[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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[339] | 3 | % function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput) |
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[332] | 4 | % |
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| 5 | % OUTPUT: |
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[371] | 6 | % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file) |
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[343] | 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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[332] | 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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[371] | 20 | % RootPath: path to the directory to be scanned |
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| 21 | % fileinput: name (without path) of the input file sample |
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[332] | 22 | % |
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| 23 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 24 | % Copyright 2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr |
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| 25 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 26 | % This file is part of the toolbox UVMAT. |
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| 27 | % |
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| 28 | % UVMAT is free software; you can redistribute it and/or modify |
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| 29 | % it under the terms of the GNU General Public License as published by |
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| 30 | % the Free Software Foundation; either version 2 of the License, or |
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| 31 | % (at your option) any later version. |
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| 32 | % |
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| 33 | % UVMAT is distributed in the hope that it will be useful, |
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| 34 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 35 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 36 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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| 37 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 38 | |
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[372] | 39 | function [RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(RootPath,fileinput,option) |
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[332] | 40 | %------------------------------------------------------------------------ |
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[372] | 41 | if ~exist('option','var') |
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| 42 | option='all'; |
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| 43 | end |
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[332] | 44 | %% get input root name and nomenclature type |
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[371] | 45 | [tild,tild,RootFile,tild,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fileinput); |
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| 46 | fullfileinput=fullfile(RootPath,fileinput); |
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[332] | 47 | |
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| 48 | %% check for particular file types: images, movies, civ data |
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| 49 | FileType=''; |
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| 50 | Object=[]; |
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[339] | 51 | i1_series=zeros(1,1,1); |
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| 52 | i2_series=zeros(1,1,1); |
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| 53 | j1_series=zeros(1,1,1); |
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| 54 | j2_series=zeros(1,1,1); |
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[371] | 55 | |
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[334] | 56 | switch FileExt |
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| 57 | % ancillary files, no field indexing |
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| 58 | case {'.civ','.log','.cmx','.cmx2','.txt','.bat'} |
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| 59 | FileType='txt'; |
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| 60 | NomType=''; |
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| 61 | case '.fig' |
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| 62 | FileType='figure'; |
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| 63 | NomType=''; |
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| 64 | case '.xml' |
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| 65 | FileType='xml'; |
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| 66 | NomType=''; |
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| 67 | case '.xls' |
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| 68 | FileType='xls'; |
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| 69 | NomType=''; |
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| 70 | otherwise |
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[371] | 71 | |
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[334] | 72 | if ~isempty(FileExt)&& ~isempty(imformats(FileExt(2:end))) |
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[339] | 73 | try |
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[371] | 74 | imainfo=imfinfo(fullfileinput); |
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[339] | 75 | FileType='image'; |
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| 76 | if length(imainfo) >1 %case of image with multiple frames |
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| 77 | NomType='*'; |
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| 78 | FileType='multimage'; |
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[354] | 79 | i1_series=(1:length(imainfo))'; |
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[371] | 80 | [RootPath,RootFile]=fileparts(fullfileinput); |
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[339] | 81 | end |
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[334] | 82 | end |
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[332] | 83 | else |
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[334] | 84 | try |
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[371] | 85 | Data=nc2struct(fullfileinput,'ListGlobalAttribute','absolut_time_T0','Conventions'); |
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[334] | 86 | if ~isempty(Data.absolut_time_T0') |
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| 87 | FileType='civx'; % test for civx velocity fields |
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[354] | 88 | elseif strcmp(Data.Conventions,'uvmat/civdata') |
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[334] | 89 | FileType='civdata'; % test for civx velocity fields |
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| 90 | else |
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| 91 | FileType='netcdf'; |
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| 92 | end |
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| 93 | end |
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| 94 | try |
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[354] | 95 | if exist('VideoReader','file')%recent version of Matlab |
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[371] | 96 | Object=VideoReader(fullfileinput); |
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[354] | 97 | else |
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[371] | 98 | Object=mmreader(fullfileinput);%older Matlab function for movies |
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[354] | 99 | end |
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[334] | 100 | NomType='*'; |
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[360] | 101 | FileType='video'; |
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[354] | 102 | i1_series=(1:get(Object,'NumberOfFrames'))'; |
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[334] | 103 | end |
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| 104 | end |
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[332] | 105 | end |
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[339] | 106 | |
