source: trunk/src/find_file_series.m @ 456

Last change on this file since 456 was 456, checked in by sommeria, 13 years ago

various bugs corrected
File size: 12.1 KB
Line 
1%'find_file_series': check the content of an input file and find the corresponding file series
2%--------------------------------------------------------------------------
3% function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(fileinput)
4%
5% OUTPUT:
6% RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
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
8%  (ref_i+1 is used to deal with the image index zero sometimes used)
9% NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string)
10% FileType: type of file, =
11%       = 'image', usual image as recognised by Matlab
12%       = 'multimage', image series stored in a single file
13%       = 'civx', netcdf file with civx convention
14%       = 'civdata', civ data with new convention
15%       = 'netcdf' other netcdf files
16%       = 'video': movie recognised by VideoReader (e;g. avi)
17% Object: video object (=[] otherwise)
18%
19%INPUT
20% RootPath: path to the directory to be scanned
21% fileinput: name (without path) of the input file sample
22%
23%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24%  Copyright  2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr
25%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26%     This file is part of the toolbox UVMAT.
27%
28%     UVMAT is free software; you can redistribute it and/or modify
29%     it under the terms of the GNU General Public License as published by
30%     the Free Software Foundation; either version 2 of the License, or
31%     (at your option) any later version.
32%
33%     UVMAT is distributed in the hope that it will be useful,
34%     but WITHOUT ANY WARRANTY; without even the implied warranty of
35%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
36%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
37%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38
39function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput)
40%------------------------------------------------------------------------
41
42%% get input root name and nomenclature type
43fullfileinput=fullfile(FilePath,fileinput);% input file name with path
44[RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput);
45
46
47%% check for particular file types: images, movies, civ data
48i1_series=zeros(1,1,1);
49i2_series=zeros(1,1,1);
50j1_series=zeros(1,1,1);
51j2_series=zeros(1,1,1);
52% ifile_min=1;%default
53[FileType,FileInfo,Object]=get_file_type(fullfileinput);
54NbFrame=1;
55
56switch FileType
57    case 'multimage'
58%    NomType='*';
59%    i1_series=(1:FileInfo.NbFrame)';
60    NbFrame=FileInfo.NbFrame;
61    case {'video','mmreader'}
62    NomType='*';
63    NbFrame=FileInfo.NumberOfFrames;
64%     i1_series=(1:FileInfo.NumberOfFrames)';
65end
66% if strcmp( FileType,'multimage')||strcmp( FileType,'video')||strcmp( FileType,'mmreader')
67%     NomType='*';
68%     i1_series=(1:FileInfo.NumberOfFrames)';
69% end
70RootFile_i='';
71NomTypePref='';
72if strcmp(NomType,'')||strcmp(NomType,'*')
73    if exist(fullfileinput,'file')
74        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
75    else
76        RootFile='';
77    end
78    i1_input=1;% the index now refer to the frame in the movie, choose 1 at opening
79    i2_input=[];
80    j1_input=[];
81    j2_input=[];
82else
83    %% possibly include the first index in the root name, if there exists a corresponding xml file
84    r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
85    if ~isempty(r)
86        fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
87        if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
88            rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
89        else% if a separator '_' is  detected
90            rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
91        end
92        if ~isempty(rr)
93            RootFile_i=[RootFile rr.i1];
94           % checkpair=~isempty(regexp(NomType,'-','once'))||~isempty(regexp(NomType,'ab$','once'))||~isempty(regexp(NomType,'AB$','once'));%case of PIV results
95            if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') %|| (checkpair && exist(fullfile(fileparts(RootPath),[RootFile_i '.xml']),'file'))
96                RootFile=RootFile_i;
97                NomTypePref=r.tiretnum;
98                NomType=regexprep(NomType,['^'  NomTypePref],'');
99                i1_input=j1_input;
100                i2_input=j2_input;
101                j1_input=[];
102                j2_input=[];
103            end       
104        end
105    end
106    %% analyse the list of existing files when relevant
107    sep1='';
108    i1_str='(?<i1>)';%will set i1=[];
109    i1_star='';
110    %     r.sep2='';
111    i2_str='(?<i2>)';%will set i2=[];
112    i2_star='';
113    %     sep3='';
114    j1_str='(?<j1>)';%will set j1=[];
115    j1_star='';
116    %     sep4='';
117    j2_str='(?<j2>)';%will set j2=[];
118    j2_star='';
119    %   NomTypeStr=NomType;
120    %Look for cases with letter indexing for the second index
121    r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
122    if ~isempty(r)
123        sep1=r.sep1;
124        i1_str='(?<i1>\d+)';
125        if strcmp(lower(r.j1),r.j1)% lower case index
126            j1_str='(?<j1>[a-z])';
127        else
128           j1_str='(?<j1>[A-Z])'; % upper case index
129        end
130        j1_star='*';
131        if ~isempty(r.j2)
132           if strcmp(lower(r.j1),r.j1)
133            j2_str='(?<j2>[a-z])';
134            else
135           j2_str='(?<j2>[A-Z])';
136           end
137            j2_star='*';
138        end
139    else %numerical indexing
140        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names');
141        if ~isempty(r)
142            sep1=r.sep1;
143            i1_str='(?<i1>\d+)';
144            i1_star='*';
145            if ~isempty(r.i2)
146                i2_str='(?<i2>-\d+)';
147                i2_star='-*';
148            end
149            if ~isempty(r.j1)
150                j1_str='(?<j1>_\d+)';
151                j1_star='_*';
152            end
153            if ~isempty(r.j2)
154                j2_str='(?<j2>-\d+)';
155                j2_star='-*';
156            end
157        end
158    end
159    detect_string=['^' RootFile sep1 i1_str i2_str j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
160    %find the string used to extract the relevant files with the command dir
161    star_string=[RootFile sep1 i1_star i2_star  j1_star j2_star FileExt];
162    wd=pwd;%current working directory
163    cd (FilePath)% move to the local dir to save time in the operation dir.
