source: trunk/src/find_file_series.m @ 644

Last change on this file since 644 was 635, checked in by sommeria, 8 years ago
File size: 13.1 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,i1_input,i2_input,j1_input,j2_input]=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(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
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% MovieObject: 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 [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput)
40%------------------------------------------------------------------------
41
42%% get input root name and nomenclature type
43fullfileinput=fullfile(FilePath,fileinput);% input file name with path
44[RootPath,SubDir,RootFile,i1_input,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fullfileinput);
45
46
47%% check for particular file types: images, movies, civ data
48i1_series=zeros(1,1,1);
49i2_series=zeros(1,1,1);
50j1_series=zeros(1,1,1);
51j2_series=zeros(1,1,1);
52[FileType,FileInfo,MovieObject]=get_file_type(fullfileinput);
53if ~exist(FilePath,'dir')
54    return % don't go further if the dir path does not exist
55end
56NomTypePref='';
57if isempty(NomType)
58    if exist(fullfileinput,'file')
59        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
60    else
61        RootFile='';
62    end
63else
64    %% possibly include the first index in the root name, if there exists a corresponding xml file
65    r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
66    if ~isempty(r) %if NomType begins by a number or _1
67        fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
68        if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
69            rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
70        else% if a separator '_' is  detected
71            rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
72        end
73        if ~isempty(rr)
74            RootFile_i=[RootFile rr.i1];% new root file
75            %look for an xml file correspoonding to the new root name
76            if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
77                RootFile=RootFile_i;
78                NomTypePref=r.tiretnum;
79                NomType=regexprep(NomType,['^'  NomTypePref],'');
80                i1_input=j1_input;
81                i2_input=j2_input;
82                j1_input=[];
83                j2_input=[];
84            end       
85        end
86    end
87    %% analyse the list of existing files when relevant
88    sep1='';
89    sep2='';
90    i1_str='(?<i1>)';%will set i1=[];
91    i1_star='';
92    i2_str='(?<i2>)';%will set i2=[];
93    i2_star='';
94    j1_str='(?<j1>)';%will set j1=[];
95    j1_star='';
96    j2_str='(?<j2>)';%will set j2=[];
97    j2_star='';
98    %Look for cases with letter indexing for the second index
99    r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
100    if ~isempty(r)
101        sep1=r.sep1;
102        sep2=r.sep2;
103        i1_str='(?<i1>\d+)';
104        i1_star='*';
105        if strcmp(lower(r.j1),r.j1)% lower case index
106            j1_str='(?<j1>[a-z])';
107        else
108           j1_str='(?<j1>[A-Z])'; % upper case index
109        end
110        j1_star='*';
111        if ~isempty(r.j2)
112           if strcmp(lower(r.j1),r.j1)
113            j2_str='(?<j2>[a-z])';
114            else
115           j2_str='(?<j2>[A-Z])';
116           end
117            j2_star='*';
118        end
119    else %numerical indexing
120        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','names');
121        if ~isempty(r)
122            sep1=r.sep1;
123            i1_str='(?<i1>\d+)';
124            i1_star='*';
125            if ~isempty(r.i2)
126                i2_str='(?<i2>-\d+)';
127                i2_star='-*';
128            end
129            if ~isempty(r.j1)
130                j1_str='(?<j1>_\d+)';
131                j1_star='_*';
132            end
133            if ~isempty(r.j2)
134                j2_str='(?<j2>-\d+)';
135                j2_star='-*';
136            end
137        end
138    end
139    detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
140    %find the string used to extract the relevant files with the command dir
141    star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt];
142    wd=pwd;%current working directory
143    cd (FilePath)% move to the local dir to save time in the operation dir.
