeSet->push_back ( rangeSet->at(i) );
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->back();
+ }
+ }
+ }
+
+ size = classSet->size();
+
+ classSet->swap ( *newClassSet );
+ weightsSet->swap( *newWeightsSet );
+ indexSet->swap ( *newIndexSet );
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+ classSetMemory->swap ( *newClassSetMemory );
+
+ delete newClassSet;
+ delete newWeightsSet;
+ delete newIndexSet;
+ delete newSpatialSet;
+ delete newRangeSet;
+ delete newClassSetMemory;
+ }
+}
+
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorDistance(float &dist, std::vector<T> &a, std::vector<T> &b)
+{
+ dist = 0.0;
+
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ dist += ( a[i]-b[i] )*( a[i]-b[i] );
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::InfiniteNorm(bool &dist, RangeVectorType &a, RangeVectorType &b)
+{
+ dist = true;
+
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ {
+ if(((a[i]-b[i])*(a[i]-b[i])) > 1)
+ {
+ dist = false;
+ i = a.size();
+ }
+ }
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::MergeInfiniteNorm(bool &dist, RangeVectorType &a, RangeVectorType &b)
+{
+ dist = true;
+
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ {
+ if(((a[i]-b[i])*(a[i]-b[i])) > (1/mergeFactor))
+ {
+ dist = false;
+ i = a.size();
+ }
+ }
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorAcc(std::vector<T> &a, std::vector<T> &b)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] += b[i];
+}
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorWeightedAcc(std::vector<T> &a, std::vector<T> &b, unsigned int &b_w)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] += b_w*b[i];
+}
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorWeightedAcc(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i){
+ a[i] *= a_w;
+ a[i] += b_w*b[i];
+ }
+}
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorWeightedMean(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] = ( (a[i]*a_w )+(b[i]*b_w) )/( a_w+b_w );
+
+ a_w += b_w;
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorMul(std::vector<T> &a, unsigned int &coeff)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] *= coeff;
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorDiv(std::vector<T> &a, unsigned int &coeff)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] /= coeff;
+}
+
+} // end of namespace itkSTMS
+
+#endif // itkmsSTMS_BlurringSTMS_TXX
--- /dev/null
+/*
+ #
+ # File : itkSTMS_BlurringSTMS_Spine.h
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_BlurringSTMS_Spine_H
+#define itkSTMS_BlurringSTMS_Spine_H
+
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+#include "itkSTMS_ImageSequenceToTemporalSet_Spine.h"
+#include "itkImageFileReader.h"
+
+namespace itkSTMS_Spine
+{
+ template < class IndexType, class SpatialType, class PixelType, class ImageType>
+ class itkSTMS_BlurringSTMS
+ {
+ public:
+
+ typedef itkSTMS_Spine::ParamsAnalysisOutputType ParametersType;
+
+ // Sample set typedefs
+ typedef std::vector< SpatialType > SpatialVectorType;
+ typedef std::vector< PixelType > RangeVectorType;
+
+ typedef std::vector< IndexType > IndexSampleSetType;
+ typedef std::vector< SpatialVectorType > SpatialSampleSetType;
+ typedef std::vector< RangeVectorType > RangeSampleSetType;
+
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef itk::ImageFileReader<ImageType> ReaderType;
+ typedef typename ReaderType::Pointer ReaderPointer;
+
+ // Image typedefs
+ typedef typename ImageType::IndexType ImageIndexType;
+ typedef std::vector<ImageIndexType> ImageIndexSetType;
+
+ // Methods
+ itkSTMS_BlurringSTMS( IndexSampleSetType* idx,
+ IndexSampleSetType* cla,
+ IndexSampleSetType* wei,
+ SpatialSampleSetType* sp,
+ RangeSampleSetType* ra,
+ ParametersType* params );
+
+ inline ~itkSTMS_BlurringSTMS(){ delete classSetMemory;
+ delete spatialSetMemory; }
+
+ inline IndexSampleSetType* GetIndexSet (){ return indexSet; }
+ inline IndexSampleSetType* GetClassSet (){ return classSet; }
+ inline IndexSampleSetType* GetWeightsSet (){ return weightsSet; }
+ inline SpatialSampleSetType* GetSpatialSet (){ return spatialSet; }
+ inline RangeSampleSetType* GetRangeSet (){ return rangeSet; }
+ inline IndexSampleSetType* GetClassMemory (){ return classSetMemory; }
+ inline SpatialSampleSetType* GetSpatialMemory (){ return spatialSetMemory; }
+
+ void GenerateData();
+ void NoMergeSTMSFiltering();
+ void ClassificationNoMergeSTMSFiltering();
+ void MergeSTMSFiltering();
+ void MergeSamples();
+ void FinalMerging();
+
+ template<class T> void VectorDistance(float &dist, std::vector< T > &a, std::vector< T > &b);
+ void InfiniteNorm (bool &dist, RangeVectorType &a, RangeVectorType &b);
+ void MergeInfiniteNorm(bool &dist, RangeVectorType &a, RangeVectorType &b);
+
+ template<class T> void VectorWeightedMean(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w);
+ template<class T> void VectorWeightedAcc(std::vector<T> &a, std::vector<T> &b, unsigned int &b_w);
+ template<class T> void VectorWeightedAcc(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w);
+ template<class T> void VectorMul(std::vector<T> &a, unsigned int &coeff);
+ template<class T> void VectorDiv(std::vector<T> &a, unsigned int &coeff);
+ template<class T> void VectorAcc(std::vector<T> &a, std::vector<T> &b);
+
+ private:
+ // Attributes
+ float mergeFactor;
+
+ ParametersType* stmsParams;
+ IndexSampleSetType* classSetMemory;
+ SpatialSampleSetType* spatialSetMemory;
+ IndexSampleSetType* indexSet;
+ IndexSampleSetType* classSet;
+ IndexSampleSetType* weightsSet;
+ SpatialSampleSetType* spatialSet;
+ RangeSampleSetType * rangeSet;
+ };
+
+} // end of namespace itkSTMS
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSTMS_BlurringSTMS_Spine.txx"
+#endif
+
+#endif // itkSTMS_BlurringSTMS_Spine_H
--- /dev/null
+/*
+ #
+ # File : itkSTMS_BlurringSTMS_Spine.txx
+ # ( C++ header file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL C
+ # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#ifndef itkSTMS_BlurringSTMS_TXX
+#define itkSTMS_BlurringSTMS_TXX
+
+#include <random>
+#include <algorithm>
+#include <iterator>
+#include "itkSTMS_BlurringSTMS_Spine.h"
+
+
+double gettime()
+{
+ struct timespec timestamp;
+
+ clock_gettime(CLOCK_REALTIME, ×tamp);
