source: trunk/src/civ.m @ 142

Last change on this file since 142 was 137, checked in by sommeria, 14 years ago

suppression of the replacement of ./fsnet (pb now solved on the cluster). Various cleaning.

File size: 181.7 KB
RevLine 
[112]1%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
[2]2%------------------------------------------------------------------------
3%  provides an interface for the software CIVx
4% function varargout = civ(varargin)
5% provides an interface for the software CIVx
6%
7%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
9%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
[112]10%     This file is part of the toolbox UVMAT.
11%
[2]12%     UVMAT is free software; you can redistribute it and/or modify
13%     it under the terms of the GNU General Public License as published by
14%     the Free Software Foundation; either version 2 of the License, or
15%     (at your option) any later version.
[112]16%
[2]17%     UVMAT is distributed in the hope that it will be useful,
18%     but WITHOUT ANY WARRANTY; without even the implied warranty of
19%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
21%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22function varargout = civ(varargin)
23
[71]24% Last Modified by GUIDE v2.5 27-Mar-2010 13:41:11
[2]25% Begin initialization code - DO NOT EDIT
26gui_Singleton = 1;
27gui_State = struct('gui_Name',       mfilename, ...
[112]28    'gui_Singleton',  gui_Singleton, ...
29    'gui_OpeningFcn', @civ_OpeningFcn, ...
30    'gui_OutputFcn',  @civ_OutputFcn, ...
31    'gui_LayoutFcn',  [] , ...
32    'gui_Callback',   []);
[2]33if nargin && ischar(varargin{1})
34    gui_State.gui_Callback = str2func(varargin{1});
35end
36
37if nargout
38    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
39else
40    gui_mainfcn(gui_State, varargin{:});
41end
42% End initialization code - DO NOT EDIT
43
[12]44%------------------------------------------------------------------------
[2]45% --- Executes just before civ is made visible.
[71]46function civ_OpeningFcn(hObject, eventdata, handles, param)
[12]47%------------------------------------------------------------------------
[2]48% This function has no output args, see OutputFcn.
49% hObject    handle to figure
50% eventdata  reserved - to be defined in a future version of MATLAB
51% handles    structure with handles and user data (see GUIDATA)
52% varargin   command line arguments to civ (see VARARGIN)
[84]53global patch_newBin %=1 if new patch processing available
[112]54%filebase: root name
[2]55%nom_type: nomencalture used ('png_old','_i_j'...)
56%list of field numbers to process
[112]57%subdir: subdirectory of the opened netcdf file
[2]58%ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2),
59%ind_a_opening ind_b_opening chosen pair from the opened netcdf file
60% Choose default command line output for civ
61handles.output = hObject;
62% Update handles structure
63guidata(hObject, handles);
64
65%default initial parameters
66filebase=''; % root file name ('filebase'.civ)
67ext=[];
[112]68testall=0;
[71]69%default input parameters:
70num1=1; % set of field i numbers
[122]71num2=1; % set of field i numbers
[71]72num_a=1; % set of field j numbers (fields a)
73num_b=1; % second set of field j numbers (fields b)
74subdir='A'; % subdir for the netcdf result files
[112]75ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
76%load the initial parameters if the interface is started from uvmat
[71]77if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
78    filebase=param.RootName;
79    nom_type_read=param.NomType;
80    num1=param.num1;
81    num2=param.num2;
82    num_a=param.num_a;
83    num_b=param.num_b;
84    subdir=param.SubDir;
85    ind_opening=param.IndOpening;
86    ext=param.ImaExt;
[2]87end
[122]88browse.num_i1=num1;
89browse.num_i2=num2;
90browse.num_j1=num_a;
91browse.num_j2=num_b;
92if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
[112]93    set(handles.ImaExt,'String',ext)
[128]94    browse.ext_ima=ext;
[112]95    if exist('nom_type_read','var')
96        browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
97    end
[2]98elseif isequal(ext,'.nc')
99    if exist('nom_type_read','var')
100        browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
101    end
102end
[71]103set(handles.RootName,'String',filebase);
[2]104set(handles.ImaDoc,'UserData',testall);
105set(handles.ImaDoc,'String',ext)
106
[122]107%read names of the .exe file to adjust the interface according to available binaries
[2]108path_uvmat=which('uvmat');% check the path detected for source file uvmat
109path_UVMAT=fileparts(path_uvmat); %path to UVMAT
[45]110errormsg=[];%default error message
[111]111% xmlfile=fullfile(path_UVMAT,'PARAM.xml');
112% if ~exist(xmlfile,'file')
[112]113xmlfile='PARAM.xml';
[111]114% end
[54]115if exist(xmlfile,'file')
116    try
[112]117        t=xmltree(xmlfile);
118        sparam=convert(t);
[54]119    catch
[112]120        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
[2]121    end
[54]122else
123    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
[2]124end
[71]125
[110]126
[45]127if ~isempty(errormsg)
[112]128    msgbox_uvmat('ERROR',errormsg);
[45]129end
[71]130% patch_newBin='';
131test_batch=0;%default: ,no batch mode available
132if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
133    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
[2]134end
135if test_batch==0
[84]136    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
[2]137    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
138end
[94]139if isfield(sparam.RunParam,'CivBin')
140    if ~exist(sparam.RunParam.CivBin,'file')
[112]141        sparam.RunParam.CivBin=fullfile(path_UVMAT,sparam.RunParam.CivBin);
[94]142    end
[97]143else
144    sparam.RunParam.CivBin='';
[94]145end
[96]146patch_newBin=exist(sparam.RunParam.CivBin,'file');
[2]147set(handles.subdir_civ1,'String',subdir)%default subdir on which uvmat was working
148set(handles.subdir_civ2,'String',subdir)%default subdir on which uvmat was working
149
150%initiate advised operations
151if isequal(ind_opening,[])
152    ind_opening=1; % default
153end
154% set default operation options
[112]155enable_civ1(handles,'off')
156enable_civ2(handles,'off')
157enable_pair1(handles,'on')
158enable_fix1(handles,'off')
159desable_patch1(handles)
160desable_fix2(handles)
161desable_patch2(handles)
162set(handles.CIV1,'Value',0)
163set(handles.FIX1,'Value',0)
164set(handles.PATCH1,'Value',0)
165set(handles.CIV2,'Value',0)
166set(handles.FIX2,'Value',0)
167set(handles.PATCH2,'Value',0)
168set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
[2]169if isequal(ind_opening,1)
170    set(handles.CIV1,'Value',1)
171    enable_civ1(handles,'on')
172elseif isequal(ind_opening,2)
173    set(handles.FIX1,'Value',1)
174    enable_fix1(handles,'on')
175elseif isequal(ind_opening,3)
176    set(handles.PATCH1,'Value',1)
177    enable_patch1(handles)
178elseif isequal(ind_opening,4)
179    set(handles.CIV2,'Value',1)
180    enable_civ2(handles,1)
181elseif isequal(ind_opening,5)
182    set(handles.FIX2,'Value',1)
183    enable_fix2(handles)
[112]184    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
185    set(handles.list_pair_civ2,'Enable','On')
186    set(handles.list_pair_civ2,'Enable','On')
187    enable_pair1(handles,'off')
[2]188elseif isequal(ind_opening,6)
189    set(handles.PATCH2,'Value',1)
190    enable_patch2(handles)
191    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
192    set(handles.list_pair_civ2,'Enable','On')
193    enable_pair1(handles,'off')
194end
195
196% set the range of fields (1:1 by default) and selected pair
[89]197if isnan(num2)||isequal(num2,num1)
[2]198    num_ref_i=num1;
199else
200    num_ref_i=floor((num1+num2)/2);
201    browse.incr_pair(1)=num2-num1;
202    browse.incr_pair(2)=0;
203end
[89]204if isnan(num_b)||isequal(num_a,num_b)
205    if isnan(num_a)
[2]206        num_ref_j=1;
207    else
208        num_ref_j=num_a;
209    end
210else
211    num_ref_j=floor((num_a+num_b)/2);
[112]212    browse.incr_pair(2)=num_b-num_a;
[2]213end
214set(handles.first_i,'String',num2str(num_ref_i));
215set(handles.last_i,'String',num2str(num_ref_i));
216set(handles.first_j,'String',num2str(num_ref_j));
217set(handles.last_j,'String',num2str(num_ref_j));
218set(handles.ref_i,'String',num2str(num_ref_i));
219set(handles.ref_j,'String',num2str(num_ref_j));
[71]220set(handles.ref_i_civ2,'String',num2str(num_ref_i));
221set(handles.ref_j_civ2,'String',num2str(num_ref_j));
[2]222set(handles.browse_root,'UserData',browse);
[71]223if exist('param','var')%varargin the interface is opened from uvmat
[112]224    RootName_Callback(hObject, eventdata, handles);
[2]225end
226
227set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001])
228set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001])
229set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001])
230set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001])
231
[12]232%------------------------------------------------------------------------
[2]233% --- Outputs from this function are returned to the command line.
234function varargout = civ_OutputFcn(hObject, eventdata, handles)
[12]235%------------------------------------------------------------------------
[2]236% varargout  cell array for returning output args (see VARARGOUT);
237% hObject    handle to figure
238% eventdata  reserved - to be defined in a future version of MATLAB
239% handles    structure with handles and user data (see GUIDATA)
240% Get default command line output from handles structure
241varargout{1} = handles.output;
242
[12]243%------------------------------------------------------------------------
[2]244% --- Executes on button press in browse_root.
245function browse_root_Callback(hObject, eventdata, handles)
[12]246%------------------------------------------------------------------------
[2]247%get the input file properties
[71]248filebase=get(handles.RootName,'String');
[2]249oldfile=''; %default
[39]250if isempty(filebase)|| isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
[112]251    dir_perso=prefdir;
252    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
253    if exist(profil_perso,'file')
254        h=load (profil_perso);
255        if isfield(h,'filebase')&& ischar(h.filebase)
256            oldfile=h.filebase;
257        end
258        if isfield(h,'RootPath') && ischar(h.RootPath)
259            oldfile=h.RootPath;
260        end
261    end
262else
263    oldfile=filebase;
264end
[2]265testall=get(handles.ImaDoc,'UserData');
266ind_opening=1;%default
267browse.incr_pair=[0 0]; %default
[112]268if testall
[2]269    menu={'*.*', 'All Files (*.*)'; '*.xml; *.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ...
270        '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc','.nc files'};
271else % menu selecting only .civ or .avi files
[112]272    menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ...
[2]273        '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';...
274        '*.*', 'All Files (*.*)'};
275end
276[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
[112]277fileinput=[PathName FileName];%complete file name
[2]278sizf=size(fileinput);
279if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
280[path,name,ext]=fileparts(fileinput);
281testeditxml=0;
282if isequal(ext,'.xml')
283    testeditxml=1;
284    t_browse=xmltree(fileinput);
285    head_element=get(t_browse,1);
[45]286    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
[2]287        testeditxml=0;
288    end
289end
[45]290if testeditxml==1 || isequal(ext,'.xls')
[112]291    heditxml=editxml({fileinput});
292    set(heditxml,'Tag','browser')
293    waitfor(heditxml,'Tag','idle')
294    if ~ishandle(heditxml)
295        return
296    end
297    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
298    set(handles.browse,'UserData',fileinput)% store for future opening with browser
299    fileinput=get(attr,'UserData');
300    if ~exist(fileinput,'file')
301        return
302    end
[2]303end
[82]304[RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
[2]305filebase=fullfile(RootPath,RootFile);
[89]306num_i1=str2double(str1);
307if isnan(num_i1),num_i1=1;end
308num_i2=str2double(str2);
309if isnan(num_i2),num_i2=num_i1;end
[54]310num_j1=stra2num(str_a);
[89]311if isnan(num_j1),num_j1=1;end
[54]312num_j2=stra2num(str_b);
[112]313if isnan(num_j2),num_j2=num_j1;end
[2]314if isequal(get(handles.compare,'Value'),1)
315    browse=[];%initialisation
316else
317    browse=get(handles.browse_root,'UserData');
318end
[122]319browse.num_i1=num_i1;
320browse.num_i2=num_i2;
321browse.num_j1=num_j1;
322browse.num_j2=num_j2;
323if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
324%     set(handles.ImaExt,'String',ext)
[2]325    browse.nom_type_ima=nom_type;
[122]326    browse.ext_ima=ext;
[2]327end
328set(handles.ImaDoc,'String',ext);
329
330%%%%% read the state of the selected netcdf file to advise default operation
331if isequal(ext,'.nc')
332    browse.nom_type_nc=nom_type;
[112]333    ind_opening=2;% propose 'fix' as the default option
[2]334    Data=nc2struct(fileinput,[]);
[112]335    if isfield(Data,'absolut_time_T0')%test for civx files
[2]336        if isfield(Data,'fix') && isequal(Data.fix,1)
337            ind_opening=3;
338        end
339        if isfield(Data,'patch') && isequal(Data.patch,1)
340            ind_opening=4;
341        end
342        if isfield(Data,'civ2') && isequal(Data.civ2,1)
343            ind_opening=5;
344        end
345        if isfield(Data,'fix2') && isequal(Data.fix2,1)
346            ind_opening=6;
347        end
348        testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
349    else
[112]350        ind_opening=3; %GUI used only for patch
[2]351        testciv=0;
352    end
353    set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results
354    set(handles.subdir_civ2,'String',subdir);
355    browse.testciv=testciv;
356    browse.ind_opening=ind_opening;
357end
[71]358set(handles.RootName,'String',filebase);
[2]359set(handles.ImaDoc,'String',ext);
[45]360if ~isempty(num_i1)
[82]361    ref_i=num_i1;
[45]362    if ~isempty(num_i2)
363        ref_i=floor((ref_i+num_i2)/2);% reference image number corresponding to the file
364        browse.incr_pair(1)=num_i2-num_i1;
[2]365        browse.incr_pair(2)=0;
366    end
367    set(handles.first_i,'String',num2str(ref_i));
368    set(handles.last_i,'String',num2str(ref_i));
[71]369    set(handles.ref_i,'String',num2str(ref_i));
370    set(handles.ref_i_civ2,'String',num2str(ref_i))
[2]371end
[45]372if isempty(num_j1)
[2]373    set(handles.ref_j,'String','1');
[71]374    set(handles.ref_j_civ2,'String','1');
[2]375else
[45]376    ref_j=num_j1;
377    if ~isempty(num_j2)
378        ref_j=floor((num_j1+num_j2)/2);
[112]379        browse.incr_pair(2)=num_j2-num_j1;
[2]380    end
381    set(handles.first_j,'String',num2str(ref_j));
382    set(handles.last_j,'String',num2str(ref_j));
[112]383    set(handles.ref_j,'String',num2str(ref_j));
[71]384    set(handles.ref_j_civ2,'String',num2str(ref_j));
[2]385end
386
387% set default operation options
388enable_civ1(handles,'off')
389enable_civ2(handles,'off')
390enable_pair1(handles,'on')
391enable_fix1(handles,'off')
392desable_patch1(handles)
393desable_fix2(handles)
394desable_patch2(handles)
395set(handles.CIV1,'Value',0)
396set(handles.FIX1,'Value',0)
397set(handles.PATCH1,'Value',0)
398set(handles.CIV2,'Value',0)
399set(handles.FIX2,'Value',0)
400set(handles.PATCH2,'Value',0)
401set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
402if isequal(ind_opening,1)
403    set(handles.CIV1,'Value',1)
404    enable_civ1(handles,'on')
405elseif isequal(ind_opening,2)
406    set(handles.FIX1,'Value',1)
407    enable_fix1(handles,'on')
408elseif isequal(ind_opening,3)
409    set(handles.PATCH1,'Value',1)
410    enable_patch1(handles)
411elseif isequal(ind_opening,4)
412    set(handles.CIV2,'Value',1)
413    enable_civ2(handles,1)
414elseif isequal(ind_opening,5)
415    enable_pair1(handles,'off')
416    set(handles.FIX2,'Value',1)
417    enable_fix2(handles)
