1 | %'find_file_series': check the content of an input file and find the corresponding file series |
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2 | %-------------------------------------------------------------------------- |
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3 | % function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml) |
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4 | % |
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5 | % OUTPUT: |
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6 | % RootPath: path to the dir containing the input file |
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7 | % SubDir: data dir containing the input file series |
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8 | % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file) |
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9 | % i1_series(pair,ref_j+1, ref_i+1),i2_series,j1_series,j2_series: set of indices (i1,i2,j1,j2) sorted by ref index ref_i, ref_j, and pairindex in case of multiple pairs with the same ref |
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10 | % (ref_i+1 is used to deal with the image index zero sometimes used) |
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11 | % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string) |
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12 | % FileInfo: structure containing info on the input files (assumed identical on the whole series) |
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13 | % FileInfo.FileType: type of file, = |
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14 | % = 'image', usual image as recognised by Matlab |
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15 | % = 'multimage', image series stored in a single file |
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16 | % = 'civx', netcdf file with civx convention |
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17 | % = 'civdata', civ data with new convention |
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18 | % = 'netcdf' other netcdf files |
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19 | % = 'video': movie recognised by VideoReader (e;g. avi) |
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20 | % MovieObject: video object (=[] otherwise |
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21 | % i1_input,i2_input,j1_input,j2_input: indices of the input file, or of the first file in the series if the input file does not exist |
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22 | % |
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23 | %INPUT |
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24 | % FilePath: path to the directory to be scanned |
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25 | % fileinput: name (without path) of the input file sample |
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26 | % checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile |
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27 | % =0: do not take into account xml file existence |
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28 | |
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29 | %======================================================================= |
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30 | % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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31 | % http://www.legi.grenoble-inp.fr |
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32 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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33 | % |
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34 | % This file is part of the toolbox UVMAT. |
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35 | % |
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36 | % UVMAT is free software; you can redistribute it and/or modify |
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37 | % it under the terms of the GNU General Public License as published |
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38 | % by the Free Software Foundation; either version 2 of the license, |
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39 | % or (at your option) any later version. |
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40 | % |
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41 | % UVMAT is distributed in the hope that it will be useful, |
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42 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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43 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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44 | % GNU General Public License (see LICENSE.txt) for more details. |
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45 | %======================================================================= |
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46 | |
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47 | function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml) |
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48 | %------------------------------------------------------------------------ |
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49 | |
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50 | %% get input root name and nomenclature type |
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51 | fullfileinput=fullfile(FilePath,fileinput);% input file name with path |
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52 | [FileInfo,MovieObject]=get_file_info(fullfileinput); |
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53 | |
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54 | %% check for particular file types: images, movies, civ data |
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55 | checkfileindexing=0; |
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56 | if isfield(FileInfo,'FileIndexing') && strcmp(FileInfo.FileIndexing,'on') |
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57 | [RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput); |
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58 | i1_series=zeros(1,1,1); |
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59 | i2_series=zeros(1,1,1); |
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60 | j1_series=zeros(1,1,1); |
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61 | j2_series=zeros(1,1,1); |
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62 | checkfileindexing=1; |
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63 | else % no file indexing |
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64 | [PathDir,RootFile]=fileparts(fullfileinput); |
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65 | [RootPath,SubDir,DirExt]=fileparts(PathDir); |
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66 | SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension) |
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67 | NomType='*'; |
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68 | i1_series=[];i2_series=[];j1_series=[];j2_series=[]; |
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69 | i1_input=1;i2_input=[];j1_input=[];j2_input=[]; |
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70 | if ~exist(fullfileinput,'file') |
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71 | RootFile=''; |
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72 | return |
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73 | end |
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74 | end |
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75 | if ~exist(FilePath,'dir') |
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76 | return % don't go further if the dir path does not exist |
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77 | end |
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78 | if checkfileindexing |
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79 | NomTypePref=''; |
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80 | if isempty(NomType)||strcmp(NomType,'*') |
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81 | if exist(fullfileinput,'file') |
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82 | [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension |
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83 | else |
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84 | RootFile=''; |
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85 | end |
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86 | else |
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87 | %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file |
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88 | if ~exist('checkxml','var')||checkxml |
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89 | r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType |
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90 | if ~isempty(r) %if NomType begins by a number or _1 |
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91 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
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92 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
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93 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
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94 | else% if a separator '_' is detected |
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95 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
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96 | end |
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97 | if ~isempty(rr) |
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98 | RootFile_i=[RootFile rr.i1];% new root file |
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99 | %look for an xml file correspoonding to the new root name |
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100 | if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file')) |
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101 | RootFile=RootFile_i; |
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102 | NomTypePref=r.tiretnum; |
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103 | NomType=regexprep(NomType,['^' NomTypePref],''); |
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104 | i1_input=j1_input; |
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105 | i2_input=j2_input; |
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106 | j1_input=[]; |
