3 # File : itkSTMS_TemporalSetToImageSequence.h
4 # ( C++ header file - STMS )
6 # Description : STMS lib that implements the STMS filter and clustering.
7 # This file is a part of the STMS Library project.
8 # ( https://www.creatis.insa-lyon.fr/site7/fr/realisations )
10 # [1] S. Mure, Grenier, T., Meier, S., Guttmann, R. G., et Benoit-Cattin, H.,
11 # « Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification »,
12 # Pattern Recognition Letters, vol. 68, Part 1, p. 48 - 55, 2015.
14 # Copyright : Thomas GRENIER - Simon MURE
15 # ( https://www.creatis.insa-lyon.fr/~grenier/ )
18 # ( http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt )
20 # This software is governed by the CeCILL license under French law and
21 # abiding by the rules of distribution of free software. You can use,
22 # modify and/ or redistribute the software under the terms of the CeCILL
23 # license as circulated by CEA, CNRS and INRIA at the following URL
24 # "http://www.cecill.info".
26 # As a counterpart to the access to the source code and rights to copy,
27 # modify and redistribute granted by the license, users are provided only
28 # with a limited warranty and the software's author, the holder of the
29 # economic rights, and the successive licensors have only limited
32 # In this respect, the user's attention is drawn to the risks associated
33 # with loading, using, modifying and/or developing or reproducing the
34 # software by the user in light of its specific status of free software,
35 # that may mean that it is complicated to manipulate, and that also
36 # therefore means that it is reserved for developers and experienced
37 # professionals having in-depth computer knowledge. Users are therefore
38 # encouraged to load and test the software's suitability as regards their
39 # requirements in conditions enabling the security of their systems and/or
40 # data to be ensured and, more generally, to use and operate it in the
41 # same conditions as regards security.
43 # The fact that you are presently reading this means that you have had
44 # knowledge of the CeCILL license and that you accept its terms.
47 /* Please don't forget to cite our work :
49 title = {Unsupervised spatio-temporal filtering of image sequences. A mean-shift specification},
50 journal = {Pattern Recognition Letters},
51 volume = {68, Part 1},
55 doi = {http://dx.doi.org/10.1016/j.patrec.2015.07.021},
56 url = {http://www.sciencedirect.com/science/article/pii/S0167865515002305},
57 author = {S. Mure and T Grenier and Meier, S. and Guttmann, R.G. and H. Benoit-Cattin}
60 #ifndef itkSTMS_TemporalSetToImageSequence_h
61 #define itkSTMS_TemporalSetToImageSequence_h
69 #include "itkImageFileReader.h"
70 #include "itkImageFileWriter.h"
71 #include "itkImageRegionIteratorWithIndex.h"
74 #ifndef STMS_NUMBERING_FORM_ONE
75 #define STMS_NUMBERING_FORM_ONE "1"
80 template < class ImageType, class ClassImageType >
81 class itkSTMS_TemporalSetToImageSequence
84 // Reader and writer typedefs
85 typedef itk::ImageFileReader< ImageType > ReaderType;
86 typedef typename ReaderType::Pointer ReaderPointer;
87 typedef itk::ImageFileWriter< ImageType > WriterType;
88 typedef typename WriterType::Pointer WriterPointer;
89 typedef itk::ImageFileWriter< ClassImageType > ClassWriterType;
90 typedef typename ClassWriterType::Pointer ClassWriterPointer;
92 // Sample set typedefs
93 typedef unsigned int IndexType;
94 typedef float SpatialType;
95 typedef typename ImageType::PixelType PixelType;
97 typedef std::vector< SpatialType > SpatialVectorType;
98 typedef std::vector< PixelType > RangeVectorType;
100 typedef std::vector< IndexType > IndexSampleSetType;
101 typedef std::vector< SpatialVectorType > SpatialSampleSetType;
102 typedef std::vector< RangeVectorType > RangeSampleSetType;
105 typedef typename ImageType::IndexType SpatialIndexType;
106 typedef typename ImageType::RegionType RegionType;
108 typedef typename ImageType::Pointer ImagePointer;
109 typedef typename ImageType::ConstPointer ImageConstPointer;
110 typedef typename ImageType::SizeType SizeType;
112 typedef typename ClassImageType::Pointer ClassImagePointer;
113 typedef typename ClassImageType::RegionType ClassRegionType;
117 itkSTMS_TemporalSetToImageSequence( IndexSampleSetType* cl,
118 SpatialSampleSetType* sp,
119 RangeSampleSetType* ra,
120 itkSTMS::ParamsAnalysisOutputType* params,
121 itkSTMS::ParserOutputType* desc );
123 void GenerateImageSequence();
125 //! To generate CSV File from all classes. The file contains the class ID, the number of pixels of this class and then all filtered values along time.
126 //! You can pass a delimiter (ie a record separator) to this function.
127 void GenerateCSVFile(const std::string &delimiter = std::string(", "));
131 itkSTMS::ParserOutputType* expDescription;
132 itkSTMS::ParamsAnalysisOutputType* stmsParameters;
134 IndexSampleSetType* classSet;
135 SpatialSampleSetType* spatialSet;
136 RangeSampleSetType* rangeSet;
138 }; // end of class itkSTMS_TemporalSetToImageSequence
139 } // end of namespace itkstms
141 #ifndef ITK_MANUAL_INSTANTIATION
142 #include "itkSTMS_TemporalSetToImageSequence.txx"