[112]418    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
419    set(handles.list_pair_civ2,'Enable','On')
420    set(handles.list_pair_civ2,'Enable','On')
[2]421elseif isequal(ind_opening,6)
422    enable_pair1(handles,'off')
423    set(handles.PATCH2,'Value',1)
424    enable_patch2(handles)
425    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
426    set(handles.list_pair_civ2,'Enable','On')
427end
428set(handles.browse_root,'UserData',browse);% store information from browser
429testall=isequal(menu(filtindex,1),{'*.*'});
430set(handles.ImaDoc,'UserData',testall);
431
[71]432RootName_Callback(hObject, eventdata, handles);
[2]433
[12]434%------------------------------------------------------------------------
[2]435function ImaDoc_Callback(hObject, eventdata, handles)
[12]436%------------------------------------------------------------------------
[71]437RootName_Callback(hObject, eventdata, handles)
[2]438
[12]439%------------------------------------------------------------------------
[54]440% --- function activated when a new filebase (image series) is introduced
[71]441function RootName_Callback(hObject, eventdata, handles)
[12]442%------------------------------------------------------------------------
[2]443set(handles.compare,'Visible','on')
[122]444%ext_ima=get(handles.ImaExt,'String');
445ext_ima='';%default
[2]446nom_type_ima=[];%default
447field_count=1;%default
448nom_type_nc=[];
449time=[];
[71]450TimeUnit='frame'; %default
451CoordUnit='px';%default
[2]452pxcmx_search=[];%default
453pxcmy_search=[];%default
[71]454filebase=get(handles.RootName,'String');
[128]455ext_imadoc=get(handles.ImaDoc,'String');
[135]456browse=get(handles.browse_root,'UserData');%default
[122]457if isfield(browse,'nom_type_ima')
458    nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
[133]459end
460if isfield(browse,'ext_ima')
[122]461    ext_ima=browse.ext_ima;
[2]462end
[122]463if isfield(browse,'nom_type_nc')
464    nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
465end
466if isfield(browse,'num_i1')
467    field_count=browse.num_i1;% get an image index type already determined by an input file
468end
[2]469
470%default first_i and j and increments
[137]471first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
472if isnan(first_i)|| first_i < 1
[2]473    first_i=1; %default first_i
474end
[137]475last_i=str2double(get(handles.last_i,'String'));
476if isnan(last_i)|| last_i < first_i
[2]477    last_i=first_i;  %default last_i
478end
[137]479first_j=str2double(get(handles.first_j,'String'));
480if isnan(first_j)|| first_j < 1
[2]481    first_j=1; %default first_j
482end
[137]483last_j=str2double(get(handles.last_j,'String'));
484if isnan(last_j)|| last_j < first_j
[2]485    last_j=first_j; %default last_j
486end
[137]487incr_i=str2double(get(handles.incr_i,'String'));
488if isnan(incr_i) || incr_i < 1;
[2]489    set(handles.incr_i,'String','1') %default incr_i
490end
[137]491incr_j=str2double(get(handles.incr_j,'String'));
492if isnan(incr_j) || incr_j < 1;
[2]493    set(handles.incr_j,'String','1') %default incr_j
494end
495dt=[];%default
496testmode=0;%default
497nbfield=[]; %default
498nburst=[];%default
499pxcmx=1;
[112]500pxcmy=1;
[2]501
[112]502%look for an image documentation file
[128]503if ~strcmp(ext_imadoc,'.xml') && ~strcmp(ext_imadoc,'.civ')&& ~strcmpi(ext_imadoc,'.avi')
[2]504    if exist([filebase '.xml'],'file')
[128]505        ext_imadoc='.xml';
[2]506    elseif exist([filebase '.civxml'],'file')
[128]507        ext_imadoc='.civxml';
[2]508    elseif exist([filebase '.civ'],'file')
[128]509        ext_imadoc='.civ';
[112]510    elseif exist([filebase '.avi'],'file')
[128]511        ext_imadoc='.avi';
[2]512    elseif exist([filebase '.AVI'],'file')
[128]513        ext_imadoc='.AVI';
[2]514    end
[128]515    set(handles.ImaDoc,'String',ext_imadoc)
[2]516end
517
518%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
[84]519mode=''; %default
520set(handles.ImaDoc,'BackgroundColor',[1 1 0])
521drawnow
[128]522if isequal(ext_imadoc,'.civxml') || isequal(ext_imadoc,'.xml')|| isequal(ext_imadoc,'.civ')
[2]523    set(handles.ref_i,'Visible','On')%use a reference index
524    set(handles.ref_j,'Visible','On')
[128]525elseif isequal(ext_imadoc,'.avi') || isequal(ext_imadoc,'.AVI')
[2]526    set(handles.ref_j,'Visible','Off')
527else
528    set(handles.ref_i,'Visible','Off')
529    set(handles.ref_j,'Visible','Off')
530end
[12]531testima_xml=0;
[128]532if isequal(ext_imadoc,'.civxml')%TO ABANDON
[122]533    [nbfield,nbfield2,time]=read_civxml([filebase '.civxml']);
[2]534    mode='pair j1-j2';
535    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
[112]536        nom_type_ima='_i_j';
[2]537    end
[128]538elseif isequal(ext_imadoc,'.xml')
[73]539    [XmlData,warntext]=imadoc2struct([filebase '.xml']);
[2]540    ext_ima_read=[];
541    nom_type_read=[];
[12]542    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
[2]543        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
[112]544        fullname=fullfile(fileparts(filebase),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
[45]545        if ~exist(fullname,'file')
[12]546            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
547        end
[2]548    end
[84]549    if isfield(XmlData,'Time')
[85]550        time=XmlData.Time;
[84]551        nbfield=size(time,1);
[122]552        nbfield2=size(time,2);
[127]553        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
[122]554        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
[127]555            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D'))
[84]556                time=time';
[122]557                nbfield=nbfield2;
558                nbfield2=1;
[84]559            end
560        end
561    end
[71]562    if isfield(XmlData,'TimeUnit')
563        TimeUnit=XmlData.TimeUnit;
[2]564    end
[71]565    if isfield(XmlData,'Npx')
566        npx=XmlData.Npx;
567        npy=XmlData.Npy;
568    end
[2]569    pxcmx_search=1;
570    pxcmy_search=1;
571    if isfield(XmlData,'GeometryCalib')
572        tsai=XmlData.GeometryCalib;
[112]573        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
574            rot2D=tsai.R(1:2,[1,2]);
575            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
576            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
[2]577        end
[112]578        if isfield(tsai,'CoordUnit')
579            CoordUnit=tsai.CoordUnit;
[2]580        end
[112]581    end
[128]582%     if ~isempty(ext_ima_read) && ~isempty(nom_type_read)
583% %         if isempty(ext_ima)
584% %             ext_ima=ext_ima_read;% define image extension from the xml file if an image has not been opened previously
585% %         else   %keep the image extension
586% %             if  ~strcmp(ext_ima_read,ext_ima)
587% %                 msgbox_uvmat('WARNING',['FirtsImage extension ' ext_ima_read ' announced in the xml file inconsistent with the selected image'])
588% %             end
589% %         end
590%         nom_type_ima=nom_type_read;
591%     end
592elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
[112]593    [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']);
594    if error==2, msgbox_uvmat('WARNING',['no file ' filebase '.civ']);
595    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
596    end
[128]597    nom_type_ima='001a';
598elseif strcmpi(ext_imadoc,'.avi')
[112]599    nom_type_ima='*';
[128]600    ext_ima=ext_imadoc;
[112]601    set(handles.mode,'String',{'series(Di)'})
602    dt=0.04;%default
[128]603    if exist([filebase ext_imadoc],'file')==2
604        info=aviinfo([filebase ext_imadoc]);%read infos on the avi movie
[112]605        dt=1/info.FramesPerSecond;%time interval between successive frames
606        nbfield=info.NumFrames;%number of frames
607    end
608    time=(dt*(0:nbfield-1))';%list of image times
609    %set(handles.dt,'String',num2str(dt*1000));%store the time interval between successive images
[2]610end
611if isempty(time)
612    set(handles.ImaDoc,'String',''); %xml file not used for timing
613end
614set(handles.ImaDoc,'BackgroundColor',[1 1 1])
615
[122]616%get the imabe nomenclature type if not defined by the input file nor by the xml file
617dirima=[];%default
[12]618if isempty(nom_type_ima)
619    %look for double image series '_i_j'
620    dirima=dir([filebase '_' num2str(first_i) '_' num2str(first_j) '.*']);
621    if isempty(dirima)
[112]622        % look for images series  with sub marker '_'
623        dirima=dir([filebase '_*' num2str(first_i) '.*']);
624        if isempty(dirima)
625            % look for other images series
626            dirima=dir([filebase '*' num2str(first_i) '.*']);
[122]627            if isempty(dirima)
628                % look for other images series witth letter appendix
629                appendix=char(96+first_j);
630                dirima=dir([filebase '*' num2str(first_i) appendix '.*']);
[112]631            end
632        end
[12]633    end
[112]634end
[122]635for ilist=1:numel(dirima)
636    [pp,ff,fc,str2,str_a,str_b,ext_list,nom_type_list]=name2display(dirima(ilist).name);
637    form=imformats(ext_list(2:end));
638    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
639        ext_ima=ext_list;
640        nom_type_ima=nom_type_list;
641            break
642    end
643end
644% no image documentation file found: look for a series of existing files,images by priority or .nc files
645if isempty(nom_type_ima)
[128]646    ext_search=ext_imadoc;
[122]647    nom_type_search=nom_type_nc;
648else
649    ext_search=ext_ima;
650    nom_type_search=nom_type_ima;
651end
652if isempty(time) && ~strcmp(nom_type_search,'none') && ~strcmp(nom_type_search,'') && ~strcmp(nom_type_search,'*')
[12]653    subdir=get(handles.subdir_civ1,'String');
654    incr_pair=[0 0];%default
655    if isfield(browse,'incr_pair')
[112]656        incr_pair=browse.incr_pair;
[12]657    end
[112]658    %     nbdetect=0;%test of detected images
[122]659    field_i=browse.num_i2;
[12]660    idetect=1;
[112]661    while idetect==1 %look for the maximum file number in the series
[122]662        imagename=name_generator(filebase,field_i+1,1,ext_search,nom_type_search);
[81]663        idetect=(exist(imagename,'file')==2);
664        if idetect
[12]665            field_i=field_i+1;
[81]666        end
[112]667        %SEE CASE OF NETCDF FILES
668        %             nbdetect=nbdetect+(exist(imagename,'file')==2);
[12]669    end
[122]670    nbfield=field_i;% last detected field number
671    field_i=browse.num_i1;%look for the minimum file number in the series
[12]672    idetect=1;
[112]673    while idetect==1
[122]674        imagename=name_generator(filebase,field_i-1,1,ext_search,nom_type_search);
[81]675        idetect=(exist(imagename,'file')==2);
676        if idetect
[112]677            field_i=field_i-1;
[81]678        end
[12]679    end
[122]680    first_i=max(field_i,1);
681    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
682        field_i=browse.num_i1;
683        field_j=browse.num_j2;
[89]684        jdetect=1;
685        while jdetect==1 %look for the maximum file number in the series
[122]686            imagename=name_generator(filebase,field_i,field_j,ext_search,nom_type_search);
[89]687            jdetect=(exist(imagename,'file')==2);
688            if jdetect
689                field_j=field_j+1;
690            end
691            %SEE CASE OF NETCDF FILES
692            %             nbdetect=nbdetect+(exist(imagename,'file')==2);
693        end
[122]694        nbfield2=field_j;% last detected field number
[120]695     end
[122]696 
[89]697    %determine the set of times and possible intervals for CIV
[137]698    %   dt=(1/1000)*str2double(get(handles.dt,'String'));
[122]699    time=(0:nbfield-1)';% time=file index -1  by default
700    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
701%     switch nom_type_search 
702%         case {'_i_j','%01dA','%02dA','%03dA','%04dA'}
[112]703        % time=[0:nb_field-1]'*ones(1,nb_field_j);% time=file index -1  by default
[122]704        [x,y]=meshgrid(0:nbfield2-1,0:nbfield-1);
[120]705        time=x+y;
706%         time=[0:nb_field-1]'*[0:nb_field_j-1];% time=file index -1  by default
[89]707    end
[122]708%     set(handles.mode,'String',{'series(Di)'})
[2]709end
[120]710
[2]711if exist('time','var')
712    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
713        nbfield=size(time,1);
714        nbfield2=size(time,2);
[71]715        set(handles.RootName,'UserData',time); %store the set of times
716        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
717        set(handles.dt_unit_civ2,'String',['dt in m' TimeUnit]);
718        set(handles.TimeUnit,'String',TimeUnit);
[2]719        set(handles.nb_field,'String',num2str(nbfield));
720        set(handles.nb_field2,'String',num2str(nbfield2));
721    end
722end
[71]723set(handles.CoordUnit,'String',CoordUnit)
[2]724set(handles.calcul_search,'UserData',[pxcmx_search pxcmy_search]);
725% npxy=[npy npx];
[71]726set(handles.ImaExt,'String',ext_ima)
[2]727set(handles.first_i,'String',num2str(first_i));
728set(handles.last_i,'String',num2str(last_i));%
729set(handles.first_j,'String',num2str(first_j));
730set(handles.last_j,'String',num2str(last_j));%
731browse.nom_type_ima=nom_type_ima;
732set(handles.browse_root,'UserData',browse)% store the nomenclature type
733
[112]734%%%%%%%%%%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
[122]735test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D'));%images with single indexing
736if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
[2]737    set(handles.mode,'String',{'series(Di)'})
738    set(handles.mode,'Value',1)
739elseif (nbfield==1)% simple series in j
740    set(handles.mode,'String',{'series(Dj)'})
741    set(handles.mode,'Value',1)
742else
743    set(handles.mode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
[122]744    if nbfield2 <= 10
[112]745        set(handles.mode,'Value',1)% advice 'pair j1-j2' for small burst
[2]746    end
747end
748
[112]749%update the subdir
[2]750pathdir=fileparts(filebase);%path to the current xml file
751listot=dir(pathdir);
752idir=0;
753listdir={''};%default
754for ilist=1:length(listot)
755    if listot(ilist).isdir
756        name=listot(ilist).name;
757        if ~isequal(name,'.') && ~isequal(name,'..')
758            idir=idir+1;
759            listdir{idir,1}=listot(ilist).name;
760        end
761    end
762end
[112]763set(handles.list_subdir_civ1,'Value',1)
[2]764set(handles.list_subdir_civ2,'Value',1)
[107]765set(handles.list_subdir_civ1,'String',[{'browse...'};listdir])
766set(handles.list_subdir_civ2,'String',[{'browse...'};listdir])
[2]767%check wether the current subdir exists:
768subdir_civ1=get(handles.subdir_civ1,'String');
769subdir_civ2=get(handles.subdir_civ2,'String');
770
[112]771mode_Callback(hObject, eventdata, handles)
[2]772
773%%%%%% initialize waitbars and RUN button
774set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
775set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
776set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
777set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
778set(handles.RUN, 'Enable','On')
779set(handles.RUN,'BackgroundColor',[1 0 0])
[122]780set(handles.BATCH,'Enable','On')
781set(handles.BATCH,'BackgroundColor',[1 0 0])
[112]782
[2]783%%%%% store the root input filename for future opening
784dir_perso=prefdir;
785profil_perso=fullfile(prefdir,'uvmat_perso.mat');
786RootPath=fileparts(filebase);
787if exist(profil_perso,'file')
788    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
789else
790    txt=ver;
791    Release=txt(1).Release;
[137]792    relnumb=str2double(Release(3:4));
[2]793    if relnumb >= 14
[112]794        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
[2]795    else
796        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
797    end
798end
799% save(profil_perso, 'filebase'); %store the root name for future opening of uvmat
800set(gcf,'Pointer','arrow')
801
[12]802%------------------------------------------------------------------------
[2]803% --- Executes on button press in mode.