+ return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
+}
+
+
+namespace itkSTMS_Spine
+{
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::itkSTMS_BlurringSTMS( IndexSampleSetType* idx, IndexSampleSetType* cla, IndexSampleSetType* wei,
+ SpatialSampleSetType* sp, RangeSampleSetType* ra, ParametersType* params )
+{
+ this->indexSet = idx;
+ this->classSet = cla;
+ this->weightsSet = wei;
+ this->spatialSet = sp;
+ this->rangeSet = ra;
+
+ this->classSetMemory = new IndexSampleSetType ( *this->classSet );
+ this->spatialSetMemory = new SpatialSampleSetType( *this->spatialSet );
+
+ this->stmsParams = params;
+
+ this->mergeFactor = 1000;
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::GenerateData()
+{
+ double dtime;
+
+ if( !stmsParams->merge )
+ {
+ std::cout<< std::endl<<"No merge Filtering!"<<std::endl<<"numSamples: "<< indexSet->size() <<std::endl<< std::endl;
+ NoMergeSTMSFiltering();
+
+ dtime=gettime();
+ ClassificationNoMergeSTMSFiltering();
+ dtime = gettime()-dtime;
+ std::cout<< std::endl<<"Classif: " << dtime/1000 << " s" <<std::endl;
+ FinalMerging();
+ }
+ else
+ {
+ std::cout<<std::endl<<"Merge Filtering!"<<std::endl<<"numSamples: "<< indexSet->size() <<std::endl<< std::endl;
+ MergeSTMSFiltering();
+ FinalMerging();
+ // ClassificationNoMergeSTMSFiltering();
+ }
+}
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::ClassificationNoMergeSTMSFiltering()
+{
+
+ IndexSampleSetType* newClassSet
+ = new IndexSampleSetType();
+ newClassSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newWeightsSet
+ = new IndexSampleSetType();
+ newWeightsSet->reserve( indexSet->size() );
+
+ IndexSampleSetType* newIndexSet
+ = new IndexSampleSetType();
+ newIndexSet->reserve ( indexSet->size() );
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType();
+
+ newSpatialSet->reserve( indexSet->size() );
+
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType();
+ newRangeSet->reserve ( indexSet->size() );
+
+
+ newClassSet->push_back ( 1 );
+ newWeightsSet->push_back( 1 );
+ newIndexSet->push_back ( indexSet->at(0) );
+ newSpatialSet->push_back( spatialSet->at(0) );
+ newRangeSet->push_back ( rangeSet->at(0) );
+ classSetMemory->at( indexSet->at(0) ) = newClassSet->at(0);
+
+
+ unsigned int k;
+ bool newC;
+ float spDist;
+ bool raNorm;
+
+ for(unsigned int i=1 ; i<indexSet->size() ; ++i)
+ {
+ newC = true;
+ k=0;
+
+ while( (k<newClassSet->size()) && newC )
+ {
+ VectorDistance( spDist, newSpatialSet->at(k), spatialSet->at(i) );
+ if( spDist<=1 )
+ {
+ InfiniteNorm( raNorm, newRangeSet->at(k), rangeSet->at(i) );
+ if( raNorm )
+ {
+ VectorWeightedMean( newSpatialSet->at(k), newWeightsSet->at(k), spatialSet->at(i), weightsSet->at(i) );
+ VectorWeightedMean( newRangeSet->at(k) , newWeightsSet->at(k), rangeSet->at(i) , weightsSet->at(i) );
+
+ classSetMemory->at( indexSet->at(i) ) = newClassSet->at(k);
+ newC = false;
+ }
+ else
+ ++k;
+ }
+ else
+ ++k;
+ }
+
+ if( newC )
+ {
+ newClassSet->push_back( (IndexType)newClassSet->back()+1 );
+ newWeightsSet->push_back( 1 );
+ newIndexSet->push_back ( indexSet->at(i) );
+ newSpatialSet->push_back( spatialSet->at(i) );
+ newRangeSet->push_back ( rangeSet->at(i) );
+ classSetMemory->at( indexSet->at(i) ) = newClassSet->back();
+ }
+ }
+
+ classSet->swap ( *newClassSet );
+ weightsSet->swap( *newWeightsSet );
+ indexSet->swap ( *newIndexSet );
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+
+ delete newClassSet;
+ delete newWeightsSet;
+ delete newIndexSet;
+ delete newSpatialSet;
+ delete newRangeSet;
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::NoMergeSTMSFiltering()
+{
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType( indexSet->size(), SpatialVectorType(stmsParams->dim, 0) );
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType( indexSet->size(), RangeVectorType(stmsParams->numTimePoints, 0) );
+
+ float globalEvolution = INFINITY;
+ float epsilon = (stmsParams->epsilon)*(stmsParams->epsilon);
+ float spDist, raDist;
+ bool raNorm;
+ unsigned int iter = 0;
+
+ double dtime;
+ while( (globalEvolution>epsilon) & (iter<stmsParams->maxIt) )
+ {
+ dtime=gettime();
+ globalEvolution = 0.0;
+
+ #pragma omp parallel for reduction(+:globalEvolution) private(spDist, raDist, raNorm)
+ for(unsigned int i=0 ; i<indexSet->size() ; ++i)
+ {
+ unsigned int count = 0;
+ SpatialVectorType tmpSpatial( stmsParams->dim, 0 );
+ RangeVectorType tmpRange ( stmsParams->numTimePoints, 0 );
+
+ for(unsigned int j=0 ; j<indexSet->size() ; ++j)
+ {
+ VectorDistance( spDist, spatialSet->at(i), spatialSet->at(j));
+
+ if( spDist<=1 )
+ {
+ InfiniteNorm(raNorm, rangeSet->at(i), rangeSet->at(j));
+
+ if( raNorm )
+ {
+ VectorAcc( tmpSpatial, spatialSet->at(j) );
+ VectorAcc( tmpRange , rangeSet->at(j) );
+
+ ++count;
+ }
+ }
+ }
+
+ if( count>1 )
+ {
+ VectorDiv( tmpSpatial, count );
+ VectorDiv( tmpRange , count );
+ }
+
+ VectorDistance(spDist, spatialSet->at(i), tmpSpatial);
+ VectorDistance(raDist, rangeSet->at(i), tmpRange);
+
+ globalEvolution += (spDist+raDist);
+
+ #pragma omp critical
+ {
+ newSpatialSet->at(i) = tmpSpatial;
+ newRangeSet->at(i) = tmpRange;
+ }
+ }
+
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+
+ ++iter;
+ dtime = gettime()-dtime;
+ std::cout<< "Iter: " << iter <<" "<< dtime/1000 << " s" <<" GE: "<< globalEvolution <<std::endl;
+ }
+
+ delete newSpatialSet;
+ delete newRangeSet;
+}
+
+
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::MergeSTMSFiltering()
+{
+
+ float globalEvolution = INFINITY;
+ float epsilon = (stmsParams->epsilon)*(stmsParams->epsilon);
+ float spDist, raDist;
+ bool raNorm, mergeNorm;
+ unsigned int iter = 0;
+ unsigned int merging;
+
+ double dtime;
+ while( (globalEvolution>epsilon) & (iter<stmsParams->maxIt) )
+ {
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType( *spatialSet );
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType ( *rangeSet );
+
+ dtime=gettime();
+ globalEvolution = 0.0;
+ merging = 0;
+
+ #pragma omp parallel for reduction(+:globalEvolution, merging) private(spDist, raDist, raNorm, mergeNorm)
+ for(unsigned int i=0 ; i<indexSet->size() ; ++i)
+ {
+ unsigned int weight = 0;
+ bool merge = false;
+ SpatialVectorType tmpSpatial( stmsParams->dim, 0 );
