source: trunk/src/find_file_series.m @ 372

Last change on this file since 372 was 372, checked in by sommeria, 12 years ago

many bugs repaired.
File size: 11.3 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,option)
40%------------------------------------------------------------------------
41if ~exist('option','var')
42    option='all';
43end
44%% get input root name and nomenclature type
45[tild,tild,RootFile,tild,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fileinput);
46fullfileinput=fullfile(RootPath,fileinput);
47
48%% check for particular file types: images, movies, civ data
49FileType='';
50Object=[];
51i1_series=zeros(1,1,1);
52i2_series=zeros(1,1,1);
53j1_series=zeros(1,1,1);
54j2_series=zeros(1,1,1);
55
56switch FileExt
57    % ancillary files, no field indexing
58    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}
59        FileType='txt';
60        NomType='';
61    case '.fig'
62        FileType='figure';
63        NomType='';
64    case '.xml'
65        FileType='xml';
66        NomType='';
67    case '.xls'
68        FileType='xls';
69        NomType='';
70    otherwise
71     
72        if ~isempty(FileExt)&& ~isempty(imformats(FileExt(2:end)))
73            try
74                imainfo=imfinfo(fullfileinput);
75                FileType='image';
76                if length(imainfo) >1 %case of image with multiple frames
77                    NomType='*';
78                    FileType='multimage';
79                    i1_series=(1:length(imainfo))';
80                    [RootPath,RootFile]=fileparts(fullfileinput);
81                end
82            end
83        else
84            try
85                Data=nc2struct(fullfileinput,'ListGlobalAttribute','absolut_time_T0','Conventions');
86                if ~isempty(Data.absolut_time_T0')
87                    FileType='civx'; % test for civx velocity fields
88                elseif strcmp(Data.Conventions,'uvmat/civdata')
89                    FileType='civdata'; % test for civx velocity fields
90                else
91                    FileType='netcdf';
92                end
93            end
94            try
95                if exist('VideoReader','file')%recent version of Matlab
96                    Object=VideoReader(fullfileinput);
97                else
98                    Object=mmreader(fullfileinput);%older Matlab function for movies
99                end
100                NomType='*';
101                FileType='video';
102                i1_series=(1:get(Object,'NumberOfFrames'))';
103            end
104        end
105end
106
107if strcmp(NomType,'')||strcmp(NomType,'*')||strcmp(option,'filetype')
108    if exist(fullfileinput,'file')
109        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
110    else     
111        RootFile='';
112    end
113else   
114    %% analyse the list of existing files when relevant
115    sep1='';
116    i1_str='(?<i1>)';
117    i1_star='';
118    sep2='';
119    i2_str='(?<i2>)';
120    i2_star='';
121    sep3='';
122    j1_str='(?<j1>)';
123    j1_star='';
124    sep4='';
125    j2_str='(?<j2>)';
126    j2_star='';
127    NomTypeStr=NomType;
128    if ~isempty(regexp(NomTypeStr,'^_\d'))
129        sep1='_';
130        NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr
131    end
132    r=regexp(NomTypeStr,'^(?<num1>\d+)','names');%look for a number at the beginning of NomTypeStr
133    if ~isempty(r)
134        i1_str='(?<i1>\d+)';
135        i1_star='*';
136        NomTypeStr=regexprep(NomTypeStr,['^' r.num1],'');
137        r=regexp(NomTypeStr,'^-(?<num2>\d+)','names');%look for a pair i1-i2
138        if ~isempty(r)
139            sep2='-';
140            i2_str='(?<i2>\d+)';
141            i2_star='*';
142            NomTypeStr=regexprep(NomTypeStr,['^-' r.num2],'');
143        end
144        if ~isempty(regexp(NomTypeStr,'^_'));
145            sep3='_';
146            NomTypeStr(1)=[];%remove '_' from the beginning of NomTypeStr
147        end
148        if ~isempty(regexp(NomTypeStr,'^[a|A]'));
149            j1_str='(?<j1>[a-z]|[A-Z])';
150            j1_star='*';
151            if ~isempty(regexp(NomTypeStr,'[b|B]$'));
152                j2_str='(?<j2>[a-z]|[A-Z])';
153                j2_star='*';
154            end
155        else
156            r=regexp(NomTypeStr,'^(?<num3>\d+)','names');
157            if ~isempty(r)
158                j1_str='(?<j1>\d+)';
159                 j1_star='*';
160                NomTypeStr=regexprep(NomTypeStr,['^' r.num3],'');
161            end
162            r=regexp(NomTypeStr,'-(?<num4>\d+)','names');
163            if ~isempty(r)
164                sep4='-';
165                j2_str='(?<j2>\d+)';
166                 j2_star='*';
167            end
168        end
169    end
170    detect_string=['^' RootFile sep1 i1_str sep2 i2_str sep3 j1_str sep4 j2_str FileExt '$'];%string used in regexp to detect file indices
171    %find the string used to extract the relevant files with the command dir
172    star_string=[RootFile sep1 i1_star sep2 i2_star sep3 j1_star sep4 j2_star '*'];
173    wd=pwd;%current working directory
174    %RR=fullfile(RootPath,SubDir);
175    cd (RootPath)% move to the local dir to save time in the operation dir.
