%'find_file_series': check the content of an input file and find the corresponding file series %-------------------------------------------------------------------------- % 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) % % OUTPUT: % RootPath: path to the dir containing the input file % SubDir: data dir containing the input file series % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file) % 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 % (ref_i+1 is used to deal with the image index zero sometimes used) % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string) % FileInfo: structure containing info on the input files (assumed identical on the whole series) % FileInfo.FileType: type of file, = % = 'image', usual image as recognised by Matlab % = 'multimage', image series stored in a single file % = 'civx', netcdf file with civx convention % = 'civdata', civ data with new convention % = 'netcdf' other netcdf files % = 'video': movie recognised by VideoReader (e;g. avi) % MovieObject: video object (=[] otherwise % 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 % %INPUT % FilePath: path to the directory to be scanned % fileinput: name (without path) of the input file sample % checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile % =0: do not take into account xml file existence %======================================================================= % Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= 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) %------------------------------------------------------------------------ %% get input root name and nomenclature type fullfileinput=fullfile(FilePath,fileinput);% input file name with path [FileInfo,MovieObject]=get_file_info(fullfileinput); %% check for particular file types: images, movies, civ data checkfileindexing=0; if isfield(FileInfo,'FileIndexing') && strcmp(FileInfo.FileIndexing,'on') [RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput); i1_series=zeros(1,1,1); i2_series=zeros(1,1,1); j1_series=zeros(1,1,1); j2_series=zeros(1,1,1); checkfileindexing=1; else % no file indexing [PathDir,RootFile]=fileparts(fullfileinput); [RootPath,SubDir,DirExt]=fileparts(PathDir); SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension) NomType='*'; i1_series=[];i2_series=[];j1_series=[];j2_series=[]; i1_input=1;i2_input=[];j1_input=[];j2_input=[]; if exist(fullfileinput,'file')~=2 RootFile=''; return end end if ~exist(FilePath,'dir') return % don't go further if the dir path does not exist end if checkfileindexing NomTypePref=''; if isempty(NomType)||strcmp(NomType,'*') if exist(fullfileinput,'file') [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension else RootFile=''; end else %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file if ~exist('checkxml','var')||checkxml r=regexp(NomType,'^(?_|\d+)','names');%look for a number or _1 at the beginning of NomType if ~isempty(r) %if NomType begins by a number or _1 fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected rr=regexp(fileinput_end,'^(?\d+)','names'); else% if a separator '_' is detected rr=regexp(fileinput_end,'^(?_\d+)','names'); end if ~isempty(rr) RootFile_i=[RootFile rr.i1];% new root file %look for an xml file correspoonding to the new root name if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file')) RootFile=RootFile_i; NomTypePref=r.tiretnum; NomType=regexprep(NomType,['^' NomTypePref],''); i1_input=j1_input; i2_input=j2_input; j1_input=[]; j2_input=[]; elseif exist([RootPath '.xml'],'file')% new convention with j indices in sub-folders level0, 1... rj=regexp(SubDir,'^level(?\d+)$','names'); if ~isempty(rj) j1_input=rj.j1; NomType='level'; [RootPath,SubDir]=fileparts(RootPath); end end end end end %% analyse the list of existing files when relevant sep1=''; sep2=''; i1_str='(?)';%will set i1=[]; i1_star=''; i2_str='(?)';%will set i2=[]; i2_star=''; j1_str='(?)';%will set j1=[]; j1_star=''; j2_str='(?)';%will set j2=[]; j2_star=''; %Look for cases with letter indexing for the second index r=regexp(NomType,'^(?_?)(?\d+)(?_?)(?[a|A])(?[b|B]?)$','names'); if ~isempty(r) sep1=r.sep1; sep2=r.sep2; i1_str='(?\d+)'; i1_star='*'; if strcmp(lower(r.j1),r.j1)% lower case index j1_str='(?[a-z])'; else j1_str='(?[A-Z])'; % upper case index end j1_star='*'; if ~isempty(r.j2) if strcmp(lower(r.j1),r.j1) j2_str='(?[a-z])'; else j2_str='(?[A-Z])'; end j2_star='*'; end else %numerical indexing r=regexp(NomType,'^(?_?)(?\d+)(?(-\d+)?)(?(_\d+)?)(?(-\d+)?)$','names'); if ~isempty(r) sep1=r.sep1; i1_str='(?\d+)'; i1_star='*'; if ~isempty(r.i2) i2_str='(?-\d+)'; i2_star='-*'; end if ~isempty(r.j1) j1_str='(?_\d+)'; j1_star='_*'; end if ~isempty(r.j2) j2_str='(?-\d+)'; j2_star='-*'; end end end if strcmp(NomType,'level') star_string=[RootFile '*' FileExt]; detect_string=['^' RootFile '(?\d+)' FileExt '$'];%string used in regexp to detect file indices wd=pwd;%current working directory cd (FilePath)% move to the local dir to save time in the operation dir. dirpair=dir(star_string);% look for relevant files in the file directory cd(wd) nbpair=numel(dirpair); i1_series=zeros(1,nbpair); if nbpair==0% no detected file RootFile=''; end % scan the list of relevant files, extract the indices for ifile=1:nbpair rr=regexp(dirpair(ifile).name,detect_string,'names'); if ~isempty(rr) i1_series(ifile)=str2num(rr.i1); end end % look for the list of subfolders level# cd (fullfile(RootPath,SubDir))% move to the local dir to save time in the operation dir. dirpair=dir('level*');% look for relevant files in the file directory cd(wd) nbpair=numel(dirpair); jfile=0; for ifile=1:nbpair rr=regexp(dirpair(ifile).name,'^level(?