+ RangeVectorType tmpRange ( stmsParams->numTimePoints, 0 );
+
+ for(unsigned int j=0 ; j<indexSet->size() ; ++j)
+ {
+ VectorDistance( spDist, spatialSet->at(i), spatialSet->at(j));
+
+ if( spDist<=1 )
+ {
+ InfiniteNorm(raNorm, rangeSet->at(i), rangeSet->at(j));
+
+ if( raNorm )
+ {
+ VectorWeightedAcc(tmpSpatial, spatialSet->at(j), weightsSet->at(j));
+ VectorWeightedAcc(tmpRange , rangeSet->at(j) , weightsSet->at(j));
+
+ weight += weightsSet->at(j);
+
+ MergeInfiniteNorm(mergeNorm, rangeSet->at(i), rangeSet->at(j));
+ if( (spDist <= (1/mergeFactor)) && mergeNorm )
+ merge = true;
+ }
+ }
+ }
+
+ if(weight > weightsSet->at(i))
+ {
+ if( merge )
+ merging += 1;
+ else
+ merge = 0;
+ }
+ else
+ merge = 0;
+
+
+ VectorDiv( tmpSpatial, weight );
+ VectorDiv( tmpRange , weight );
+
+ #pragma omp critical
+ {
+ newSpatialSet->at(i) = tmpSpatial;
+ newRangeSet->at(i) = tmpRange;
+ }
+
+ VectorDistance(spDist, spatialSet->at(i), tmpSpatial);
+ VectorDistance(raDist, rangeSet->at(i), tmpRange);
+
+ globalEvolution += (spDist+raDist);
+ }
+
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+
+ delete newSpatialSet;
+ delete newRangeSet;
+
+ if(merging > 0)
+ MergeSamples();
+
+ ++iter;
+ dtime = gettime()-dtime;
+ std::cout<< "Iter: " << iter <<" "<< dtime/1000 << " s" <<" GE: "<< globalEvolution << " numSamples: "<< classSet->size() <<std::endl;
+ }
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::MergeSamples()
+{
+
+ IndexSampleSetType* newClassSet
+ = new IndexSampleSetType();
+ newClassSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newWeightsSet
+ = new IndexSampleSetType();
+ newWeightsSet->reserve( indexSet->size() );
+
+ IndexSampleSetType* newIndexSet
+ = new IndexSampleSetType();
+ newIndexSet->reserve ( indexSet->size() );
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType();
+
+ newSpatialSet->reserve( indexSet->size() );
+
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType();
+ newRangeSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newClassSetMemory
+ = new IndexSampleSetType( *classSetMemory );
+
+ IndexSampleSetType* indexes
+ = new IndexSampleSetType( *classSet );
+
+ std::random_device rd;
+ std::mt19937 g(rd());
+
+ std::shuffle(indexes->begin(), indexes->end(), g);
+
+
+ newClassSet->push_back ( 1 );
+ newWeightsSet->push_back( weightsSet->at( indexes->at(0)-1 ) );
+ newIndexSet->push_back ( indexSet->at ( indexes->at(0)-1 ) );
+ newSpatialSet->push_back( spatialSet->at( indexes->at(0)-1 ) );
+ newRangeSet->push_back ( rangeSet->at ( indexes->at(0)-1 ) );
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(indexes->at(0)-1))
+ newClassSetMemory->at(l) = 1;
+ }
+
+ unsigned int k;
+ bool newC;
+ float spDist;
+ bool raNorm;
+ unsigned int i;
+
+ for(unsigned int m=1 ; m<indexes->size() ; ++m)
+ {
+ i = indexes->at(m)-1;
+
+ newC = true;
+ k=0;
+
+ while( (k<newClassSet->size()) && newC )
+ {
+ VectorDistance( spDist, newSpatialSet->at(k), spatialSet->at(i) );
+ MergeInfiniteNorm( raNorm, newRangeSet->at(k), rangeSet->at(i) );
+ if( (spDist<=1/mergeFactor)&&raNorm )
+ {
+ VectorWeightedAcc( newSpatialSet->at(k), newWeightsSet->at(k), spatialSet->at(i), weightsSet->at(i) );
+ VectorWeightedAcc( newRangeSet->at(k) , newWeightsSet->at(k), rangeSet->at(i) , weightsSet->at(i) );
+
+ newWeightsSet->at(k) += weightsSet->at(i);
+
+ VectorDiv(newSpatialSet->at(k), newWeightsSet->at(k));
+ VectorDiv(newRangeSet->at(k), newWeightsSet->at(k));
+
+ for(unsigned int l=0 ; l<classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->at(k);
+ }
+
+ newC = false;
+ }
+ else
+ ++k;
+ }
+
+ if( newC )
+ {
+ newClassSet->push_back( newClassSet->back()+1 );
+ newWeightsSet->push_back( weightsSet->at(i) );
+ newIndexSet->push_back ( indexSet->at(i) );
+ newSpatialSet->push_back( spatialSet->at(i) );
+ newRangeSet->push_back ( rangeSet->at(i) );
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->back();
+ }
+ }
+ }
+
+ classSet->swap ( *newClassSet );
+ weightsSet->swap( *newWeightsSet );
+ indexSet->swap ( *newIndexSet );
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+ classSetMemory->swap ( *newClassSetMemory );
+
+ delete newClassSet;
+ delete newWeightsSet;
+ delete newIndexSet;
+ delete newSpatialSet;
+ delete newRangeSet;
+ delete newClassSetMemory;
+ delete indexes;
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::FinalMerging()
+{
+ unsigned int size = INFINITY;
+ while(size > classSet->size()){
+ IndexSampleSetType* newClassSet
+ = new IndexSampleSetType();
+ newClassSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newWeightsSet
+ = new IndexSampleSetType();
+ newWeightsSet->reserve( indexSet->size() );
+
+ IndexSampleSetType* newIndexSet
+ = new IndexSampleSetType();
+ newIndexSet->reserve ( indexSet->size() );
+
+ SpatialSampleSetType* newSpatialSet
+ = new SpatialSampleSetType();
+
+ newSpatialSet->reserve( indexSet->size() );
+
+ RangeSampleSetType* newRangeSet
+ = new RangeSampleSetType();
+ newRangeSet->reserve ( indexSet->size() );
+
+ IndexSampleSetType* newClassSetMemory
+ = new IndexSampleSetType( *classSetMemory );
+
+ newClassSet->push_back ( 1 );
+ newWeightsSet->push_back( 1 );
+ newIndexSet->push_back ( indexSet->at(0) );
+ newSpatialSet->push_back( spatialSet->at(0) );
+ newRangeSet->push_back ( rangeSet->at(0) );
+
+ unsigned int k;
+ bool newC;
+ bool raNorm;
+
+ for(unsigned int i=1 ; i<classSet->size() ; ++i)
+ {
+ newC = true;
+ k=0;
+
+ while( (k<newClassSet->size()) && newC )
+ {
+ InfiniteNorm( raNorm, newRangeSet->at(k), rangeSet->at(i) );
+ if( raNorm ){
+
+ ReaderPointer reader = ReaderType::New();
+ ImagePointer image = ImageType::New();
+
+ reader->SetFileName( *stmsParams->images.begin() );
+ reader->Update();
+ image = reader->GetOutput();
+ image->FillBuffer( 0 );
+
+ ImageIndexSetType* refClass = new ImageIndexSetType();
+ ImageIndexSetType* candClass = new ImageIndexSetType();
+ refClass->reserve( classSet->size()/2 );
+ candClass->reserve( classSet->size()/2 );
+
+
+ for(unsigned int m=0 ; m<newClassSetMemory->size() ; ++m)
+ {
+ ImageIndexType idx;
+ if(newClassSetMemory->at(m) == classSet->at(i)){
+
+ #pragma omp simd
+ for(unsigned int n=0 ; n<stmsParams->dim ; ++n)
+ idx[n] = spatialSetMemory->at(m)[n]*stmsParams->spScales[n];
+