176    dirpair=dir([star_string FileExt]);% look for relevant files in the file directory
177    cd(wd)
178    nbpair=numel(dirpair);
179    ref_i_list=zeros(1,nbpair);
180    ref_j_list=zeros(1,nbpair);
181    if nbpair==0% no detected file
182        RootPath='';
183        RootFile='';
184    end
185    % scan the list of relevant files, extract the indices
186    for ifile=1:nbpair
187        rr=regexp(dirpair(ifile).name,detect_string,'names');
188        if ~isempty(rr)
189        i1=str2num(rr.i1);
190        i2=str2num(rr.i2);
191        j1=stra2num(rr.j1);
192        j2=stra2num(rr.j2);
193        ref_i=i1;
194        if isempty(i2_input)
195            if ~isempty(i2)% invalid file name if i2 does not exist in the input file
196                break
197            end
198        else
199            ref_i=floor((i1+i2)/2);
200        end
201        ref_j=1;
202        if isempty(j1_input)
203            if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
204                break
205            end
206        else %j1_input is not empty
207            if isempty(j1)% the detected name does not fit with the input
208                break
209            else
210                ref_j=j1;
211                if isempty(j2_input)
212                    if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
213                        break
214                    end
215                else
216                    ref_j=floor((j1+j2)/2);
217                end
218            end
219        end
220        % update the detected index series
221        ref_i_list(ifile)=ref_i;
222        ref_j_list(ifile)=ref_j;
223        nb_pairs=0;
224        if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
225            if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
226                nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
227            end
228        end
229        i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
230        if ~isempty(i2_input)
231            i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
232        end
233        if ~isempty(j1_input)
234            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
235        end
236        if ~isempty(j2_input)
237            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
238            j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
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    [tild,ifile_min]=min(ref_ij(ref_ij>0));
250    if isempty(ifile_min)
251        RootPath='';
252        RootFile='';
253        NomType='';
254    else
255        [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)
256    end
257end
258
259%% update the file type if the input file does not exist (pb of 0001)
260if strcmp(option,'filetype')
261    return
262elseif isempty(FileType)
263    [tild,tild, tild,tild,tild,tild,FileType,Object]=find_file_series(RootPath,dirpair(ifile_min).name,'filetype');
264end
265
266%% set to empty array the irrelevant index series
267if isequal(i1_series,0), i1_series=[]; end
268if isequal(i2_series,0), i2_series=[]; end
269if isequal(j1_series,0), j1_series=[]; end
270if isequal(j2_series,0), j2_series=[]; end
271
272%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
273if size(i2_series,3)>1 %pairs i1 -i2
274    diff_index=abs(i2_series-i1_series);
275    [tild,ind_pair]=sort(diff_index,3,'descend');
276    for ref_i=1:size(i1_series,1)
277        for ref_j=1:size(j1_series,2)
278            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
279            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
280            if ~isempty(j1_series)
281                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
282            end
283        end
284    end
285elseif size(j2_series,3)>1 %pairs j1 -j2
286    diff_index=abs(j2_series-j1_series);
287    [tild,ind_pair]=sort(diff_index,3,'descend');
288    for ref_i=1:size(i1_series,1)
289        for ref_j=1:size(j1_series,2)
290            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
291            if ~isempty(i2_series)
292                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
293            end
294            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
295            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
296        end
297    end
298end
299
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