source: trunk/src/find_file_series.m @ 801

Last change on this file since 801 was 801, checked in by g7moreau, 10 years ago
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1%'find_file_series': check the content of an input file and find the corresponding file series
2%--------------------------------------------------------------------------
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)
4%
5% OUTPUT:
6% RootPath: path to the dir containing the input file
7% SubDir: data dir containing the input file series
8% RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
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
10%  (ref_i+1 is used to deal with the image index zero sometimes used)
11% NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string)
12% FileInfo: structure containing info on the input files (assumed identical on the whole series)
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)
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
22%
23%INPUT
24% FilePath: path to the directory to be scanned
25% fileinput: name (without path) of the input file sample
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
28%
29%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30%  Copyright 2011-2014, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr
31%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
32%     This file is part of the toolbox UVMAT.
33%
34%     UVMAT is free software; you can redistribute it and/or modify
35%     it under the terms of the GNU General Public License as published by
36%     the Free Software Foundation; either version 2 of the License, or
37%     (at your option) any later version.
38%
39%     UVMAT is distributed in the hope that it will be useful,
40%     but WITHOUT ANY WARRANTY; without even the implied warranty of
41%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
42%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
43%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44
45function [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)
46%------------------------------------------------------------------------
47
48%% get input root name and nomenclature type
49fullfileinput=fullfile(FilePath,fileinput);% input file name with path
50[FileInfo,MovieObject]=get_file_info(fullfileinput);
51
52%% check for particular file types: images, movies, civ data
53checkfileindexing=0;
54if isfield(FileInfo,'FileIndexing') && strcmp(FileInfo.FileIndexing,'on')
55    [RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput);
56    i1_series=zeros(1,1,1);
57    i2_series=zeros(1,1,1);
58    j1_series=zeros(1,1,1);
59    j2_series=zeros(1,1,1);
60    checkfileindexing=1;
61else % no file indexing
62    [PathDir,RootFile]=fileparts(fullfileinput);
63    [RootPath,SubDir,DirExt]=fileparts(PathDir);
64    SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension)
65    NomType='*';
66    i1_series=[];i2_series=[];j1_series=[];j2_series=[];
67    i1_input=1;i2_input=[];j1_input=[];j2_input=[];
68end
69if ~exist(FilePath,'dir')
70    return % don't go further if the dir path does not exist
71end
72if checkfileindexing
73NomTypePref='';
74if isempty(NomType)
75    if exist(fullfileinput,'file')
76        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
77    else
78        RootFile='';
79    end
80else
81    %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file
82    if ~exist('checkxml','var')||checkxml
83        r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
84        if ~isempty(r) %if NomType begins by a number or _1
85            fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
86            if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
87                rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
88            else% if a separator '_' is  detected
89                rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
90            end
91            if ~isempty(rr)
92                RootFile_i=[RootFile rr.i1];% new root file
93                %look for an xml file correspoonding to the new root name
94                if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
95                    RootFile=RootFile_i;
96                    NomTypePref=r.tiretnum;
97                    NomType=regexprep(NomType,['^'  NomTypePref],'');
98                    i1_input=j1_input;
99                    i2_input=j2_input;
100                    j1_input=[];
101                    j2_input=[];
102                end
103            end
104        end
105    end
106    %% analyse the list of existing files when relevant
107    sep1='';
108    sep2='';
109    i1_str='(?<i1>)';%will set i1=[];
110    i1_star='';
111    i2_str='(?<i2>)';%will set i2=[];
112    i2_star='';
113    j1_str='(?<j1>)';%will set j1=[];
114    j1_star='';
115    j2_str='(?<j2>)';%will set j2=[];
116    j2_star='';
117    %Look for cases with letter indexing for the second index
118    r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
119    if ~isempty(r)
120        sep1=r.sep1;
121        sep2=r.sep2;
122        i1_str='(?<i1>\d+)';
123        i1_star='*';
124        if strcmp(lower(r.j1),r.j1)% lower case index
125            j1_str='(?<j1>[a-z])';
126        else
127           j1_str='(?<j1>[A-Z])'; % upper case index
128        end
129        j1_star='*';
130        if ~isempty(r.j2)
131           if strcmp(lower(r.j1),r.j1)
132            j2_str='(?<j2>[a-z])';
133            else
134           j2_str='(?<j2>[A-Z])';
135           end
136            j2_star='*';
137        end
138    else %numerical indexing
139        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names');
140        if ~isempty(r)
141            sep1=r.sep1;
142            i1_str='(?<i1>\d+)';
143            i1_star='*';
144            if ~isempty(r.i2)
145                i2_str='(?<i2>-\d+)';
146                i2_star='-*';
147            end
148            if ~isempty(r.j1)
149                j1_str='(?<j1>_\d+)';
150                j1_star='_*';
151            end
152            if ~isempty(r.j2)
153                j2_str='(?<j2>-\d+)';
154                j2_star='-*';
155            end
156        end
157    end
158    detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
159    %find the string used to extract the relevant files with the command dir
160    star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt];
161    wd=pwd;%current working directory
162    cd (FilePath)% move to the local dir to save time in the operation dir.