804function mode_Callback(hObject, eventdata, handles)
[12]805%------------------------------------------------------------------------
[2]806browse=get(handles.browse_root,'UserData');
807compare_list=get(handles.compare,'String');
808val=get(handles.compare,'Value');
809compare=compare_list{val};
810if strcmp(compare,'displacement')
811    mode='displacement';
812else
813    mode_list=get(handles.mode,'String');
814    mode_value=get(handles.mode,'Value');
815    mode=mode_list{mode_value};
816end
817displ_num=[];%default
[137]818ref_i=str2double(get(handles.ref_i,'String'));
[2]819% last_i=str2num(get(handles.last_i,'String'));
[71]820time=get(handles.RootName,'UserData'); %get the set of times
[2]821siztime=size(time);
822nbfield=siztime(1);
823nbfield2=siztime(2);
824indchosen=1;  %%first pair selected by default
825if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
826    dt=1;
827    displ='';
828    index=0;
829    numlist_a=[];
830    numlist_B=[];
831    %get all the time intervals in bursts
832    displ_dt=1;%default
833    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
834    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
835        for numod_b=(numod_a+1):nbfield2
[112]836            index=index+1;
837            numlist_a(index)=numod_a;
838            numlist_b(index)=numod_b;
839            if ~isempty(time)
[54]840                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
[2]841                displ_dt(index)=dt(numod_a,numod_b);
[112]842            else
843                displ_dt(index)=1;
844            end
845        end
846    end
847    [dtsort,indsort]=sort(displ_dt);
848    if ~isempty(numlist_a)
849        displ_num(1,:)=numlist_a(indsort);
850        displ_num(2,:)=numlist_b(indsort);
851    end
852    displ_num(3,:)=0;
853    displ_num(4,:)=0;
854    set(handles.jtext,'Visible','Off')
[2]855    set(handles.first_j,'Visible','Off')
856    set(handles.last_j,'Visible','Off')
857    set(handles.incr_j,'Visible','Off')
858    set(handles.nb_field2,'Visible','Off')
859    set(handles.ref_j,'Visible','Off')
860elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
[112]861    for index=1:min(nbfield2-1,200)
862        displ_num(1,index)=-floor(index/2);
863        displ_num(2,index)=ceil(index/2);
864        displ_num(3,index)=0;
865        displ_num(4,index)=0;
866    end
867    set(handles.jtext,'Visible','On')
868    set(handles.first_j,'Visible','On')
869    set(handles.last_j,'Visible','On')
870    set(handles.incr_j,'Visible','On')
871    set(handles.nb_field2,'Visible','On')
872    set(handles.ref_j,'Visible','On')
873    if nbfield > 1
[2]874        set(handles.itext,'Visible','On')
875        set(handles.first_i,'Visible','On')
876        set(handles.last_i,'Visible','On')
877        set(handles.incr_i,'Visible','On')
878        set(handles.nb_field,'Visible','On')
879        set(handles.ref_i,'Visible','On')
880    else
881        set(handles.itext,'Visible','Off')
882        set(handles.first_i,'Visible','Off')
883        set(handles.last_i,'Visible','Off')
884        set(handles.incr_i,'Visible','Off')
885        set(handles.nb_field,'Visible','Off')
886        set(handles.ref_i,'Visible','Off')
887    end
[112]888elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
889    for index=1:200%min(nbfield-1,200)
890        displ_num(1,index)=0;
891        displ_num(2,index)=0;
892        displ_num(3,index)=-floor(index/2);
893        displ_num(4,index)=ceil(index/2);
894    end
895    set(handles.itext,'Visible','On')
896    set(handles.first_i,'Visible','On')
897    set(handles.last_i,'Visible','On')
898    set(handles.incr_i,'Visible','On')
899    set(handles.nb_field,'Visible','On')
900    set(handles.ref_i,'Visible','On')
901    if nbfield2 > 1
[2]902        set(handles.jtext,'Visible','On')
903        set(handles.first_j,'Visible','On')
904        set(handles.last_j,'Visible','On')
905        set(handles.incr_j,'Visible','On')
906        set(handles.nb_field2,'Visible','On')
907        set(handles.ref_j,'Visible','On')
[112]908    else
[2]909        set(handles.jtext,'Visible','Off')
910        set(handles.first_j,'Visible','Off')
911        set(handles.last_j,'Visible','Off')
912        set(handles.incr_j,'Visible','Off')
913        set(handles.nb_field2,'Visible','Off')
914        set(handles.ref_j,'Visible','Off')
915    end
916elseif isequal(mode,'displacement')%the pairs have the same indices
[112]917    displ_num(1,1)=0;
918    displ_num(2,1)=0;
919    displ_num(3,1)=0;
920    displ_num(4,1)=0;
921    if nbfield > 1
[2]922        set(handles.itext,'Visible','On')
923        set(handles.first_i,'Visible','On')
924        set(handles.last_i,'Visible','On')
925        set(handles.incr_i,'Visible','On')
926        set(handles.nb_field,'Visible','On')
927        set(handles.ref_i,'Visible','On')
928    else
929        set(handles.itext,'Visible','Off')
930        set(handles.first_i,'Visible','Off')
931        set(handles.last_i,'Visible','Off')
932        set(handles.incr_i,'Visible','Off')
933        set(handles.nb_field,'Visible','Off')
934        set(handles.ref_i,'Visible','Off')
935    end
936    if nbfield2 > 1
[112]937        set(handles.jtext,'Visible','On')
938        set(handles.first_j,'Visible','On')
939        set(handles.last_j,'Visible','On')
940        set(handles.incr_j,'Visible','On')
941        set(handles.nb_field2,'Visible','On')
942        set(handles.ref_j,'Visible','On')
[2]943    else
944        set(handles.jtext,'Visible','Off')
945        set(handles.first_j,'Visible','Off')
946        set(handles.last_j,'Visible','Off')
947        set(handles.incr_j,'Visible','Off')
948        set(handles.nb_field2,'Visible','Off')
949        set(handles.ref_j,'Visible','Off')
950    end
[112]951end
[2]952set(handles.list_pair_civ1,'UserData',displ_num);
953find_netcpair_civ1(hObject, eventdata, handles)
954find_netcpair_civ2(hObject, eventdata, handles)
955
[12]956%------------------------------------------------------------------------
[2]957% determine the menu for civ1 pairs depending on existing netcdf file at the middle of
958% the field series set by first_i, incr, last_i
959function find_netcpair_civ1(hObject, eventdata, handles)
[12]960%------------------------------------------------------------------------
[2]961set(gcf,'Pointer','watch')
962%nomenclature types
[71]963filebase=get(handles.RootName,'String');
[2]964[filepath,Nme,ext_dir]=fileparts(filebase);
965browse=get(handles.browse_root,'UserData');
966compare_list=get(handles.compare,'String');
967val=get(handles.compare,'Value');
968compare=compare_list{val};
969if strcmp(compare,'displacement')
970    mode='displacement';
971else
972    mode_list=get(handles.mode,'String');
973    mode_value=get(handles.mode,'Value');
974    mode=mode_list{mode_value};
975end
976
977% nomenclature type of the .nc files
978nom_type_ima=[];%default
979if isfield(browse,'nom_type_ima')
980    nom_type_ima=browse.nom_type_ima;
981end
982
[112]983%determine nom_type_nc:
[2]984nom_type_nc=[];%default
985if isfield(browse,'nom_type_nc')
986    nom_type_nc=browse.nom_type_nc;
987end
988if isempty(nom_type_nc)
[112]989    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
[2]990end
991browse.nom_type_nc=nom_type_nc;
992set(handles.browse_root,'UserData',browse)
993
994%reads .nc subdirectoy and image numbers from the interface
995subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
[45]996% first_i=str2num(get(handles.first_i,'String'));
997% last_i=str2num(get(handles.last_i,'String'));
998% incr=str2num(get(handles.incr_i,'String'));
999% num1=first_i:incr:last_i;
1000% if isempty(num1)
1001%     set(handles.list_pair_civ1,'String',{''});
1002%     return
1003% end
1004ref_i=str2double(get(handles.ref_i,'String'));
[2]1005if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1006    ref_j=0;
1007else
[45]1008    ref_j=str2double(get(handles.ref_j,'String'));
[2]1009end
[71]1010time=get(handles.RootName,'UserData');%get the set of times
[2]1011if isempty(time)
1012    time=[0 1];
[112]1013end
[71]1014%dt_unit=str2double(get(handles.dt,'String'));% used when there is no image documentation file
1015dt_unit=1000;%default
[2]1016displ_num=get(handles.list_pair_civ1,'UserData');
1017
[112]1018%eliminate the first pairs inconsistent with the position
1019if isempty(displ_num)
1020    nbpair=0;
1021else
[2]1022    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1023    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
1024        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1025    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1026        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1027    end
[112]1028end
[2]1029nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1030
[112]1031%look for existing processed pairs involving the field at the middle of the series if civ1 will not
[2]1032% be performed, while the result is needed for next steps.
1033displ_pair={''};
1034select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1035testpair=0;
1036if get(handles.CIV1,'Value')==0 %
[112]1037    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
1038        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
1039        set(handles.list_pair_civ1,'String',{});
1040        return
[2]1041    end
[112]1042    for ipair=1:nbpair
[2]1043        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
[112]1044            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
[2]1045        select(ipair)=exist(filename,'file')==2;
1046    end
1047    if ~exist('select','var') || isequal(select,zeros(size(1:nbpair)))
[112]1048        if isfield(browse,'incr_pair')
[2]1049            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1050            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
1051            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1052            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
1053            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
1054            select(1)=exist(filename,'file')==2;
1055            testpair=1;
1056        else
[112]1057            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
[2]1058                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
1059            else
1060                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
1061            end
[112]1062            set(handles.list_pair_civ1,'String',{''});
1063            %COMPLETER CAS STEREO
[2]1064            return
1065        end
1066    end
1067end
1068if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
1069    if testpair
[73]1070        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1071        %     elseif ~isequal(get(handles.root_txt,'String'),'dt(ms)=')
1072        %        for ipair=1:nbpair
1073        %           if select(ipair)
1074        %               if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1075        %               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1076        %               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1077        %               end
1078        %           else
1079        %              displ_pair{ipair}='...'; %pair not displayed in the menu
1080        %           end
1081        %        end
[2]1082    else
[73]1083        for ipair=1:nbpair
1084            if select(ipair)
1085                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1086                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1087                    displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1088                else
1089                    displ_pair{ipair}='...'; %pair not displayed in the menu
1090                end
1091            end
1092        end
[2]1093    end
1094elseif isequal(mode,'series(Dj)')%|isequal(mode,'st_series(Dj)')% series on the j index
1095    if testpair
[112]1096        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
[2]1097    else
[112]1098        for ipair=1:nbpair
1099            if select(ipair)
1100                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1101                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1102                    displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1103                end
1104            elseif testpair
1105                displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))];
1106            else
1107                displ_pair{ipair}='...'; %pair not displayed in the menu
1108            end
1109        end
1110    end
[2]1111elseif isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')%case of pairs
1112    for ipair=1:nbpair
1113        if select(ipair)
[112]1114            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
1115            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1116                ' :dt= ' num2str(dt*1000)];
1117        else
1118            displ_pair{ipair}='...'; %pair not displayed in the menu
1119        end
1120    end
[2]1121elseif isequal(mode,'displacement')
[112]1122    displ_pair={'Di=Dj=0'};
1123end
[2]1124set(handles.list_pair_civ1,'String',displ_pair');
1125ichoice=min(find(select));
[45]1126if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1127initial=get(handles.list_pair_civ1,'Value');%initial choice of pair
[112]1128if initial>nbpair
1129    set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
[45]1130end
1131if numel(select)>=initial && ~isequal(select(initial),1)
[2]1132    set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
1133end
[45]1134
[2]1135%set(handles.list_pair_civ2,'String',displ_pair');
1136initial=get(handles.list_pair_civ2,'Value');
1137if initial>length(displ_pair')%|~isequal(select(initial),1)
1138    if ichoice <= length(displ_pair')
1139        set(handles.list_pair_civ2,'Value',ichoice);% same pair proposed by default for civ2
1140    else
1141        set(handles.list_pair_civ2,'Value',1);% same pair proposed by default for civ2
1142    end
1143end
1144set(handles.list_pair_civ2,'String',displ_pair');
1145set(gcf,'Pointer','arrow')
[12]1146
1147%------------------------------------------------------------------------
[112]1148% determine the menu for civ2 pairs depending on the existing netcdf file at the
1149%middle of the series set by first_i, incr, last_i
[2]1150function find_netcpair_civ2(hObject, eventdata, handles)
[12]1151%------------------------------------------------------------------------
[2]1152set(gcf,'Pointer','watch')
1153%nomenclature types
[71]1154filebase=get(handles.RootName,'String');
[2]1155[filepath,Nme,ext_dir]=fileparts(filebase);
1156browse=get(handles.browse_root,'UserData');
1157compare_list=get(handles.compare,'String');
1158val=get(handles.compare,'Value');
1159compare=compare_list{val};
1160if strcmp(compare,'displacement')
1161    mode='displacement';
1162else
1163    mode_list=get(handles.mode,'String');
1164    mode_value=get(handles.mode,'Value');
1165    mode=mode_list{mode_value};
1166end
1167
1168% nomenclature type of the .nc files
1169nom_type_ima='ima_num';%default
1170if isfield(browse,'nom_type_ima')
1171    nom_type_ima=browse.nom_type_ima;
1172end
1173nom_type_nc='_i1-i2';%default
1174if isfield(browse,'nom_type_nc')
1175    nom_type_nc=browse.nom_type_nc;
1176end
[94]1177if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
[2]1178    nom_type_nc='netc_old';%nom_type for the netcdf files
[94]1179elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
[2]1180    nom_type_nc='none';
[94]1181elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
[112]1182    nom_type_nc='_i1-i2';
[2]1183else
1184    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
1185        nom_type_nc='_i1-i2_j'; % PIV in volume
1186    else
1187        nom_type_nc='_i_j1-j2';
[112]1188    end
[2]1189end
1190browse.nom_type_nc=nom_type_nc;
1191set(handles.browse_root,'UserData',browse)
1192
1193%reads .nc subdirectory and image numbers from the interface
1194subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
1195subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data
[45]1196% first_i=str2num(get(handles.first_i,'String'));
1197% last_i=str2num(get(handles.last_i,'String'));
1198% incr=str2num(get(handles.incr_i,'String'));
1199% num1=first_i:incr:last_i;
1200% if isempty(num1)
1201%     set(handles.list_pair_civ2,'Value',1);
1202%     set(handles.list_pair_civ2,'String',{''});
1203%     return
1204% end
[137]1205ref_i=str2double(get(handles.ref_i_civ2,'String'));
[2]1206if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1207    ref_j=0;
1208else
[137]1209    ref_j=str2double(get(handles.ref_j_civ2,'String'));
[2]1210end
[71]1211time=get(handles.RootName,'UserData'); %get the set of times
[2]1212if isempty(time)
1213    time=[0 1];%default
1214end
[71]1215%dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
[73]1216%dt_unit=1000;
[2]1217displ_num=get(handles.list_pair_civ1,'UserData');
1218
1219
[112]1220%eliminate the first pairs inconsistent with the position
[2]1221if isempty(displ_num)
1222    nbpair=0;
1223else
1224    nbpair=length(displ_num(1,:));%nbre of displayed pairs
[112]1225    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
[2]1226        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
[112]1227    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
[2]1228        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1229    end
1230end
1231nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1232
[112]1233%look for existing processed pairs involving the field at the middle of the series if civ1 will not
[2]1234% be performed, while the result is needed for next steps.
1235displ_pair={''}; %default
1236select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1237if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&...
