1 | %'find_file_series': check the content onf an input field and find the corresponding file series |
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2 | %-------------------------------------------------------------------------- |
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3 | % function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput) |
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4 | % |
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5 | % OUTPUT: |
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6 | % RootPath,RootFile: root path and root name detected in fileinput, possibly modified for movies (indexing is then done on image view, not file) |
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7 | % i1_series(ref_i+1, ref_j+1,pair),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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8 | % (ref_i+1 is used to deal with the image index zero sometimes used) |
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9 | % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string) |
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10 | % FileType: type of file, = |
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11 | % = 'image', usual image as recognised by Matlab |
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12 | % = 'multimage', image series stored in a single file |
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13 | % = 'civx', netcdf file with civx convention |
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14 | % = 'civdata', civ data with new convention |
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15 | % = 'netcdf' other netcdf files |
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16 | % = 'video': movie recognised by VideoReader (e;g. avi) |
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17 | % Object: video object (=[] otherwise) |
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18 | % |
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19 | %INPUT |
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20 | % fileinput: name (including path) of the input file |
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21 | % |
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22 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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23 | % Copyright 2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr |
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24 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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25 | % This file is part of the toolbox UVMAT. |
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26 | % |
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27 | % UVMAT is free software; you can redistribute it and/or modify |
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28 | % it under the terms of the GNU General Public License as published by |
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29 | % the Free Software Foundation; either version 2 of the License, or |
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30 | % (at your option) any later version. |
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31 | % |
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32 | % UVMAT is distributed in the hope that it will be useful, |
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33 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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34 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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35 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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36 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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37 | |
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38 | function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput) |
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39 | %------------------------------------------------------------------------ |
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40 | |
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41 | %% get input root name and nomenclature type |
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42 | [RootPath,SubDir,RootFile,tild,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fileinput); |
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43 | |
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44 | %% check for particular file types: images, movies, civ data |
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45 | FileType=''; |
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46 | Object=[]; |
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47 | i1_series=zeros(1,1,1); |
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48 | i2_series=zeros(1,1,1); |
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49 | j1_series=zeros(1,1,1); |
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50 | j2_series=zeros(1,1,1); |
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51 | switch FileExt |
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52 | % ancillary files, no field indexing |
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53 | case {'.civ','.log','.cmx','.cmx2','.txt','.bat'} |
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54 | FileType='txt'; |
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55 | NomType=''; |
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56 | case '.fig' |
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57 | FileType='figure'; |
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58 | NomType=''; |
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59 | case '.xml' |
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60 | FileType='xml'; |
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61 | NomType=''; |
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62 | case '.xls' |
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63 | FileType='xls'; |
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64 | NomType=''; |
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65 | otherwise |
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66 | if ~isempty(FileExt)&& ~isempty(imformats(FileExt(2:end))) |
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67 | try |
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68 | imainfo=imfinfo(fileinput); |
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69 | FileType='image'; |
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70 | if length(imainfo) >1 %case of image with multiple frames |
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71 | NomType='*'; |
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72 | FileType='multimage'; |
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73 | i1_series=(1:length(imainfo))'; |
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74 | [RootPath,RootFile]=fileparts(fileinput); |
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75 | end |
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76 | end |
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77 | else |
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78 | try |
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79 | Data=nc2struct(fileinput,'ListGlobalAttribute','absolut_time_T0','Conventions'); |
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80 | if ~isempty(Data.absolut_time_T0') |
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81 | FileType='civx'; % test for civx velocity fields |
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82 | elseif strcmp(Data.Conventions,'uvmat/civdata') |
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83 | FileType='civdata'; % test for civx velocity fields |
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84 | else |
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85 | FileType='netcdf'; |
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86 | end |
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87 | end |
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88 | try |
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89 | if exist('VideoReader','file')%recent version of Matlab |
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90 | Object=VideoReader(fileinput); |
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91 | else |
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92 | Object=mmreader(fileinput);%older Matlab function for movies |
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93 | end |
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94 | NomType='*'; |
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95 | FileType='video'; |
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96 | i1_series=(1:get(Object,'NumberOfFrames'))'; |
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97 | end |
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98 | end |
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99 | end |
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100 | |
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101 | %% get the list of existing files when relevant |
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102 | if strcmp(NomType,'')||strcmp(NomType,'*') |
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103 | if exist(fileinput,'file') |
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104 | [RootPath,RootFile]=fileparts(fileinput);% case of constant name (no indexing) |
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105 | else |
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106 | RootPath=''; |
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107 | RootFile=''; |
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108 | end |
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109 | else |
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110 | if strcmp(SubDir,'') |
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111 | filebasesub=fullfile(RootPath,RootFile); |
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112 | else |
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113 | filebasesub=fullfile(RootPath,SubDir,RootFile); |
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114 | end |
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115 | detect_string=regexprep(NomType,'\d','*');%replace numbers by '*' |