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[372] | 107 | if strcmp(NomType,'')||strcmp(NomType,'*')||strcmp(option,'filetype') |
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[371] | 108 | if exist(fullfileinput,'file') |
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| 109 | [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing) |
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| 110 | else |
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[360] | 111 | RootFile=''; |
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[339] | 112 | end |
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[360] | 113 | else |
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| 114 | %% analyse the list of existing files when relevant |
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| 115 | sep1=''; |
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| 116 | i1_str='(?<i1>)'; |
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| 117 | i1_star=''; |
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| 118 | sep2=''; |
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| 119 | i2_str='(?<i2>)'; |
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| 120 | i2_star=''; |
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| 121 | sep3=''; |
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| 122 | j1_str='(?<j1>)'; |
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| 123 | j1_star=''; |
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| 124 | sep4=''; |
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| 125 | j2_str='(?<j2>)'; |
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| 126 | j2_star=''; |
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| 127 | NomTypeStr=NomType; |
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| 128 | if ~isempty(regexp(NomTypeStr,'^_\d')) |
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| 129 | sep1='_'; |
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| 130 | NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr |
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[332] | 131 | end |
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[360] | 132 | r=regexp(NomTypeStr,'^(?<num1>\d+)','names');%look for a number at the beginning of NomTypeStr |
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| 133 | if ~isempty(r) |
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| 134 | i1_str='(?<i1>\d+)'; |
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| 135 | i1_star='*'; |
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| 136 | NomTypeStr=regexprep(NomTypeStr,['^' r.num1],''); |
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| 137 | r=regexp(NomTypeStr,'^-(?<num2>\d+)','names');%look for a pair i1-i2 |
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| 138 | if ~isempty(r) |
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| 139 | sep2='-'; |
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| 140 | i2_str='(?<i2>\d+)'; |
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| 141 | i2_star='*'; |
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| 142 | NomTypeStr=regexprep(NomTypeStr,['^-' r.num2],''); |
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| 143 | end |
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| 144 | if ~isempty(regexp(NomTypeStr,'^_')); |
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| 145 | sep3='_'; |
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| 146 | NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr |
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| 147 | end |
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| 148 | if ~isempty(regexp(NomTypeStr,'^[a|A]')); |
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| 149 | j1_str='(?<j1>[a-z]|[A-Z])'; |
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| 150 | j1_star='*'; |
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| 151 | if ~isempty(regexp(NomTypeStr,'[b|B]$')); |
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[365] | 152 | j2_str='(?<j2>[a-z]|[A-Z])'; |
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[360] | 153 | j2_star='*'; |
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| 154 | end |
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| 155 | else |
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| 156 | r=regexp(NomTypeStr,'^(?<num3>\d+)','names'); |
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| 157 | if ~isempty(r) |
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| 158 | j1_str='(?<j1>\d+)'; |
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| 159 | j1_star='*'; |
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| 160 | NomTypeStr=regexprep(NomTypeStr,['^' r.num3],''); |
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| 161 | end |
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| 162 | r=regexp(NomTypeStr,'-(?<num4>\d+)','names'); |
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| 163 | if ~isempty(r) |
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| 164 | sep4='-'; |
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| 165 | j2_str='(?<j2>\d+)'; |
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| 166 | j2_star='*'; |
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| 167 | end |
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| 168 | end |
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[332] | 169 | end |
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[371] | 170 | detect_string=['^' RootFile sep1 i1_str sep2 i2_str sep3 j1_str sep4 j2_str FileExt '$'];%string used in regexp to detect file indices |
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[360] | 171 | %find the string used to extract the relevant files with the command dir |
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[371] | 172 | star_string=[RootFile sep1 i1_star sep2 i2_star sep3 j1_star sep4 j2_star '*']; |
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[360] | 173 | wd=pwd;%current working directory |
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[371] | 174 | %RR=fullfile(RootPath,SubDir); |
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| 175 | cd (RootPath)% move to the local dir to save time in the operation dir. |
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| 176 | dirpair=dir([star_string FileExt]);% look for relevant files in the file directory |
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[360] | 177 | cd(wd) |
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[339] | 178 | nbpair=numel(dirpair); |
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| 179 | ref_i_list=zeros(1,nbpair); |
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| 180 | ref_j_list=zeros(1,nbpair); |
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| 181 | if nbpair==0% no detected file |
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| 182 | RootPath=''; |
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| 183 | RootFile=''; |
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| 184 | end |
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[360] | 185 | % scan the list of relevant files, extract the indices |
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[339] | 186 | for ifile=1:nbpair |
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[360] | 187 | rr=regexp(dirpair(ifile).name,detect_string,'names'); |
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[362] | 188 | if ~isempty(rr) |
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[360] | 189 | i1=str2num(rr.i1); |
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| 190 | i2=str2num(rr.i2); |
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| 191 | j1=stra2num(rr.j1); |
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| 192 | j2=stra2num(rr.j2); |
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[339] | 193 | ref_i=i1; |
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| 194 | if isempty(i2_input) |
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| 195 | if ~isempty(i2)% invalid file name if i2 does not exist in the input file |
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| 196 | break |
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| 197 | end |
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[334] | 198 | else |
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[339] | 199 | ref_i=floor((i1+i2)/2); |
