[356] | 1 | %'find_file_series': check the content of an input file and find the corresponding file series |
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[332] | 2 | %-------------------------------------------------------------------------- |
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[783] | 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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[332] | 4 | % |
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| 5 | % OUTPUT: |
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[783] | 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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[371] | 8 | % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file) |
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[609] | 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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[343] | 10 | % (ref_i+1 is used to deal with the image index zero sometimes used) |
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[332] | 11 | % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string) |
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[783] | 12 | % FileInfo: structure containing info on the input files (assumed identical on the whole series) |
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[1009] | 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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[783] | 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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[332] | 22 | % |
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| 23 | %INPUT |
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[783] | 24 | % FilePath: path to the directory to be scanned |
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[1009] | 25 | % fileinput: name (without path) of the input file sample |
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[667] | 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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[809] | 28 | |
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| 29 | %======================================================================= |
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[1093] | 30 | % Copyright 2008-2021, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[809] | 31 | % http://www.legi.grenoble-inp.fr |
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| 32 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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[332] | 33 | % |
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| 34 | % This file is part of the toolbox UVMAT. |
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[809] | 35 | % |
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[332] | 36 | % UVMAT is free software; you can redistribute it and/or modify |
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[809] | 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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[332] | 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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[809] | 44 | % GNU General Public License (see LICENSE.txt) for more details. |
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| 45 | %======================================================================= |
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[332] | 46 | |
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[783] | 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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[332] | 48 | %------------------------------------------------------------------------ |
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[398] | 49 | |
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[1033] | 50 | %% get input root name and info on the input file |
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[1022] | 51 | if isempty(regexp(FilePath,'^http://')) |
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[398] | 52 | fullfileinput=fullfile(FilePath,fileinput);% input file name with path |
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[1022] | 53 | else |
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| 54 | fullfileinput=[FilePath '/' fileinput]; |
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| 55 | end |
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[790] | 56 | [FileInfo,MovieObject]=get_file_info(fullfileinput); |
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[332] | 57 | |
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| 58 | %% check for particular file types: images, movies, civ data |
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[1022] | 59 | [RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput); |
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| 60 | i1_series=zeros(1,1,1); |
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| 61 | i2_series=zeros(1,1,1); |
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| 62 | j1_series=zeros(1,1,1); |
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| 63 | j2_series=zeros(1,1,1); |
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| 64 | checkfileindexing=1; |
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| 65 | if isempty(regexp(FilePath,'^http://')) && ~exist(FilePath,'dir') |
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[472] | 66 | return % don't go further if the dir path does not exist |
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| 67 | end |
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[790] | 68 | if checkfileindexing |
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[961] | 69 | NomTypePref=''; |
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| 70 | if isempty(NomType)||strcmp(NomType,'*') |
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| 71 | if exist(fullfileinput,'file') |
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| 72 | [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension |
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| 73 | else |
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| 74 | RootFile=''; |
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| 75 | end |
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[388] | 76 | else |
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[961] | 77 | %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file |
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| 78 | if ~exist('checkxml','var')||checkxml |
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| 79 | r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType |
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| 80 | if ~isempty(r) %if NomType begins by a number or _1 |
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| 81 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
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| 82 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
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| 83 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
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| 84 | else% if a separator '_' is detected |
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| 85 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
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[667] | 86 | end |
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[961] | 87 | if ~isempty(rr) |
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| 88 | RootFile_i=[RootFile rr.i1];% new root file |
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| 89 | %look for an xml file correspoonding to the new root name |
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| 90 | if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file')) |
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| 91 | RootFile=RootFile_i; |
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| 92 | NomTypePref=r.tiretnum; |
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| 93 | NomType=regexprep(NomType,['^' NomTypePref],''); |
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| 94 | i1_input=j1_input; |
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| 95 | i2_input=j2_input; |
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| 96 | j1_input=[]; |
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| 97 | j2_input=[]; |
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| 98 | end |
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| 99 | end |
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[667] | 100 | end |
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[384] | 101 | end |
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[961] | 102 | |
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| 103 | %% analyse the list of existing files when relevant |
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| 104 | sep1=''; |
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| 105 | sep2=''; |
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| 106 | i1_str='(?<i1>)';%will set i1=[]; |
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| 107 | i1_star=''; |
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| 108 | i2_str='(?<i2>)';%will set i2=[]; |
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| 109 | i2_star=''; |
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| 110 | j1_str='(?<j1>)';%will set j1=[]; |
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| 111 | j1_star=''; |
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| 112 | j2_str='(?<j2>)';%will set j2=[]; |
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| 113 | j2_star=''; |
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| 114 | %Look for cases with letter indexing for the second index |
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| 115 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names'); |
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[1022] | 116 | if ~isempty(r) %indexing image pair with letters |
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[388] | 117 | sep1=r.sep1; |
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[961] | 118 | sep2=r.sep2; |
