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 2008-2014, LEGI UMR 5519 / CNRS UJF 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 | |
---|
47 | function [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 |
---|
51 | fullfileinput=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 |
---|
55 | checkfileindexing=0; |
---|
56 | if 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; |
---|
63 | else % 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 | end |
---|
71 | if ~exist(FilePath,'dir') |
---|
72 | return % don't go further if the dir path does not exist |
---|
73 | end |
---|
74 | if checkfileindexing |
---|
75 | NomTypePref=''; |
---|
76 | if isempty(NomType) |
---|
77 | if exist(fullfileinput,'file') |
---|
78 | [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension |
---|
79 | else |
---|
80 | RootFile=''; |
---|
81 | end |
---|
82 | else |
---|
83 | %% if checkxml=1, possibly include the first index in the root name, if there exists a corresponding xml file |
---|
84 | if ~exist('checkxml','var')||checkxml |
---|
85 | r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType |
---|
86 | if ~isempty(r) %if NomType begins by a number or _1 |
---|
87 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
---|
88 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
---|
89 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
---|
90 | else% if a separator '_' is detected |
---|
91 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
---|
92 | end |
---|
93 | if ~isempty(rr) |
---|
94 | RootFile_i=[RootFile rr.i1];% new root file |
---|
95 | %look for an xml file correspoonding to the new root name |
---|
96 | if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file')) |
---|
97 | RootFile=RootFile_i; |
---|
98 | NomTypePref=r.tiretnum; |
---|
99 | NomType=regexprep(NomType,['^' NomTypePref],''); |
---|
100 | i1_input=j1_input; |
---|
101 | i2_input=j2_input; |
---|
102 | j1_input=[]; |
---|
103 | j2_input=[]; |
---|
104 | end |
---|
105 | end |
---|
106 | end |
---|
107 | end |
---|
108 | %% analyse the list of existing files when relevant |
---|
109 | sep1=''; |
---|
110 | sep2=''; |
---|
111 | i1_str='(?<i1>)';%will set i1=[]; |
---|
112 | i1_star=''; |
---|
113 | i2_str='(?<i2>)';%will set i2=[]; |
---|
114 | i2_star=''; |
---|
115 | j1_str='(?<j1>)';%will set j1=[]; |
---|
116 | j1_star=''; |
---|
117 | j2_str='(?<j2>)';%will set j2=[]; |
---|
118 | j2_star=''; |
---|
119 | %Look for cases with letter indexing for the second index |
---|
120 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names'); |
---|
121 | if ~isempty(r) |
---|
122 | sep1=r.sep1; |
---|
123 | sep2=r.sep2; |
---|
124 | i1_str='(?<i1>\d+)'; |
---|
125 | i1_star='*'; |
---|
126 | if strcmp(lower(r.j1),r.j1)% lower case index |
---|
127 | j1_str='(?<j1>[a-z])'; |
---|
128 | else |
---|
129 | j1_str='(?<j1>[A-Z])'; % upper case index |
---|
130 | end |
---|
131 | j1_star='*'; |
---|
132 | if ~isempty(r.j2) |
---|
133 | if strcmp(lower(r.j1),r.j1) |
---|
134 | j2_str='(?<j2>[a-z])'; |
---|
135 | else |
---|
136 | j2_str='(?<j2>[A-Z])'; |
---|
137 | end |
---|
138 | j2_star='*'; |
---|
139 | end |
---|
140 | else %numerical indexing |
---|
141 | r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names'); |
---|
142 | if ~isempty(r) |
---|
143 | sep1=r.sep1; |
---|
144 | i1_str='(?<i1>\d+)'; |
---|
145 | i1_star='*'; |
---|
146 | if ~isempty(r.i2) |
---|
147 | i2_str='(?<i2>-\d+)'; |
---|
148 | i2_star='-*'; |
---|
149 | end |
---|
150 | if ~isempty(r.j1) |
---|
151 | j1_str='(?<j1>_\d+)'; |
---|
152 | j1_star='_*'; |
---|
153 | end |
---|
154 | if ~isempty(r.j2) |
---|
155 | j2_str='(?<j2>-\d+)'; |
---|
156 | j2_star='-*'; |
---|
157 | end |
---|
158 | end |
---|
159 | end |
---|
160 | detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices |
---|
161 | %find the string used to extract the relevant files with the command dir |
---|