164    dirpair=dir(star_string);% look for relevant files in the file directory
165    cd(wd)
166    nbpair=numel(dirpair);
167    ref_i_list=zeros(1,nbpair);
168    ref_j_list=zeros(1,nbpair);
169    if nbpair==0% no detected file
170        RootFile='';
171    end
172    % scan the list of relevant files, extract the indices
173    for ifile=1:nbpair
174        rr=regexp(dirpair(ifile).name,detect_string,'names');
175        if ~isempty(rr)
176            i1=str2num(rr.i1);
177            i2=str2num(regexprep(rr.i2,'^-',''));
178            j1=stra2num(regexprep(rr.j1,'^_',''));
179            j2=stra2num(regexprep(rr.j2,'^-',''));
180            ref_i=i1;
181            if isempty(i2_input)
182                if ~isempty(i2)% invalid file name if i2 does not exist in the input file
183                    break
184                end
185            else
186                ref_i=floor((i1+i2)/2);
187            end
188            ref_j=1;
189            if isempty(j1_input)
190                if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
191                    break
192                end
193            else %j1_input is not empty
194                if isempty(j1)% the detected name does not fit with the input
195                    break
196                else
197                    ref_j=j1;
198                    if isempty(j2_input)
199                        if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
200                            break
201                        end
202                    else
203                        ref_j=floor((j1+j2)/2);
204                    end
205                end
206            end
207            % update the detected index series
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            i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
217            if ~isempty(i2_input)
218                i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
219            end
220            if ~isempty(j1_input)
221                j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
222            end
223            if ~isempty(j2_input)
224                j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
225                j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
226            end
227        end
228    end
229    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
230    max_j=max(ref_j_list);
231    if isempty(max_j)
232        ref_ij=ref_i_list;
233    else
234        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
235    end
236    %[tild,ifile_min]=min(ref_ij(ref_ij>0));
237    ind_select=find(ref_ij>0);
238    if isempty(ind_select)
239        %         RootPath='';
240        RootFile='';
241        NomType='';
242    else
243        [tild,ifile_min]=min(ref_ij(ind_select));
244        [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)
245        NomType=regexprep(NomType,['^' NomTypePref],'');
246    end
247    %% update the file type if the input file does not exist (pb of 0001)
248    if isempty(FileType)
249        [FileType,tild,Object]=get_file_type(dirpair(ifile_min).name);
250    end
251end
252
253%% set to empty array the irrelevant index series
254if isequal(i1_series,0), i1_series=[]; end
255if isequal(i2_series,0), i2_series=[]; end
256if isequal(j1_series,0), j1_series=[]; end
257if isequal(j2_series,0), j2_series=[]; end
258
259%% introduce the frame index in case of movies or multimage type
260if NbFrame>1
261    if isempty(i1_series)
262        i1_series=(1:NbFrame)';
263        i1_input=1;
264    else
265       j1_series=(1:NbFrame)';
266       j1_input=1;
267    end
268end
269
270%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
271if size(i2_series,3)>1 %pairs i1 -i2
272    diff_index=abs(i2_series-i1_series);
273    [tild,ind_pair]=sort(diff_index,3,'descend');
274    for ref_i=1:size(i1_series,1)
275        for ref_j=1:size(j1_series,2)
276            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
277            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
278            if ~isempty(j1_series)
279                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
280            end
281        end
282    end
283elseif size(j2_series,3)>1 %pairs j1 -j2
284    diff_index=abs(j2_series-j1_series);
285    [tild,ind_pair]=sort(diff_index,3,'descend');
286    for ref_i=1:size(i1_series,1)
287        for ref_j=1:size(j1_series,2)
288            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
289            if ~isempty(i2_series)
290                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
291            end
292            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
293            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
294        end
295    end
296end
297
298% %% deals with frame index in movies
299% switch FileType
300%     case 'multimage'
301%    NomType='*';
302%    i1_series=(1:FileInfo.NbFrame)';
303%     case {'video','mmreader'}
304%     NomType='*';
305%     i1_series=(1:FileInfo.NumberOfFrames)';
306% end
307
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