163    dirpair=dir(star_string);% look for relevant files in the file directory
164    cd(wd)
165    nbpair=numel(dirpair);
166    ref_i_list=zeros(1,nbpair);
167    ref_j_list=zeros(1,nbpair);
168    if nbpair==0% no detected file
169        RootFile='';
170    end
171    % scan the list of relevant files, extract the indices
172    for ifile=1:nbpair
173        rr=regexp(dirpair(ifile).name,detect_string,'names');
174        if ~isempty(rr)
175            i1=str2num(rr.i1);
176            i2=str2num(regexprep(rr.i2,'^-',''));
177            j1=stra2num(regexprep(rr.j1,'^_',''));
178            j2=stra2num(regexprep(rr.j2,'^-',''));
179            ref_i=i1;
180            if isempty(i2_input)
181                if ~isempty(i2)% invalid file name if i2 does not exist in the input file
182                    break
183                end
184            else
185                ref_i=floor((i1+i2)/2);
186            end
187            ref_j=1;
188            if isempty(j1_input)
189                if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
190                    break
191                end
192            else %j1_input is not empty
193                if isempty(j1)% the detected name does not fit with the input
194                    break
195                else
196                    ref_j=j1;
197                    if isempty(j2_input)
198                        if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
199                            break
200                        end
201                    else
202                        ref_j=floor((j1+j2)/2);
203                    end
204                end
205            end
206            % update the detected index series
207            if ~isempty(ref_i)&&~isempty(ref_j)
208                ref_i_list(ifile)=ref_i;
209                ref_j_list(ifile)=ref_j;
210                nb_pairs=0;
211                if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
212                    if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
213                        nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
214                    end
215                end
216                if i1==0
217                    i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
218                end
219                if j1==0
220                    j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
221                end
222                i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
223                if ~isempty(i2_input)
224                    i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
225                end
226                if ~isempty(j1_input)
227                    j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
228                end
229                if ~isempty(j2_input)
230                    j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
231                    j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
232                end
233            end
234        end
235    end
236    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
237    max_j=max(ref_j_list);
238    if isempty(max_j)
239        ref_ij=ref_i_list;
240    else
241        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
242    end
243    ind_select=find(ref_ij>0);
244   
245    if isempty(ind_select)
246%         RootFile='';
247%         NomType='';
248    else
249        [tild,ifile_min]=min(ref_ij(ind_select));
250        [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)
251        NomType=regexprep(NomType,['^' NomTypePref],'');
252        %% update the file type if the input file does not exist (pb of 0001)
253        if isempty(FileInfo.FileType)
254            [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name));
255        end
256    end
257end
258
259%% set to empty array the irrelevant index series
260if isequal(i1_series,0), i1_series=[]; end
261if isequal(i2_series,0), i2_series=[]; end
262if isequal(j1_series,0), j1_series=[]; end
263if isequal(j2_series,0), j2_series=[]; end
264end
265% %% detect rdvision format
266% if strcmp(FileExt,'.bin')
267%     if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file')
268%         FileInfo.FileType='rdvision';
269%         FileInfo.SeqFile=[RootFile '.seq'];
270%     end
271% end
272
273%% introduce the frame index in case of movies or multimage type
274if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
275    if isempty(i1_series)% if there is no file index, i denotes the frame index
276        i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
277        i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
278        i1_input=1;
279        NomType='*';
280    else  % if there is a file index, j denotes the frame index while i denotes the file index
281        if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair
282            RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices       
283            i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
284            i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
285            j1_series=[];
286            i1_input=1;
287            NomType='*';
288        else
289            i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);%
290            i1_series=[zeros(size(i1_series,1),1) i1_series];
291            j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);%
292            j1_series=[zeros(size(i1_series,1),1) j1_series];
293            %  include the first index in the root name
294            r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
295            if ~isempty(r)
296                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
297                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
298                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
299                else% if a separator '_' is  detected
300                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
301                end
302                if ~isempty(rr)
303                    j1_input=1;
304                    j2_input=[];
305                end
306            end
307        end
308    end
309end
310
311%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
312if size(i2_series,3)>1 %pairs i1 -i2
313    diff_index=abs(i2_series-i1_series);
314    [tild,ind_pair]=sort(diff_index,3,'descend');
315    for ref_i=1:size(i1_series,1)
316        for ref_j=1:size(j1_series,2)
317            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
318            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
319            if ~isempty(j1_series)
320                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
321            end
322        end
323    end
324elseif size(j2_series,3)>1 %pairs j1 -j2
325    diff_index=abs(j2_series-j1_series);
326    [tild,ind_pair]=sort(diff_index,3,'descend');
327    for ref_i=1:size(i1_series,1)
328        for ref_j=1:size(j1_series,2)
329            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
330            if ~isempty(i2_series)
331                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
332            end
333            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
334            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
335        end
336    end
337end
338i1_series=permute(i1_series,[3 2 1]);% permute dimensions
339i2_series=permute(i2_series,[3 2 1]);% permute dimensions
340j1_series=permute(j1_series,[3 2 1]);% permute dimensions
341j2_series=permute(j2_series,[3 2 1]);% permute dimensions
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