source: trunk/src/find_file_series.m @ 371

Last change on this file since 371 was 371, checked in by sommeria, 12 years ago

various bug fixes with file indexing. mode displacement from a fixed image introduced.
PIV stereo suppressed (todo: introduce in the GUI series).
find_file_series cleaned, with a change in the function arguments
File size: 10.9 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]=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 [RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(RootPath,fileinput)
40%------------------------------------------------------------------------
41
42%% get input root name and nomenclature type
43[tild,tild,RootFile,tild,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fileinput);
44fullfileinput=fullfile(RootPath,fileinput);
45
46%% check for particular file types: images, movies, civ data
47FileType='';
48Object=[];
49i1_series=zeros(1,1,1);
50i2_series=zeros(1,1,1);
51j1_series=zeros(1,1,1);
52j2_series=zeros(1,1,1);
53
54switch FileExt
55    % ancillary files, no field indexing
56    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}
57        FileType='txt';
58        NomType='';
59    case '.fig'
60        FileType='figure';
61        NomType='';
62    case '.xml'
63        FileType='xml';
64        NomType='';
65    case '.xls'
66        FileType='xls';
67        NomType='';
68    otherwise
69     
70        if ~isempty(FileExt)&& ~isempty(imformats(FileExt(2:end)))
71            try
72                imainfo=imfinfo(fullfileinput);
73                FileType='image';
74                if length(imainfo) >1 %case of image with multiple frames
75                    NomType='*';
76                    FileType='multimage';
77                    i1_series=(1:length(imainfo))';
78                    [RootPath,RootFile]=fileparts(fullfileinput);
79                end
80            end
81        else
82            try
83                Data=nc2struct(fullfileinput,'ListGlobalAttribute','absolut_time_T0','Conventions');
84                if ~isempty(Data.absolut_time_T0')
85                    FileType='civx'; % test for civx velocity fields
86                elseif strcmp(Data.Conventions,'uvmat/civdata')
87                    FileType='civdata'; % test for civx velocity fields
88                else
89                    FileType='netcdf';
90                end
91            end
92            try
93                if exist('VideoReader','file')%recent version of Matlab
94                    Object=VideoReader(fullfileinput);
95                else
96                    Object=mmreader(fullfileinput);%older Matlab function for movies
97                end
98                NomType='*';
99                FileType='video';
100                i1_series=(1:get(Object,'NumberOfFrames'))';
101            end
102        end
103end
104
105if strcmp(NomType,'')||strcmp(NomType,'*')
106    if exist(fullfileinput,'file')
107        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
108    else     
109        RootFile='';
110    end
111else   
112    %% analyse the list of existing files when relevant
113    sep1='';
114    i1_str='(?<i1>)';
115    i1_star='';
116    sep2='';
117    i2_str='(?<i2>)';
118    i2_star='';
119    sep3='';
120    j1_str='(?<j1>)';
121    j1_star='';
122    sep4='';
123    j2_str='(?<j2>)';
124    j2_star='';
125    NomTypeStr=NomType;
126    if ~isempty(regexp(NomTypeStr,'^_\d'))
127        sep1='_';
128        NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr
129    end
130    r=regexp(NomTypeStr,'^(?<num1>\d+)','names');%look for a number at the beginning of NomTypeStr
131    if ~isempty(r)
132        i1_str='(?<i1>\d+)';
133        i1_star='*';
134        NomTypeStr=regexprep(NomTypeStr,['^' r.num1],'');
135        r=regexp(NomTypeStr,'^-(?<num2>\d+)','names');%look for a pair i1-i2
136        if ~isempty(r)
137            sep2='-';
138            i2_str='(?<i2>\d+)';
139            i2_star='*';
140            NomTypeStr=regexprep(NomTypeStr,['^-' r.num2],'');
141        end
142        if ~isempty(regexp(NomTypeStr,'^_'));
143            sep3='_';
144            NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr
145        end
146        if ~isempty(regexp(NomTypeStr,'^[a|A]'));
147            j1_str='(?<j1>[a-z]|[A-Z])';
148            j1_star='*';
149            if ~isempty(regexp(NomTypeStr,'[b|B]$'));
150                j2_str='(?<j2>[a-z]|[A-Z])';
151                j2_star='*';
152            end
153        else
154            r=regexp(NomTypeStr,'^(?<num3>\d+)','names');
155            if ~isempty(r)
156                j1_str='(?<j1>\d+)';
157                 j1_star='*';
158                NomTypeStr=regexprep(NomTypeStr,['^' r.num3],'');
159            end
160            r=regexp(NomTypeStr,'-(?<num4>\d+)','names');
161            if ~isempty(r)
162                sep4='-';
163                j2_str='(?<j2>\d+)';
164                 j2_star='*';
165            end
166        end
167    end
168    detect_string=['^' RootFile sep1 i1_str sep2 i2_str sep3 j1_str sep4 j2_str FileExt '$'];%string used in regexp to detect file indices
169    %find the string used to extract the relevant files with the command dir
170    star_string=[RootFile sep1 i1_star sep2 i2_star sep3 j1_star sep4 j2_star '*'];
171    wd=pwd;%current working directory
172    %RR=fullfile(RootPath,SubDir);
173    cd (RootPath)% move to the local dir to save time in the operation dir.