+ candClass->push_back( idx );
+ image->SetPixel(candClass->back(), 1);
+ }
+ else
+ {
+ if(newClassSetMemory->at(m) == newClassSet->at(k)){
+
+ #pragma omp simd
+ for(unsigned int n=0 ; n<stmsParams->dim ; ++n)
+ idx[n] = spatialSetMemory->at(m)[n]*stmsParams->spScales[n];
+
+ refClass->push_back( idx );
+ image->SetPixel(refClass->back(), 2);
+ }
+ }
+ }
+
+ bool connex = false;
+ if(stmsParams->dim == 2)
+ {
+ if(refClass->size() < candClass->size())
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<refClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ idx[0] = refClass->at(m)[0]+x;
+ idx[1] = refClass->at(m)[1]+y;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0)
+ {
+ if(image->GetPixel(idx) == 2)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+ else
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<candClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ idx[0] = candClass->at(m)[0]+x;
+ idx[1] = candClass->at(m)[1]+y;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0)
+ {
+ if(image->GetPixel(idx) == 1)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+
+ }
+ else
+ {
+ if(refClass->size() < candClass->size())
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<refClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ for(int z=-1 ; z<=1 ; ++z)
+ {
+ idx[0] = refClass->at(m)[0]+x;
+ idx[1] = refClass->at(m)[1]+y;
+ idx[2] = refClass->at(m)[2]+z;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0 && idx[2]<image->GetBufferedRegion().GetSize()[2] && idx[2]>0)
+ {
+ if(image->GetPixel(idx) == 2)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ z = 2;
+ }
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+ else
+ {
+ unsigned int m=0;
+ ImageIndexType idx;
+ while((m<candClass->size()) && !connex)
+ {
+ for(int x=-1 ; x<=1 ; ++x)
+ {
+ for(int y=-1 ; y<=1 ; ++y)
+ {
+ for(int z=-1 ; z<=1 ; ++z)
+ {
+ idx[0] = candClass->at(m)[0]+x;
+ idx[1] = candClass->at(m)[1]+y;
+ idx[2] = candClass->at(m)[2]+z;
+
+ if(idx[0]<image->GetBufferedRegion().GetSize()[0] && idx[0]>0 && idx[1]<image->GetBufferedRegion().GetSize()[1] && idx[1]>0 && idx[2]<image->GetBufferedRegion().GetSize()[2] && idx[2]>0)
+ {
+ if(image->GetPixel(idx) == 1)
+ {
+ connex = true;
+ x = 2;
+ y = 2;
+ z = 2;
+ }
+ }
+ }
+ }
+ }
+
+ ++m;
+ }
+ }
+ }
+
+ if( connex )
+ {
+
+ VectorWeightedAcc( newSpatialSet->at(k), newWeightsSet->at(k), spatialSet->at(i), weightsSet->at(i) );
+ VectorWeightedAcc( newRangeSet->at(k) , newWeightsSet->at(k), rangeSet->at(i) , weightsSet->at(i) );
+
+ newWeightsSet->at(k) += weightsSet->at(i);
+
+ VectorDiv(newSpatialSet->at(k), newWeightsSet->at(k));
+ VectorDiv(newRangeSet->at(k), newWeightsSet->at(k));
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->at(k);
+ }
+
+ newC = false;
+ }
+ else
+ ++k;
+
+ delete refClass;
+ delete candClass;
+ }
+ else
+ ++k;
+ }
+
+ if( newC )
+ {
+ newClassSet->push_back( newClassSet->back()+1 );
+ newWeightsSet->push_back( weightsSet->at(i) );
+ newIndexSet->push_back ( indexSet->at(i) );
+ newSpatialSet->push_back( spatialSet->at(i) );
+ newRangeSet->push_back ( rangeSet->at(i) );
+
+ for(unsigned int l=0 ; l< classSetMemory->size() ; ++l)
+ {
+ if(classSetMemory->at(l) == classSet->at(i))
+ newClassSetMemory->at(l) = newClassSet->back();
+ }
+ }
+ }
+
+ size = classSet->size();
+
+ classSet->swap ( *newClassSet );
+ weightsSet->swap( *newWeightsSet );
+ indexSet->swap ( *newIndexSet );
+ spatialSet->swap( *newSpatialSet );
+ rangeSet->swap ( *newRangeSet );
+ classSetMemory->swap ( *newClassSetMemory );
+
+ delete newClassSet;
+ delete newWeightsSet;
+ delete newIndexSet;
+ delete newSpatialSet;
+ delete newRangeSet;
+ delete newClassSetMemory;
+ }
+}
+
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorDistance(float &dist, std::vector<T> &a, std::vector<T> &b)
+{
+ dist = 0.0;
+
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ dist += ( a[i]-b[i] )*( a[i]-b[i] );
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::InfiniteNorm(bool &dist, RangeVectorType &a, RangeVectorType &b)
+{
+ dist = true;
+
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ {
+ if(((a[i]-b[i])*(a[i]-b[i])) > 1)
+ {
+ dist = false;
+ i = a.size();
+ }
+ }
+}
+
+
+template < class IndexType, class SpatialType, class PixelType, class ImageType >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::MergeInfiniteNorm(bool &dist, RangeVectorType &a, RangeVectorType &b)
+{
+ dist = true;
+
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ {
+ if(((a[i]-b[i])*(a[i]-b[i])) > (1/mergeFactor))
+ {
+ dist = false;
+ i = a.size();
+ }
+ }
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorAcc(std::vector<T> &a, std::vector<T> &b)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] += b[i];
+}
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorWeightedAcc(std::vector<T> &a, std::vector<T> &b, unsigned int &b_w)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] += b_w*b[i];
+}
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorWeightedAcc(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i){
+ a[i] *= a_w;
+ a[i] += b_w*b[i];
+ }
+}
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorWeightedMean(std::vector<T> &a, unsigned int &a_w, std::vector<T> &b, unsigned int &b_w)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] = ( (a[i]*a_w )+(b[i]*b_w) )/( a_w+b_w );
+
+ a_w += b_w;
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorMul(std::vector<T> &a, unsigned int &coeff)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] *= coeff;
+}
+
+
+template< class IndexType, class SpatialType, class PixelType, class ImageType >
+template< class T >
+void
+itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType >
+::VectorDiv(std::vector<T> &a, unsigned int &coeff)
+{
+ #pragma omp simd
+ for(unsigned int i=0 ; i<a.size() ; ++i)
+ a[i] /= coeff;
+}
+
+} // end of namespace itkSTMS
+
+#endif // itkmsSTMS_BlurringSTMS_Spine_TXX
--- /dev/null
+
+CeCILL-C FREE SOFTWARE LICENSE AGREEMENT
+
+
+ Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+
+The authors of the CeCILL-C (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+INRIA, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, Rocquencourt, BP
+105, 78153 Le Chesnay cedex, France.
