source: trunk/src/find_file_series.m @ 941

Last change on this file since 941 was 935, checked in by sommeria, 5 years ago

various improvments

File size: 15.2 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%=======================================================================
30% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
31%   http://www.legi.grenoble-inp.fr
32%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
33%
34%     This file is part of the toolbox UVMAT.
35%
36%     UVMAT is free software; you can redistribute it and/or modify
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%
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
44%     GNU General Public License (see LICENSE.txt) for more details.
45%=======================================================================
46
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)
48%------------------------------------------------------------------------
49
50%% get input root name and nomenclature type
51fullfileinput=fullfile(FilePath,fileinput);% input file name with path
52[FileInfo,MovieObject]=get_file_info(fullfileinput);
53
54%% check for particular file types: images, movies, civ data
55checkfileindexing=0;
56if isfield(FileInfo,'FileIndexing') && strcmp(FileInfo.FileIndexing,'on')
57    [RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput);
58    i1_series=zeros(1,1,1);
59    i2_series=zeros(1,1,1);
60    j1_series=zeros(1,1,1);
61    j2_series=zeros(1,1,1);
62    checkfileindexing=1;
63else % no file indexing
64    [PathDir,RootFile]=fileparts(fullfileinput);
65    [RootPath,SubDir,DirExt]=fileparts(PathDir);
66    SubDir=[SubDir DirExt];% include part after . in the name (considered as a file extension)
67    NomType='*';
68    i1_series=[];i2_series=[];j1_series=[];j2_series=[];
69    i1_input=1;i2_input=[];j1_input=[];j2_input=[];
70    if exist(fullfileinput,'file')~=2
71        RootFile='';
72        return
73    end
74end
75if ~exist(FilePath,'dir')
76    return % don't go further if the dir path does not exist
77end
78if checkfileindexing
79NomTypePref='';
80if isempty(NomType)||strcmp(NomType,'*')
81    if exist(fullfileinput,'file')
82        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
83    else
84        RootFile='';
85    end
86else
87    %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file
88    if ~exist('checkxml','var')||checkxml
89        r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
90        if ~isempty(r) %if NomType begins by a number or _1
91            fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
92            if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
93                rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
94            else% if a separator '_' is  detected
95                rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
96            end
97            if ~isempty(rr)
98                RootFile_i=[RootFile rr.i1];% new root file
99                %look for an xml file correspoonding to the new root name
100                if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
101                    RootFile=RootFile_i;
102                    NomTypePref=r.tiretnum;
103                    NomType=regexprep(NomType,['^'  NomTypePref],'');
104                    i1_input=j1_input;
105                    i2_input=j2_input;
106                    j1_input=[];
107                    j2_input=[];
108                end
109            end
110        end
111    end
112    %% analyse the list of existing files when relevant
113    sep1='';
114    sep2='';
115    i1_str='(?<i1>)';%will set i1=[];
116    i1_star='';
117    i2_str='(?<i2>)';%will set i2=[];
118    i2_star='';
119    j1_str='(?<j1>)';%will set j1=[];
120    j1_star='';
121    j2_str='(?<j2>)';%will set j2=[];
122    j2_star='';
123    %Look for cases with letter indexing for the second index
124    r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
125    if ~isempty(r)
126        sep1=r.sep1;
127        sep2=r.sep2;
128        i1_str='(?<i1>\d+)';
129        i1_star='*';
130        if strcmp(lower(r.j1),r.j1)% lower case index
131            j1_str='(?<j1>[a-z])';
132        else
133           j1_str='(?<j1>[A-Z])'; % upper case index
134        end
135        j1_star='*';
136        if ~isempty(r.j2)
137           if strcmp(lower(r.j1),r.j1)
138            j2_str='(?<j2>[a-z])';
139            else
140           j2_str='(?<j2>[A-Z])';
141           end
142            j2_star='*';
143        end
144    else %numerical indexing
145        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names');
146        if ~isempty(r)
147            sep1=r.sep1;
148            i1_str='(?<i1>\d+)';
149            i1_star='*';
150            if ~isempty(r.i2)
151                i2_str='(?<i2>-\d+)';
152                i2_star='-*';
153            end
154            if ~isempty(r.j1)
155                j1_str='(?<j1>_\d+)';
156                j1_star='_*';
157            end
158            if ~isempty(r.j2)
159                j2_str='(?<j2>-\d+)';
160                j2_star='-*';
161            end
162        end
163    end
164    detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
165    %find the string used to extract the relevant files with the command dir
166    star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt];
167    wd=pwd;%current working directory
168    cd (FilePath)% move to the local dir to save time in the operation dir.
169    dirpair=dir(star_string);% look for relevant files in the file directory
170    cd(wd)
171    nbpair=numel(dirpair);
172    ref_i_list=zeros(1,nbpair);
173    ref_j_list=zeros(1,nbpair);
174    if nbpair==0% no detected file
175        RootFile='';
176    end
177    % scan the list of relevant files, extract the indices
178    for ifile=1:nbpair
179        rr=regexp(dirpair(ifile).name,detect_string,'names');
180        if ~isempty(rr)
181            i1=str2num(rr.i1);
182            i2=str2num(regexprep(rr.i2,'^-',''));
183            j1=stra2num(regexprep(rr.j1,'^_',''));
184            j2=stra2num(regexprep(rr.j2,'^-',''));
185            ref_i=i1;
186            if isempty(i2_input)
187                if ~isempty(i2)% invalid file name if i2 does not exist in the input file
188                    break
189                end
190            else
191                ref_i=floor((i1+i2)/2);
192            end
193            ref_j=1;
194            if isempty(j1_input)
195                if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
196                    break
