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
RevLine 
[356]1%'find_file_series': check the content of an input file and find the corresponding file series
[332]2%--------------------------------------------------------------------------
[398]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)
[332]4%
5% OUTPUT:
[371]6% RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
[609]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
[343]8%  (ref_i+1 is used to deal with the image index zero sometimes used)
[332]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)
[472]17% MovieObject: video object (=[] otherwise)
[332]18%
19%INPUT
[371]20% RootPath: path to the directory to be scanned
21% fileinput: name (without path) of the input file sample
[332]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
[599]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)
[332]40%------------------------------------------------------------------------
[398]41
[332]42%% get input root name and nomenclature type
[398]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);
[332]45
[398]46
[332]47%% check for particular file types: images, movies, civ data
[339]48i1_series=zeros(1,1,1);
49i2_series=zeros(1,1,1);
50j1_series=zeros(1,1,1);
51j2_series=zeros(1,1,1);
[472]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
[445]56NomTypePref='';
[483]57if isempty(NomType)
[371]58    if exist(fullfileinput,'file')
[398]59        [tild,RootFile]=fileparts(fileinput);% case of constant name (no indexing), get the filename without its extension
[388]60    else
[360]61        RootFile='';
[339]62    end
[388]63else
[395]64    %% possibly include the first index in the root name, if there exists a corresponding xml file
[562]65    r=regexp(NomType,'^(?<tiretnum>_|\d+)','names');%look for a number or _1 at the beginning of NomType
[558]66    if ~isempty(r) %if NomType begins by a number or _1
[388]67        fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
[395]68        if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
[388]69            rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
70        else% if a separator '_' is  detected
71            rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
[384]72        end
[388]73        if ~isempty(rr)
[469]74            RootFile_i=[RootFile rr.i1];% new root file
[558]75            %look for an xml file correspoonding to the new root name
[469]76            if exist(fullfile(RootPath,SubDir,[RootFile_i '.xml']),'file') || (strcmp(FileExt,'.nc') && exist(fullfile(RootPath,[RootFile_i '.xml']),'file'))
[445]77                RootFile=RootFile_i;
[391]78                NomTypePref=r.tiretnum;
[388]79                NomType=regexprep(NomType,['^'  NomTypePref],'');
[398]80                i1_input=j1_input;
[388]81                i2_input=j2_input;
82                j1_input=[];
83                j2_input=[];
[395]84            end       
[384]85        end
86    end
[360]87    %% analyse the list of existing files when relevant
88    sep1='';
[558]89    sep2='';
[388]90    i1_str='(?<i1>)';%will set i1=[];
[360]91    i1_star='';
[388]92    i2_str='(?<i2>)';%will set i2=[];
[360]93    i2_star='';
[388]94    j1_str='(?<j1>)';%will set j1=[];
[360]95    j1_star='';
[388]96    j2_str='(?<j2>)';%will set j2=[];
[360]97    j2_star='';
[388]98    %Look for cases with letter indexing for the second index
[558]99    r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<sep2>_?)(?<j1>[a|A])(?<j2>[b|B]?)$','names');
[360]100    if ~isempty(r)
[388]101        sep1=r.sep1;
[558]102        sep2=r.sep2;
[399]103        i1_str='(?<i1>\d+)';
[558]104        i1_star='*';
[399]105        if strcmp(lower(r.j1),r.j1)% lower case index
[388]106            j1_str='(?<j1>[a-z])';
107        else
[399]108           j1_str='(?<j1>[A-Z])'; % upper case index
[360]109        end
[388]110        j1_star='*';
111        if ~isempty(r.j2)
112           if strcmp(lower(r.j1),r.j1)
113            j2_str='(?<j2>[a-z])';
114            else
115           j2_str='(?<j2>[A-Z])';
116           end
117            j2_star='*';
[360]118        end
[388]119    else %numerical indexing
120        r=regexp(NomType,'^(?<sep1>_?)(?<i1>\d+)(?<i2>(-\d+)?)(?<j1>(_\d+)?)(?<j2>(-\d+)?)$','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='-*';
[360]128            end
[388]129            if ~isempty(r.j1)
130                j1_str='(?<j1>_\d+)';
131                j1_star='_*';
[360]132            end
[388]133            if ~isempty(r.j2)
134                j2_str='(?<j2>-\d+)';
135                j2_star='-*';
[360]136            end
137        end
[332]138    end
[558]139    detect_string=['^' RootFile sep1 i1_str i2_str sep2 j1_str j2_str FileExt '$'];%string used in regexp to detect file indices
[360]140    %find the string used to extract the relevant files with the command dir
[558]141    star_string=[RootFile sep1 i1_star i2_star sep2 j1_star j2_star FileExt];
[360]142    wd=pwd;%current working directory
[398]143    cd (FilePath)% move to the local dir to save time in the operation dir.
[388]144    dirpair=dir(star_string);% look for relevant files in the file directory
[360]145    cd(wd)
[339]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
[360]152    % scan the list of relevant files, extract the indices
[339]153    for ifile=1:nbpair
[360]154        rr=regexp(dirpair(ifile).name,detect_string,'names');
[362]155        if ~isempty(rr)
[388]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);
[339]167            end
[388]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);
[342]184                    end
[339]185                end
186            end
[388]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
[339]195            end
[554]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
[388]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
[334]213        end
[339]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);
[350]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
[456]222    ind_select=find(ref_ij>0);
223    if isempty(ind_select)
[350]224        RootFile='';
225        NomType='';
226    else
[456]227        [tild,ifile_min]=min(ref_ij(ind_select));
[494]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)
[384]229        NomType=regexprep(NomType,['^' NomTypePref],'');
[497]230        %% update the file type if the input file does not exist (pb of 0001)
231        if isempty(FileType)
[599]232            [FileType,FileInfo,MovieObject]=get_file_type(fullfile(FilePath,dirpair(ifile_min).name));
[497]233        end
[350]234    end
[339]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
[445]243%% introduce the frame index in case of movies or multimage type
[484]244if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
[445]245    if isempty(i1_series)
[609]246        i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
247        i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
[445]248        i1_input=1;
[483]249        NomType='*';
[445]250    else
[610]251        i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);
[635]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];
[483]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)
[485]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;
[483]270                j1_input=1;
271                j2_input=[];
272            end
273        end
[445]274    end
275end
276
[339]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);
[353]280    [tild,ind_pair]=sort(diff_index,3,'descend');
[339]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
[334]289    end
[339]290elseif size(j2_series,3)>1 %pairs j1 -j2
291    diff_index=abs(j2_series-j1_series);
[353]292    [tild,ind_pair]=sort(diff_index,3,'descend');
[339]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
[512]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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