+
+
+ Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and re-use the software governed by this license.
+
+The exercising of this right is conditional upon the obligation to make
+available to the community the modifications made to the source code of
+the software so as to contribute to its evolution.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+
+ Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+Agreement: means this license agreement, and its possible subsequent
+versions and annexes.
+
+Software: means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+Initial Software: means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+Modified Software: means the Software modified by at least one
+Integrated Contribution.
+
+Source Code: means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+Object Code: means the binary files originating from the compilation of
+the Source Code.
+
+Holder: means the holder(s) of the economic rights over the Initial
+Software.
+
+Licensee: means the Software user(s) having accepted the Agreement.
+
+Contributor: means a Licensee having made at least one Integrated
+Contribution.
+
+Licensor: means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+Integrated Contribution: means any or all modifications, corrections,
+translations, adaptations and/or new functions integrated into the
+Source Code by any or all Contributors.
+
+Related Module: means a set of sources files including their
+documentation that, without modification to the Source Code, enables
+supplementary functions or services in addition to those offered by the
+Software.
+
+Derivative Software: means any combination of the Software, modified or
+not, and of a Related Module.
+
+Parties: mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+ Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software.
+
+
+ Article 3 - ACCEPTANCE
+
+3.1 The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+
+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+
+ Article 4 - EFFECTIVE DATE AND TERM
+
+
+ 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+
+ 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+ Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+ 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+
+
+ 5.2 RIGHT OF MODIFICATION
+
+The right of modification includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software. It includes, in particular, the
+right to create a Derivative Software.
+
+The Licensee is authorized to make any or all modification to the
+Software provided that it includes an explicit notice that it is the
+author of said modification and indicates the date of the creation thereof.
+
+
+ 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows effective access to the full Source
+Code of the Software at a minimum during the entire period of its
+distribution of the Software, it being understood that the additional
+cost of acquiring the Source Code shall not exceed the cost of
+transferring the data.
+
+
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes an Integrated Contribution to the Software, the
+terms and conditions for the distribution of the resulting Modified
+Software become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows effective access to the
+full source code of the Modified Software at a minimum during the entire
+period of its distribution of the Modified Software, it being understood
+that the additional cost of acquiring the source code shall not exceed
+the cost of transferring the data.
+
+
+ 5.3.3 DISTRIBUTION OF DERIVATIVE SOFTWARE
+
+When the Licensee creates Derivative Software, this Derivative Software
+may be distributed under a license agreement other than this Agreement,
+subject to compliance with the requirement to include a notice
+concerning the rights over the Software as defined in Article 6.4.
+In the event the creation of the Derivative Software required modification
+of the Source Code, the Licensee undertakes that:
+
+ 1. the resulting Modified Software will be governed by this Agreement,
+ 2. the Integrated Contributions in the resulting Modified Software
+ will be clearly identified and documented,
+ 3. the Licensee will allow effective access to the source code of the
+ Modified Software, at a minimum during the entire period of
+ distribution of the Derivative Software, such that such
+ modifications may be carried over in a subsequent version of the
+ Software; it being understood that the additional cost of
+ purchasing the source code of the Modified Software shall not
+ exceed the cost of transferring the data.
+
+
+ 5.3.4 COMPATIBILITY WITH THE CeCILL LICENSE
+
+When a Modified Software contains an Integrated Contribution subject to
+the CeCILL license agreement, or when a Derivative Software contains a
+Related Module subject to the CeCILL license agreement, the provisions
+set forth in the third item of Article 6.4 are optional.
+
+
+ Article 6 - INTELLECTUAL PROPERTY
+
+
+ 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+ 6.2 OVER THE INTEGRATED CONTRIBUTIONS
+
+The Licensee who develops an Integrated Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ 6.3 OVER THE RELATED MODULES
+
+The Licensee who develops a Related Module is the owner of the
+intellectual property rights over this Related Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution under the conditions defined in Article 5.3.3.
+
+
+ 6.4 NOTICE OF RIGHTS
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not;
+
+ 3. to ensure that use of the Software, its intellectual property
+ notices and the fact that it is governed by the Agreement is
+ indicated in a text that is easily accessible, specifically from
+ the interface of any Derivative Software.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-à-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+ Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+ Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+ Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+ Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+ Article 11 - MISCELLANEOUS
+
+
+ 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+ 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version.
+
+
+ Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+Version 1.0 dated 2006-09-05.
--- /dev/null
+
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+Version 2.1 dated 2013-06-21
+
+
+ Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to users,
+ * secondly, the election of a governing law, French law, with which it
+ is conformant, both as regards the law of torts and intellectual
+ property law, and the protection that it offers to both authors and
+ holders of the economic rights over software.
+
+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
+public scientific, technical and industrial research establishment,
+having its principal place of business at 25 rue Leblanc, immeuble Le
+Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+Inria, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, Rocquencourt, BP
+105, 78153 Le Chesnay cedex, France.
+
+
+ Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
+
+The exercising of this right is conditional upon certain obligations for
+users so as to preserve this status for all subsequent redistributions.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+Frequently asked questions can be found on the official website of the
+CeCILL licenses family (http://www.cecill.info/index.en.html) for any
+necessary clarification.
+
+
+ Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+Agreement: means this license agreement, and its possible subsequent
+versions and annexes.
+
+Software: means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+Initial Software: means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+Modified Software: means the Software modified by at least one
+Contribution.
+
+Source Code: means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+Object Code: means the binary files originating from the compilation of
+the Source Code.
+
+Holder: means the holder(s) of the economic rights over the Initial
+Software.
+
+Licensee: means the Software user(s) having accepted the Agreement.
+
+Contributor: means a Licensee having made at least one Contribution.
+
+Licensor: means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+Contribution: means any or all modifications, corrections, translations,
+adaptations and/or new functions integrated into the Software by any or
+all Contributors, as well as any or all Internal Modules.
+
+Module: means a set of sources files including their documentation that
+enables supplementary functions or services in addition to those offered
+by the Software.
+
+External Module: means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+Internal Module: means any or all Module, connected to the Software so
+that they both execute in the same address space.
+
+GNU GPL: means the GNU General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+GNU Affero GPL: means the GNU Affero General Public License version 3 or
+any subsequent version, as published by the Free Software Foundation Inc.
+
+EUPL: means the European Union Public License version 1.1 or any
+subsequent version, as published by the European Commission.
+
+Parties: mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+ Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 <#scope> hereinafter for the whole
+term of the protection granted by the rights over said Software.
+
+
+ Article 3 - ACCEPTANCE
+
+3.1 The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical medium;
+ * (ii) the first time the Licensee exercises any of the rights granted
+ hereunder.
+
+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+<#accepting> hereinabove, and the Licensee hereby acknowledges that it
+has read and understood it.
+
+
+ Article 4 - EFFECTIVE DATE AND TERM
+
+
+ 4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1 <#accepting>.
+
+
+ 4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+ Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+ 5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+
+ 2. loading, displaying, running, or storing the Software on any or all
+ medium.
+
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission or
+ storage operation as regards the Software, that it is entitled to
+ carry out hereunder.
+
+
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+ 5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's warranty
+ and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows effective access to the full Source
+Code of the Software for a period of at least three years from the
+distribution of the Software, it being understood that the additional
+acquisition cost of the Source Code shall not exceed the cost of the
+data transfer.