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107 | j2_input=[]; |
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108 | end |
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109 | end |
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110 | end |
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111 | end |
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112 | %% analyse the list of existing files when relevant |
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113 | sep1=''; |
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114 | sep2=''; |
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115 | i1_str='(?<i1>)';%will set i1=[]; |
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116 | i1_star=''; |
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117 | i2_str='(?<i2>)';%will set i2=[]; |
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118 | i2_star=''; |
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119 | j1_str='(?<j1>)';%will set j1=[]; |
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120 | j1_star=''; |
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121 | j2_str='(?<j2>)';%will set j2=[]; |
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122 | j2_star=''; |
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123 | %Look for cases with letter indexing for the second index |
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124 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names'); |
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125 | if ~isempty(r) |
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126 | sep1=r.sep1; |
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127 | sep2=r.sep2; |
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128 | i1_str='(?<i1>\d+)'; |
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129 | i1_star='*'; |
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130 | if strcmp(lower(r.j1),r.j1)% lower case index |
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131 | j1_str='(?<j1>[a-z])'; |
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132 | else |
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133 | j1_str='(?<j1>[A-Z])'; % upper case index |
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134 | end |
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135 | j1_star='*'; |
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136 | if ~isempty(r.j2) |
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137 | if strcmp(lower(r.j1),r.j1) |
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138 | j2_str='(?<j2>[a-z])'; |
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139 | else |
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140 | j2_str='(?<j2>[A-Z])'; |
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141 | end |
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142 | j2_star='*'; |
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143 | end |
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144 | else %numerical indexing |
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145 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names'); |
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146 | if ~isempty(r) |
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147 | sep1=r.sep1; |
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148 | i1_str='(?<i1>\d+)'; |
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149 | i1_star='*'; |
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150 | if ~isempty(r.i2) |
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151 | i2_str='(?<i2>-\d+)'; |
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152 | i2_star='-*'; |
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153 | end |
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154 | if ~isempty(r.j1) |
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155 | j1_str='(?<j1>_\d+)'; |
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156 | j1_star='_*'; |
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157 | end |
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158 | if ~isempty(r.j2) |
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159 | j2_str='(?<j2>-\d+)'; |
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160 | j2_star='-*'; |
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161 | end |
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162 | end |
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163 | end |
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164 | detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices |
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165 | %find the string used to extract the relevant files with the command dir |
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166 | star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt]; |
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167 | wd=pwd;%current working directory |
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168 | cd (FilePath)% move to the local dir to save time in the operation dir. |
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169 | dirpair=dir(star_string);% look for relevant files in the file directory |
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170 | cd(wd) |
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171 | nbpair=numel(dirpair); |
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172 | ref_i_list=zeros(1,nbpair); |
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173 | ref_j_list=zeros(1,nbpair); |
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174 | if nbpair==0% no detected file |
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175 | RootFile=''; |
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176 | end |
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177 | % scan the list of relevant files, extract the indices |
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178 | for ifile=1:nbpair |
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179 | rr=regexp(dirpair(ifile).name,detect_string,'names'); |
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180 | if ~isempty(rr) |
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181 | i1=str2num(rr.i1); |
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182 | i2=str2num(regexprep(rr.i2,'^-','')); |
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183 | j1=stra2num(regexprep(rr.j1,'^_','')); |
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184 | j2=stra2num(regexprep(rr.j2,'^-','')); |
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185 | ref_i=i1; |
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186 | if isempty(i2_input) |
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187 | if ~isempty(i2)% invalid file name if i2 does not exist in the input file |
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188 | break |
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189 | end |
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190 | else |
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191 | ref_i=floor((i1+i2)/2); |
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192 | end |
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193 | ref_j=1; |
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194 | if isempty(j1_input) |
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195 | if ~isempty(j1)% invalid file name if j1 does not exist in the input file |
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196 | break |
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197 | end |
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198 | else %j1_input is not empty |
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199 | if isempty(j1)% the detected name does not fit with the input |
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200 | break |
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201 | else |
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202 | ref_j=j1; |
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203 | if isempty(j2_input) |
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204 | if ~isempty(j2)% invalid file name if j2 does not exist in the input file |
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205 | break |
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206 | end |
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207 | else |
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208 | ref_j=floor((j1+j2)/2); |
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209 | end |
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210 | end |
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211 | end |
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212 | % update the detected index series |
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213 | if ~isempty(ref_i)&&~isempty(ref_j) |
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214 | ref_i_list(ifile)=ref_i; |
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215 | ref_j_list(ifile)=ref_j; |
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216 | nb_pairs=0; |
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217 | if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs |
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218 | if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 |
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219 | nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); |
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220 | end |
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221 | end |
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222 | if i1==0 |
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223 | i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
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224 | end |
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225 | if j1==0 |
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226 | j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
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227 | end |
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228 | i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; |
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229 | if ~isempty(i2_input) |
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230 | i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; |
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231 | end |
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232 | if ~isempty(j1_input) |
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233 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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234 | end |