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116 | old_string=''; |
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117 | detect_string=regexprep(detect_string,'[ab]$','*');%suppress the possible letter ab at the end |
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118 | detect_string=regexprep(detect_string,'[AB]$','*');%suppress the possible letter ab at the end |
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119 | detect_string=regexprep(detect_string,'[a|A]$','*');%suppress a possible second letter a,A at the end |
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120 | while ~strcmp(detect_string,old_string)%removes multiple '*' |
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121 | old_string=detect_string; |
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122 | detect_string=regexprep(detect_string,'**','*'); |
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123 | end |
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124 | dirpair=dir([filebasesub detect_string FileExt]); |
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125 | nbpair=numel(dirpair); |
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126 | ref_i_list=zeros(1,nbpair); |
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127 | ref_j_list=zeros(1,nbpair); |
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128 | if nbpair==0% no detected file |
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129 | RootPath=''; |
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130 | RootFile=''; |
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131 | end |
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132 | for ifile=1:nbpair |
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133 | [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(dirpair(ifile).name); |
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134 | ref_i=i1; |
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135 | if isempty(i2_input) |
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136 | if ~isempty(i2)% invalid file name if i2 does not exist in the input file |
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137 | break |
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138 | end |
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139 | else |
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140 | ref_i=floor((i1+i2)/2); |
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141 | end |
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142 | ref_j=1; |
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143 | if isempty(j1_input) |
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144 | if ~isempty(j1)% invalid file name if j1 does not exist in the input file |
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145 | break |
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146 | end |
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147 | else %j1_input is not empty |
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148 | if isempty(j1)% the detected name does not fit with the input |
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149 | break |
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150 | else |
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151 | ref_j=j1; |
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152 | if isempty(j2_input) |
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153 | if ~isempty(j2)% invalid file name if j2 does not exist in the input file |
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154 | break |
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155 | end |
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156 | else |
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157 | ref_j=floor((j1+j2)/2); |
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158 | end |
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159 | end |
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160 | end |
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161 | % update the detected index series |
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162 | ref_i_list(ifile)=ref_i; |
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163 | ref_j_list(ifile)=ref_j; |
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164 | nb_pairs=0; |
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165 | if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs |
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166 | if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 |
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167 | nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); |
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168 | end |
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169 | end |
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170 | i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; |
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171 | if ~isempty(i2_input) |
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172 | i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; |
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173 | end |
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174 | if ~isempty(j1_input) |
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175 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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176 | end |
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177 | if ~isempty(j2_input) |
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178 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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179 | j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; |
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180 | end |
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181 | end |
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182 | % 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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183 | max_j=max(ref_j_list); |
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184 | if isempty(max_j) |
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185 | ref_ij=ref_i_list; |
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186 | else |
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187 | 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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188 | end |
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189 | [tild,ifile]=min(ref_ij(ref_ij>0)); |
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190 | if isempty(ifile) |
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191 | RootPath=''; |
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192 | RootFile=''; |
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193 | NomType=''; |
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194 | else |
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195 | [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile).name); |
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196 | end |
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197 | end |
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198 | |
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199 | %% set to empty array the irrelevant index series |
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200 | if isequal(i1_series,0), i1_series=[]; end |
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201 | if isequal(i2_series,0), i2_series=[]; end |
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202 | if isequal(j1_series,0), j1_series=[]; end |
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203 | if isequal(j2_series,0), j2_series=[]; end |
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204 | |
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205 | %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index |
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206 | if size(i2_series,3)>1 %pairs i1 -i2 |
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207 | diff_index=abs(i2_series-i1_series); |
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208 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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209 | for ref_i=1:size(i1_series,1) |
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210 | for ref_j=1:size(j1_series,2) |
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211 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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212 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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213 | if ~isempty(j1_series) |
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214 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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215 | end |
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216 | end |
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217 | end |
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218 | elseif size(j2_series,3)>1 %pairs j1 -j2 |
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219 | diff_index=abs(j2_series-j1_series); |
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220 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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221 | for ref_i=1:size(i1_series,1) |
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222 | for ref_j=1:size(j1_series,2) |
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223 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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224 | if ~isempty(i2_series) |
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225 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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226 | end |
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227 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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228 | j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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229 | end |
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230 | end |
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231 | end |
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232 | |
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