+
+
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+ 1. a copy of the Agreement,
+
+ 2. a notice relating to the limitation of both the Licensor's warranty
+ and liability as set forth in Articles 8 and 9,
+
+and, in the event that only the object code of the Modified Software is
+redistributed,
+
+ 3. a note stating the conditions of effective access to the full source
+ code of the Modified Software for a period of at least three years
+ from the distribution of the Modified Software, it being understood
+ that the additional acquisition cost of the source code shall not
+ exceed the cost of the data transfer.
+
+
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+
+ 5.3.4 COMPATIBILITY WITH OTHER LICENSES
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
+Modified or unmodified Software, and distribute that entire code under
+the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
+
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the GNU GPL,
+GNU Affero GPL and/or EUPL and distribute that entire code under the
+terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
+
+
+ Article 6 - INTELLECTUAL PROPERTY
+
+
+ 6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2 <#term>.
+
+
+ 6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+ 6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+ 6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+
+ 2. to reproduce said notices, in an identical manner, in the copies of
+ the Software modified or not.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights on the Software of the Holder and/or
+Contributors, and to take, where applicable, vis-à-vis its staff, any
+and all measures required to ensure respect of said intellectual
+property rights of the Holder and/or Contributors.
+
+
+ Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+ Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+ Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5 <#scope>).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 <#good-faith> and, in particular,
+without any warranty as to its commercial value, its secured, safe,
+innovative or relevant nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+expertise for its defense. Such technical and legal expertise shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+ Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+ Article 11 - MISCELLANEOUS
+
+
+ 11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+ 11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4
+<#compatibility>.
+
+
+ Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
--- /dev/null
+# cmake_minimum_required(VERSION 2.4)
+# SET(CMAKE_BUILD_TYPE Debug)
+#SET(CMAKE_BUILD_TYPE Release)
+
+# if(COMMAND CMAKE_POLICY)
+ # cmake_policy(SET CMP0003 NEW)
+# endif()
+
+# project(STMS)
+# include_regular_expression("^.*$")
+
+# find_package(ITK REQUIRED)
+# include(${ITK_USE_FILE})
+
+#add_executable(test_parseXML test_parseXML.cxx )
+#target_link_libraries(test_parseXML ${ITK_LIBRARIES})
+
+#add_executable(test_ArgumentsAnalysis test_ArgumentsAnalysis.cxx )
+#target_link_libraries(test_ArgumentsAnalysis ${ITK_LIBRARIES})
+
+#add_executable(test_ArgumentsAnalysis_Spine test_ArgumentsAnalysis_Spine.cxx )
+#target_link_libraries(test_ArgumentsAnalysis_Spine ${ITK_LIBRARIES})
+
+add_executable(STMS_GrayLevelFiltering STMS_GrayLevelFiltering.cxx)
+target_link_libraries(STMS_GrayLevelFiltering ${ITK_LIBRARIES})
+
+#add_executable(STMS_GrayLevelFiltering_Spine STMS_GrayLevelFiltering_Spine.cxx )
+#target_link_libraries(STMS_GrayLevelFiltering_Spine ${ITK_LIBRARIES})
+
--- /dev/null
+/*
+ #
+ # File : STMS_GrayLevelFiltering.cxx
+ # ( C++ example file - STMS )
+ #
+ # Description : STMS lib that implements the STMS filter and clustering.
+ # This file is a part of the STMS Library project.
+ # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
+ #
+ # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
+ # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
+ # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
+ #
+ # Copyright : Thomas GRENIER - Simon MURE
+ # ( https://www.creatis.insa-lyon.fr/~grenier/ )
+ #
+ # License : CeCILL V2.1
+ # ( http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.txt)
+ #
+ # This software is governed by the CeCILL license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # "http://www.cecill.info".
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # In this respect, the user's attention is drawn to the risks associated
+ # with loading, using, modifying and/or developing or reproducing the
+ # software by the user in light of its specific status of free software,
+ # that may mean that it is complicated to manipulate, and that also
+ # therefore means that it is reserved for developers and experienced
+ # professionals having in-depth computer knowledge. Users are therefore
+ # encouraged to load and test the software's suitability as regards their
+ # requirements in conditions enabling the security of their systems and/or
+ # data to be ensured and, more generally, to use and operate it in the
+ # same conditions as regards security.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL license and that you accept its terms.
+ #
+*/
+/* Please don't forget to cite our work :
+ @article {MURE-15a,
+ title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
+ journal = {Pattern Recognition Letters},
+ volume = {68, Part 1},
+ year = {2015},
+ pages = {48 - 55},
+ issn = {0167-8655},
+ doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
+ url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
+ author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
+}
+*/
+#include <iomanip>
+#include <ctime>
+
+#define STMS_NUMBERING_FORM_ONE "01"
+
+#include "itkImage.h"
+#include "itkSTMS_ArgumentsAnalysis.h"
+#include "itkSTMS_ImageSequenceToTemporalSet.h"
+#include "itkSTMS_TemporalSetToImageSequence.h"
+#include "itkSTMS_BlurringSTMS.h"
+
+#include <array>
+
+
+
+typedef float PixelType;
+
+double gettime_hp()
+{
+ struct timespec timestamp;
+
+ clock_gettime(CLOCK_REALTIME, ×tamp);
+ return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
+}
+
+// Only --expDescription and numTimePoints parameter are compulsory.