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[388] | 119 | i1_str='(?<i1>\d+)'; |
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| 120 | i1_star='*'; |
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[961] | 121 | if strcmp(lower(r.j1),r.j1)% lower case index |
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| 122 | j1_str='(?<j1>[a-z])'; |
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| 123 | else |
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| 124 | j1_str='(?<j1>[A-Z])'; % upper case index |
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[360] | 125 | end |
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[961] | 126 | j1_star='*'; |
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[388] | 127 | if ~isempty(r.j2) |
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[961] | 128 | if strcmp(lower(r.j1),r.j1) |
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| 129 | j2_str='(?<j2>[a-z])'; |
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| 130 | else |
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| 131 | j2_str='(?<j2>[A-Z])'; |
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| 132 | end |
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| 133 | j2_star='*'; |
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[360] | 134 | end |
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[961] | 135 | else %numerical indexing |
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| 136 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names'); |
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| 137 | if ~isempty(r) |
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| 138 | sep1=r.sep1; |
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| 139 | i1_str='(?<i1>\d+)'; |
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| 140 | i1_star='*'; |
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| 141 | if ~isempty(r.i2) |
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| 142 | i2_str='(?<i2>-\d+)'; |
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| 143 | i2_star='-*'; |
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| 144 | end |
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| 145 | if ~isempty(r.j1) |
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| 146 | j1_str='(?<j1>_\d+)'; |
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| 147 | j1_star='_*'; |
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| 148 | end |
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| 149 | if ~isempty(r.j2) |
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| 150 | j2_str='(?<j2>-\d+)'; |
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| 151 | j2_star='-*'; |
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| 152 | end |
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| 153 | end |
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[360] | 154 | end |
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[1033] | 155 | |
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[1009] | 156 | 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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[1033] | 157 | ListStruct=dir_uvmat(FilePath);% scan the content of the folder FilePath |
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| 158 | ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray |
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| 159 | ListFiles=ListCells(1,:);%list of file names |
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| 160 | rr=regexp(ListFiles,detect_string,'names'); |
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[1022] | 161 | nbpair=numel(rr); |
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[1009] | 162 | ref_i_list=zeros(1,nbpair); |
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| 163 | ref_j_list=zeros(1,nbpair); |
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| 164 | if nbpair==0% no detected file |
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| 165 | RootFile=''; |
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| 166 | end |
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| 167 | % scan the list of relevant files, extract the indices |
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| 168 | for ifile=1:nbpair |
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[1033] | 169 | % rr=regexp(dirpair(ifile).name,detect_string,'names'); |
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[1022] | 170 | if ~isempty(rr{ifile}) |
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| 171 | i1=str2num(rr{ifile}.i1); |
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| 172 | i2=str2num(regexprep(rr{ifile}.i2,'^-','')); |
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| 173 | j1=stra2num(regexprep(rr{ifile}.j1,'^_','')); |
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| 174 | j2=stra2num(regexprep(rr{ifile}.j2,'^-','')); |
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[1009] | 175 | ref_i=i1; |
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| 176 | if isempty(i2_input) |
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| 177 | if ~isempty(i2)% invalid file name if i2 does not exist in the input file |
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| 178 | break |
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| 179 | end |
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| 180 | else |
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| 181 | ref_i=floor((i1+i2)/2); |
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[388] | 182 | end |
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[1009] | 183 | ref_j=1; |
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| 184 | if isempty(j1_input) |
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| 185 | if ~isempty(j1)% invalid file name if j1 does not exist in the input file |
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| 186 | break |
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| 187 | end |
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| 188 | else %j1_input is not empty |
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| 189 | if isempty(j1)% the detected name does not fit with the input |
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| 190 | break |
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[388] | 191 | else |
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[1009] | 192 | ref_j=j1; |
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| 193 | if isempty(j2_input) |
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| 194 | if ~isempty(j2)% invalid file name if j2 does not exist in the input file |
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| 195 | break |
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| 196 | end |
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[961] | 197 | else |
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[1009] | 198 | ref_j=floor((j1+j2)/2); |
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[961] | 199 | end |
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| 200 | end |
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[1009] | 201 | end |
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| 202 | % update the detected index series |
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| 203 | if ~isempty(ref_i)&&~isempty(ref_j) |
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| 204 | ref_i_list(ifile)=ref_i; |
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| 205 | ref_j_list(ifile)=ref_j; |
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| 206 | nb_pairs=0; |
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| 207 | if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs |
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| 208 | if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 |
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| 209 | nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); |
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[961] | 210 | end |
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| 211 | end |
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[1009] | 212 | if i1==0 |
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| 213 | i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
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| 214 | end |
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| 215 | if j1==0 |
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| 216 | j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
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| 217 | end |
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| 218 | i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; |
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| 219 | if ~isempty(i2_input) |
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| 220 | i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; |
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| 221 | end |
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| 222 | if ~isempty(j1_input) |
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| 223 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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| 224 | end |
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| 225 | if ~isempty(j2_input) |
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| 226 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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| 227 | j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; |
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| 228 | end |
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[339] | 229 | end |
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| 230 | end |
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[1009] | 231 | end |
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| 232 | % 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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| 233 | max_j=max(ref_j_list); |
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| 234 | if isempty(max_j) |