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235 | if ~isempty(j2_input) |
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236 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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237 | j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; |
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238 | end |
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239 | end |
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240 | end |
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241 | end |
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242 | % look for the numerical string of the first files to update the NomType (take into account the 0 before the number) |
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243 | max_j=max(ref_j_list); |
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244 | if isempty(max_j) |
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245 | ref_ij=ref_i_list; |
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246 | else |
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247 | ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i. |
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248 | end |
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249 | ind_select=find(ref_ij>0); |
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250 | |
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251 | if isempty(ind_select) |
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252 | % RootFile=''; |
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253 | % NomType=''; |
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254 | else |
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255 | [tild,ifile_min]=min(ref_ij(ind_select)); |
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256 | [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ind_select(ifile_min)).name);% update the representation of indices (number of 0 before the number) |
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257 | NomType=regexprep(NomType,['^' NomTypePref],''); |
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258 | %% update the file type if the input file does not exist (pb of 0001) |
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259 | if isempty(FileInfo.FileType) |
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260 | [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name)); |
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261 | end |
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262 | end |
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263 | end |
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264 | |
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265 | %% set to empty array the irrelevant index series |
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266 | if isequal(i1_series,0), i1_series=[]; end |
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267 | if isequal(i2_series,0), i2_series=[]; end |
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268 | if isequal(j1_series,0), j1_series=[]; end |
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269 | if isequal(j2_series,0), j2_series=[]; end |
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270 | end |
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271 | % %% detect rdvision format |
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272 | % if strcmp(FileExt,'.bin') |
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273 | % if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file') |
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274 | % FileInfo.FileType='rdvision'; |
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275 | % FileInfo.SeqFile=[RootFile '.seq']; |
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276 | % end |
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277 | % end |
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278 | |
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279 | %% introduce the frame index in case of movies or multimage type |
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280 | if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 |
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281 | if isempty(i1_series)% if there is no file index, i denotes the frame index |
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282 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
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283 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
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284 | i1_input=1; |
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285 | NomType='*'; |
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286 | else % if there is a file index, j denotes the frame index while i denotes the file index |
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287 | if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair |
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288 | RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices |
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289 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
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290 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
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291 | j1_series=[]; |
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292 | i1_input=1; |
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293 | NomType='*'; |
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294 | else |
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295 | i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);% |
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296 | i1_series=[zeros(size(i1_series,1),1) i1_series]; |
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297 | j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);% |
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298 | j1_series=[zeros(size(i1_series,1),1) j1_series]; |
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299 | % include the first index in the root name |
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300 | r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType |
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301 | if ~isempty(r) |
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302 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
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303 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
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304 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
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305 | else% if a separator '_' is detected |
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306 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
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307 | end |
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308 | if ~isempty(rr) |
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309 | j1_input=1; |
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310 | j2_input=[]; |
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311 | end |
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312 | end |
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313 | end |
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314 | end |
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315 | end |
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316 | |
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317 | %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index |
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318 | if size(i2_series,3)>1 %pairs i1 -i2 |
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319 | diff_index=abs(i2_series-i1_series); |
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320 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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321 | for ref_i=1:size(i1_series,1) |
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322 | for ref_j=1:size(j1_series,2) |
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323 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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324 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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325 | if ~isempty(j1_series) |
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326 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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327 | end |
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328 | end |
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329 | end |
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330 | elseif size(j2_series,3)>1 %pairs j1 -j2 |
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331 | diff_index=abs(j2_series-j1_series); |
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332 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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333 | for ref_i=1:size(i1_series,1) |
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334 | for ref_j=1:size(j1_series,2) |
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335 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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336 | if ~isempty(i2_series) |
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337 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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338 | end |
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339 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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340 | j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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341 | end |
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342 | end |
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343 | end |
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344 | i1_series=permute(i1_series,[3 2 1]);% permute dimensions |
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345 | i2_series=permute(i2_series,[3 2 1]);% permute dimensions |
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346 | j1_series=permute(j1_series,[3 2 1]);% permute dimensions |
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347 | j2_series=permute(j2_series,[3 2 1]);% permute dimensions |
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