+
+//--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/P43_Parser.xml --imageDimension 2 --xScale 20 --yScale 20 --rScale 1 --epsilon 0.1 --maxIt 20 --numTimePoints 25 --merge
+
+//--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/L43_3_Parser.xml --imageDimension 3 --xScale 1000 --yScale 1000 --zScale 1000 --rScale 0.75 --epsilon 0.1 --maxIt 50 --numTimePoints 25 --merge
+//--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/Simu_Parser.xml --imageDimension 2 --xScale 255 --yScale 255 --rScale 0.4 --epsilon 0.01 --maxIt 50 --numTimePoints 8
+//--expDescription /run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/itkSTMS/Data/G1_Parser.xml --imageDimension 3 --xScale 1000 --yScale 1000 --zScale 1000 --rScale 0.15 --epsilon 0.01 --maxIt 50 --numTimePoints 8
+
+// --expDescription E:/Documents/Creatis/Projets/15_MUST/Data_Cardiac/Parser_AIF_Cardiac.xml --imageDimension 2 --xScale 10 --yScale 10 --rScale 10 --numTimePoints 80
+
+int main(int argc, char **argv){
+ double dtime;
+
+ std::cout << "The Numbering form is set to numbers like = " << STMS_NUMBERING_FORM_ONE << std::endl;
+ std::cout << "size : " << sizeof(STMS_NUMBERING_FORM_ONE) << std::endl;
+
+
+ itkSTMS::itkSTMS_ArgumentsAnalysis* argsAnalysis
+ = new itkSTMS::itkSTMS_ArgumentsAnalysis(argc, argv);
+ argsAnalysis->Update();
+
+ itkSTMS::ParamsAnalysisOutputType* params
+ = argsAnalysis->GetSTMSParams();
+
+
+ switch(params->dim){
+ case 2:
+ {
+ typedef itk::Image< PixelType, 2 > ImageType2D;
+ typedef itk::Image< unsigned char, 2 > MaskImageType2D;
+
+
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexType IndexType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialType SpatialType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexSampleSetType IndexSampleSetType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialSampleSetType SpatialSampleSetType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::RangeSampleSetType RangeSampleSetType;
+
+ typedef itk::Image< IndexType, 2 > ClassImageType2D;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >* preProcess
+ = new itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D > ( params );
+ preProcess->GenerateDataSets();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
+
+ IndexSampleSetType* indexSet = preProcess->GetIndexSet();
+ IndexSampleSetType* classSet = preProcess->GetClassSet();
+ IndexSampleSetType* weightsSet = preProcess->GetWeightsSet();
+ SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
+ RangeSampleSetType* rangeSet = preProcess->GetRangeSet();
+
+
+ dtime=gettime_hp();
+
+ itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >* stmsFilter
+ = new itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >
+ (indexSet, classSet, weightsSet, spatialSet, rangeSet, params, preProcess->GetExperimentDescription());
+
+ stmsFilter->GenerateData();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >* postProcess
+ = new itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >(stmsFilter->GetClassMemory(),
+ stmsFilter->GetSpatialMemory(),
+ stmsFilter->GetRangeSet(),
+ params,
+ preProcess->GetExperimentDescription());
+
+ postProcess->GenerateImageSequence();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
+
+ delete argsAnalysis;
+ delete preProcess;
+ delete stmsFilter;
+ delete postProcess;
+ break;
+ }
+
+ case 3:
+ {
+ typedef itk::Image< PixelType, 3 > ImageType3D;
+ typedef itk::Image< unsigned char, 3 > MaskImageType3D;
+
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexType IndexType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialType SpatialType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexSampleSetType IndexSampleSetType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialSampleSetType SpatialSampleSetType;
+ typedef itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::RangeSampleSetType RangeSampleSetType;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >* preProcess
+ = new itkSTMS::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D > ( params );
+ preProcess->GenerateDataSets();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
+
+ IndexSampleSetType* indexSet = preProcess->GetIndexSet();
+ IndexSampleSetType* classSet = preProcess->GetClassSet();
+ IndexSampleSetType* weightsSet = preProcess->GetWeightsSet();
+ SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
+ RangeSampleSetType* rangeSet = preProcess->GetRangeSet();
+
+
+
+
+ dtime=gettime_hp();
+
+ itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >* stmsFilter
+ = new itkSTMS::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >
+ (indexSet, classSet, weightsSet, spatialSet, rangeSet, params, preProcess->GetExperimentDescription());
+
+ stmsFilter->GenerateData();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >* postProcess
+ = new itkSTMS::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >(stmsFilter->GetClassMemory(),
+ stmsFilter->GetSpatialMemory(),
+ stmsFilter->GetRangeSet(),
+ params,
+ preProcess->GetExperimentDescription());
+
+ postProcess->GenerateImageSequence();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
+
+
+ delete argsAnalysis;
+ delete preProcess;
+ delete stmsFilter;
+ delete postProcess;
+ break;
+ }
+
+ default:
+ {
+ delete argsAnalysis;
+
+ std::cout << std::endl << "Image dimensionality should be equal to 2 or 3.";
+ std::exit( EXIT_FAILURE );
+ break;
+ }
+ }
+
+ return EXIT_SUCCESS;
+}
--- /dev/null
+#include <iomanip>
+#include <ctime>
+#include "itkImage.h"
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+#include "itkSTMS_ImageSequenceToTemporalSet_Spine.h"
+#include "itkSTMS_TemporalSetToImageSequence_Spine.h"
+#include "itkSTMS_BlurringSTMS_Spine.h"
+
+
+typedef float PixelType;
+
+double gettime_hp()
+{
+ struct timespec timestamp;
+
+ clock_gettime(CLOCK_REALTIME, ×tamp);
+ return timestamp.tv_sec * 1000.0 + timestamp.tv_nsec * 1.0e-6;
+}
+
+// Only --expDescription and --outFolder parameters are compulsory.
+/* --image ../../itkSTMS/Data/Images/Simu/Simu1.nii --image ../../itkSTMS/Data/Images/Simu/Simu2.nii --image ../../itkSTMS/Data/Images/Simu/Simu3.nii
+--image ../../itkSTMS/Data/Images/Simu/Simu4.nii --image ../../itkSTMS/Data/Images/Simu/Simu5.nii --image ../../itkSTMS/Data/Images/Simu/Simu6.nii
+--image ../../itkSTMS/Data/Images/Simu/Simu7.nii --image ../../itkSTMS/Data/Images/Simu/Simu8.nii --outFolder ../../itkSTMS/Data/Images/Simu_Outputs-Spine/
+--imageDimension 2 --xScale 1000 --yScale 1000 --rScale 0.5 --mask ../../itkSTMS/Data/Images/Simu/Mask.nii --imageExtension .nii
+
+--image ../../itkSTMS/Data/Images/Simu/Simu1.nii --image ../../itkSTMS/Data/Images/Simu/Simu2.nii --image ../../itkSTMS/Data/Images/Simu/Simu3.nii
+--image ../../itkSTMS/Data/Images/Simu/Simu4.nii --image ../../itkSTMS/Data/Images/Simu/Simu5.nii --image ../../itkSTMS/Data/Images/Simu/Simu6.nii
+--image ../../itkSTMS/Data/Images/Simu/Simu7.nii --image ../../itkSTMS/Data/Images/Simu/Simu8.nii --outFolder ../../itkSTMS/Data/Images/Simu_Outputs-Spine/
+--imageDimension 2 --xScale 1000 --yScale 1000 --rScale 0.5 --imageExtension .nii
+*/
+int main(int argc, char **argv){
+ double dtime;
+
+ itkSTMS_Spine::itkSTMS_ArgumentsAnalysis* argsAnalysis
+ = new itkSTMS_Spine::itkSTMS_ArgumentsAnalysis(argc, argv);
+ argsAnalysis->Update();
+
+ itkSTMS_Spine::ParamsAnalysisOutputType* params
+ = argsAnalysis->GetSTMSParams();
+
+
+ switch(params->dim){
+ case 2:
+ {
+ typedef itk::Image< PixelType, 2 > ImageType2D;
+ typedef itk::Image< unsigned int, 2 > MaskImageType2D;