162 | star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt]; |
---|
163 | wd=pwd;%current working directory |
---|
164 | cd (FilePath)% move to the local dir to save time in the operation dir. |
---|
165 | dirpair=dir(star_string);% look for relevant files in the file directory |
---|
166 | cd(wd) |
---|
167 | nbpair=numel(dirpair); |
---|
168 | ref_i_list=zeros(1,nbpair); |
---|
169 | ref_j_list=zeros(1,nbpair); |
---|
170 | if nbpair==0% no detected file |
---|
171 | RootFile=''; |
---|
172 | end |
---|
173 | % scan the list of relevant files, extract the indices |
---|
174 | for ifile=1:nbpair |
---|
175 | rr=regexp(dirpair(ifile).name,detect_string,'names'); |
---|
176 | if ~isempty(rr) |
---|
177 | i1=str2num(rr.i1); |
---|
178 | i2=str2num(regexprep(rr.i2,'^-','')); |
---|
179 | j1=stra2num(regexprep(rr.j1,'^_','')); |
---|
180 | j2=stra2num(regexprep(rr.j2,'^-','')); |
---|
181 | ref_i=i1; |
---|
182 | if isempty(i2_input) |
---|
183 | if ~isempty(i2)% invalid file name if i2 does not exist in the input file |
---|
184 | break |
---|
185 | end |
---|
186 | else |
---|
187 | ref_i=floor((i1+i2)/2); |
---|
188 | end |
---|
189 | ref_j=1; |
---|
190 | if isempty(j1_input) |
---|
191 | if ~isempty(j1)% invalid file name if j1 does not exist in the input file |
---|
192 | break |
---|
193 | end |
---|
194 | else %j1_input is not empty |
---|
195 | if isempty(j1)% the detected name does not fit with the input |
---|
196 | break |
---|
197 | else |
---|
198 | ref_j=j1; |
---|
199 | if isempty(j2_input) |
---|
200 | if ~isempty(j2)% invalid file name if j2 does not exist in the input file |
---|
201 | break |
---|
202 | end |
---|
203 | else |
---|
204 | ref_j=floor((j1+j2)/2); |
---|
205 | end |
---|
206 | end |
---|
207 | end |
---|
208 | % update the detected index series |
---|
209 | if ~isempty(ref_i)&&~isempty(ref_j) |
---|
210 | ref_i_list(ifile)=ref_i; |
---|
211 | ref_j_list(ifile)=ref_j; |
---|
212 | nb_pairs=0; |
---|
213 | if ~isempty(i2_input)|| ~isempty(j2_input) %deals with pairs |
---|
214 | if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1 |
---|
215 | nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0)); |
---|
216 | end |
---|
217 | end |
---|
218 | if i1==0 |
---|
219 | i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
---|
220 | end |
---|
221 | if j1==0 |
---|
222 | j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0) |
---|
223 | end |
---|
224 | i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1; |
---|
225 | if ~isempty(i2_input) |
---|
226 | i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2; |
---|
227 | end |
---|
228 | if ~isempty(j1_input) |
---|
229 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
---|
230 | end |
---|
231 | if ~isempty(j2_input) |
---|
232 | j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1; |
---|
233 | j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2; |
---|
234 | end |
---|
235 | end |
---|
236 | end |
---|
237 | end |
---|
238 | % look for the numerical string of the first files to update the NomType (take into account the 0 before the number) |
---|
239 | max_j=max(ref_j_list); |
---|
240 | if isempty(max_j) |
---|
241 | ref_ij=ref_i_list; |
---|
242 | else |
---|
243 | ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i. |
---|
244 | end |
---|
245 | ind_select=find(ref_ij>0); |
---|
246 | |
---|
247 | if isempty(ind_select) |
---|
248 | % RootFile=''; |
---|
249 | % NomType=''; |
---|
250 | else |
---|
251 | [tild,ifile_min]=min(ref_ij(ind_select)); |
---|
252 | [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) |
---|
253 | NomType=regexprep(NomType,['^' NomTypePref],''); |
---|
254 | %% update the file type if the input file does not exist (pb of 0001) |
---|
255 | if isempty(FileInfo.FileType) |
---|
256 | [FileInfo,MovieObject]=get_file_info(fullfile(FilePath,dirpair(ifile_min).name)); |
---|
257 | end |
---|
258 | end |
---|
259 | end |
---|
260 | |
---|
