[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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| 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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[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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[371] | 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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| 30 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF 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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[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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[332] | 50 | %% get input root name and nomenclature type |
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[398] | 51 | fullfileinput=fullfile(FilePath,fileinput);% input file name with path |
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[790] | 52 | [FileInfo,MovieObject]=get_file_info(fullfileinput); |
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[332] | 53 | |
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| 54 | %% check for particular file types: images, movies, civ data |
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[790] | 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 | end |
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[472] | 71 | if ~exist(FilePath,'dir') |
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| 72 | return % don't go further if the dir path does not exist |
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| 73 | end |
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[790] | 74 | if checkfileindexing |
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[445] | 75 | NomTypePref=''; |
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[483] | 76 | if isempty(NomType) |
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[371] | 77 | if exist(fullfileinput,'file') |
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[398] | 78 | [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension |
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[388] | 79 | else |
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[360] | 80 | RootFile=''; |
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[339] | 81 | end |
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[388] | 82 | else |
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[667] | 83 | %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file |
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| 84 | if ~exist('checkxml','var')||checkxml |
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| 85 | r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType |
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| 86 | if ~isempty(r) %if NomType begins by a number or _1 |
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| 87 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
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| 88 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
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| 89 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
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| 90 | else% if a separator '_' is detected |
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| 91 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
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| 92 | end |
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| 93 | if ~isempty(rr) |
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| 94 | RootFile_i=[RootFile rr.i1];% new root file |
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| 95 | %look for an xml file correspoonding to the new root name |
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| 96 | if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file')) |
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| 97 | RootFile=RootFile_i; |
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| 98 | NomTypePref=r.tiretnum; |
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| 99 | NomType=regexprep(NomType,['^' NomTypePref],''); |
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| 100 | i1_input=j1_input; |
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| 101 | i2_input=j2_input; |
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| 102 | j1_input=[]; |
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| 103 | j2_input=[]; |
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| 104 | end |
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| 105 | end |
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[384] | 106 | end |
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| 107 | end |
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[360] | 108 | %% analyse the list of existing files when relevant |
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| 109 | sep1=''; |
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[558] | 110 | sep2=''; |
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[388] | 111 | i1_str='(?<i1>)';%will set i1=[]; |
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[360] | 112 | i1_star=''; |
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[388] | 113 | i2_str='(?<i2>)';%will set i2=[]; |
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[360] | 114 | i2_star=''; |
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[388] | 115 | j1_str='(?<j1>)';%will set j1=[]; |
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[360] | 116 | j1_star=''; |
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[388] | 117 | j2_str='(?<j2>)';%will set j2=[]; |
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[360] | 118 | j2_star=''; |
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[388] | 119 | %Look for cases with letter indexing for the second index |
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[558] | 120 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names'); |
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[360] | 121 | if ~isempty(r) |
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[388] | 122 | sep1=r.sep1; |
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[558] | 123 | sep2=r.sep2; |
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[399] | 124 | i1_str='(?<i1>\d+)'; |
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[558] | 125 | i1_star='*'; |
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[399] | 126 | if strcmp(lower(r.j1),r.j1)% lower case index |
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[388] | 127 | j1_str='(?<j1>[a-z])'; |
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| 128 | else |
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[399] | 129 | j1_str='(?<j1>[A-Z])'; % upper case index |
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[360] | 130 | end |
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[388] | 131 | j1_star='*'; |
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| 132 | if ~isempty(r.j2) |
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| 133 | if strcmp(lower(r.j1),r.j1) |
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| 134 | j2_str='(?<j2>[a-z])'; |
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| 135 | else |
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| 136 | j2_str='(?<j2>[A-Z])'; |
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| 137 | end |
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| 138 | j2_star='*'; |
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[360] | 139 | end |
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[388] | 140 | else %numerical indexing |
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| 141 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names'); |
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| 142 | if ~isempty(r) |
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| 143 | sep1=r.sep1; |
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| 144 | i1_str='(?<i1>\d+)'; |
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| 145 | i1_star='*'; |
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| 146 | if ~isempty(r.i2) |
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| 147 | i2_str='(?<i2>-\d+)'; |
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| 148 | i2_star='-*'; |
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[360] | 149 | end |
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[388] | 150 | if ~isempty(r.j1) |
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| 151 | j1_str='(?<j1>_\d+)'; |
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| 152 | j1_star='_*'; |
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[360] | 153 | end |