+
+
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexType IndexType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialType SpatialType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::IndexSampleSetType IndexSampleSetType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::SpatialSampleSetType SpatialSampleSetType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >::RangeSampleSetType RangeSampleSetType;
+
+ typedef itk::Image< IndexType, 2 > ClassImageType2D;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D >* preProcess
+ = new itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType2D, MaskImageType2D > ( params );
+ preProcess->GenerateDataSets();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
+
+ IndexSampleSetType* indexSet = preProcess->GetIndexSet();
+ IndexSampleSetType* classSet = preProcess->GetClassSet();
+ IndexSampleSetType* weightsSet = preProcess->GetWeightsSet();
+ SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
+ RangeSampleSetType* rangeSet = preProcess->GetRangeSet();
+
+
+ dtime=gettime_hp();
+
+ itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >* stmsFilter
+ = new itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType2D >
+ (indexSet, classSet, weightsSet, spatialSet, rangeSet, params );
+
+ stmsFilter->GenerateData();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
+
+
+
+ dtime=gettime_hp();
+
+ itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >* postProcess
+ = new itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType2D, ClassImageType2D >(stmsFilter->GetClassMemory(),
+ stmsFilter->GetSpatialMemory(),
+ stmsFilter->GetRangeSet(),
+ params );
+
+ postProcess->GenerateImageSequence();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
+
+ delete argsAnalysis;
+ delete preProcess;
+ delete stmsFilter;
+ delete postProcess;
+ break;
+ }
+
+ case 3:
+ {
+ typedef itk::Image< PixelType, 3 > ImageType3D;
+ typedef itk::Image< unsigned int, 3 > MaskImageType3D;
+
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexType IndexType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialType SpatialType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::IndexSampleSetType IndexSampleSetType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::SpatialSampleSetType SpatialSampleSetType;
+ typedef itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >::RangeSampleSetType RangeSampleSetType;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D >* preProcess
+ = new itkSTMS_Spine::itkSTMS_ImageSequenceToTemporalSet< ImageType3D, MaskImageType3D > ( params );
+ preProcess->GenerateDataSets();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Characteristics extraction: " << dtime/1000 << " s" <<std::endl;
+
+ IndexSampleSetType* indexSet = preProcess->GetIndexSet();
+ IndexSampleSetType* classSet = preProcess->GetClassSet();
+ IndexSampleSetType* weightsSet = preProcess->GetWeightsSet();
+ SpatialSampleSetType* spatialSet = preProcess->GetSpatialSet();
+ RangeSampleSetType* rangeSet = preProcess->GetRangeSet();
+
+
+
+
+ dtime=gettime_hp();
+
+ itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >* stmsFilter
+ = new itkSTMS_Spine::itkSTMS_BlurringSTMS< IndexType, SpatialType, PixelType, ImageType3D >
+ (indexSet, classSet, weightsSet, spatialSet, rangeSet, params );
+
+ stmsFilter->GenerateData();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "STMS filtering: " << dtime/1000 << " s" <<std::endl;
+
+
+ dtime=gettime_hp();
+
+ itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >* postProcess
+ = new itkSTMS_Spine::itkSTMS_TemporalSetToImageSequence< ImageType3D, MaskImageType3D >(stmsFilter->GetClassMemory(),
+ stmsFilter->GetSpatialMemory(),
+ stmsFilter->GetRangeSet(),
+ params );
+
+ postProcess->GenerateImageSequence();
+
+ dtime = gettime_hp()-dtime;
+ std::cout<<std::endl<< std::setw(30) << std::left << "Image sequence saving: " << dtime/1000 << " s" <<std::endl;
+
+
+ delete argsAnalysis;
+ delete preProcess;
+ delete stmsFilter;
+ delete postProcess;
+ break;
+ }
+
+ default:
+ {
+ delete argsAnalysis;
+
+ std::cout << std::endl << "Image dimensionality should be equal to 2 or 3.";
+ std::exit( EXIT_FAILURE );
+ break;
+ }
+ }
+
+ return EXIT_SUCCESS;
+}
--- /dev/null
+#include <string>
+#include "itkSTMS_ArgumentsAnalysis.h"
+
+//--expDescription ../xmlFile.xml --xScale 10 --yScale 10 --zScale 10 --rScale 1.0 --epsilon 0.1 --maxIt 50
+// Only --expDescription parameter is compulsory.
+
+int main(int argc, char **argv)
+{
+ itkSTMS::itkSTMS_ArgumentsAnalysis* argsAnalysis = new itkSTMS::itkSTMS_ArgumentsAnalysis(argc, argv);
+ argsAnalysis->Update();
+
+ itkSTMS::ParamsAnalysisOutputType* params = argsAnalysis->GetSTMSParams();
+
+
+ std::cout << params->expDescription << std::endl;
+ std::cout << params->xScale << std::endl;
+ std::cout << params->yScale << std::endl;
+ std::cout << params->zScale << std::endl;
+ std::cout << params->rScale << std::endl;
+ std::cout << params->epsilon << std::endl;
+ std::cout << params->maxIt << std::endl;
+
+
+ delete argsAnalysis;
+ return EXIT_SUCCESS;
+}
--- /dev/null
+#include <string>
+#include "itkSTMS_ArgumentsAnalysis_Spine.h"
+
+
+// --image image1.nii --xScale 15.2 --image image2.nii --yScale 16.3 --zScale 17.4 --rScale 10.6 --mask mask.nii --image image3.nii --outFolder outFolder/ --epsilon 0.1 --imageDimension 2 --maxIt 20
+int main(int argc, char **argv)
+{
+ itkSTMS::itkSTMS_ArgumentsAnalysis* argsAnalysis = new itkSTMS::itkSTMS_ArgumentsAnalysis(argc, argv);
+ argsAnalysis->Update();
+
+ itkSTMS::ParamsAnalysisOutputType* params = argsAnalysis->GetSTMSParams();
+
+
+ std::cout << "images:"<<std::endl;
+
+ for (std::list<std::string>::iterator it = params->images.begin(); it != params->images.end(); ++it)
+ {
+ std::cout<< *it << std::endl;
+ }
+
+ std::cout << std::endl << "x :"<< params->spScales[0] << std::endl<< std::endl;
+ std::cout << std::endl << "y :"<< params->spScales[1] << std::endl<< std::endl;
+ std::cout << std::endl << "z :"<< params->spScales[2] << std::endl<< std::endl;
+ std::cout << std::endl << "r :"<< params->rScale << std::endl<< std::endl;
+ std::cout << std::endl << "mask :"<< params->mask << std::endl<< std::endl;
+ std::cout << std::endl << "outFolder :"<< params->outFolder << std::endl<< std::endl;
+ std::cout << std::endl << "ntp :"<< params->numTimePoints << std::endl<< std::endl;
+ std::cout << std::endl << "eps :"<< params->epsilon << std::endl<< std::endl;
+ std::cout << std::endl << "imDim :"<< params->dim << std::endl<< std::endl;
+ std::cout << std::endl << "maxIt :"<< params->maxIt << std::endl<< std::endl;
+ std::cout << std::endl << "merge :"<< params->merge << std::endl<< std::endl;
+
+ std::cout << std::endl << "1st element:"<< *params->images.begin()<< std::endl<< std::endl;
+
+ delete argsAnalysis;
+ return EXIT_SUCCESS;
+}
--- /dev/null
+//#include <string>
+//#include "itkDOMNodeXMLReader.h"
+//#include "itkFancyString.h"
+
+#include <string>
+#include "itkSTMS_XMLFileParser.h"
+
+int main(int argc, char **argv)
+{
+ std::string fileName = "/run/media/mure/HDD/Recherche/These/CVS/Mure/Dev/Cpp/STMS/Data/G1_Parser.xml";
+
+ itkSTMS::itkSTMS_XMLFileParser* parser = new itkSTMS::itkSTMS_XMLFileParser();
+ parser->SetFileName( fileName );
+ parser->Update();
+
+ itkSTMS::ParserOutputType* expDescritpion = parser->GetXMLParams();
+
+ std::cout << expDescritpion->experimentPath <<std::endl;
+
+
+
+ delete parser;
+ return EXIT_SUCCESS;
+}
git://git.creatis.insa-lyon.fr / STMS.git / commitdiff