source: trunk/src/find_file_series.m @ 789

Last change on this file since 789 was 788, checked in by sommeria, 10 years ago
File size: 14.6 KB
Line 
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, LEGI / CNRS-UJF-INPG, 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[RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput);
51
52
53%% check for particular file types: images, movies, civ data
54i1_series=zeros(1,1,1);
55i2_series=zeros(1,1,1);
56j1_series=zeros(1,1,1);
57j2_series=zeros(1,1,1);
58[FileInfo,MovieObject]=get_file_info(fullfileinput);
59if ~exist(FilePath,'dir')
60    return % don't go further if the dir path does not exist
61end
62NomTypePref='';
63if isempty(NomType)
64    if exist(fullfileinput,'file')
65        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
66    else
67        RootFile='';
68    end
69else
70    %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file
71    if ~exist('checkxml','var')||checkxml
72        r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
73        if ~isempty(r) %if NomType begins by a number or _1
74            fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
75            if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
76                rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
77            else% if a separator '_' is  detected
78                rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
79            end
80            if ~isempty(rr)
81                RootFile_i=[RootFile rr.i1];% new root file
82                %look for an xml file correspoonding to the new root name
83                if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
84                    RootFile=RootFile_i;
85                    NomTypePref=r.tiretnum;
86                    NomType=regexprep(NomType,['^'  NomTypePref],'');
87                    i1_input=j1_input;
88                    i2_input=j2_input;
89                    j1_input=[];
90                    j2_input=[];
91                end
92            end
93        end
94    end
95    %% analyse the list of existing files when relevant
96    sep1='';
97    sep2='';
98    i1_str='(?<i1>)';%will set i1=[];
99    i1_star='';
100    i2_str='(?<i2>)';%will set i2=[];
101    i2_star='';
102    j1_str='(?<j1>)';%will set j1=[];
103    j1_star='';
104    j2_str='(?<j2>)';%will set j2=[];
105    j2_star='';
106    %Look for cases with letter indexing for the second index
107    r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
108    if ~isempty(r)
109        sep1=r.sep1;
110        sep2=r.sep2;
111        i1_str='(?<i1>\d+)';
112        i1_star='*';
113        if strcmp(lower(r.j1),r.j1)% lower case index
114            j1_str='(?<j1>[a-z])';
115        else
116           j1_str='(?<j1>[A-Z])'; % upper case index
117        end
118        j1_star='*';
119        if ~isempty(r.j2)
120           if strcmp(lower(r.j1),r.j1)
121            j2_str='(?<j2>[a-z])';
122            else
123           j2_str='(?<j2>[A-Z])';
124           end
125            j2_star='*';
126        end
127    else %numerical indexing
128        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names');
129        if ~isempty(r)
130            sep1=r.sep1;
131            i1_str='(?<i1>\d+)';
132            i1_star='*';
133            if ~isempty(r.i2)
134                i2_str='(?<i2>-\d+)';
135                i2_star='-*';
136            end
137            if ~isempty(r.j1)
138                j1_str='(?<j1>_\d+)';
139                j1_star='_*';
140            end
141            if ~isempty(r.j2)
142                j2_str='(?<j2>-\d+)';
143                j2_star='-*';
144            end
145        end
146    end
147    detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
148    %find the string used to extract the relevant files with the command dir
149    star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt];
150    wd=pwd;%current working directory
151    cd (FilePath)% move to the local dir to save time in the operation dir.
