3 # File : itkSTMS_ImageSequenceToTemporalSet.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_ImageSequenceToTemporalSet_h
61 #define itkSTMS_ImageSequenceToTemporalSet_h
68 #include "itkSTMS_XMLFileParser.h"
69 #include "itkSTMS_ArgumentsAnalysis.h"
70 #include "itkImageFileReader.h"
71 #include "itkImageRegionConstIteratorWithIndex.h"
72 #include "itkMinimumMaximumImageCalculator.h"
74 #ifndef STMS_NUMBERING_FORM_ONE
75 #define STMS_NUMBERING_FORM_ONE "1"
80 template < class ImageType, class MaskImageType >
81 class itkSTMS_ImageSequenceToTemporalSet
86 typedef itk::ImageFileReader< ImageType > ReaderType;
87 typedef typename ReaderType::Pointer ReaderPointer;
88 typedef itk::ImageFileReader< MaskImageType > MaskReaderType;
89 typedef typename MaskReaderType::Pointer MaskReaderPointer;
91 // Mask processing typedefs
92 typedef itk::MinimumMaximumImageCalculator< MaskImageType >
94 typedef typename MinMaxCalculatorType::Pointer MinMaxCalculatorPointer;
97 typedef itk::ImageRegionConstIteratorWithIndex< ImageType > IteratorType;
98 typedef itk::ImageRegionConstIteratorWithIndex< MaskImageType > MaskIteratorType;
100 // Sample set typedefs
101 typedef unsigned int IndexType;
102 typedef float SpatialType;
103 typedef typename ImageType::PixelType PixelType;
105 typedef typename ImageType::Pointer ImagePointer;
106 typedef typename ImageType::ConstPointer ImageConstPointer;
107 typedef typename ImageType::SizeType SizeType;
109 typedef std::vector< SpatialType > SpatialVectorType;
110 typedef std::vector< PixelType > RangeVectorType;
112 typedef std::vector< IndexType > IndexSampleSetType;
113 typedef std::vector< SpatialVectorType > SpatialSampleSetType;
114 typedef std::vector< RangeVectorType > RangeSampleSetType;
116 // Mask image typedefs
117 typedef typename MaskImageType::PixelType MaskPixelType;
118 typedef typename MaskImageType::Pointer MaskImagePointer;
119 typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
122 itkSTMS_ImageSequenceToTemporalSet( itkSTMS::ParamsAnalysisOutputType* stmsParameters );
123 inline ~itkSTMS_ImageSequenceToTemporalSet(){ delete xmlParser; }
125 void GenerateDataSets();
127 inline IndexSampleSetType* GetIndexSet (){ return &indexSet; }
128 inline IndexSampleSetType* GetClassSet (){ return &classSet; }
129 inline IndexSampleSetType* GetMergingSet(){ return &mergingSet; }
130 inline IndexSampleSetType* GetWeightsSet(){ return &weightsSet; }
131 inline SpatialSampleSetType* GetSpatialSet(){ return &spatialSet; }
132 inline RangeSampleSetType* GetRangeSet (){ return &rangeSet; }
134 inline itkSTMS::ParserOutputType* GetExperimentDescription(){ return expDescription; }
138 itkSTMS::itkSTMS_XMLFileParser* xmlParser;
139 itkSTMS::ParserOutputType* expDescription;
140 itkSTMS::ParamsAnalysisOutputType* stmsParameters;
142 IndexSampleSetType indexSet,
146 SpatialSampleSetType spatialSet;
147 RangeSampleSetType rangeSet;
149 MaskPixelType maskValue;
150 MaskImagePointer mask;
151 MaskReaderPointer mReader;
152 MinMaxCalculatorPointer MinMaxCalculator;
153 std::string maskPath;
154 MaskIteratorType mIt;
156 }; // end of class itkSTMS_ImageSequenceToTemporalSet
157 } // end of namespace itkstms
159 #ifndef ITK_MANUAL_INSTANTIATION
160 #include "itkSTMS_ImageSequenceToTemporalSet.txx"