\d+)$','names'); if ~isempty(rr) jfile=jfile+1; j1_series(jfile)=str2num(rr.i1); end end [i1_series,j1_series]=meshgrid(i1_series,j1_series); i1_series=reshape(i1_series,1,[]); j1_series=reshape(j1_series,1,[]); else detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices %find the string used to extract the relevant files with the command dir star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt]; wd=pwd;%current working directory cd (FilePath)% move to the local dir to save time in the operation dir. dirpair=dir(star_string);% look for relevant files in the file directory cd(wd) nbpair=numel(dirpair); ref_i_list=zeros(1,nbpair); ref_j_list=zeros(1,nbpair); if nbpair==0% no detected file RootFile=''; end % scan the list of relevant files, extract the indices for ifile=1:nbpair rr=regexp(dirpair(ifile).name,detect_string,'names'); if ~isempty(rr) i1=str2num(rr.i1); i2=str2num(regexprep(rr.i2,'^-','')); j1=stra2num(regexprep(rr.j1,'^_','')); j2=stra2num(regexprep(rr.j2,'^-','')); ref_i=i1; if isempty(i2_input) if ~isempty(i2)% invalid file name if i2 does not exist in the input file break end else ref_i=floor((i1+i2)/2); end ref_j=1; if isempty(j1_input) if ~isempty(j1)% invalid file name if j1 does not exist in the input file break end else %j1_input is not empty if isempty(j1)% the detected name does not fit with the input break else ref_j=j1; if isempty(j2_input) if ~isempty(j2)% invalid file name if j2 does not exist in the input file break end else ref_j=floor((j1+j2)/2); end end end % update the detected index series if ~isempty(ref_i)&&~isempty(ref_j) ref_i_list(ifile)=ref_i; ref_j_list(ifile)=ref_j; nb_pairs=0; if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); end end if i1==0 i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) end if j1==0 j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) end i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; if ~isempty(i2_input) i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; end if ~isempty(j1_input) j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; end if ~isempty(j2_input) j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; end end end end % look for the numerical string of the first files to update the NomType (take into account the 0 before the number) max_j=max(ref_j_list); if isempty(max_j) ref_ij=ref_i_list; else ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i. end ind_select=find(ref_ij>0); if ~isempty(ind_select) [tild,ifile_min]=min(ref_ij(ind_select)); [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) NomType=regexprep(NomType,['^' NomTypePref],''); %% update the file type if the input file does not exist (pb of 0001) if isempty(FileInfo.FileType) [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name)); end end end end %% set to empty array the irrelevant index series if isequal(i1_series,0), i1_series=[]; end if isequal(i2_series,0), i2_series=[]; end if isequal(j1_series,0), j1_series=[]; end if isequal(j2_series,0), j2_series=[]; end end % %% detect rdvision format % if strcmp(FileExt,'.bin') % if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file') % FileInfo.FileType='rdvision'; % FileInfo.SeqFile=[RootFile '.seq']; % end % end %% introduce the frame index in case of movies or multimage type if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 if isempty(i1_series)% if there is no file index, i denotes the frame index i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 i1_input=1; NomType='*'; else % if there is a file index, j denotes the frame index while i denotes the file index if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 j1_series=[]; i1_input=1; NomType='*'; else i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);% i1_series=[zeros(size(i1_series,1),1) i1_series]; j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);% j1_series=[zeros(size(i1_series,1),1) j1_series]; % include the first index in the root name r=regexp(NomType,'^(?_?\d+)','names');%look for a number or _1 at the beginning of NomType if ~isempty(r) fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected rr=regexp(fileinput_end,'^(?\d+)','names'); else% if a separator '_' is detected rr=regexp(fileinput_end,'^(?_\d+)','names'); end if ~isempty(rr) j1_input=1; j2_input=[]; end end end end end %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index if size(i2_series,3)>1 %pairs i1 -i2 diff_index=abs(i2_series-i1_series); [tild,ind_pair]=sort(diff_index,3,'descend'); for ref_i=1:size(i1_series,1) for ref_j=1:size(j1_series,2) i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); if ~isempty(j1_series) j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); end end end elseif size(j2_series,3)>1 %pairs j1 -j2 diff_index=abs(j2_series-j1_series); [tild,ind_pair]=sort(diff_index,3,'descend'); for ref_i=1:size(i1_series,1) for ref_j=1:size(j1_series,2) i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); if ~isempty(i2_series) i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); end j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); end end end i1_series=permute(i1_series,[3 2 1]);% permute dimensions i2_series=permute(i2_series,[3 2 1]);% permute dimensions j1_series=permute(j1_series,[3 2 1]);% permute dimensions j2_series=permute(j2_series,[3 2 1]);% permute dimensions