152    dirpair=dir(star_string);% look for relevant files in the file directory
153    cd(wd)
154    nbpair=numel(dirpair);
155    ref_i_list=zeros(1,nbpair);
156    ref_j_list=zeros(1,nbpair);
157    if nbpair==0% no detected file
158        RootFile='';
159    end
160    % scan the list of relevant files, extract the indices
161    for ifile=1:nbpair
162        rr=regexp(dirpair(ifile).name,detect_string,'names');
163        if ~isempty(rr)
164            i1=str2num(rr.i1);
165            i2=str2num(regexprep(rr.i2,'^-',''));
166            j1=stra2num(regexprep(rr.j1,'^_',''));
167            j2=stra2num(regexprep(rr.j2,'^-',''));
168            ref_i=i1;
169            if isempty(i2_input)
170                if ~isempty(i2)% invalid file name if i2 does not exist in the input file
171                    break
172                end
173            else
174                ref_i=floor((i1+i2)/2);
175            end
176            ref_j=1;
177            if isempty(j1_input)
178                if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
179                    break
180                end
181            else %j1_input is not empty
182                if isempty(j1)% the detected name does not fit with the input
183                    break
184                else
185                    ref_j=j1;
186                    if isempty(j2_input)
187                        if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
188                            break
189                        end
190                    else
191                        ref_j=floor((j1+j2)/2);
192                    end
193                end
194            end
195            % update the detected index series
196            if ~isempty(ref_i)&&~isempty(ref_j)
197                ref_i_list(ifile)=ref_i;
198                ref_j_list(ifile)=ref_j;
199                nb_pairs=0;
200                if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
201                    if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
202                        nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
203                    end
204                end
205                if i1==0
206                    i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
207                end
208                if j1==0
209                    j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
210                end
211                i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
212                if ~isempty(i2_input)
213                    i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
214                end
215                if ~isempty(j1_input)
216                    j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
217                end
218                if ~isempty(j2_input)
219                    j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
220                    j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
221                end
222            end
223        end
224    end
225    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
226    max_j=max(ref_j_list);
227    if isempty(max_j)
228        ref_ij=ref_i_list;
229    else
230        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
231    end
232    ind_select=find(ref_ij>0);
233   
234    if isempty(ind_select)
235%         RootFile='';
236%         NomType='';
237    else
238        [tild,ifile_min]=min(ref_ij(ind_select));
239        [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)
240        NomType=regexprep(NomType,['^' NomTypePref],'');
241        %% update the file type if the input file does not exist (pb of 0001)
242        if isempty(FileInfo.FileType)
243            [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name));
244        end
245    end
246end
247
248%% set to empty array the irrelevant index series
249if isequal(i1_series,0), i1_series=[]; end
250if isequal(i2_series,0), i2_series=[]; end
251if isequal(j1_series,0), j1_series=[]; end
252if isequal(j2_series,0), j2_series=[]; end
253
254%% detect rdvision format
255if strcmp(FileExt,'.bin')
256    if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file')
257        FileInfo.FileType='rdvision';
258        FileInfo.SeqFile=[RootFile '.seq'];
259    end
260end
261
262%% introduce the frame index in case of movies or multimage type
263if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
264    if isempty(i1_series)% if there is no file index, i denotes the frame index
265        i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
266        i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
267        i1_input=1;
268        NomType='*';
269    else  % if there is a file index, j denotes the frame index while i denotes the file index
270        if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair
271            RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices       
272            i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
273            i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
274            j1_series=[];
275            i1_input=1;
276            NomType='*';
277        else
278            i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);%
279            i1_series=[zeros(size(i1_series,1),1) i1_series];
280            j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);%
281            j1_series=[zeros(size(i1_series,1),1) j1_series];
282            %  include the first index in the root name
283            r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
284            if ~isempty(r)
285                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
286                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
287                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
288                else% if a separator '_' is  detected
289                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
290                end
291                if ~isempty(rr)
292                    j1_input=1;
293                    j2_input=[];
294                end
295            end
296        end
297    end
298end
299
300%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
301if size(i2_series,3)>1 %pairs i1 -i2
302    diff_index=abs(i2_series-i1_series);
303    [tild,ind_pair]=sort(diff_index,3,'descend');
304    for ref_i=1:size(i1_series,1)
305        for ref_j=1:size(j1_series,2)
306            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
307            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
308            if ~isempty(j1_series)
309                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
310            end
311        end
312    end
313elseif size(j2_series,3)>1 %pairs j1 -j2
314    diff_index=abs(j2_series-j1_series);
315    [tild,ind_pair]=sort(diff_index,3,'descend');
316    for ref_i=1:size(i1_series,1)
317        for ref_j=1:size(j1_series,2)
318            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
319            if ~isempty(i2_series)
320                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
321            end
322            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
323            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
324        end
325    end
326end
327i1_series=permute(i1_series,[3 2 1]);% permute dimensions
328i2_series=permute(i2_series,[3 2 1]);% permute dimensions
329j1_series=permute(j1_series,[3 2 1]);% permute dimensions
330j2_series=permute(j2_series,[3 2 1]);% permute dimensions
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