source: trunk/src/find_file_series.m

Last change on this file was 1164, checked in by sommeria, 5 months ago

civ3D updated

File size: 15.7 KB
RevLine 
[356]1%'find_file_series': check the content of an input file and find the corresponding file series
[332]2%--------------------------------------------------------------------------
[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)
[332]4%
5% OUTPUT:
[783]6% RootPath: path to the dir containing the input file
7% SubDir: data dir containing the input file series
[371]8% RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
[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
[343]10%  (ref_i+1 is used to deal with the image index zero sometimes used)
[332]11% NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string)
[783]12% FileInfo: structure containing info on the input files (assumed identical on the whole series)
[1009]13% FileInfo.FileType: type of file, =
14%       = 'image', usual image as recognised by Matlab
15%       = 'multimage', image series stored in a single file
16%       = 'civx', netcdf file with civx convention
17%       = 'civdata', civ data with new convention
18%       = 'netcdf' other netcdf files
19%       = 'video': movie recognised by VideoReader (e;g. avi)
[783]20% MovieObject: video object (=[] otherwise
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
[332]22%
23%INPUT
[783]24% FilePath: path to the directory to be scanned
[1009]25% fileinput: name (without path) of the input file sample
[667]26% checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile
27%           =0: do not take into account xml file existence
[809]28
29%=======================================================================
[1126]30% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[809]31%   http://www.legi.grenoble-inp.fr
[1127]32%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
[332]33%
34%     This file is part of the toolbox UVMAT.
[809]35%
[332]36%     UVMAT is free software; you can redistribute it and/or modify
[809]37%     it under the terms of the GNU General Public License as published
38%     by the Free Software Foundation; either version 2 of the license,
39%     or (at your option) any later version.
40%
[332]41%     UVMAT is distributed in the hope that it will be useful,
42%     but WITHOUT ANY WARRANTY; without even the implied warranty of
43%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
[809]44%     GNU General Public License (see LICENSE.txt) for more details.
45%=======================================================================
[332]46
[783]47function [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)
[332]48%------------------------------------------------------------------------
[398]49
[1033]50%% get input root name and info on the input file
[1164]51if isempty(regexp(FilePath,'^http://','once'))% case of usual file input
[398]52fullfileinput=fullfile(FilePath,fileinput);% input file name with path
[1022]53else
[1164]54  fullfileinput=[FilePath '/' fileinput]; % case of web input
[1022]55end
[790]56[FileInfo,MovieObject]=get_file_info(fullfileinput);
[332]57
58%% check for particular file types: images, movies, civ data
[1022]59[RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput);
60i1_series=zeros(1,1,1);
61i2_series=zeros(1,1,1);
62j1_series=zeros(1,1,1);
63j2_series=zeros(1,1,1);
64checkfileindexing=1;
65if isempty(regexp(FilePath,'^http://')) && ~exist(FilePath,'dir')
[472]66    return % don't go further if the dir path does not exist
67end
[790]68if checkfileindexing
[961]69    NomTypePref='';
70    if isempty(NomType)||strcmp(NomType,'*')
71        if exist(fullfileinput,'file')
72            [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
73        else
74            RootFile='';
75        end
[388]76    else
[961]77        %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file
78        if ~exist('checkxml','var')||checkxml
79            r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
80            if ~isempty(r) %if NomType begins by a number or _1
81                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
82                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
83                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
84                else% if a separator '_' is  detected
85                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
[667]86                end
[961]87                if ~isempty(rr)
88                    RootFile_i=[RootFile rr.i1];% new root file
89                    %look for an xml file correspoonding to the new root name
90                    if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
91                        RootFile=RootFile_i;
92                        NomTypePref=r.tiretnum;
93                        NomType=regexprep(NomType,['^'  NomTypePref],'');
94                        i1_input=j1_input;
95                        i2_input=j2_input;
96                        j1_input=[];
97                        j2_input=[];
98                    end
99                end
[667]100            end
[384]101        end
[961]102       
103        %% analyse the list of existing files when relevant
104        sep1='';
105        sep2='';
106        i1_str='(?<i1>)';%will set i1=[];
