source: trunk/src/find_file_series.m @ 343

Last change on this file since 343 was 343, checked in by sommeria, 12 years ago

-bugs repaired in civ
-change in find_file_series to account for possible file index 0
-name2display suppressed in all functions, replaced by fileparts_uvmat (except incorporated in civ_3D)
-open_uvmat introduced to open files from a list

File size: 8.9 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,RootFile,~,~,~,~,FileExt,NomType,SubDir]=name2display(fileinput);
43[RootPath,SubDir,RootFile,~,i2_input,j1_input,j2_input,FileExt,NomType]=fileparts_uvmat(fileinput);
44
45%% check for particular file types: images, movies, civ data
46FileType='';
47Object=[];
48i1_series=zeros(1,1,1);
49i2_series=zeros(1,1,1);
50j1_series=zeros(1,1,1);
51j2_series=zeros(1,1,1);
52switch FileExt
53    % ancillary files, no field indexing
54    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}
55        FileType='txt';
56        NomType='';
57    case '.fig'
58        FileType='figure';
59        NomType='';
60    case '.xml'
61        FileType='xml';
62        NomType='';
63    case '.xls'
64        FileType='xls';
65        NomType='';
66    otherwise
67        if ~isempty(FileExt)&& ~isempty(imformats(FileExt(2:end)))
68            try
69                imainfo=imfinfo(fileinput);
70                FileType='image';
71                if length(imainfo) >1 %case of image with multiple frames
72                    NomType='*';
73                    FileType='multimage';
74                    i1_series=1:length(imainfo);
75                    [RootPath,RootFile]=fileparts(fileinput);
76                end
77            end
78        else
79            try
80                Data=nc2struct(fileinput,'ListGlobalAttribute','absolut_time_T0','Conventions');
81                if ~isempty(Data.absolut_time_T0')
82                    FileType='civx'; % test for civx velocity fields
83                elseif strcmp(Data.Conventions','uvmat/civdata')
84                    FileType='civdata'; % test for civx velocity fields
85                else
86                    FileType='netcdf';
87                end
88            end
89            try
90                Object=VideoReader(fileinput);
91                NomType='*';
92                FileType='video';
93                i1_series=[1:get(Object,'NumberOfFrames')];
94                [RootPath,RootFile]=fileparts(fileinput);
95            end
96        end
97end
98
99%% get the list of existing files when relevant
100if strcmp(NomType,'')||strcmp(NomType,'*')
101    if exist(fileinput,'file')
102    [RootPath,RootFile]=fileparts(fileinput);% case of constant name (no indexing)
103    else
104       RootPath='';
105       RootFile='';
106    end
107else
108    if strcmp(SubDir,'')
109        filebasesub=fullfile(RootPath,RootFile);
110    else
111        filebasesub=fullfile(RootPath,SubDir,RootFile);
112    end
113    detect_string=regexprep(NomType,'\d','*');%replace numbers by '*'
114    old_string='';
115    detect_string=regexprep(detect_string,'[ab]$','*');%suppress the possible letter ab at the end
116    detect_string=regexprep(detect_string,'[AB]$','*');%suppress the possible letter ab at the end
117    detect_string=regexprep(detect_string,'[a|A]$','*');%suppress a possible second letter a,A at the end
118    while ~strcmp(detect_string,old_string)%removes multiple '*'
119        old_string=detect_string;
120        detect_string=regexprep(detect_string,'**','*');
121    end
122    dirpair=dir([filebasesub detect_string FileExt]);
123    nbpair=numel(dirpair);
124    ref_i_list=zeros(1,nbpair);
125    ref_j_list=zeros(1,nbpair);
126    if nbpair==0% no detected file
127        RootPath='';
128        RootFile='';
129    end
130    for ifile=1:nbpair
131        [~,~,~,i1,i2,j1,j2]=fileparts_uvmat(dirpair(ifile).name);
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+1 && size(i1_series,2)>=ref_j+1
165                nb_pairs=numel(find(i1_series(ref_i+1,ref_j+1,:)~=0));
166            end
167        end
168        i1_series(ref_i+1,ref_j+1,nb_pairs+1)=i1;
169        if ~isempty(i2_input)
170            i2_series(ref_i+1,ref_j+1,nb_pairs+1)=i2;
171        end
172        if ~isempty(j1_input)
173            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
174        end
175        if ~isempty(j2_input)
176            j1_series(ref_i+1,ref_j+1,nb_pairs+1)=j1;
177            j2_series(ref_i+1,ref_j+1,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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