source: trunk/src/find_file_series.m @ 354

Last change on this file since 354 was 354, checked in by sommeria, 9 years ago
File size: 9.2 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+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% fileinput: name (including path)  of the input file
21%
22%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23%  Copyright  2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr
24%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25%     This file is part of the toolbox UVMAT.
26%
27%     UVMAT is free software; you can redistribute it and/or modify
28%     it under the terms of the GNU General Public License as published by
29%     the Free Software Foundation; either version 2 of the License, or
30%     (at your option) any later version.
31%
32%     UVMAT is distributed in the hope that it will be useful,
33%     but WITHOUT ANY WARRANTY; without even the implied warranty of
34%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
35%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
36%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37
38function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput)
39%------------------------------------------------------------------------
40
41%% get input root name and nomenclature type
42[RootPath,SubDir,RootFile,tild,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                if exist('VideoReader','file')%recent version of Matlab
90                    Object=VideoReader(fileinput);   
91                else
92                    Object=mmreader(fileinput);%older Matlab function for movies               
93                end
94                NomType='*';
95                FileType='video'; 
96                i1_series=(1:get(Object,'NumberOfFrames'))';
97            end
98        end
99end
100
101%% get the list of existing files when relevant
102if strcmp(NomType,'')||strcmp(NomType,'*')
103    if exist(fileinput,'file')
104    [RootPath,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
105    else
106       RootPath='';
107       RootFile='';
108    end
109else
110    if strcmp(SubDir,'')
111        filebasesub=fullfile(RootPath,RootFile);
112    else
113        filebasesub=fullfile(RootPath,SubDir,RootFile);
114    end
115    detect_string=regexprep(NomType,'\d','*');%replace numbers by '*'
116    old_string='';
117    detect_string=regexprep(detect_string,'[ab]$','*');%suppress the possible letter ab at the end
118    detect_string=regexprep(detect_string,'[AB]$','*');%suppress the possible letter ab at the end
119    detect_string=regexprep(detect_string,'[a|A]$','*');%suppress a possible second letter a,A at the end
120    while ~strcmp(detect_string,old_string)%removes multiple '*'
121        old_string=detect_string;
122        detect_string=regexprep(detect_string,'**','*');
123    end
124    dirpair=dir([filebasesub detect_string FileExt]);
125    nbpair=numel(dirpair);
126    ref_i_list=zeros(1,nbpair);
127    ref_j_list=zeros(1,nbpair);
128    if nbpair==0% no detected file
129        RootPath='';
130        RootFile='';
131    end
132    for ifile=1:nbpair
133        [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(dirpair(ifile).name);
134        ref_i=i1;
135        if isempty(i2_input)
136            if ~isempty(i2)% invalid file name if i2 does not exist in the input file
137                break
138            end
139        else
140            ref_i=floor((i1+i2)/2);
141        end
142        ref_j=1;
143        if isempty(j1_input)
144            if  ~isempty(j1)% invalid file name if j1 does not exist in the input file
145                break
146            end
147        else %j1_input is not empty
148            if isempty(j1)% the detected name does not fit with the input
149                break
150            else
151                ref_j=j1;
152                if isempty(j2_input)
153                    if  ~isempty(j2)% invalid file name if j2 does not exist in the input file
154                        break
155                    end
156                else
157                    ref_j=floor((j1+j2)/2);
158                end
159            end
160        end
161        % update the detected index series
162        ref_i_list(ifile)=ref_i;
163        ref_j_list(ifile)=ref_j;
164        nb_pairs=0;
165        if ~isempty(i2_input)|| ~isempty(j2_input) %deals with  pairs
166            if size(i1_series,1)>=ref_i+1 && size(i1_series,2)>=ref_j+1
167                nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
168            end
169        end
170        i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
171        if ~isempty(i2_input)
172            i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
173        end
174        if ~isempty(j1_input)
175            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
176        end
177        if ~isempty(j2_input)
178            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
179            j2_series(ref_i+1,ref_j+1,nb_pairs+1)=j2;
180        end
181    end
182    % look for the numerical string of the first files to update the NomType (take into account the 0 before the number)
183    max_j=max(ref_j_list);
184    if isempty(max_j)
185        ref_ij=ref_i_list;
186    else
187        ref_ij=ref_i_list*max_j+ref_j_list; % ordered by index i, then by j for a given i.
188    end
189    [tild,ifile]=min(ref_ij(ref_ij>0));
190    if isempty(ifile)
191        RootPath='';
192        RootFile='';
193        NomType='';
194    else
195    [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile).name);
196    end
197end
198
199%% set to empty array the irrelevant index series
200if isequal(i1_series,0), i1_series=[]; end
201if isequal(i2_series,0), i2_series=[]; end
202if isequal(j1_series,0), j1_series=[]; end
203if isequal(j2_series,0), j2_series=[]; end
204
205%% sort pairs by decreasing index differences in case of multiple pairs at the same reference index
206if size(i2_series,3)>1 %pairs i1 -i2
207    diff_index=abs(i2_series-i1_series);
208    [tild,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            i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
213            if ~isempty(j1_series)
214                j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
215            end
216        end
217    end
218elseif size(j2_series,3)>1 %pairs j1 -j2
219    diff_index=abs(j2_series-j1_series);
220    [tild,ind_pair]=sort(diff_index,3,'descend');
221    for ref_i=1:size(i1_series,1)
222        for ref_j=1:size(j1_series,2)
223            i1_series(ref_i,ref_j,:)=i1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
224            if ~isempty(i2_series)
225                i2_series(ref_i,ref_j,:)=i2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
226            end
227            j1_series(ref_i,ref_j,:)=j1_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
228            j2_series(ref_i,ref_j,:)=j2_series(ref_i,ref_j,ind_pair(ref_i,ref_j,:));
229        end
230    end
231end
232
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