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| 235 | ref_ij=ref_i_list; |
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| 236 | else |
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| 237 | 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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| 238 | end |
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| 239 | ind_select=find(ref_ij>0); |
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| 240 | |
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| 241 | if ~isempty(ind_select) |
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| 242 | [tild,ifile_min]=min(ref_ij(ind_select)); |
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[1022] | 243 | [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(ListFiles{ind_select(ifile_min)});% update the representation of indices (number of 0 before the number) |
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[1009] | 244 | NomType=regexprep(NomType,['^' NomTypePref],''); |
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| 245 | %% update the file type if the input file does not exist (pb of 0001) |
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| 246 | if isempty(FileInfo.FileType) |
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[1050] | 247 | [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,ListFiles{ifile_min})); |
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[961] | 248 | end |
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[334] | 249 | end |
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[1009] | 250 | % end |
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[339] | 251 | end |
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[1009] | 252 | |
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| 253 | %% set to empty array the irrelevant index series |
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| 254 | if isequal(i1_series,0), i1_series=[]; end |
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| 255 | if isequal(i2_series,0), i2_series=[]; end |
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| 256 | if isequal(j1_series,0), j1_series=[]; end |
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| 257 | if isequal(j2_series,0), j2_series=[]; end |
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| 258 | |
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| 259 | %% case of isolated input file, not member of an indexed series |
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| 260 | if isempty(i1_series) |
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| 261 | [PathDir,RootFile]=fileparts(fullfileinput); |
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| 262 | [RootPath,SubDir,DirExt]=fileparts(PathDir); |
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| 263 | SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension) |
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| 264 | NomType='*'; |
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| 265 | i2_series=[];j1_series=[];j2_series=[]; |
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[1033] | 266 | % i1_input=1;i2_input=[];j1_input=[];j2_input=[]; |
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[1009] | 267 | if ~exist(fullfileinput,'file') |
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| 268 | RootFile=''; |
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| 269 | return |
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| 270 | end |
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| 271 | end |
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[784] | 272 | end |
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| 273 | |
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[445] | 274 | %% introduce the frame index in case of movies or multimage type |
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[484] | 275 | if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 |
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[783] | 276 | if isempty(i1_series)% if there is no file index, i denotes the frame index |
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[609] | 277 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
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| 278 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
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[445] | 279 | i1_input=1; |
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[483] | 280 | NomType='*'; |
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[783] | 281 | else % if there is a file index, j denotes the frame index while i denotes the file index |
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[788] | 282 | if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair |
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[1009] | 283 | 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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[783] | 284 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
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| 285 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
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| 286 | j1_series=[]; |
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| 287 | i1_input=1; |
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| 288 | NomType='*'; |
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| 289 | else |
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| 290 | i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);% |
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| 291 | i1_series=[zeros(size(i1_series,1),1) i1_series]; |
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| 292 | j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);% |
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| 293 | j1_series=[zeros(size(i1_series,1),1) j1_series]; |
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| 294 | % include the first index in the root name |
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| 295 | r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType |
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| 296 | if ~isempty(r) |
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| 297 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
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| 298 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
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| 299 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
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| 300 | else% if a separator '_' is detected |
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| 301 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
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| 302 | end |
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| 303 | if ~isempty(rr) |
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| 304 | j1_input=1; |
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| 305 | j2_input=[]; |
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| 306 | end |
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[483] | 307 | end |
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| 308 | end |
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[445] | 309 | end |
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| 310 | end |
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| 311 | |
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[339] | 312 | %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index |
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| 313 | if size(i2_series,3)>1 %pairs i1 -i2 |
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| 314 | diff_index=abs(i2_series-i1_series); |
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[353] | 315 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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[339] | 316 | for ref_i=1:size(i1_series,1) |
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| 317 | for ref_j=1:size(j1_series,2) |
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| 318 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 319 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 320 | if ~isempty(j1_series) |
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| 321 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 322 | end |
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| 323 | end |
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[334] | 324 | end |
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[339] | 325 | elseif size(j2_series,3)>1 %pairs j1 -j2 |
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| 326 | diff_index=abs(j2_series-j1_series); |
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[353] | 327 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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[339] | 328 | for ref_i=1:size(i1_series,1) |
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| 329 | for ref_j=1:size(j1_series,2) |
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| 330 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 331 | if ~isempty(i2_series) |
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| 332 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 333 | end |
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| 334 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 335 | j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 336 | end |
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| 337 | end |
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| 338 | end |
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[1009] | 339 | i1_series=permute(i1_series,[3 2 1]);% permute dimensions |
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[512] | 340 | i2_series=permute(i2_series,[3 2 1]);% permute dimensions |
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[1009] | 341 | j1_series=permute(j1_series,[3 2 1]);% permute dimensions |
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[512] | 342 | j2_series=permute(j2_series,[3 2 1]);% permute dimensions |
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