[112]1238    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
1239        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
1240        set(handles.list_pair_civ2,'Value',1);
1241        set(handles.list_pair_civ2,'String',{''});
1242        return
[2]1243    end
[112]1244    for ipair=1:nbpair
[2]1245        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
[112]1246            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
[2]1247        select(ipair)=exist(filename,'file')==2;
1248    end
1249    if  isequal(select,zeros(size(1:nbpair)))
[112]1250        if isfield(browse,'incr_pair')
[2]1251            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1252            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
1253            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1254            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
1255            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
1256            select(1)=exist(filename,'file')==2;
1257        else
[112]1258            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
[2]1259                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
1260            else
1261                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
1262            end
[112]1263            set(handles.list_pair_civ2,'Value',1);
1264            set(handles.list_pair_civ2,'String',{''});
[2]1265            return
1266        end
1267    end
1268end
[112]1269if isequal(mode,'series(Di)') % | isequal(mode,'st_series(Di)')
1270    for ipair=1:nbpair
1271        if select(ipair)
1272            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
[2]1273                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1274                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
[112]1275            end
1276        else
1277            displ_pair{ipair}='...'; %pair not displayed in the menu
1278        end
1279    end
[2]1280elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
[112]1281    for ipair=1:nbpair
1282        if select(ipair)
1283            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1284                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1285                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1286            end
1287        else
1288            displ_pair{ipair}='...'; %pair not displayed in the menu
1289        end
1290    end
[2]1291elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
1292    for ipair=1:nbpair
1293        if select(ipair)
[112]1294            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
1295            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1296                ' :dt= ' num2str(dt*1000)];
1297        else
1298            displ_pair{ipair}='...'; %pair not displayed in the menu
1299        end
1300    end
[2]1301elseif isequal(mode,'displacement')
[112]1302    displ_pair={'Di=Dj=0'};
1303end
[2]1304val=get(handles.list_pair_civ2,'Value');
1305ichoice=min(find(select));
[137]1306if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1307if get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0
[2]1308    val=ichoice;% first valid pair proposed by default in the menu
1309end
1310if val>length(displ_pair')
1311    set(handles.list_pair_civ2,'Value',1);% first valid pair proposed by default in the menu
1312else
1313    set(handles.list_pair_civ2,'Value',val);
1314end
1315set(handles.list_pair_civ2,'String',displ_pair');
[12]1316set(gcf,'Pointer','arrow')
[2]1317
[12]1318%------------------------------------------------------------------------
[112]1319%  determine the list of index pairs of processing file
[2]1320function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1321    find_pair_indices(handles,mode)
[12]1322%------------------------------------------------------------------------
[112]1323first_i=str2double(get(handles.first_i,'String'));%first index i
1324last_i=str2double(get(handles.last_i,'String'));%last index i
[45]1325incr=str2double(get(handles.incr_i,'String'));% increment
[137]1326num_i=first_i:incr:last_i;% list of i indices (reference values for each pair)
[2]1327if isequal(get(handles.first_j,'Visible'),'on')
[45]1328    first_j=str2double(get(handles.first_j,'String'));%first index j
[112]1329    last_j=str2double(get(handles.last_j,'String'));%last index j
[45]1330    incr_j=str2double(get(handles.incr_j,'String'));% increment
[2]1331else
1332    first_j=1;
1333    last_j=1;
1334    incr_j=1;
1335end
[36]1336num_j=[first_j:incr_j:last_j];% list of j indices (reference values for each pair)
[2]1337list_civ1=get(handles.list_pair_civ1,'String');
1338index_civ1=get(handles.list_pair_civ1,'Value');
[36]1339str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
[2]1340if isempty(str_civ1)||isequal(str_civ1,'')
1341    msgbox_uvmat('ERROR','no image pair selected for civ1')
1342    return
1343end
1344list_civ2=get(handles.list_pair_civ2,'String');
1345index_civ2=get(handles.list_pair_civ2,'Value');
1346if index_civ2>length(list_civ2)
1347    list_civ2=list_civ1;
1348    index_civ2=index_civ1;
1349end
[36]1350str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
1351if isempty(first_i)||isempty(first_j), msgbox_uvmat('ERROR','first field number not defined'),...
[112]1352        return,end;
[39]1353if isequal(last_i,[])|| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),...
[112]1354        return,end;
[39]1355if isequal(incr,[])|| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),...
[112]1356        return,end;
[39]1357if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
[112]1358        return,end;
1359if isequal (mode,'series(Di)')
1360    %recognize the pair civ1 from the display
1361    indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters
[2]1362    str_raw=str_civ1(indsel);
1363    indsepar=find(str_raw=='|'); %character index of the separator
[137]1364    d1=str2double(str_civ1(indsel(indsepar-1)+1:indsel(indsepar)-1));
[2]1365    if indsepar==length(str_raw)
[137]1366        d2=str2double(str_civ1(indsel(indsepar)+1:end));
[2]1367    else
[137]1368        d2=str2double(str_civ1(indsel(indsepar)+1:indsel(indsepar+1)-1));
[112]1369    end
[39]1370    num1_civ1=num_i-d1;% set of first image numbers
1371    num2_civ1=num_i+d2;
[2]1372    num_a_civ1=num_j;
1373    num_b_civ1=num_j;
1374   
1375    %recognize the pair civ2 from the display
1376    indsel=find((double(str_civ2)<48)|(double(str_civ2)>57));% character indices of non numerical characters
1377    str_raw=str_civ2(indsel);
1378    indsepar=find(str_raw=='|'); %character index of the separator
[137]1379    d1=str2double(str_civ2(indsel(indsepar-1)+1:indsel(indsepar)-1));
[2]1380    if indsepar==length(str_raw)
[137]1381        d2=str2double(str_civ2(indsel(indsepar)+1:end));
[2]1382    else
[137]1383        d2=str2double(str_civ2(indsel(indsepar)+1:indsel(indsepar+1)-1));
[112]1384    end
[137]1385    if isnan(d1)
[39]1386        num1_civ2=num_i;
[2]1387    else
[39]1388        num1_civ2=num_i-d1;% set of first image numbers
[2]1389    end
[137]1390    if isnan(d2)
[39]1391        num2_civ2=num_i;
[2]1392    else
[39]1393        num2_civ2=num_i+d2;
[2]1394    end
1395    num_a_civ2=num_j;
1396    num_b_civ2=num_j;
1397   
1398    % adjust the first and last field number
[137]1399    lastfield=str2double(get(handles.nb_field,'String'));
[2]1400    if isequal(lastfield,[])
1401        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
1402    else
1403        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
1404    end
1405    if length(indsel)>=1
1406        firstind=indsel(1);
1407        lastind=indsel(end);
[39]1408        set(handles.first_i,'String',num2str(num_i(firstind)))%update the display of first and last fields
1409        set(handles.last_i,'String',num2str(num_i(lastind)))
1410        num_i=num_i(indsel);
[2]1411        num1_civ1=num1_civ1(indsel);
1412        num1_civ2=num1_civ2(indsel);
1413        num2_civ1=num2_civ1(indsel);
1414        num2_civ2=num2_civ2(indsel);
1415    end
[36]1416elseif isequal (mode,'series(Dj)')
[137]1417    lastfield_j=str2double(get(handles.nb_field2,'String'));
[39]1418    num1_civ1=num_i;% set of first image numbers
1419    num2_civ1=num_i;
[2]1420    num_a_civ1=num_j-floor(index_civ1/2)*ones(size(num_j));
1421    num_b_civ1=num_j+ceil(index_civ1/2)*ones(size(num_j));
[39]1422    num1_civ2=num_i;
1423    num2_civ2=num_i;
[2]1424    num_a_civ2=num_j-floor(index_civ2/2)*ones(size(num_j));
1425    num_b_civ2=num_j+ceil(index_civ2/2)*ones(size(num_j));
1426    % adjust the first and last field number
[137]1427    if isnan(lastfield_j)
[2]1428        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
1429    else
1430        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
1431    end
1432    if length(indsel)>=1
1433        firstind=indsel(1);
1434        lastind=indsel(end);
1435        set(handles.first_j,'String',num2str(num_j(firstind)))%update the display of first and last fields
1436        set(handles.last_j,'String',num2str(num_j(lastind)))
1437        num_j=num_j(indsel);
1438        num_a_civ1=num_a_civ1(indsel);
1439        num_a_civ2=num_a_civ2(indsel);
1440        num_b_civ1=num_b_civ1(indsel);
1441        num_b_civ2=num_b_civ2(indsel);
1442    end
[36]1443elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
[39]1444    num1_civ1=num_i;
1445    num1_civ2=num_i;
[2]1446    displ_num=get(handles.list_pair_civ1,'UserData');
[39]1447    num2_civ1=num_i;
[2]1448    num_a_civ1=displ_num(1,index_civ1);
1449    num_b_civ1=displ_num(2,index_civ1);
[39]1450    num2_civ2=num_i;
[2]1451    num_a_civ2=displ_num(1,index_civ2);
1452    num_b_civ2=displ_num(2,index_civ2);
1453elseif isequal(mode,'displacement')
[39]1454    num1_civ1=num_i;
1455    num2_civ1=num_i;
[2]1456    num_a_civ1=num_j;
1457    num_b_civ1=num_j;
[39]1458    num1_civ2=num_i;
1459    num2_civ2=num_i;
[2]1460    num_a_civ2=num_j;
1461    num_b_civ2=num_j;
1462end
1463
[41]1464
[12]1465%------------------------------------------------------------------------
[2]1466% --- Executes on selection change in list_pair_civ1.
1467function list_pair_civ1_Callback(hObject, eventdata, handles)
[12]1468%------------------------------------------------------------------------
[2]1469%reproduce by default the chosen pair in the civ2 menu
1470list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
1471index_pair=get(handles.list_pair_civ1,'Value');
1472displ_num=get(handles.list_pair_civ1,'UserData');
[137]1473% num_a=displ_num(1,index_pair);
1474% num_b=displ_num(2,index_pair);
[2]1475list_pair2=get(handles.list_pair_civ2,'String');%get the menu of image pairs
1476if index_pair<=length(list_pair2)
1477    set(handles.list_pair_civ2,'Value',index_pair);
1478end
1479
[112]1480%update first_i and last_i according to the chosen image pairs
[2]1481mode_list=get(handles.mode,'String');
1482mode_value=get(handles.mode,'Value');
1483mode=mode_list{mode_value};
1484if isequal(mode,'series(Di)')
[137]1485    first_i=str2double(get(handles.first_i,'String'));
1486    last_i=str2double(get(handles.last_i,'String'));
1487    incr_i=str2double(get(handles.incr_i,'String'));
[2]1488    num1=first_i:incr_i:last_i;
[137]1489    lastfield=str2double(get(handles.nb_field,'String'));
1490    if ~isnan(lastfield)
[2]1491        ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ...
[112]1492            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
[2]1493        num1=num1(ind);
1494    end
1495    set(handles.first_i,'String',num2str(num1(1)));
1496    set(handles.last_i,'String',num2str(num1(end)));
1497elseif isequal(mode,'series(Dj)')
[137]1498    first_j=str2double(get(handles.first_j,'String'));
1499    last_j=str2double(get(handles.last_j,'String'));
1500    incr_j=str2double(get(handles.incr_j,'String'));
[2]1501    num_j=first_j:incr_j:last_j;
[137]1502    lastfield2=str2double(get(handles.nb_field2,'String'));
1503    if ~isnan(lastfield2)
[2]1504        ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
[112]1505            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
[2]1506        num1=num_j(ind);
1507    end
1508    set(handles.first_j,'String',num2str(num1(1)));
1509    set(handles.last_j,'String',num2str(num1(end)));
[112]1510end
[2]1511
[12]1512%------------------------------------------------------------------------
[2]1513% --- Executes on selection change in list_pair_civ2.
1514function list_pair_civ2_Callback(hObject, eventdata, handles)
[12]1515%------------------------------------------------------------------------
[112]1516index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu
[2]1517
[112]1518%update first_i and last_i according to the chosen image pairs
[2]1519mode_list=get(handles.mode,'String');
1520mode_value=get(handles.mode,'Value');
1521mode=mode_list{mode_value};
1522if isequal(mode,'series(Di)')
[137]1523    first_i=str2double(get(handles.first_i,'String'));
1524    last_i=str2double(get(handles.last_i,'String'));
1525    incr_i=str2double(get(handles.incr_i,'String'));
[2]1526    num1=first_i:incr_i:last_i;
[137]1527    lastfield=str2double(get(handles.nb_field,'String'));
1528    if ~isnan(lastfield)
[2]1529        ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ...
[112]1530            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
[2]1531        num1=num1(ind);
1532    end
1533    set(handles.first_i,'String',num2str(num1(1)));
1534    set(handles.last_i,'String',num2str(num1(end)));
1535elseif isequal(mode,'series(Dj)')
[137]1536    first_j=str2double(get(handles.first_j,'String'));
1537    last_j=str2double(get(handles.last_j,'String'));
1538    incr_j=str2double(get(handles.incr_j,'String'));
[2]1539    num_j=first_j:incr_j:last_j;
[137]1540    lastfield2=str2double(get(handles.nb_field2,'String'));
1541    if ~isnan(lastfield2)
[2]1542        ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
[112]1543            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
[2]1544        num1=num_j(ind);
1545    end
1546    set(handles.first_j,'String',num2str(num1(1)));
1547    set(handles.last_j,'String',num2str(num1(end)));
[112]1548end
[2]1549
[67]1550function RUN_Callback(hObject, eventdata, handles)
1551%------------------------------------------------------------------------
1552% global civ1_exe civ2_exe patch_exe patch_new_exe sge
[73]1553set(handles.RUN, 'Enable','Off')
1554set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
[67]1555batch=0;
1556launch_jobs(hObject, eventdata, handles,batch);
[73]1557set(handles.RUN, 'Enable','On')
1558set(handles.RUN,'BackgroundColor',[1 0 0])
[36]1559
[12]1560%------------------------------------------------------------------------
[2]1561% --- Executes on button press in BATCH: remote processing
1562function BATCH_Callback(hObject, eventdata, handles)
[133]1563%% -----------------------------------------------------------------------
[67]1564%global civ1_exe civ2_exe patch_exe patch_new_exe fix_exe todo_path sge Civ_exe % probabely to remove
[73]1565set(handles.BATCH, 'Enable','Off')
1566set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
[67]1567batch=1;
1568launch_jobs(hObject, eventdata, handles, batch)
[73]1569set(handles.BATCH, 'Enable','On')
1570set(handles.BATCH,'BackgroundColor',[1 0 0])
[67]1571
1572%------------------------------------------------------------------------
[133]1573% --- Lauch command called by RUN and BATCH: remote processing
[67]1574function launch_jobs(hObject, eventdata, handles, batch)
1575%-----------------------------------------------------------------------
[133]1576%% check the selected list of operations:
[2]1577operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'};
1578box_test(1)=get(handles.CIV1,'Value');
1579box_test(2)=get(handles.FIX1,'Value');
1580box_test(3)=get(handles.PATCH1,'Value');
1581box_test(4)=get(handles.CIV2,'Value');
1582box_test(5)=get(handles.FIX2,'Value');
1583box_test(6)=get(handles.PATCH2,'Value');
1584index=find(box_test==1);
1585if isempty(index)
1586    msgbox_uvmat('ERROR','no selected operation')
1587    return
1588end
1589index_first=min(index);
1590index_last=max(index);
1591box_used=box_test([index_first : index_last]);
1592[box_missing,ind_missing]=min(box_used);
1593if isequal(box_missing,0)
1594    msgbox_uvmat('ERROR',['missing' cell2mat(operations(ind_missing))]);
1595    return
1596end
1597
1598%check mask if selecetd
1599if isequal(get(handles.get_mask_civ1,'Value'),1)
[12]1600    maskname=get(handles.mask_civ1,'String');
1601    if ~exist(maskname,'file')
1602        get_mask_civ1_Callback(hObject, eventdata, handles);
1603    end
[2]1604end
1605if isequal(get(handles.get_mask_fix1,'Value'),1)
[12]1606    maskname=get(handles.mask_fix1,'String');
1607    if ~exist(maskname,'file')
1608        get_mask_fix1_Callback(hObject, eventdata, handles);
1609    end
[2]1610end
1611if isequal(get(handles.get_mask_civ2,'Value'),1)
[12]1612    maskname=get(handles.mask_civ2,'String');
1613    if ~exist(maskname,'file')
[112]1614        get_mask_civ2_Callback(hObject, eventdata, handles);
[12]1615    end
[2]1616end
1617if isequal(get(handles.get_mask_fix2,'Value'),1)
[12]1618    maskname=get(handles.mask_fix2,'String');
1619    if ~exist(maskname,'file')
[112]1620        get_mask_fix2_Callback(hObject, eventdata, handles);
[12]1621    end
[2]1622end
1623
[137]1624%% initialize the waitbars: TO suppress, waitbar not used
[133]1625set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
1626set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
1627set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
1628set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
1629drawnow
1630
1631%% set the list of files and check them
1632display('checking the files...')
1633compare=get(handles.compare,'Value');%test for usual PIV (compare=1) or displacement (=2) or stereo PIV (=3)
1634[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=...
1635    set_civ_filenames(handles,compare,box_test);
[137]1636if isempty(filecell)% (error message displayed in fct set_civ_filenames)
[133]1637    return
1638end
1639nbfield=numel(num1_civ1);
1640nbslice=numel(num_a_civ1);
1641
1642%% choice of batch priority
1643ind_answer=2;
1644if batch
1645    [s,w]=unix('qstat -q civ.q|grep job_| wc -l'); %check the waiting list (command unix)
1646    if isequal(s,0)
1647        w(end)=[];
1648        str_displ={[w ' jobs in the waiting list'];'Select a priority:'};
1649        str={'urgent';'normal';'low'};
1650        [ind_answer,v] = listdlg('PromptString',str_displ,...
1651            'SelectionMode','single',...