107        i2_str='(?<i2>)';%will set i2=[];
108        j1_str='(?<j1>)';%will set j1=[];
109        j2_str='(?<j2>)';%will set j2=[];
[1164]110
[961]111        %Look for cases with letter indexing for the second index
112        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
[1022]113        if ~isempty(r) %indexing image pair with letters
[388]114            sep1=r.sep1;
[961]115            sep2=r.sep2;
[388]116            i1_str='(?<i1>\d+)';
[961]117            if strcmp(lower(r.j1),r.j1)% lower case index
118                j1_str='(?<j1>[a-z])';
119            else
120                j1_str='(?<j1>[A-Z])'; % upper case index
[360]121            end
[388]122            if ~isempty(r.j2)
[961]123                if strcmp(lower(r.j1),r.j1)
124                    j2_str='(?<j2>[a-z])';
125                else
126                    j2_str='(?<j2>[A-Z])';
127                end
[360]128            end
[961]129        else %numerical indexing
130            r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names');
131            if ~isempty(r)
132                sep1=r.sep1;
133                i1_str='(?<i1>\d+)';
134                if ~isempty(r.i2)
135                    i2_str='(?<i2>-\d+)';
136                end
137                if ~isempty(r.j1)
138                    j1_str='(?<j1>_\d+)';
139                end
140                if ~isempty(r.j2)
141                    j2_str='(?<j2>-\d+)';
142                end
143            end
[360]144        end
[1033]145       
[1009]146        detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
[1033]147        ListStruct=dir_uvmat(FilePath);% scan the content of the folder FilePath
148        ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
149        ListFiles=ListCells(1,:);%list of file names
150        rr=regexp(ListFiles,detect_string,'names');
[1022]151        nbpair=numel(rr);
[1009]152        ref_i_list=zeros(1,nbpair);
153        ref_j_list=zeros(1,nbpair);
154        if nbpair==0% no detected file
155            RootFile='';
156        end
157        % scan the list of relevant files, extract the indices
158        for ifile=1:nbpair
[1033]159            %             rr=regexp(dirpair(ifile).name,detect_string,'names');
[1022]160            if ~isempty(rr{ifile})
161                i1=str2num(rr{ifile}.i1);
162                i2=str2num(regexprep(rr{ifile}.i2,'^-',''));
163                j1=stra2num(regexprep(rr{ifile}.j1,'^_',''));
164                j2=stra2num(regexprep(rr{ifile}.j2,'^-',''));
[1009]165                ref_i=i1;
166                if isempty(i2_input)
167                    if ~isempty(i2)% invalid file name if i2 does not exist in the input file
168                        break
169                    end
170                else
171                    ref_i=floor((i1+i2)/2);
[388]172                end
[1009]173                ref_j=1;
174                if isempty(j1_input)
175                    if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
176                        break
177                    end
178                else %j1_input is not empty
179                    if isempty(j1)% the detected name does not fit with the input
180                        break
[388]181                    else
[1009]182                        ref_j=j1;
183                        if isempty(j2_input)
184                            if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
185                                break
186                            end
[961]187                        else
[1009]188                            ref_j=floor((j1+j2)/2);
[961]189                        end
190                    end
[1009]191                end
192                % update the detected index series
193                if ~isempty(ref_i)&&~isempty(ref_j)
194                    ref_i_list(ifile)=ref_i;
195                    ref_j_list(ifile)=ref_j;
196                    nb_pairs=0;
197                    if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
198                        if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
199                            nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
[961]200                        end
201                    end
[1009]202                    if i1==0
203                        i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
204                    end
205                    if j1==0
206                        j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
207                    end
208                    i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
209                    if ~isempty(i2_input)
210                        i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
211                    end
212                    if ~isempty(j1_input)
213                        j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
214                    end
215                    if ~isempty(j2_input)
216                        j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
217                        j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
218                    end
[339]219                end
220            end
[1009]221        end
222        % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
