source: trunk/src/find_file_series.m @ 342

Last change on this file since 342 was 342, checked in by sommeria, 12 years ago

various bugs corrected

File size: 8.8 KB
Line 
1%'find_file_series': check the content onf an input field 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% RootPath,RootFile: root path and root name detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
7% i1_series(ref_i, ref_j,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% NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string)
9% FileType: type of file, =
10%       = 'image', usual image as recognised by Matlab
11%       = 'multimage', image series stored in a single file
12%       = 'civx', netcdf file with civx convention
13%       = 'civdata', civ data with new convention
14%       = 'netcdf' other netcdf files
15%       = 'video': movie recognised by VideoReader (e;g. avi)
16% Object: video object (=[] otherwise)
17%
18%INPUT
19% fileinput: name (including path)  of the input file
20%
21%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22%  Copyright  2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr
23%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24%     This file is part of the toolbox UVMAT.
25%
26%     UVMAT is free software; you can redistribute it and/or modify
27%     it under the terms of the GNU General Public License as published by
28%     the Free Software Foundation; either version 2 of the License, or
29%     (at your option) any later version.
30%
31%     UVMAT is distributed in the hope that it will be useful,
32%     but WITHOUT ANY WARRANTY; without even the implied warranty of
33%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
34%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
35%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36
37function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput)
38%------------------------------------------------------------------------
39
40%% get input root name and nomenclature type
41% [RootPath,RootFile,~,~,~,~,FileExt,NomType,SubDir]=name2display(fileinput);
42[RootPath,SubDir,RootFile,~,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fileinput);
43
44%% check for particular file types: images, movies, civ data
45FileType='';
46Object=[];
47i1_series=zeros(1,1,1);
48i2_series=zeros(1,1,1);
49j1_series=zeros(1,1,1);
50j2_series=zeros(1,1,1);
51switch FileExt
52    % ancillary files, no field indexing
53    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}
54        FileType='txt';
55        NomType='';
56    case '.fig'
57        FileType='figure';
58        NomType='';
59    case '.xml'
60        FileType='xml';
61        NomType='';
62    case '.xls'
63        FileType='xls';
64        NomType='';
65    otherwise
66        if ~isempty(FileExt)&& ~isempty(imformats(FileExt(2:end)))
67            try
68                imainfo=imfinfo(fileinput);
69                FileType='image';
70                if length(imainfo) >1 %case of image with multiple frames
71                    NomType='*';
72                    FileType='multimage';
73                    i1_series=1:length(imainfo);
74                    [RootPath,RootFile]=fileparts(fileinput);
75                end
76            end
77        else
78            try
79                Data=nc2struct(fileinput,'ListGlobalAttribute','absolut_time_T0','Conventions');
80                if ~isempty(Data.absolut_time_T0')
81                    FileType='civx'; % test for civx velocity fields
82                elseif strcmp(Data.Conventions','uvmat/civdata')
83                    FileType='civdata'; % test for civx velocity fields
84                else
85                    FileType='netcdf';
86                end
87            end
88            try
89                Object=VideoReader(fileinput);
90                NomType='*';
91                FileType='video';
92                i1_series=[1:get(Object,'NumberOfFrames')];
93                [RootPath,RootFile]=fileparts(fileinput);
94            end
95        end
96end
97
98%% get the list of existing files when relevant
99if strcmp(NomType,'')||strcmp(NomType,'*')
100    if exist(fileinput,'file')
101    [RootPath,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
102    else
103       RootPath='';
104       RootFile='';
105    end
106else
107    if strcmp(SubDir,'')
108        filebasesub=fullfile(RootPath,RootFile);
109    else
110        filebasesub=fullfile(RootPath,SubDir,RootFile);
111    end
112    detect_string=regexprep(NomType,'\d','*');%replace numbers by '*'
113    old_string='';
114    detect_string=regexprep(detect_string,'[ab]$','*');%suppress the possible letter ab at the end
115    detect_string=regexprep(detect_string,'[AB]$','*');%suppress the possible letter ab at the end
116    detect_string=regexprep(detect_string,'[a|A]$','*');%suppress a possible second letter a,A at the end
117    while ~strcmp(detect_string,old_string)%removes multiple '*'
118        old_string=detect_string;
119        detect_string=regexprep(detect_string,'**','*');
120    end
121    dirpair=dir([filebasesub detect_string FileExt]);
122    nbpair=numel(dirpair);
123    ref_i_list=zeros(1,nbpair);
124    ref_j_list=zeros(1,nbpair);
125    if nbpair==0% no detected file
126        RootPath='';
127        RootFile='';
128    end
129    for ifile=1:nbpair
130        [~,~,~,i1,i2,j1,j2]=fileparts_uvmat(dirpair(ifile).name);
131        %             i1_series(ifile)=i1;
132        ref_i=i1;
133        if isempty(i2_input)
134            if ~isempty(i2)% invalid file name if i2 does not exist in the input file
135                break
136            end
137        else
138            ref_i=floor((i1+i2)/2);
139        end
140        ref_j=1;
141        if isempty(j1_input)
142            if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
143                break
144            end
145        else %j1_input is not empty
146            if isempty(j1)% the detected name does not fit with the input
147                break
148            else
149                ref_j=j1;
150                if isempty(j2_input)
151                    if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
152                        break
153                    end
154                else
155                    ref_j=floor((j1+j2)/2);
156                end
157            end
158        end
159        % update the detected index series
160        ref_i_list(ifile)=ref_i;
161        ref_j_list(ifile)=ref_j;
162        nb_pairs=0;
163        if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
164            if size(i1_series,1)>=ref_i && size(i1_series,2)>=ref_j
165                nb_pairs=numel(find(i1_series(ref_i,ref_j,:)~=0));
166            end
167        end
168        i1_series(ref_i,ref_j,nb_pairs+1)=i1;
169        if ~isempty(i2_input)
170            i2_series(ref_i,ref_j,nb_pairs+1)=i2;
171        end
172        if ~isempty(j1_input)
173            j1_series(ref_i,ref_j,nb_pairs+1)=j1;
174        end
175        if ~isempty(j2_input)
176            j1_series(ref_i,ref_j,nb_pairs+1)=j1;
177            j2_series(ref_i,ref_j,nb_pairs+1)=j2;
178        end
179    end
180    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
181    max_j=max(ref_j_list);
182    ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
183    [~,ifile]=min(ref_ij(ref_ij>0));
184    [~,~,~,~,~,~,~,~,NomType]=fileparts_uvmat(dirpair(ifile).name);
185end
186
187%% set to empty array the irrelevant index series
188if isequal(i1_series,0), i1_series=[]; end
189if isequal(i2_series,0), i2_series=[]; end
190if isequal(j1_series,0), j1_series=[]; end
191if isequal(j2_series,0), j2_series=[]; end
192
193%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
194if size(i2_series,3)>1 %pairs i1 -i2
195    diff_index=abs(i2_series-i1_series);
196    [~,ind_pair]=sort(diff_index,3,'descend');
197    for ref_i=1:size(i1_series,1)
198        for ref_j=1:size(j1_series,2)
199            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
200            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
201            if ~isempty(j1_series)
202                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
203            end
204        end
205    end
206elseif size(j2_series,3)>1 %pairs j1 -j2
207    diff_index=abs(j2_series-j1_series);
208    [~,ind_pair]=sort(diff_index,3,'descend');
209    for ref_i=1:size(i1_series,1)
210        for ref_j=1:size(j1_series,2)
211            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
212            if ~isempty(i2_series)
213                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
214            end
215            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
216            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
217        end
218    end
219end
220
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