1652            'ListString',str,'ListSize',[200 200],'Name','job priority','InitialValue',3);
1653        if isequal(v,0) % to handle Cancel button and figure close,
1654            return % a better way should be create
1655        end
1656    else
1657        msgbox_uvmat('ERROR','batch system not available')
1658        return
1659    end
1660else
1661    if isunix
1662        [xx,w]=unix('ps faux |grep civ|wc -l');
1663        w(end)=[];
1664        if str2double(w)+numel(num1_civ1)> 50
1665            msgbox_uvmat('ERROR',{['There are already ' w ' civ processes running locally'];'Use BATCH or submit RUN later'})
1666            return
1667        end
1668    end
1669end
1670
1671
1672%% read names of the .exe files for PIV and patch
1673path_UVMAT=fileparts(which('uvmat')); %path to the source directory of uvmat
[112]1674xmlfile='PARAM.xml';
[133]1675if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
[54]1676    t=xmltree(xmlfile);
[67]1677    s=convert(t);
[2]1678end
[127]1679test_interp=0;
1680if batch
[67]1681    if isfield(s,'BatchParam')
1682        sparam=s.BatchParam;
1683        if ~ismember(sparam.BatchMode,{'sge'})
1684            msgbox_uvmat('ERROR',['batch mode ' sparam.BatchMode ' not supported by UVMAT'])
1685        end
1686    else
1687        msgbox_uvmat('ERROR','no batch mode defined in PARAM.xml')
1688        return
1689    end
1690else
1691    if isfield(s,'RunParam')
1692        sparam=s.RunParam;
1693    else
1694        msgbox_uvmat('ERROR','no civ binaries defined in PARAM.xml')
1695        return
1696    end
[112]1697    if isfield(sparam,'CivBin')
1698        if ~exist(sparam.CivBin,'file')
1699            sparam.CivBin=fullfile(path_UVMAT,sparam.CivBin);
1700        end
[94]1701    end
[112]1702    if isfield(sparam,'Civ1Bin')
1703        if ~exist(sparam.Civ1Bin,'file')
1704            sparam.Civ1Bin=fullfile(path_UVMAT,sparam.Civ1Bin);
1705        end
[94]1706    end
[112]1707    if isfield(sparam,'Civ2Bin')
1708        if ~exist(sparam.Civ2Bin,'file')
1709            sparam.Civ2Bin=fullfile(path_UVMAT,sparam.Civ2Bin);
1710        end
[94]1711    end
[112]1712    %test_interp=get(handles.test_interp,'Value');
[116]1713
[112]1714    if  isfield(sparam,'PatchBin')
1715        if ~exist(sparam.PatchBin,'file')
1716            sparam.PatchBin=fullfile(path_UVMAT,sparam.PatchBin);
1717        end
[94]1718    end
[112]1719    % if test_interp && isfield(sparam,'PatchNewBin')
1720    %     if ~exist(sparam.PatchNewBin,'file')
1721    %          sparam.PatchNewBin=fullfile(path_UVMAT,sparam.PatchNewBin);
1722    %     end
1723    % end
1724    if isfield(sparam,'FixBin')
1725        if ~exist(sparam.FixBin,'file')
1726            sparam.FixBin=fullfile(path_UVMAT,sparam.FixBin);
1727        end
[94]1728    end
[73]1729end
[67]1730if batch
1731    if isfield(sparam,'BatchMode')
1732        batch_mode=sparam.BatchMode;
[2]1733    end
[67]1734else
[133]1735%     MaxCivProcesses=50;
1736%     if isfield(sparam,'MaxCivProcesses')
1737%         MaxCivProcesses=str2double(sparam.MaxCivProcesses);
1738%     end
[2]1739end
1740
1741
[133]1742%% get civ1 parameters:
[112]1743display('files OK, processing...')
1744%get civ parameters
[2]1745if box_test(1)==1
1746    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1,1});
[112]1747end
[2]1748
[133]1749%% get fix1 parameters
[112]1750if box_test(2)==1
[2]1751    flagindex1(1)=get(handles.vec_Fmin2, 'Value');
1752    flagindex1(2)=get(handles.vec_F3, 'Value');
1753    flagindex1(3)=get(handles.vec_F2, 'Value');
[127]1754    thresh_vecC1=str2double(get(handles.thresh_vecC,'String'));%threshold on image correlation vec_C
1755    thresh_vel1=str2double(get(handles.thresh_vel,'String'));%threshold on velocity modulus
[2]1756    test_mask=get(handles.get_mask_fix1,'Value');
1757    nbslice_mask=get(handles.mask_fix1,'UserData'); % get the number of slices (= number of masks)
1758    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX
[112]1759    %     inf_sup=get(handles.inf_sup1,'Value');80
1760    %     fileref=get(handles.ref_fix1,'String');
1761    %     refpath=get(handles.ref_fix1,'UserData');
1762    %     fileref=fullfile(refpath,fileref);
[2]1763    menu=get(handles.field_ref1,'String');
1764    index=get(handles.field_ref1,'Value');
1765    if isempty(menu)
1766        fieldchoice='';
1767    else
1768        fieldchoice=menu{index};
[112]1769        msgbox_uvmat('WARNING','reference field is not used presently with batch, use RUN option')
1770    end
[2]1771end
[112]1772
[133]1773%% get patch1 parameters
[67]1774if box_test(3)==1
[127]1775    rho_patch1=str2double(get(handles.rho_patch1,'String'));
1776    if isnan(rho_patch1)
[112]1777        rho_patch1='1000';
1778        set(handles.rho_patch1,'String','1')
1779    else
1780        rho_patch1=num2str(1000*rho_patch1);
1781    end
1782    nx_patch1=get(handles.nx_patch1,'String');
1783    ny_patch1=get(handles.ny_patch1,'String');
[127]1784    if isnan(str2double(nx_patch1))
[112]1785        nx_patch1='50' ;%default
1786        set(handles.nx_patch1,'String','50');
1787    end
[127]1788    if isnan(str2double(ny_patch1))
[112]1789        ny_patch1='50' ;%default
1790        set(handles.ny_patch1,'String','50');
1791    end
1792    subdomain_patch1=get(handles.subdomain_patch1,'String');
1793    thresh_patch1=get(handles.thresh_patch1,'String');
1794end
1795
[133]1796%% get civ2 parameters:
[2]1797if box_test(4)==1
1798    par_civ2=read_param_civ2(handles,cell2mat(filecell.ima1.civ2(1,1)));
1799end
1800
[133]1801%% get fix2 parameters
[112]1802if box_test(5)==1
[2]1803    flagindex2(1)=get(handles.vec_Fmin2_2, 'Value');
1804    flagindex2(2)=get(handles.vec_F3_2, 'Value');
1805    flagindex2(3)=get(handles.vec_F4, 'Value');
[127]1806    thresh_vec2C=str2double(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C
1807    thresh_vel2=str2double(get(handles.thresh_vel2,'String'));%threshold on velocity modulus
[2]1808    test_mask=get(handles.get_mask_fix2,'Value');
1809    nbslice_mask=get(handles.mask_fix2,'UserData'); % get the number of slices (= number of masks)
[112]1810    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX AVEC REF FILE ET OPTION inf_sup=2
1811    %     inf_sup=get(handles.inf_sup2,'Value');
1812    %     ref=get(handles.ref_fix2,'UserData');
1813   
[2]1814    %%%%%%%%%%%%%%%%%%%
1815end
1816
[133]1817%% get patch2 parameters
[2]1818if box_test(6)==1
[127]1819    rho_patch2=str2double(get(handles.rho_patch2,'String'));
1820    if isnan(rho_patch2)
[2]1821        rho_patch2='1000';
1822        set(handles.rho_patch2,'String','1')
1823    else
1824        rho_patch2=num2str(1000*rho_patch2);
1825    end
1826    nx_patch2=get(handles.nx_patch2,'String');
1827    ny_patch2=get(handles.ny_patch2,'String');
[127]1828    if isnan(str2double(nx_patch2))
[2]1829        nx_patch2='50' ;%default
1830        set(handles.nx_patch2,'String','50');
1831    end
[127]1832    if isnan(str2double(ny_patch2))
[2]1833        ny_patch2='50' ;%default
1834        set(handles.ny_patch2,'String','50');
1835    end
1836    subdomain_patch2=get(handles.subdomain_patch2,'String');
1837    thresh_patch2=get(handles.thresh_patch2,'String');
[112]1838    %              test_interp=get(handles.test_interp,'Value');
[2]1839end
1840
[133]1841%% MAIN LOOP
[71]1842time=get(handles.RootName,'UserData'); %get the set of times
[112]1843civAll=get(handles.Experimental,'Value'); % Boolean for new civ excution method
[134]1844super_cmd=[];
1845
[2]1846for ifile=1:nbfield
1847    for j=1:nbslice
[112]1848        i_cmd=0;
[2]1849        cmd='';
[73]1850        if isunix % check: necessaire aussi en RUN?
[112]1851            %fid=fopen([filename '.cmx'],'w')
1852            cmd='#!/bin/bash \n';
1853            cmd=[cmd '#$ -cwd \n'];
1854            cmd=[cmd 'hostname && date \n'];
[117]1855            cmd=[cmd 'umask 002 \n'];
[2]1856        end
1857        if civAll
1858            civAllxml=xmltree;% xml contents,  all parameters
[73]1859            civAllCmd='';
[2]1860            civAllxml=set(civAllxml,1,'name','CivDoc');
1861        end
[73]1862        filename_cmx=filecell.nc.civ1{ifile,j};%output netcdf file
[127]1863        filename_cmx(end-1:end+1)='cmx';%name of cmx file
[2]1864       
[112]1865        %CIV1
[2]1866        if box_test(1)==1
[41]1867            par_civ1.filename_ima_a=filecell.ima1.civ1{ifile,j};
[112]1868            par_civ1.filename_ima_b=filecell.ima2.civ1{ifile,j};
[2]1869            namelog=[filename_cmx([1:end-3]) 'log'];
1870            par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j)));
[112]1871            par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2);
[2]1872            par_civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE?
[112]1873            par_civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);%
[2]1874            test_mask=get(handles.get_mask_civ1,'Value');
[112]1875            if test_mask==0
[2]1876                par_civ1.maskname='noFile use default';
1877                par_civ1.maskflag='n';
1878            else
1879                maskdispl=get(handles.mask_civ1,'String');
[12]1880                if exist(maskdispl,'file')
1881                    par_civ1.maskname=maskdispl;
[112]1882                    par_civ1.maskflag='y';
[2]1883                else
[136]1884                    maskbase=[filecell.filebase '_' maskdispl]; %
[137]1885                    nbslice_mask=str2double(maskdispl(1:end-4)); %
[12]1886                    num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1887                    par_civ1.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1888                    if exist(par_civ1.maskname,'file')
[82]1889                        par_civ1.maskflag='y';
[12]1890                    else
1891                        par_civ1.maskname='noFile use default';
[112]1892                        par_civ1.maskflag='n';
[12]1893                    end
[2]1894                end
1895            end
1896           
1897            test_grid=get(handles.browse_gridciv1,'Value');
1898            if test_grid
1899                par_civ1.gridflag='y';
1900                gridname=get(handles.grid_civ1,'String');
1901                if isequal(gridname(end-3:end),'grid')
[137]1902                    nbslice_grid=str2double(gridname(1:end-4)); %
1903                    if ~isnan(nbslice_grid)
[2]1904                        num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
[136]1905                        par_civ1.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
[2]1906                        if ~exist(par_civ1.gridname,'file')
[112]1907                            msgbox_uvmat('ERROR','grid file absent for civ1')
[2]1908                        end
1909                    elseif exist(gridname,'file')
[112]1910                        par_civ1.gridname=gridname;
[2]1911                    else
1912                        msgbox_uvmat('ERROR','grid file absent for civ1')
1913                    end
1914                end
1915            else
[112]1916                par_civ1.gridname='noFile use default';
1917                par_civ1.gridflag='n';
[2]1918            end
[112]1919            %
[2]1920            i_cmd=i_cmd+1;
1921            if isequal(civAll,0)
[94]1922                cmd=[cmd CIV1_CMD(filename_cmx(1:end-4),namelog,par_civ1,handles,sparam) '\n'];
[2]1923            else
[112]1924                civAllCmd=[civAllCmd ' civ1 '];
1925                str=CIV1_CMD_Unified(filename_cmx([1:end-4]),namelog,par_civ1);
1926                fieldnames=fields(str);
[2]1927                [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1');
1928                for ilist=1:length(fieldnames)
[112]1929                    val=eval(['str.' fieldnames{ilist}]);
1930                    if ischar(val)
1931                        [civAllxml,uid_t]=add(civAllxml,uid_civ1,'element',fieldnames{ilist});
1932                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
1933                    end
1934                end
[2]1935            end
1936        end
1937       
[112]1938        % FIX1
1939        if box_test(2)==1
1940            test_mask=get(handles.get_mask_fix1,'Value');
1941            if test_mask==0
[2]1942                maskname='';
[112]1943            else
[2]1944                maskdispl=get(handles.mask_fix1,'String');
[137]1945                nbslice_mask=str2double(maskdispl(1:end-4)); %
[2]1946                num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
[136]1947                maskbase=[filecell.filebase '_' maskdispl];
[2]1948                maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
[112]1949            end
1950            if isequal(civAll,0)
[94]1951                cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(flagindex1(1)) ...