261 | %% set to empty array the irrelevant index series |
---|
262 | if isequal(i1_series,0), i1_series=[]; end |
---|
263 | if isequal(i2_series,0), i2_series=[]; end |
---|
264 | if isequal(j1_series,0), j1_series=[]; end |
---|
265 | if isequal(j2_series,0), j2_series=[]; end |
---|
266 | end |
---|
267 | % %% detect rdvision format |
---|
268 | % if strcmp(FileExt,'.bin') |
---|
269 | % if exist(fullfile(RootPath,SubDir,[RootFile '.seq']),'file') |
---|
270 | % FileInfo.FileType='rdvision'; |
---|
271 | % FileInfo.SeqFile=[RootFile '.seq']; |
---|
272 | % end |
---|
273 | % end |
---|
274 | |
---|
275 | %% introduce the frame index in case of movies or multimage type |
---|
276 | if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 |
---|
277 | if isempty(i1_series)% if there is no file index, i denotes the frame index |
---|
278 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
---|
279 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
---|
280 | i1_input=1; |
---|
281 | NomType='*'; |
---|
282 | else % if there is a file index, j denotes the frame index while i denotes the file index |
---|
283 | if ~isempty(regexp(NomType,'ab$', 'once'))% recognized as a pair |
---|
284 | RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices |
---|
285 | i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 |
---|
286 | i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 |
---|
287 | j1_series=[]; |
---|
288 | i1_input=1; |
---|
289 | NomType='*'; |
---|
290 | else |
---|
291 | i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);% |
---|
292 | i1_series=[zeros(size(i1_series,1),1) i1_series]; |
---|
293 | j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);% |
---|
294 | j1_series=[zeros(size(i1_series,1),1) j1_series]; |
---|
295 | % include the first index in the root name |
---|
296 | r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType |
---|
297 | if ~isempty(r) |
---|
298 | fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput |
---|
299 | if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected |
---|
300 | rr=regexp(fileinput_end,'^(?<i1>\d+)','names'); |
---|
301 | else% if a separator '_' is detected |
---|
302 | rr=regexp(fileinput_end,'^(?<i1>_\d+)','names'); |
---|
303 | end |
---|
304 | if ~isempty(rr) |
---|
305 | j1_input=1; |
---|
306 | j2_input=[]; |
---|
307 | end |
---|
308 | end |
---|
309 | end |
---|
310 | end |
---|
311 | end |
---|
312 | |
---|
313 | %% sort pairs by decreasing index differences in case of multiple pairs at the same reference index |
---|
314 | if size(i2_series,3)>1 %pairs i1 -i2 |
---|
315 | diff_index=abs(i2_series-i1_series); |
---|
316 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
---|
317 | for ref_i=1:size(i1_series,1) |
---|
318 | for ref_j=1:size(j1_series,2) |
---|
319 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
320 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
321 | if ~isempty(j1_series) |
---|
322 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
323 | end |
---|
324 | end |
---|
325 | end |
---|
326 | elseif size(j2_series,3)>1 %pairs j1 -j2 |
---|
327 | diff_index=abs(j2_series-j1_series); |
---|
328 | [tild,ind_pair]=sort(diff_index,3,'descend'); |
---|
329 | for ref_i=1:size(i1_series,1) |
---|
330 | for ref_j=1:size(j1_series,2) |
---|
331 | i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
332 | if ~isempty(i2_series) |
---|
333 | i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
334 | end |
---|
335 | j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
336 | j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:)); |
---|
337 | end |
---|
338 | end |
---|
339 | end |
---|
340 | i1_series=permute(i1_series,[3 2 1]);% permute dimensions |
---|
341 | i2_series=permute(i2_series,[3 2 1]);% permute dimensions |
---|
342 | j1_series=permute(j1_series,[3 2 1]);% permute dimensions |
---|
343 | j2_series=permute(j2_series,[3 2 1]);% permute dimensions |
---|