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[334] | 200 | end |
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[339] | 201 | ref_j=1; |
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| 202 | if isempty(j1_input) |
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| 203 | if ~isempty(j1)% invalid file name if j1 does not exist in the input file |
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| 204 | break |
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| 205 | end |
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[342] | 206 | else %j1_input is not empty |
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| 207 | if isempty(j1)% the detected name does not fit with the input |
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| 208 | break |
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| 209 | else |
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| 210 | ref_j=j1; |
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| 211 | if isempty(j2_input) |
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| 212 | if ~isempty(j2)% invalid file name if j2 does not exist in the input file |
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| 213 | break |
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| 214 | end |
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| 215 | else |
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| 216 | ref_j=floor((j1+j2)/2); |
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[339] | 217 | end |
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| 218 | end |
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[332] | 219 | end |
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[339] | 220 | % update the detected index series |
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| 221 | ref_i_list(ifile)=ref_i; |
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| 222 | ref_j_list(ifile)=ref_j; |
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| 223 | nb_pairs=0; |
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| 224 | if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs |
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[343] | 225 | if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 |
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| 226 | nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); |
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[339] | 227 | end |
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[334] | 228 | end |
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[343] | 229 | i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; |
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[339] | 230 | if ~isempty(i2_input) |
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[343] | 231 | i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; |
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[332] | 232 | end |
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[339] | 233 | if ~isempty(j1_input) |
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[343] | 234 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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[332] | 235 | end |
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[339] | 236 | if ~isempty(j2_input) |
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[343] | 237 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
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| 238 | j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; |
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[339] | 239 | end |
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[362] | 240 | end |
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[339] | 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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[350] | 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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[360] | 249 | [tild,ifile_min]=min(ref_ij(ref_ij>0)); |
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| 250 | if isempty(ifile_min) |
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[350] | 251 | RootPath=''; |
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| 252 | RootFile=''; |
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| 253 | NomType=''; |
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| 254 | else |
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[372] | 255 | [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile_min).name);% update the representation of indices (number of 0 before the number) |
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[350] | 256 | end |
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[339] | 257 | end |
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| 258 | |
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[372] | 259 | %% update the file type if the input file does not exist (pb of 0001) |
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| 260 | if strcmp(option,'filetype') |
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| 261 | return |
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| 262 | elseif isempty(FileType) |
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| 263 | [tild,tild, tild,tild,tild,tild,FileType,Object]=find_file_series(RootPath,dirpair(ifile_min).name,'filetype'); |
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| 264 | end |
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| 265 | |
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[339] | 266 | %% set to empty array the irrelevant index series |
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| 267 | if isequal(i1_series,0), i1_series=[]; end |
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| 268 | if isequal(i2_series,0), i2_series=[]; end |
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| 269 | if isequal(j1_series,0), j1_series=[]; end |
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| 270 | if isequal(j2_series,0), j2_series=[]; end |
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| 271 | |
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| 272 | %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index |
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| 273 | if size(i2_series,3)>1 %pairs i1 -i2 |
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| 274 | diff_index=abs(i2_series-i1_series); |
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[353] | 275 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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[339] | 276 | for ref_i=1:size(i1_series,1) |
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| 277 | for ref_j=1:size(j1_series,2) |
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| 278 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 279 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 280 | if ~isempty(j1_series) |
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| 281 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 282 | end |
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| 283 | end |
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[334] | 284 | end |
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[339] | 285 | elseif size(j2_series,3)>1 %pairs j1 -j2 |
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| 286 | diff_index=abs(j2_series-j1_series); |
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[353] | 287 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
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[339] | 288 | for ref_i=1:size(i1_series,1) |
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| 289 | for ref_j=1:size(j1_series,2) |
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| 290 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 291 | if ~isempty(i2_series) |
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| 292 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 293 | end |
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| 294 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 295 | j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
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| 296 | end |
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| 297 | end |
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| 298 | end |
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| 299 | |
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