[112]1952                    ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1953                    ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName ' maskname];
[94]1954                cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
1955                cmd=[cmd cmd_FIX '\n'];
[112]1956            else
[2]1957                fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1958                fix1.fi1=num2str(flagindex1(1));
1959                fix1.fi2=num2str(flagindex1(2));
1960                fix1.fi3=num2str(flagindex1(3));
1961                fix1.threshC=num2str(thresh_vecC1);
[112]1962                fix1.threshV=num2str(thresh_vel1);
[2]1963                fieldnames=fields(fix1);
1964                [civAllxml,uid_fix1]=add(civAllxml,1,'element','fix1');
1965                for ilist=1:length(fieldnames)
[112]1966                    val=eval(['fix1.' fieldnames{ilist}]);
1967                    if ischar(val)
1968                        [civAllxml,uid_t]=add(civAllxml,uid_fix1,'element',fieldnames{ilist});
1969                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
1970                    end
1971                end
1972                civAllCmd=[civAllCmd ' fix1 '];
1973            end
1974        end
1975       
1976        %PATCH1
1977        if box_test(3)==1
1978            if isequal(civAll,0)
1979                cmd_PATCH=PATCH_CMD(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp,sparam.PatchBin);
1980                cmd_PATCH=regexprep(cmd_PATCH,'\\','\\\\');
1981                cmd=[cmd cmd_PATCH '\n'];
1982            else
1983                patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1984                patch1.nopt=subdomain_patch1;
1985                patch1.maxdiff=thresh_patch1;
1986                patch1.ro=rho_patch1;
1987                test_grid=get(handles.get_gridpatch1,'Value');
1988                if test_grid
1989                    patch1.gridflag='y';
1990                    gridname=get(handles.grid_patch1,'String');
1991                    if isequal(gridname(end-3:end),'grid')
[137]1992                        nbslice_grid=str2double(gridname(1:end-4)); %
1993                        if ~isnan(nbslice_grid)
[112]1994                            num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
[136]1995                            patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
[112]1996                            if ~exist(patch1.gridPatch,'file')
1997                                msgbox_uvmat('ERROR','grid file absent for patch1')
1998                            end
1999                        elseif exist(gridname,'file')
2000                            patch1.gridPatch=gridname;
2001                        else
2002                            msgbox_uvmat('ERROR','grid file absent for patch1')
[2]2003                        end
2004                    end
[112]2005                else
2006                    patch1.gridPatch='none';
2007                    patch1.gridflag='n';
2008                    patch1.m=nx_patch1;
2009                    patch1.n=ny_patch1;
[2]2010                end
[112]2011                patch1.convectFlow='n';
2012                fieldnames=fields(patch1);
[2]2013                [civAllxml,uid_patch1]=add(civAllxml,1,'element','patch1');
2014                for ilist=1:length(fieldnames)
[112]2015                    val=eval(['patch1.' fieldnames{ilist}]);
2016                    if ischar(val)
2017                        [civAllxml,uid_t]=add(civAllxml,uid_patch1,'element',fieldnames{ilist});
2018                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2019                    end
2020                end
2021                civAllCmd=[civAllCmd ' patch1 '];
2022            end
[2]2023        end
[112]2024       
[127]2025        if box_test(4)==1 || box_test(5)==1 || box_test(6)==1
[112]2026            filename_cmx=filecell.nc.civ2{ifile,j};%output netcdf file
[127]2027            filename_cmx([end-1:end+1])=[ 'cmx'];%name of cmx file
2028%             filename_cmx=[filename_cmx 'x'];
[112]2029        end
2030       
2031        if box_test(4)==1
[2]2032            par_civ2.filename_ima_a=filecell.ima1.civ2{ifile,j};
2033            %par_civ2.filename_ima_a([end-3:end])=[];%remove .png extension
2034            par_civ2.filename_ima_b=filecell.ima2.civ2{ifile,j};
2035            %par_civ2.filename_ima_b([end-3:end])=[];%remove .png extension
2036            namelog=[filename_cmx([1:end-3]) 'log'];
2037            par_civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j)));
[112]2038            par_civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2);
[2]2039            par_civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc);
[112]2040            par_civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc);
[2]2041            par_civ2.filename_nc1=filecell.nc.civ1{ifile,j};
2042            par_civ2.filename_nc1([end-2:end])=[]; % remove '.nc'
2043            test_mask=get(handles.get_mask_civ2,'Value');
[112]2044            if test_mask==0
[2]2045                par_civ2.maskname='noFile use default';
2046                par_civ2.maskflag='n';
2047            else
2048                maskdispl=get(handles.mask_civ2,'String');
[12]2049                if exist(maskdispl,'file')
2050                    par_civ2.maskname=maskdispl;
2051                    par_civ2.maskflag='y';
[2]2052                else
[136]2053                    maskbase=[filecell.filebase '_' maskdispl]; %
[137]2054                    nbslice_mask=str2double(maskdispl(1:end-4)); %
[12]2055                    num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
2056                    par_civ2.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
2057                    if exist(par_civ2.maskname,'file')
[112]2058                        par_civ2.maskflag='y';
[12]2059                    else
2060                        par_civ2.maskname='noFile use default';
[112]2061                        par_civ2.maskflag='n';
[12]2062                    end
[2]2063                end
2064            end
2065            %TESTgrid
[137]2066            %test_grid=get(handles.browse_gridciv2,'Value');
[2]2067            gridname=get(handles.grid_civ2,'String');
[137]2068            %gridflag='y';
[2]2069            if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid')
[137]2070                nbslice_grid=str2double(gridname(1:end-4)); %
2071                if ~isnan(nbslice_grid)
[2]2072                    par_civ2.gridflag='y';
2073                    num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
[136]2074                    par_civ2.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
[2]2075                    if exist(par_civ2.gridname,'file')
[112]2076                        par_civ2.gridflag='y';
[2]2077                    else
2078                        par_civ2.gridname='noFile use default';
[112]2079                        par_civ2.gridflag='n';
[2]2080                    end
2081                elseif exist(gridname,'file')
[112]2082                    par_civ2.gridflag='y';
[2]2083                else
2084                    par_civ2.gridname='noFile use default';
[112]2085                    par_civ2.gridflag='n';
[2]2086                end
2087            end
2088            %endTESTgrid
2089            i_cmd=i_cmd+1;
[134]2090            cmd_CIV2=CIV2_CMD(filename_cmx(1:end-4),namelog,par_civ2,sparam);
[2]2091            if isequal(civAll,0)
2092                if(isunix)
[90]2093                    cmd=[cmd 'cp -f ' filename_cmx '2 ' filename_cmx '\n' cmd_CIV2 '\n'];
[2]2094                else
[94]2095                    filename_cmx=regexprep(filename_cmx,'\\','\\\\');
[90]2096                    cmd=[cmd 'copy /Y ' filename_cmx '2 ' filename_cmx '\n' cmd_CIV2 '\n'];
[2]2097                end
2098            else
[112]2099                civAllCmd=[civAllCmd ' civ2 '];
2100                str=CIV2_CMD_Unified(filename_cmx([1:end-4]),namelog,par_civ2);
2101                fieldnames=fields(str);
[2]2102                [civAllxml,uid_civ2]=add(civAllxml,1,'element','civ2');
2103                for ilist=1:length(fieldnames)
2104                    val=eval(['str.' fieldnames{ilist}]);
2105                    if ischar(val)
[112]2106                        [civAllxml,uid_t]=add(civAllxml,uid_civ2,'element',fieldnames{ilist});
2107                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
[2]2108                    end
[112]2109                end
[2]2110            end
[112]2111        end
2112       
2113        % FIX2
2114        if box_test(5)==1
2115            test_mask=get(handles.get_mask_fix2,'Value');
2116            if test_mask==0
2117                maskname=''; %no mask used
[2]2118            else
2119                maskdispl=get(handles.mask_fix2,'String');
[136]2120                maskbase=[filecell.filebase '_' maskdispl]; %
[137]2121                nbslice_mask=str2double(maskdispl(1:end-4)); %
[2]2122                num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
2123                maskname =name_generator(maskbase,num1_mask,1,'.png','_i');
[112]2124            end
2125            if isequal(civAll,0)
[94]2126                cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ...
[112]2127                    ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2128                    ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName ' maskname];
2129                cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
2130                cmd=[cmd cmd_FIX '\n'];
2131            else
[2]2132                fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
2133                fix2.fi1=num2str(flagindex2(1));
2134                fix2.fi2=num2str(flagindex2(2));
2135                fix2.fi3=num2str(flagindex2(3));
2136                fix2.threshC=num2str(thresh_vec2C);
[112]2137                fix2.threshV=num2str(thresh_vel2);
[2]2138                fieldnames=fields(fix2);
2139                [civAllxml,uid_fix2]=add(civAllxml,1,'element','fix2');
2140                for ilist=1:length(fieldnames)
[112]2141                    val=eval(['fix2.' fieldnames{ilist}]);
2142                    if ischar(val)
2143                        [civAllxml,uid_t]=add(civAllxml,uid_fix2,'element',fieldnames{ilist});
2144                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2145                    end
2146                end
2147                civAllCmd=[civAllCmd ' fix2 '];
2148            end
2149        end
2150       
2151        %PATCH2
2152        if box_test(6)==1
[12]2153            if isequal(civAll,0)
[94]2154                cmd_PATCH=PATCH_CMD(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,test_interp,sparam.PatchBin);
2155                cmd_PATCH=regexprep(cmd_PATCH,'\\','\\\\');
[90]2156                cmd=[cmd cmd_PATCH '\n'];
[12]2157            else
2158                patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
2159                patch2.nopt=subdomain_patch1;
2160                patch2.maxdiff=thresh_patch1;
2161                patch2.ro=rho_patch1;
2162                test_grid=get(handles.get_gridpatch2,'Value');
2163                if test_grid
2164                    patch2.gridflag='y';
2165                    gridname=get(handles.grid_patch2,'String');
2166                    if isequal(gridname(end-3:end),'grid')
[137]2167                        nbslice_grid=str2double(gridname(1:end-4)); %
2168                        if ~isnan(nbslice_grid)
[12]2169                            num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
[136]2170                            patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
[12]2171                            if ~exist(patch2.gridPatch,'file')
[112]2172                                msgbox_uvmat('ERROR','grid file absent for patch2')
[12]2173                            end
2174                        elseif exist(gridname,'file')
[112]2175                            patch2.gridPatch=gridname;
[12]2176                        else
2177                            msgbox_uvmat('ERROR','grid file absent for patch2')
[2]2178                        end
2179                    end
[12]2180                else
[112]2181                    patch2.gridPatch='none';
2182                    patch2.gridflag='n';
2183                    patch2.m=nx_patch2;
2184                    patch2.n=ny_patch2;
[2]2185                end
[12]2186                patch2.convectFlow='n';
2187                fieldnames=fields(patch2);
2188                [civAllxml,uid_patch2]=add(civAllxml,1,'element','patch2');
2189                for ilist=1:length(fieldnames)
[112]2190                    val=eval(['patch2.' fieldnames{ilist}]);
2191                    if ischar(val)
2192                        [civAllxml,uid_t]=add(civAllxml,uid_patch2,'element',fieldnames{ilist});
2193                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2194                    end
2195                end
[12]2196                civAllCmd=[civAllCmd ' patch2 '];
[112]2197            end
[12]2198        end
2199        if isequal(civAll,1)
2200            save(civAllxml,[filename_cmx([1:end-4]) '.xml']);
[73]2201            %cmd=char({cmd;[CivBin ' -f ' [filename_cmx([1:end-4]) '.xml'] ' ' civAllCmd]});
[90]2202            cmd=[cmd CivBin ' -f ' filename_cmx(1:end-4) '.xml '  civAllCmd  '\n'];
[12]2203        end
[112]2204        % create the .bat file:
[67]2205        if batch
[112]2206            [Rootbat,Filebat,extbat]=fileparts(filename_cmx);
2207            filename_bat=fullfile(Rootbat,['job_' Filebat extbat]);
[136]2208         else
[12]2209            filename_bat=filename_cmx;
2210        end
2211        filename_bat(end-2:end)='bat';
2212        fid=fopen(filename_bat,'w');
[39]2213        fprintf(fid,cmd);
2214        fclose(fid);
[12]2215        %dlmwrite(filename_bat,cmd,'');%write commands in filename_bat
[67]2216        if batch
2217            switch batch_mode
2218                case 'sge'
2219                    pvalue=num2str((1-ind_answer)*500);
[133]2220                    %namelog=[filename_bat '.patch.log'];
[73]2221                    display(['!qsub -p ' pvalue ' -q civ.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]);
[67]2222                    eval(  ['!qsub -p ' pvalue ' -q civ.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]);
2223            end
[12]2224        else
[112]2225            %% to lauch the jobs locally :
[12]2226            if(isunix)
[135]2227                cmd_str=['. ' filename_bat];
2228                % cmd_str=['!at -qb now -f ' filename_bat ' &']; %ou at -qb now -f bad idea...
[133]2229            else %case of Windows
[135]2230                cmd_str=['@call ' regexprep(filename_bat,'\\','\\\\')];
[2]2231            end
[135]2232            super_cmd=[super_cmd cmd_str '\n'];         
2233            %             eval(cmd_str);
2234            disp(cmd_str);
[12]2235        end
[112]2236    end
[2]2237end
[134]2238
[137]2239if ~batch
[134]2240    [Rootbat,Filebat,extbat]=fileparts(filename_cmx);
[135]2241    filename_superbat=fullfile(Rootbat,['job_list.bat']);
[134]2242    fid=fopen(filename_superbat,'w');
2243    fprintf(fid,super_cmd');
2244    fclose(fid);
[135]2245    if(isunix)
2246        eval(['!. ' filename_superbat ' &']);
2247    else
2248        eval(['!' filename_superbat ' &']);
2249    end
[133]2250end
[2]2251
[137]2252%% save interface state
[2]2253if isfield(filecell,'nc')
2254    if isfield(filecell.nc,'civ2')
2255        fileresu=filecell.nc.civ2{1,1};
2256    else
2257        fileresu=filecell.nc.civ1{1,1};
2258    end
2259end
2260[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
2261namedoc=fullfile(RootPath,subdir,RootFile);
[112]2262detect=1;
[2]2263while detect==1
2264    namefigfull=[namedoc '.fig'];
2265    hh=dir(namefigfull);
2266    if ~isempty(hh)
2267        detect=1;
2268        namedoc=[namedoc '.0'];
2269    else
2270        detect=0;
2271    end
2272end
2273saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
2274
[134]2275
2276
[2]2277function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
2278    set_civ_filenames(handles,compare,box_test)
[12]2279%------------------------------------------------------------------------
[85]2280filecell=[];%default
[136]2281
2282%% get the root names nomenclature and numbers
[71]2283filebase=get(handles.RootName,'String');
[136]2284
2285if isempty(filebase)||isequal(filebase,'')
2286    msgbox_uvmat('ERROR','no input files')
2287    return
2288end
2289
[137]2290%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
[136]2291filecell.filebase=filebase;
2292
[2]2293browse=get(handles.browse_root,'UserData');
2294compare_list=get(handles.compare,'String');
2295val=get(handles.compare,'Value');
2296compare=compare_list{val};
2297if strcmp(compare,'displacement')
2298    mode='displacement';
2299else
2300    mode_list=get(handles.mode,'String');
2301    mode_value=get(handles.mode,'Value');
2302    mode=mode_list{mode_value};
2303end
[137]2304%time=get(handles.RootName,'UserData'); %get the set of times
[71]2305ext_ima=get(handles.ImaExt,'String');
[2]2306nom_type_nc=browse.nom_type_nc;
[122]2307if isfield(browse,'nom_type_ima')
2308    nom_type_ima2=browse.nom_type_ima;
2309end
2310if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
2311if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
[2]2312[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2313    find_pair_indices(handles,mode);
2314%determine the new filebase for 'displacement' mode (comparison of two series)
2315filebase_B=filebase;% root name of the second field series for stereo
2316if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
[127]2317%     test_disp=1;
[2]2318    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
2319    [Path2,Name2]=fileparts(filebase_B);
2320    Path1=Path2;
[71]2321    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
[2]2322    filebase_A=fullfile(Path1,Name1);
2323    if length(Name1)>6
2324        Name1=Name1(end-5:end);
2325    end
2326    if length(Name2)>6
2327        Name2=Name2(end-5:end);
2328    end
2329    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
2330else
[127]2331%     test_disp=0;
[2]2332    filebase_A=filebase;
2333    nom_type_ima1=nom_type_ima2;
2334    filebase_AB=filebase;
2335end
2336if strcmp(compare,'displacement')
[112]2337    filebase_ima1=filebase_A;
2338    filebase_ima2=filebase_B;
2339    filebase_nc=filebase_AB; %root name for the result of civ2
[2]2340else
[112]2341    filebase_ima1=filebase_B;
2342    filebase_ima2=filebase_B;
2343    filebase_nc=filebase_B;
2344end
[2]2345
2346%determine reference files for fix:
2347file_ref_fix1={};%default
2348file_ref_fix2={};
2349nbfield=length(num1_civ1);
2350nbslice=length(num_a_civ1);
2351if box_test(2)==1% fix1 performed
2352    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
2353    if ~isempty(ref)
[137]2354        first_i=str2double(get(handles.first_i,'String'));
2355        last_i=str2double(get(handles.last_i,'String'));
2356        incr_i=str2double(get(handles.incr_i,'String'));
2357        first_j=str2double(get(handles.first_j,'String'));
2358        last_j=str2double(get(handles.last_j,'String'));
2359        incr_j=str2double(get(handles.incr_j,'String'));
[127]2360        num_i_ref=first_i:incr_i:last_i;
2361        num_j_ref=first_j:incr_j:last_j;
[2]2362        if isequal(mode,'displacement')
2363            num_i1=num_i_ref;
2364            num_i2=num_i_ref;
2365            num_j1=num_j_ref;
2366            num_j2=num_j_ref;
2367        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2368            num_i1=num_i_ref;
2369            num_i2=num_i1;
2370            num_j1=ref.num_a*ones(size(num_i_ref));
2371            num_j2=ref.num_b*ones(size(num_i_ref));
2372        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2373            delta1=floor((ref.num2-ref.num1)/2);
2374            delta2=ceil((ref.num2-ref.num1)/2);
2375            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2376            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2377            if isempty(ref.num_a)
2378                ref.num_a=1;
2379            end
2380            num_j1=ref.num_a*ones(size(num_i1));
2381            num_j2=num_j1;
2382        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2383            delta1=floor((ref.num_b-ref.num_a)/2);
2384            delta2=ceil((ref.num_b-ref.num_a)/2);
2385            num_i1=ref.num1*ones(size(num_i_ref));
2386            num_i2=num_i1;
2387            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2388            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2389        end
2390        for ifile=1:nbfield
2391            for j=1:nbslice
2392                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
2393                file_ref_fix1(ifile,j)={file_ref};
2394                if ~exist(file_ref,'file')
2395                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
[12]2396                    filecell=[];
[2]2397                    return
2398                end
2399            end
2400        end
2401    end
2402end
2403
2404%determine reference files for fix2:
2405if box_test(5)==1% fix2 performed
2406    ref=get(handles.ref_fix2,'UserData');
2407    if ~isempty(ref)
[127]2408        first_i=str2double(get(handles.first_i,'String'));
2409        last_i=str2double(get(handles.last_i,'String'));
2410        incr_i=str2double(get(handles.incr_i,'String'));
2411        first_j=str2double(get(handles.first_j,'String'));
2412        last_j=str2double(get(handles.last_j,'String'));
2413        incr_j=str2double(get(handles.incr_j,'String'));
[2]2414        num_i_ref=[first_i:incr_i:last_i];
2415        num_j_ref=[first_j:incr_j:last_j];
2416        if isequal(mode,'displacement')
2417            num_i1=num_i_ref;
2418            num_i2=num_i_ref;
2419            num_j1=num_j_ref;
2420            num_j2=num_j_ref;
2421        elseif isequal(mode,'pair j1-j2')
2422            num_i1=num_i_ref;
2423            num_i2=num_i1;
2424            num_j1=ref.num_a;
2425            num_j2=ref.num_b;
2426        elseif isequal(mode,'series(Di)')
2427            delta1=floor((ref.num2-ref.num1)/2);
2428            delta2=ceil((ref.num2-ref.num1)/2);
2429            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2430            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2431            num_j1=ref.num_a*ones(size(num_i1));
2432            num_j2=num_j1;
2433        elseif isequal(mode,'series(Dj)')
2434            delta1=floor((ref.num_b-ref.num_a)/2);
2435            delta2=ceil((ref.num_b-ref.num_a)/2);
2436            num_i1=ref.num1*ones(size(num_i_ref));
2437            num_i2=num_i1;
2438            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2439            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2440        end
2441        for ifile=1:nbfield
2442            for j=1:nbslice
2443                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
2444                file_ref_fix2(ifile,j)={file_ref};
2445                if ~exist(file_ref,'file')
2446                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
[122]2447                    filecell={};
[2]2448                    return
2449                end
2450            end
2451        end
2452    end
2453end
2454
2455%check dir
2456subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data
2457subdir_civ2=get(handles.subdir_civ2,'String');
2458if isequal(subdir_civ1,''),subdir_civ1='A'; end% put default subdir
2459if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
[135]2460currentdir=pwd;%store the current working directory
[2]2461[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
2462if ~exist(Path_ima,'dir')
[12]2463    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
[122]2464    filecell={};
[2]2465    return
2466end
[127]2467[xx,message]=fileattrib(Path_ima);
[122]2468if ~isempty(message) && ~isequal(message.UserWrite,1)
[112]2469    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
[122]2470    filecell={};
[112]2471    cd(currentdir);
2472    return
[2]2473end
2474
2475%check the existence of the netcdf and image files involved
2476% %%%%%%%%%%%%  case CIV1 activated   %%%%%%%%%%%%%