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[388] | 154 | if ~isempty(r.j2) |
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| 155 | j2_str='(?<j2>-\d+)'; |
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| 156 | j2_star='-*'; |
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[360] | 157 | end |
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| 158 | end |
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[332] | 159 | end |
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[558] | 160 | 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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[360] | 161 | %find the string used to extract the relevant files with the command dir |
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[558] | 162 | star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt]; |
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[360] | 163 | wd=pwd;%current working directory |
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[398] | 164 | cd (FilePath)% move to the local dir to save time in the operation dir. |
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[388] | 165 | dirpair=dir(star_string);% look for relevant files in the file directory |
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[360] | 166 | cd(wd) |
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[339] | 167 | nbpair=numel(dirpair); |
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| 168 | ref_i_list=zeros(1,nbpair); |
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| 169 | ref_j_list=zeros(1,nbpair); |
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| 170 | if nbpair==0% no detected file |
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| 171 | RootFile=''; |
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| 172 | end |
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[360] | 173 | % scan the list of relevant files, extract the indices |
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[339] | 174 | for ifile=1:nbpair |
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[360] | 175 | rr=regexp(dirpair(ifile).name,detect_string,'names'); |
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[362] | 176 | if ~isempty(rr) |
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[388] | 177 | i1=str2num(rr.i1); |
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| 178 | i2=str2num(regexprep(rr.i2,'^-','')); |
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| 179 | j1=stra2num(regexprep(rr.j1,'^_','')); |
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| 180 | j2=stra2num(regexprep(rr.j2,'^-','')); |
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| 181 | ref_i=i1; |
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| 182 | if isempty(i2_input) |
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| 183 | if ~isempty(i2)% invalid file name if i2 does not exist in the input file |
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| 184 | break |
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| 185 | end |
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| 186 | else |
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| 187 | ref_i=floor((i1+i2)/2); |
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[339] | 188 | end |
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[388] | 189 | ref_j=1; |
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| 190 | if isempty(j1_input) |
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| 191 | if ~isempty(j1)% invalid file name if j1 does not exist in the input file |
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| 192 | break |
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| 193 | end |
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| 194 | else %j1_input is not empty |
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| 195 | if isempty(j1)% the detected name does not fit with the input |
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| 196 | break |
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| 197 | else |
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| 198 | ref_j=j1; |
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| 199 | if isempty(j2_input) |
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| 200 | if ~isempty(j2)% invalid file name if j2 does not exist in the input file |
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| 201 | break |
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| 202 | end |
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| 203 | else |
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| 204 | ref_j=floor((j1+j2)/2); |
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[342] | 205 | end |
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[339] | 206 | end |
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| 207 | end |
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[388] | 208 | % update the detected index series |
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[788] | 209 | if ~isempty(ref_i)&&~isempty(ref_j) |
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| 210 | ref_i_list(ifile)=ref_i; |
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| 211 | ref_j_list(ifile)=ref_j; |
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| 212 | nb_pairs=0; |
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| 213 | if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs |
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| 214 | if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 |
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| 215 | nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); |
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| 216 | end |
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[388] | 217 | end |
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[788] | 218 | if i1==0 |
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| 219 | i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
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| 220 | end |
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| 221 | if j1==0 |
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| 222 | j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
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| 223 | end |
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| 224 | i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; |
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| 225 | if ~isempty(i2_input) |
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| 226 | i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; |
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| 227 | end |
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| 228 | if ~isempty(j1_input) |
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| 229 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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| 230 | end |
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| 231 | if ~isempty(j2_input) |
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| 232 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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| 233 | j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; |
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| 234 | end |
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[339] | 235 | end |
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[334] | 236 | end |
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[339] | 237 | end |
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| 238 | % 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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| 239 | max_j=max(ref_j_list); |
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[350] | 240 | if isempty(max_j) |
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| 241 | ref_ij=ref_i_list; |
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| 242 | else |
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| 243 | 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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| 244 | end |
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[456] | 245 | ind_select=find(ref_ij>0); |
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[788] | 246 | |
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[456] | 247 | if isempty(ind_select) |
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[788] | 248 | % RootFile=''; |
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| 249 | % NomType=''; |
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[350] | 250 | else |