144    dirpair=dir(star_string);% look for relevant files in the file directory
145    cd(wd)
146    nbpair=numel(dirpair);
147    ref_i_list=zeros(1,nbpair);
148    ref_j_list=zeros(1,nbpair);
149    if nbpair==0% no detected file
150        RootFile='';
151    end
152    % scan the list of relevant files, extract the indices
153    for ifile=1:nbpair
154        rr=regexp(dirpair(ifile).name,detect_string,'names');
155        if ~isempty(rr)
156            i1=str2num(rr.i1);
157            i2=str2num(regexprep(rr.i2,'^-',''));
158            j1=stra2num(regexprep(rr.j1,'^_',''));
159            j2=stra2num(regexprep(rr.j2,'^-',''));
160            ref_i=i1;
161            if isempty(i2_input)
162                if ~isempty(i2)% invalid file name if i2 does not exist in the input file
163                    break
164                end
165            else
166                ref_i=floor((i1+i2)/2);
167            end
168            ref_j=1;
169            if isempty(j1_input)
170                if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
171                    break
172                end
173            else %j1_input is not empty
174                if isempty(j1)% the detected name does not fit with the input
175                    break
176                else
177                    ref_j=j1;
178                    if isempty(j2_input)
179                        if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
180                            break
181                        end
182                    else
183                        ref_j=floor((j1+j2)/2);
184                    end
185                end
186            end
187            % update the detected index series
188            ref_i_list(ifile)=ref_i;
189            ref_j_list(ifile)=ref_j;
190            nb_pairs=0;
191            if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
192                if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
193                    nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
194                end
195            end
196            if i1==0
197                i1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
198            end
199            if j1==0
200                j1=-1;% set index 0 to -1 to distinguish from the absent index (set to 0)
201            end
202            i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
203            if ~isempty(i2_input)
204                i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
205            end
206            if ~isempty(j1_input)
207                j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
208            end
209            if ~isempty(j2_input)
210                j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
211                j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
212            end
213        end
214    end
215    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
216    max_j=max(ref_j_list);
217    if isempty(max_j)
218        ref_ij=ref_i_list;
219    else
220        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
221    end
222    ind_select=find(ref_ij>0);
223    if isempty(ind_select)
224        RootFile='';
225        NomType='';
226    else
227        [tild,ifile_min]=min(ref_ij(ind_select));
228        [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)
229        NomType=regexprep(NomType,['^' NomTypePref],'');
230        %% update the file type if the input file does not exist (pb of 0001)
231        if isempty(FileType)
232            [FileType,FileInfo,MovieObject]=get_file_type(fullfile(FilePath,dirpair(ifile_min).name));
233        end
234    end
235end
236
237%% set to empty array the irrelevant index series
238if isequal(i1_series,0), i1_series=[]; end
239if isequal(i2_series,0), i2_series=[]; end
240if isequal(j1_series,0), j1_series=[]; end
241if isequal(j2_series,0), j2_series=[]; end
242
243%% introduce the frame index in case of movies or multimage type
244if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
245    if isempty(i1_series)
246        i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
247        i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
248        i1_input=1;
249        NomType='*';
250    else
251        i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);
252        i1_series=[zeros(size(i1_series,1),1) i1_series];
253        j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);
254        j1_series=[zeros(size(i1_series,1),1) j1_series];
255        %  include the first index in the root name
256        r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
257        if ~isempty(r)
258            fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
259            if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
260                rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
261            else% if a separator '_' is  detected
262                rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
263            end
264            if ~isempty(rr)
265%                 RootFile=[RootFile rr.i1];% new root file
266%                 NomTypePref=r.tiretnum;
267%                 NomType=regexprep(NomType,['^'  NomTypePref],'');
268              %  i1_input=j1_input;
269              %  i2_input=j2_input;
270                j1_input=1;
271                j2_input=[];
272            end
273        end
274    end
275end
276
277%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
278if size(i2_series,3)>1 %pairs i1 -i2
279    diff_index=abs(i2_series-i1_series);
280    [tild,ind_pair]=sort(diff_index,3,'descend');
281    for ref_i=1:size(i1_series,1)
282        for ref_j=1:size(j1_series,2)
283            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
284            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
285            if ~isempty(j1_series)
286                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
287            end
288        end
289    end
290elseif size(j2_series,3)>1 %pairs j1 -j2
291    diff_index=abs(j2_series-j1_series);
292    [tild,ind_pair]=sort(diff_index,3,'descend');
293    for ref_i=1:size(i1_series,1)
294        for ref_j=1:size(j1_series,2)
295            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
296            if ~isempty(i2_series)
297                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
298            end
299            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
300            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
301        end
302    end
303end
304i1_series=permute(i1_series,[3 2 1]);% permute dimensions
305i2_series=permute(i2_series,[3 2 1]);% permute dimensions
306j1_series=permute(j1_series,[3 2 1]);% permute dimensions
307j2_series=permute(j2_series,[3 2 1]);% permute dimensions
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