223        max_j=max(ref_j_list);
224        if isempty(max_j)
225            ref_ij=ref_i_list;
226        else
227            ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
228        end
229        ind_select=find(ref_ij>0);
230       
231        if ~isempty(ind_select)
232            [tild,ifile_min]=min(ref_ij(ind_select));
[1022]233            [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)
[1009]234            NomType=regexprep(NomType,['^' NomTypePref],'');
235            %% update the file type if the input file does not exist (pb of 0001)
236            if isempty(FileInfo.FileType)
[1050]237                [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,ListFiles{ifile_min}));
[961]238            end
[334]239        end
[1009]240        %         end
[339]241    end
[1009]242   
243    %% set to empty array the irrelevant index series
244    if isequal(i1_series,0), i1_series=[]; end
245    if isequal(i2_series,0), i2_series=[]; end
246    if isequal(j1_series,0), j1_series=[]; end
247    if isequal(j2_series,0), j2_series=[]; end
248   
249    %% case of isolated input file, not member of an  indexed series
250    if isempty(i1_series)
251        [PathDir,RootFile]=fileparts(fullfileinput);
252        [RootPath,SubDir,DirExt]=fileparts(PathDir);
253        SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension)
254        NomType='*';
255        i2_series=[];j1_series=[];j2_series=[];
[1033]256        %         i1_input=1;i2_input=[];j1_input=[];j2_input=[];
[1009]257        if ~exist(fullfileinput,'file')
258            RootFile='';
259            return
260        end
261    end
[784]262end
263
[445]264%% introduce the frame index in case of movies or multimage type
[484]265if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
[783]266    if isempty(i1_series)% if there is no file index, i denotes the frame index
[609]267        i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
268        i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
[445]269        i1_input=1;
[483]270        NomType='*';
[783]271    else  % if there is a file index, j denotes the frame index while i denotes the file index
[788]272        if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair
[1009]273            RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices
[783]274            i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
275            i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
276            j1_series=[];
277            i1_input=1;
278            NomType='*';
279        else
280            i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);%
281            i1_series=[zeros(size(i1_series,1),1) i1_series];
[1164]282            if ~isempty(i2_series)
283                i2_series=i2_series(:,2)*ones(1,FileInfo.NumberOfFrames);%
284            i2_series=[zeros(size(i2_series,1),1) i2_series];
285            end
[783]286            j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);%
287            j1_series=[zeros(size(i1_series,1),1) j1_series];
288            %  include the first index in the root name
289            r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
290            if ~isempty(r)
291                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
292                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
293                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
294                else% if a separator '_' is  detected
295                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
296                end
297                if ~isempty(rr)
298                    j1_input=1;
299                    j2_input=[];
300                end
[483]301            end
302        end
[445]303    end
304end
305
[339]306%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
307if size(i2_series,3)>1 %pairs i1 -i2
308    diff_index=abs(i2_series-i1_series);
[353]309    [tild,ind_pair]=sort(diff_index,3,'descend');
[339]310    for ref_i=1:size(i1_series,1)
311        for ref_j=1:size(j1_series,2)
312            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
313            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
314            if ~isempty(j1_series)
315                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
316            end
317        end
[334]318    end
[339]319elseif size(j2_series,3)>1 %pairs j1 -j2
320    diff_index=abs(j2_series-j1_series);
[353]321    [tild,ind_pair]=sort(diff_index,3,'descend');
[339]322    for ref_i=1:size(i1_series,1)
323        for ref_j=1:size(j1_series,2)
324            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
325            if ~isempty(i2_series)
326                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
327            end
328            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
329            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
330        end
331    end
332end
[1009]333i1_series=permute(i1_series,[3 2 1]);% permute dimensions
[512]334i2_series=permute(i2_series,[3 2 1]);% permute dimensions
[1009]335j1_series=permute(j1_series,[3 2 1]);% permute dimensions
[512]336j2_series=permute(j2_series,[3 2 1]);% permute dimensions
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