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[456] | 251 | [tild,ifile_min]=min(ref_ij(ind_select)); |
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[494] | 252 | [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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[384] | 253 | NomType=regexprep(NomType,['^' NomTypePref],''); |
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[497] | 254 | %% update the file type if the input file does not exist (pb of 0001) |
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[783] | 255 | if isempty(FileInfo.FileType) |
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[784] | 256 | [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name)); |
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[497] | 257 | end |
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[350] | 258 | end |
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[339] | 259 | end |
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| 260 | |
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| 261 | %% set to empty array the irrelevant index series |
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| 262 | if isequal(i1_series,0), i1_series=[]; end |
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| 263 | if isequal(i2_series,0), i2_series=[]; end |
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| 264 | if isequal(j1_series,0), j1_series=[]; end |
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| 265 | if isequal(j2_series,0), j2_series=[]; end |
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[784] | 266 | end |
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[790] | 267 | % %% detect rdvision format |
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| 268 | % if strcmp(FileExt,'.bin') |
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| 269 | % if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file') |
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| 270 | % FileInfo.FileType='rdvision'; |
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| 271 | % FileInfo.SeqFile=[RootFile '.seq']; |
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| 272 | % end |
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| 273 | % end |
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[784] | 274 | |
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[445] | 275 | %% introduce the frame index in case of movies or multimage type |
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[484] | 276 | if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 |
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[783] | 277 | if isempty(i1_series)% if there is no file index, i denotes the frame index |
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[609] | 278 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
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| 279 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
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[445] | 280 | i1_input=1; |
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[483] | 281 | NomType='*'; |
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[783] | 282 | else % if there is a file index, j denotes the frame index while i denotes the file index |
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[788] | 283 | if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair |
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[783] | 284 | 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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| 285 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
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| 286 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
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| 287 | j1_series=[]; |
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| 288 | i1_input=1; |
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| 289 | NomType='*'; |
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| 290 | else |
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| 291 | i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);% |
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| 292 | i1_series=[zeros(size(i1_series,1),1) i1_series]; |
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| 293 | j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);% |
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| 294 | j1_series=[zeros(size(i1_series,1),1) j1_series]; |
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| 295 | % include the first index in the root name |
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| 296 | r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType |
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| 297 | if ~isempty(r) |
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| 298 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
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| 299 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
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| 300 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
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| 301 | else% if a separator '_' is detected |
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| 302 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
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| 303 | end |
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| 304 | if ~isempty(rr) |
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| 305 | j1_input=1; |
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| 306 | j2_input=[]; |
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| 307 | end |
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[483] | 308 | end |
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| 309 | end |
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[445] | 310 | end |
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| 311 | end |
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| 312 | |
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[339] | 313 | %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index |
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| 314 | if size(i2_series,3)>1 %pairs i1 -i2 |
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| 315 | diff_index=abs(i2_series-i1_series); |
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[353] | 316 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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[339] | 317 | for ref_i=1:size(i1_series,1) |
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| 318 | for ref_j=1:size(j1_series,2) |
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| 319 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 320 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 321 | if ~isempty(j1_series) |
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| 322 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 323 | end |
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| 324 | end |
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[334] | 325 | end |
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[339] | 326 | elseif size(j2_series,3)>1 %pairs j1 -j2 |
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| 327 | diff_index=abs(j2_series-j1_series); |
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[353] | 328 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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[339] | 329 | for ref_i=1:size(i1_series,1) |
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| 330 | for ref_j=1:size(j1_series,2) |
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| 331 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 332 | if ~isempty(i2_series) |
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| 333 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 334 | end |
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| 335 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 336 | j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 337 | end |
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| 338 | end |
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| 339 | end |
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[512] | 340 | i1_series=permute(i1_series,[3 2 1]);% permute dimensions |
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| 341 | i2_series=permute(i2_series,[3 2 1]);% permute dimensions |
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| 342 | j1_series=permute(j1_series,[3 2 1]);% permute dimensions |
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| 343 | j2_series=permute(j2_series,[3 2 1]);% permute dimensions |
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