174    dirpair=dir([star_string FileExt]);% look for relevant files in the file directory
175    cd(wd)
176    nbpair=numel(dirpair);
177    ref_i_list=zeros(1,nbpair);
178    ref_j_list=zeros(1,nbpair);
179    if nbpair==0% no detected file
180        RootPath='';
181        RootFile='';
182    end
183    % scan the list of relevant files, extract the indices
184    for ifile=1:nbpair
185        rr=regexp(dirpair(ifile).name,detect_string,'names');
186        if ~isempty(rr)
187        i1=str2num(rr.i1);
188        i2=str2num(rr.i2);
189        j1=stra2num(rr.j1);
190        j2=stra2num(rr.j2);
191        ref_i=i1;
192        if isempty(i2_input)
193            if ~isempty(i2)% invalid file name if i2 does not exist in the input file
194                break
195            end
196        else
197            ref_i=floor((i1+i2)/2);
198        end
199        ref_j=1;
200        if isempty(j1_input)
201            if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
202                break
203            end
204        else %j1_input is not empty
205            if isempty(j1)% the detected name does not fit with the input
206                break
207            else
208                ref_j=j1;
209                if isempty(j2_input)
210                    if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
211                        break
212                    end
213                else
214                    ref_j=floor((j1+j2)/2);
215                end
216            end
217        end
218        % update the detected index series
219        ref_i_list(ifile)=ref_i;
220        ref_j_list(ifile)=ref_j;
221        nb_pairs=0;
222        if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
223            if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
224                nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
225            end
226        end
227        i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
228        if ~isempty(i2_input)
229            i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
230        end
231        if ~isempty(j1_input)
232            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
233        end
234        if ~isempty(j2_input)
235            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
236            j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
237        end
238        end
239    end
240    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
241    max_j=max(ref_j_list);
242    if isempty(max_j)
243        ref_ij=ref_i_list;
244    else
245        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
246    end
247    [tild,ifile_min]=min(ref_ij(ref_ij>0));
248    if isempty(ifile_min)
249        RootPath='';
250        RootFile='';
251        NomType='';
252    else
253        [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile_min).name);
254    end
255end
256
257%% set to empty array the irrelevant index series
258if isequal(i1_series,0), i1_series=[]; end
259if isequal(i2_series,0), i2_series=[]; end
260if isequal(j1_series,0), j1_series=[]; end
261if isequal(j2_series,0), j2_series=[]; end
262
263%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
264if size(i2_series,3)>1 %pairs i1 -i2
265    diff_index=abs(i2_series-i1_series);
266    [tild,ind_pair]=sort(diff_index,3,'descend');
267    for ref_i=1:size(i1_series,1)
268        for ref_j=1:size(j1_series,2)
269            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
270            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
271            if ~isempty(j1_series)
272                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
273            end
274        end
275    end
276elseif size(j2_series,3)>1 %pairs j1 -j2
277    diff_index=abs(j2_series-j1_series);
278    [tild,ind_pair]=sort(diff_index,3,'descend');
279    for ref_i=1:size(i1_series,1)
280        for ref_j=1:size(j1_series,2)
281            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
282            if ~isempty(i2_series)
283                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
284            end
285            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
286            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
287        end
288    end
289end
290
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