2477if box_test(1)==1;
[112]2478    detect=1;
[127]2479    vers=0;
2480    subdir_civ1_new=subdir_civ1;
[137]2481    ind_test=0;
2482    while detect==1 && ind_test<10%create a new subdir if the netcdf files already exist
[122]2483        for ifile=1:nbfield
[112]2484            for j=1:nbslice
[122]2485                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);
[112]2486                detect=exist(filename,'file')==2;
2487                if detect% if a netcdf file already exists
[137]2488                    indstr=regexp(subdir_civ1_new,'\D');
2489                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2490                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2491                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
[127]2492                    else
2493                        vers=vers+1;
[137]2494                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
[127]2495                    end
[137]2496                    subdir_civ2=subdir_civ1_new;
[112]2497                    break
2498                end
2499                filecell.nc.civ1(ifile,j)={filename};
2500            end
2501            if detect% if a netcdf file already exists
2502                break
2503            end
2504        end
[134]2505 
[112]2506        %create the new subdir_civ1
[127]2507        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
[134]2508            cd(Path_ima);         
[128]2509            [xx,msg1]=mkdir(subdir_civ1_new);
[134]2510
[128]2511            if ~strcmp(msg1,'')
2512                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
[122]2513                filecell={};
2514                return
[134]2515            else         
[128]2516                [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2517                if ~strcmp(msg2,'')
[134]2518                    msgbox_uvmat('ERROR',['pb of permission for  ' subdir_civ1_new ': ' msg2])%error message for directory creation
[128]2519                    filecell={};
2520                    return
2521                end
[112]2522            end
[134]2523            cd(currentdir);
[112]2524        end
2525        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2526            for ifile=1:nbfield
2527                for j=1:nbslice
[122]2528                    filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);%
[112]2529                    detect=exist(filename,'file')==2;
[2]2530                    if detect% if a netcdf file already exists
[137]2531                       indstr=regexp(subdir_civ1_new,'\D');
2532                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2533                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2534                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
[127]2535                       else
2536                           vers=vers+1;
[137]2537                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
[127]2538                       end
2539                       subdir_civ2=subdir_civ1;
2540                       break
[2]2541                    end
[112]2542                    filecell.ncA.civ1(ifile,j)={filename};
2543                end
2544                if detect% if a netcdf file already exists
2545                    break
2546                end
2547            end
2548            %create the new subdir_civ1
[134]2549            if exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2550                   cd(Path_ima);         
[128]2551                [xx,msg1]=mkdir(subdir_civ1_new);
[134]2552                            cd(currentdir);
[128]2553                if ~strcmpl(msg1,'')
2554                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
[122]2555                    cd(currentdir)
2556                    filecell={};
2557                    return
[128]2558                else
2559                    [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2560                    if ~strcmp(msg2,'')
2561                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2562                        cd(currentdir)
2563                        filecell={};
2564                        return
2565                    end
[112]2566                end
2567            end
2568        end
2569    end
[127]2570    subdir_civ1=subdir_civ1_new;
[2]2571    % get image names
2572    for ifile=1:nbfield
[112]2573        for j=1:nbslice
[2]2574            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2575            idetect(j)=exist(filename,'file')==2;
2576            filecell.ima1.civ1(ifile,j)={filename}; %first image
2577            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2578            idetect_1(j)=exist(filename,'file')==2;
2579            filecell.ima2.civ1(ifile,j)={filename};%second image
[112]2580        end
2581        [idetectmin,indexj]=min(idetect);
2582        if idetectmin==0,
2583            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
[122]2584            filecell={};
2585            cd(currentdir)
[112]2586            return
2587        end
2588        [idetectmin,indexj]=min(idetect_1);
2589        if idetectmin==0,
2590            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
[122]2591            filecell={};
[112]2592            cd(currentdir)
2593            return
2594        end
2595    end
2596    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2597        for ifile=1:nbfield
2598            for j=1:nbslice
2599                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2600                idetect(j)=exist(filename,'file')==2;
2601                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2602                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2603                idetect_1(j)=exist(filename,'file')==2;
2604                filecell.imaA2.civ1(ifile,j)={filename};%second image
2605            end
[2]2606            [idetectmin,indexj]=min(idetect);
[112]2607            if idetectmin==0,
2608                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
[122]2609                filecell={};
[112]2610                cd(currentdir)
[2]2611                return
[112]2612            end
[2]2613            [idetectmin,indexj]=min(idetect_1);
[112]2614            if idetectmin==0,
2615                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
[122]2616                filecell={};
[2]2617                cd(currentdir)
2618                return
[112]2619            end
2620        end
[2]2621    end
[112]2622   
2623    %%%%%%%%%%%%%  fix1 or patch1 activated but no civ1   %%%%%%%%%%%%%
2624elseif (box_test(2)==1 || box_test(3)==1);
[2]2625    for ifile=1:nbfield
2626        for j=1:nbslice
2627            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
[112]2628                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2629            detect=exist(filename,'file')==2;
[122]2630            if detect==0
2631                msgbox_uvmat('ERROR',[filename ' not found'])
2632                filecell={};
2633                cd(currentdir)
2634                return
2635            end
[2]2636            filecell.nc.civ1(ifile,j)={filename};
2637        end
2638    end
2639    if strcmp(compare,'stereo PIV')
[112]2640        for ifile=1:nbfield
2641            for j=1:nbslice
2642                filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2643                filecell.ncA.civ1(ifile,j)={filename};
2644                if ~exist(filename,'file')
2645                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2646                    set(handles.RUN, 'Enable','On')
2647                    set(handles.RUN,'BackgroundColor',[1 0 0])
[122]2648                    filecell={};
[112]2649                    cd(currentdir)
2650                    return
[2]2651                end
2652            end
[112]2653        end
[2]2654    end
2655end
2656
2657%%%%%%%%%%%%%  if civ2 performed with pairs different than civ1  %%%%%%%%%%%%%
2658testdiff=0;
2659if (box_test(4)==1)&&...
[127]2660        ((get(handles.list_pair_civ1,'Value')~=get(handles.list_pair_civ2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
[2]2661    testdiff=1;
[112]2662    detect=1;
[127]2663    vers=0;
2664    subdir_civ2_new=subdir_civ2;
[2]2665    while detect==1 %create a new subdir if the netcdf files already exist
[112]2666        for ifile=1:nbfield
2667            for j=1:nbslice
[127]2668                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2_new);%
[112]2669                detect=exist(filename,'file')==2;
2670                if detect% if a netcdf file already exists
[127]2671                    indstr=regexp(subdir_civ2,'\D');
2672                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2673                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2674                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2675                    else
2676                        vers=vers+1;
2677                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2678                    end
[112]2679                    break
2680                end
2681                filecell.nc.civ2(ifile,j)={filename};
2682            end
2683            if detect% if a netcdf file already exists
2684                break
2685            end
2686        end
[128]2687        %create the new subdir_civ2_new
2688        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2689            [xx,m2]=mkdir(subdir_civ2_new);
2690            [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
[112]2691            if ~isequal(m2,'')
[128]2692                msgbox_uvmat('ERROR',['cannot create ' subdir_civ2_new ': ' m2])
[122]2693                filecell={};
2694                cd(currentdir)
2695                return
[112]2696            end
2697        end
2698        if strcmp(compare,'stereo PIV')%check second nc series
2699            for ifile=1:nbfield
2700                for j=1:nbslice
2701                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
[122]2702                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
[112]2703                    detect=exist(filename,'file')==2;
[2]2704                    if detect% if a netcdf file already exists
[127]2705                        indstr=regexp(subdir_civ2,'\D');
2706                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2707                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2708                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2709                        else
2710                           vers=vers+1;
2711                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2712                        end
[112]2713                        break
[2]2714                    end
[112]2715                    filecell.ncA.civ2(ifile,j)={filename};
2716                end
2717                if detect% if a netcdf file already exists
2718                    break
2719                end
2720            end
[122]2721            subdir_civ2=subdir_civ2_new;
[112]2722            %create the new subdir_civ1
[127]2723            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2724                [xx,m2]=mkdir(subdir_civ2_new);
[128]2725                 [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
[112]2726                if ~isequal(m2,'')
[128]2727                    msgbox_uvmat('ERROR', ['cannot create ' subdir_civ2_new ': ' m2])%error message for directory creation
[122]2728                    cd(currentdir)
2729                    filecell={};
2730                    return
[112]2731                end
2732            end
2733        end
2734    end
[127]2735    subdir_civ2=subdir_civ2_new;
[2]2736end
2737cd(currentdir);%come back to the current working directory
2738
2739%%%%%%%%%%%%%  if civ2 results are obtained or used  %%%%%%%%%%%%%
2740if box_test(4)==1 || box_test(5)==1 || box_test(6)==1 %civ2
2741    %check source netcdf file of civ1 estimates
2742    if box_test(1)==0; %no civ1 performed
2743        for ifile=1:nbfield
2744            for j=1:nbslice
2745                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2746                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2747                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2748                if ~exist(filename,'file')
2749                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
[122]2750                    filecell={};
[2]2751                    return
2752                end
2753                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2754                    if box_test(4)==0 ; %check the existence of civ2 if it is not calculated
2755                        Data=nc2struct(filename,'ListGlobalAttribute','civ2');
2756                        if isempty(Data.civ2)||isequal(Data.civ2,0)
2757                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
[12]2758                            filecell=[];
[2]2759                            return
[112]2760                        end
[2]2761                    elseif box_test(3)==0; %check the existence of patch if it is not calculated
2762                        Data=nc2struct(filename,'ListGlobalAttribute','patch');
2763                        if isempty(Data.patch)||isequal(Data.patch,0)
2764                            msgbox_uvmat('ERROR',['no patch data in ' filename])
[12]2765                            filecell=[];
[2]2766                            return
2767                        end
[112]2768                    end
[2]2769                end
2770            end
2771        end
2772        if strcmp(compare,'stereo PIV')
2773            for ifile=1:nbfield
2774                for j=1:nbslice
2775                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2776                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2777                    filecell.ncA.civ2(ifile,j)={filename};
2778                    if ~exist(filename,'file')
2779                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2780                        set(handles.RUN, 'Enable','On')
2781                        set(handles.RUN,'BackgroundColor',[1 0 0])
2782                        return
2783                    end
2784                end
2785            end
2786        end
2787    end
[112]2788   
2789    detect=1;
2790    %     while detect==1%creates a new subdir if the netcdf files already contain civ2 data
2791    for ifile=1:nbfield
2792        for j=1:nbslice
2793            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
[2]2794                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
[112]2795            detect=exist(filename,'file')==2;
2796            filecell.nc.civ2(ifile,j)={filename};
[2]2797        end
[112]2798    end
[2]2799    %get first image names for civ2
2800    if box_test(1)==1 & isequal(num1_civ1,num1_civ2) & isequal(num_a_civ1,num_a_civ2)
2801        filecell.ima1.civ2=filecell.ima1.civ1;
2802    elseif box_test(4)==1
2803        for ifile=1:nbfield
2804            for j=1:nbslice
2805                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2806                idetect_2(j)=exist(filename,'file')==2;
2807                filecell.ima1.civ2(ifile,j)={filename};%first image
2808            end
[112]2809            [idetectmin,indexj]=min(idetect_2);
[2]2810            if idetectmin==0,
[112]2811                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2812                filecell=[];
2813                return
[2]2814            end
2815        end
2816    end
2817   
2818    %get second image names for civ2
2819    if box_test(1)==1 & isequal(num2_civ1,num2_civ2) & isequal(num_b_civ1,num_b_civ2)
2820        filecell.ima2.civ2=filecell.ima2.civ1;
2821    elseif box_test(4)==1
2822        for ifile=1:nbfield
2823            for j=1:nbslice
2824                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2825                idetect_3(j)=exist(filename,'file')==2;
2826                filecell.ima2.civ2(ifile,j)={filename};%first image
2827            end
[112]2828            [idetectmin,indexj]=min(idetect_3);
[2]2829            if idetectmin==0,
[112]2830                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2831                filecell=[];
2832                return
[2]2833            end
2834        end
2835    end
2836end
2837if (box_test(5)==1 || box_test(6)==1 ) && box_test(4)==0  % need to read an existing netcdf civ2 file
2838    if ~testdiff
2839        filecell.nc.civ2=filecell.nc.civ1;% file already checked
[112]2840    else     % check the civ2 files
[2]2841        for ifile=1:nbfield
2842            for j=1:nbslice
2843                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
[112]2844                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
[2]2845                filecell.nc.civ2(ifile,j)={filename};
2846                if ~exist(filename,'file')
2847                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
[12]2848                    filecell=[];
[2]2849                    return
2850                else
2851                    Data=nc2struct(filename,'ListGlobalAttribute','civ2');
[112]2852                    if isempty(Data.civ2)||isequal(Data.civ2,0)
[2]2853                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
[12]2854                        filecell=[];
[2]2855                        return
2856                    end
2857                end
2858            end
2859        end
2860    end
2861end
2862
2863%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2864if strcmp(compare,'stereo PIV')
[127]2865    if  box_test(3)==1 && isequal(get(handles.test_stereo1,'Value'),1)
[2]2866        for ifile=1:nbfield
2867            for j=1:nbslice
2868                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2869                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2870                filecell.st(ifile,j)={filename};
2871            end
2872        end
2873    end
[127]2874    if  box_test(6)==1 && isequal(get(handles.test_stereo2,'Value'),1)
[2]2875        for ifile=1:nbfield
2876            for j=1:nbslice
2877                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2878                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2879                filecell.st(ifile,j)={filename};
2880            end
2881        end
[112]2882    end
[2]2883end
2884set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box
2885set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box
2886browse.nom_type_nc=nom_type_nc;
2887set(handles.browse_root,'UserData',browse); %update the nomenclature type for uvmat
2888
2889
2890%COPY IMAGES TO THE FORMAT .png IF NEEDED
[45]2891if isequal(nom_type_ima1,'*')%case of movie files
2892    nom_type_imanew1='_i';
[2]2893else
2894    nom_type_imanew1=nom_type_ima1;
2895end
[45]2896if isequal(nom_type_ima2,'*')%case of movie files
2897    nom_type_imanew2='_i';
[2]2898else
2899    nom_type_imanew2=nom_type_ima2;
2900end
2901if ~isequal(ext_ima,'.png')
[45]2902    %%type of image file
2903    type_ima1='none';%default
2904    movieobject1=[];%default
[133]2905    if strcmpi(ext_ima,'.avi')
[45]2906        hhh=which('mmreader');
2907        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2908            type_ima1='movie';
2909            movieobject1=mmreader([filebase_ima2 ext_ima]);
2910        else
2911            type_ima1='avi';
2912        end
[133]2913    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
[112]2914        form=imformats(ext_ima(2:end));
2915        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2916            if isequal(nom_type_ima1,'*');
2917                type_ima1='multimage';%image series in a single image file
2918            else
2919                type_ima1='image';
2920            end
2921        end
[45]2922    end
2923    type_ima2='none';%default
2924    movieobject2=[];
[133]2925    if strcmpi(ext_ima,'.avi')
[45]2926        hhh=which('mmreader');
2927        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2928            type_ima2='movie';
2929            movieobject2=mmreader([filebase_ima2 ext_ima]);
2930        else
2931            type_ima2='avi';
2932        end
[133]2933    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
[112]2934        form=imformats(ext_ima(2:end));
2935        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2936            if isequal(nom_type_ima1,'*');
2937                type_ima2='multimage';%image series in a single image file
2938            else
2939                type_ima2='image';
2940            end
2941        end
[45]2942    end
[71]2943    %npxy=get(handles.ImaExt,'UserData');
[112]2944    % %     if numel(npxy)<2
2945    %
2946    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2947    %         A=imread(filename);
2948    %         npxy=size(A);
2949    % %     end
2950    %     npy=npxy(1);
2951    %     npx=npxy(2);
[2]2952    if box_test(1)==1 %if civ1 is performed
[112]2953        h = waitbar(0,['copy images to the .png format for civ1']);% display a wait bar
2954        for ifile=1:nbfield
[2]2955            waitbar(ifile/nbfield);
2956            for j=1:nbslice
[112]2957                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2958                if ~exist(filename,'file')
2959                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2960                    imwrite(A,filename,'BitDepth',16);
2961                end
2962                filecell.ima1.civ1(ifile,j)={filename};
2963                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2964                if ~exist(filename,'file')
2965                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2966                    imwrite(A,filename,'BitDepth',16);
2967                end
2968                filecell.ima2.civ1(ifile,j)={filename};
[2]2969            end
2970        end
2971        close(h)
2972    end
2973    if box_test(4)==1 %if civ2 is performed
[112]2974        h = waitbar(0,['copy images to the .png format for civ2']);% display a wait bar
[2]2975        for ifile=1:nbfield
2976            waitbar(ifile/nbfield);
2977            for j=1:nbslice
[112]2978                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
2979                if ~exist(filename,'file')
2980                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
2981                    imwrite(A,filename,'BitDepth',16);
2982                end
2983                filecell.ima1.civ2(ifile,j)={filename};
2984                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
2985                if ~exist(filename,'file')
2986                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
2987                    imwrite(A,filename,'BitDepth',16);
2988                end
2989                filecell.ima2.civ2(ifile,j)={filename};
[2]2990            end
2991        end
2992        close(h);
2993    end
2994end
2995
[12]2996%------------------------------------------------------------------------
2997% --- PATCH
[94]2998function cmd_PATCH=PATCH_CMD(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp,PatchBin)
[12]2999%------------------------------------------------------------------------
[112]3000namelog=[filename_nc([1:end-3]) '_patch.log'];
3001if test_interp==0
3002    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3003        '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3004else %nouveau programme patch
3005    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
3006        ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3007end
[12]3008
3009%------------------------------------------------------------------------
3010% --- STEREO Interp
[67]3011function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
[12]3012%------------------------------------------------------------------------
[2]3013namelog=[filename_nc([1:end-3]) '_stinterp.log'];
[67]3014cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
[2]3015    ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB '  -xy  x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file
3016
[12]3017%------------------------------------------------------------------------
[2]3018% --- Executes on button press in CIV1.