197                end
198            else %j1_input is not empty
199                if isempty(j1)% the detected name does not fit with the input
200                    break
201                else
202                    ref_j=j1;
203                    if isempty(j2_input)
204                        if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
205                            break
206                        end
207                    else
208                        ref_j=floor((j1+j2)/2);
209                    end
210                end
211            end
212            % update the detected index series
213            if ~isempty(ref_i)&&~isempty(ref_j)
214                ref_i_list(ifile)=ref_i;
215                ref_j_list(ifile)=ref_j;
216                nb_pairs=0;
217                if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
218                    if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
219                        nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
220                    end
221                end
222                if i1==0
223                    i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
224                end
225                if j1==0
226                    j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
227                end
228                i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
229                if ~isempty(i2_input)
230                    i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
231                end
232                if ~isempty(j1_input)
233                    j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
234                end
235                if ~isempty(j2_input)
236                    j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
237                    j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
238                end
239            end
240        end
241    end
242    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
243    max_j=max(ref_j_list);
244    if isempty(max_j)
245        ref_ij=ref_i_list;
246    else
247        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
248    end
249    ind_select=find(ref_ij>0);
250   
251    if isempty(ind_select)
252%         RootFile='';
253%         NomType='';
254    else
255        [tild,ifile_min]=min(ref_ij(ind_select));
256        [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)
257        NomType=regexprep(NomType,['^' NomTypePref],'');
258        %% update the file type if the input file does not exist (pb of 0001)
259        if isempty(FileInfo.FileType)
260            [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name));
261        end
262    end
263end
264
265%% set to empty array the irrelevant index series
266if isequal(i1_series,0), i1_series=[]; end
267if isequal(i2_series,0), i2_series=[]; end
268if isequal(j1_series,0), j1_series=[]; end
269if isequal(j2_series,0), j2_series=[]; end
270end
271% %% detect rdvision format
272% if strcmp(FileExt,'.bin')
273%     if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file')
274%         FileInfo.FileType='rdvision';
275%         FileInfo.SeqFile=[RootFile '.seq'];
276%     end
277% end
278
279%% introduce the frame index in case of movies or multimage type
280if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
281    if isempty(i1_series)% if there is no file index, i denotes the frame index
282        i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
283        i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
284        i1_input=1;
285        NomType='*';
286    else  % if there is a file index, j denotes the frame index while i denotes the file index
287        if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair
288            RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices       
289            i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
290            i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
291            j1_series=[];
292            i1_input=1;
293            NomType='*';
294        else
295            i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);%
296            i1_series=[zeros(size(i1_series,1),1) i1_series];
297            j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);%
298            j1_series=[zeros(size(i1_series,1),1) j1_series];
299            %  include the first index in the root name
300            r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
301            if ~isempty(r)
302                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
303                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
304                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
305                else% if a separator '_' is  detected
306                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
307                end
308                if ~isempty(rr)
309                    j1_input=1;
310                    j2_input=[];
311                end
312            end
313        end
314    end
315end
316
317%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
318if size(i2_series,3)>1 %pairs i1 -i2
319    diff_index=abs(i2_series-i1_series);
320    [tild,ind_pair]=sort(diff_index,3,'descend');
321    for ref_i=1:size(i1_series,1)
322        for ref_j=1:size(j1_series,2)
323            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
324            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
325            if ~isempty(j1_series)
326                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
327            end
328        end
329    end
330elseif size(j2_series,3)>1 %pairs j1 -j2
331    diff_index=abs(j2_series-j1_series);
332    [tild,ind_pair]=sort(diff_index,3,'descend');
333    for ref_i=1:size(i1_series,1)
334        for ref_j=1:size(j1_series,2)
335            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
336            if ~isempty(i2_series)
337                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
338            end
339            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
340            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
341        end
342    end
343end
344i1_series=permute(i1_series,[3 2 1]);% permute dimensions
345i2_series=permute(i2_series,[3 2 1]);% permute dimensions
346j1_series=permute(j1_series,[3 2 1]);% permute dimensions
347j2_series=permute(j2_series,[3 2 1]);% permute dimensions
Note: See TracBrowser for help on using the repository browser.