3019function CIV1_Callback(hObject, eventdata, handles)
[12]3020%------------------------------------------------------------------------
[2]3021val=get(handles.CIV1,'Value');
3022if isequal(val,1)
3023    enable_civ1(handles,'on')
3024    enable_pair1(handles,'on')
3025else
3026    enable_civ1(handles,'off')
3027end
3028find_netcpair_civ1(hObject, eventdata, handles);
3029
[12]3030%------------------------------------------------------------------------
[2]3031% --- Executes on button press in FIX1.
3032function FIX1_Callback(hObject, eventdata, handles)
[12]3033%------------------------------------------------------------------------
[2]3034enable_fix1(handles,get(handles.FIX1,'Value'))
3035
[12]3036%------------------------------------------------------------------------
[2]3037% --- Executes on button press in PATCH1.
3038function PATCH1_Callback(hObject, eventdata, handles)
[12]3039%------------------------------------------------------------------------
[2]3040if get(handles.PATCH1,'Value')==1
[12]3041    enable_patch1(handles)
[2]3042else
[12]3043    desable_patch1(handles)
[2]3044end
3045
[12]3046%------------------------------------------------------------------------
[2]3047% --- Executes on button press in CIV2.
3048function CIV2_Callback(hObject, eventdata, handles)
[12]3049%------------------------------------------------------------------------
[2]3050state=get(handles.CIV2,'Value');
3051enable_civ2(handles,state)
3052if state
3053    find_netcpair_civ2(hObject, eventdata, handles)
3054    enable_pair1(handles,'on')
3055end
3056
[12]3057%------------------------------------------------------------------------
[2]3058% --- Executes on button press in FIX2.
3059function FIX2_Callback(hObject, eventdata, handles)
[12]3060%------------------------------------------------------------------------
[2]3061if get(handles.FIX2,'Value')==1
3062    enable_fix2(handles)
3063    if get(handles.CIV2,'Value')==0
3064        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3065    end
3066else
3067    desable_fix2(handles)
3068end
3069
[12]3070%------------------------------------------------------------------------
[2]3071% --- Executes on button press in PATCH2.
3072function PATCH2_Callback(hObject, eventdata, handles)
[12]3073%------------------------------------------------------------------------
[2]3074if get(handles.PATCH2,'Value')==1
3075    enable_patch2(handles)
3076    if get(handles.CIV2,'Value')==0
3077        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3078    end
3079else
3080    desable_patch2(handles)
3081end
3082
[12]3083%------------------------------------------------------------------------
3084function first_i_Callback(hObject, eventdata, handles)
3085%------------------------------------------------------------------------
3086% last_i_Callback(hObject, eventdata, handles)
[137]3087first_i=str2double(get(handles.first_i,'String'));
[12]3088% last_i=str2num(get(handles.last_i,'String'));
3089% ref_i=ceil((first_i+last_i)/2);
3090set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
[71]3091set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
[12]3092ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
[2]3093
[12]3094%------------------------------------------------------------------------
3095function first_j_Callback(hObject, eventdata, handles)
3096%------------------------------------------------------------------------
3097first_j=str2num(get(handles.first_j,'String'));
3098set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3099ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
[2]3100
[12]3101%------------------------------------------------------------------------
[2]3102% --- Executes on button press in calcul_search: determine the search range isx,isy
3103function calcul_search_Callback(hObject, eventdata, handles)
[12]3104%------------------------------------------------------------------------
[2]3105%determine pair numbers
3106list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
3107index=get(handles.list_pair_civ1,'Value');
3108displ_num=get(handles.list_pair_civ1,'UserData');
[71]3109time=get(handles.RootName,'UserData'); %get the set of times
[2]3110pxcm_xy=get(handles.calcul_search,'UserData');
3111pxcmx=pxcm_xy(1);
3112pxcmy=pxcm_xy(2);
3113mode_list=get(handles.mode,'String');
3114mode_value=get(handles.mode,'Value');
3115mode=mode_list{mode_value};
3116if isequal (mode, 'series(Di)' )
[137]3117    ref_i=str2double(get(handles.ref_i,'String'));
[2]3118    num1=ref_i-floor(index/2);%  first image numbers
3119    num2=ref_i+ceil(index/2);
3120    num_a=1;
3121    num_b=1;
[112]3122elseif isequal (mode, 'series(Dj)')
[2]3123    num1=1;
3124    num2=1;
[137]3125    ref_j=str2double(get(handles.ref_j,'String'));
[2]3126    num_a=ref_j-floor(index/2);%  first image numbers
3127    num_b=ref_j+ceil(index/2);
3128elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
[137]3129    ref_i=str2double(get(handles.ref_i,'String'));
[2]3130    num1=ref_i;
3131    num2=ref_i;
3132    num_a=displ_num(1,index);
3133    num_b=displ_num(2,index);
3134end
3135dt=time(num2,num_b)-time(num1,num_a);
[137]3136ibx=str2double(get(handles.ibx,'String'));
3137iby=str2double(get(handles.iby,'String'));
3138umin=dt*pxcmx*str2double(get(handles.umin,'String'));
3139umax=dt*pxcmx*str2double(get(handles.umax,'String'));
3140vmin=dt*pxcmy*str2double(get(handles.vmin,'String'));
3141vmax=dt*pxcmy*str2double(get(handles.vmax,'String'));
[2]3142shiftx=round((umin+umax)/2);
3143shifty=round((vmin+vmax)/2);
3144isx=(umax+2-shiftx)*2+ibx;
3145isx=2*ceil(isx/2)+1;
3146isy=(vmax+2-shifty)*2+iby;
3147isy=2*ceil(isy/2)+1;
3148set(handles.shiftx,'String',num2str(shiftx));
3149set(handles.shifty,'String',num2str(shifty));
3150set(handles.isx,'String',num2str(isx));
3151set(handles.isy,'String',num2str(isy));
3152
[12]3153%------------------------------------------------------------------------
3154% --- Executes on carriage return on the subdir civ1 edit window
[2]3155function subdir_civ1_Callback(hObject, eventdata, handles)
[12]3156%------------------------------------------------------------------------
[2]3157subdir=get(handles.subdir_civ1,'String');
3158set(handles.subdir_civ2,'String',subdir);
[112]3159if get(handles.CIV1,'Value')==0
[2]3160    find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
3161end
3162
[12]3163%------------------------------------------------------------------------
3164% --- Executes on carriage return on the subdir civ1 edit window
[2]3165function subdir_civ2_Callback(hObject, eventdata, handles)
[12]3166%------------------------------------------------------------------------
[2]3167%update the list of available pairs from netcdf files in the new directory
3168if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0
3169    find_netcpair_civ2(hObject, eventdata, handles);
3170end
3171
[12]3172%------------------------------------------------------------------------
[133]3173% --- Executes on button press in get_mask_civ1: select box for mask option
[2]3174function get_mask_civ1_Callback(hObject, eventdata, handles)
[12]3175%------------------------------------------------------------------------
[2]3176maskval=get(handles.get_mask_civ1,'Value');
3177if isequal(maskval,0)
3178    set(handles.mask_civ1,'String','')
3179else
3180    mask_displ='no mask'; %default
[71]3181    filebase=get(handles.RootName,'String');
[2]3182    [ nbslice_mask, flag_mask]=get_mask(filebase,handles);
3183    if isequal(flag_mask,1)
[112]3184        mask_displ=[num2str(nbslice_mask) 'mask'];
[2]3185    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
[112]3186        common_path=fileparts(filebase);
3187        filebase_a=fullfile(common_path,get(handles.RootName_1,'String'));
3188        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3189        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice_mask)
3190            mask_displ='no mask';
3191        end
[2]3192    end
3193    if isequal(mask_displ,'no mask')
[12]3194        [FileName, PathName, filterindex] = uigetfile( ...
[112]3195            {'*.png', ' (*.png)';
3196            '*.png',  '.png files '; ...
3197            '*.*', 'All Files (*.*)'}, ...
3198            'Pick a mask file *.png',filebase);
3199        mask_displ=fullfile(PathName,FileName);
[12]3200        if ~exist(mask_displ,'file')
3201            mask_displ='no mask';
3202        end
3203    end
3204    if isequal(mask_displ,'no mask')
[2]3205        set(handles.get_mask_civ1,'Value',0)
3206        set(handles.get_mask_fix1,'Value',0)
3207        set(handles.get_mask_civ2,'Value',0)
3208        set(handles.get_mask_fix2,'Value',0)
3209    else
3210        set(handles.get_mask_fix1,'Value',1)
3211        set(handles.get_mask_fix2,'Value',1)
3212    end
3213    set(handles.mask_civ1,'String',mask_displ)
3214    set(handles.mask_fix1,'String',mask_displ)
3215    set(handles.mask_civ2,'String',mask_displ)
3216    set(handles.mask_fix2,'String',mask_displ)
3217end
[133]3218set(handles.get_mask_civ2,'Value',maskval)%update the civ2 mask with the same option as civ1
[2]3219
[12]3220%------------------------------------------------------------------------
[2]3221% --- Executes on button press in get_mask_fix1.
3222function get_mask_fix1_Callback(hObject, eventdata, handles)
[12]3223%------------------------------------------------------------------------
[2]3224maskval=get(handles.get_mask_fix1,'Value');
3225if isequal(maskval,0)
3226    set(handles.mask_fix1,'String','')
3227else
[112]3228    mask_displ='no mask'; %default
3229    filebase=get(handles.RootName,'String');
3230    [nbslice, flag_mask]=get_mask(filebase,handles);
3231    if isequal(flag_mask,1)
3232        mask_displ=[num2str(nbslice) 'mask'];
3233    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
[71]3234        filebase_a=get(handles.RootName_1,'String');
[2]3235        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3236        if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
3237            mask_displ='no mask';
3238        end
[112]3239    end
3240    if isequal(mask_displ,'no mask')
3241        [FileName, PathName, filterindex] = uigetfile( ...
3242            {'*.png', ' (*.png)';
[12]3243            '*.png',  '.png files '; ...
3244            '*.*', 'All Files (*.*)'}, ...
3245            'Pick a mask file *.png',filebase);
[112]3246        mask_displ=fullfile(PathName,FileName);
3247        if ~exist(mask_displ,'file')
3248            mask_displ='no mask';
3249        end
[12]3250    end
[112]3251    if isequal(mask_displ,'no mask')
3252        set(handles.get_mask_fix1,'Value',0)
3253        set(handles.get_mask_civ2,'Value',0)
3254        set(handles.get_mask_fix2,'Value',0)
3255    else
3256        %set(handles.get_mask_civ2,'Value',1)
3257        set(handles.get_mask_fix2,'Value',1)
3258    end
3259    set(handles.mask_fix1,'String',mask_displ)
3260    set(handles.mask_civ2,'String',mask_displ)
3261    set(handles.mask_fix2,'String',mask_displ)
[12]3262end
3263
3264%------------------------------------------------------------------------
[133]3265% --- Executes on button press in get_mask_civ2: select box for mask option
[2]3266function get_mask_civ2_Callback(hObject, eventdata, handles)
[12]3267%------------------------------------------------------------------------
[2]3268maskval=get(handles.get_mask_civ2,'Value');
3269if isequal(maskval,0)
3270    set(handles.mask_civ2,'String','')
3271else
[112]3272    mask_displ='no mask'; %default
3273    filebase=get(handles.RootName,'String');
3274    [nbslice, flag_mask]=get_mask(filebase,handles);
3275    if isequal(flag_mask,1)
3276        mask_displ=[num2str(nbslice) 'mask'];
3277    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
[71]3278        filebase_a=get(handles.RootName_1,'String');
[2]3279        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3280        if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
3281            mask_displ='no mask';
3282        end
[112]3283    end
3284    if isequal(mask_displ,'no mask')
3285        [FileName, PathName, filterindex] = uigetfile( ...
3286            {'*.png', ' (*.png)';
[12]3287            '*.png',  '.png files '; ...
3288            '*.*', 'All Files (*.*)'}, ...
3289            'Pick a mask file *.png',filebase);
[112]3290        mask_displ=fullfile(PathName,FileName);
3291        if ~exist(mask_displ,'file')
3292            mask_displ='no mask';
3293        end
[12]3294    end
[112]3295    if isequal(mask_displ,'no mask')
3296        set(handles.get_mask_civ2,'Value',0)
3297        set(handles.get_mask_fix2,'Value',0)
3298    else
3299        set(handles.get_mask_fix2,'Value',1)
3300    end
3301    set(handles.mask_civ2,'String',mask_displ)
3302    set(handles.mask_fix2,'String',mask_displ)
[12]3303end
3304
3305%------------------------------------------------------------------------
[2]3306% --- Executes on button press in get_mask_fix2.
3307function get_mask_fix2_Callback(hObject, eventdata, handles)
[12]3308%------------------------------------------------------------------------
[2]3309maskval=get(handles.get_mask_fix2,'Value');
3310if isequal(maskval,0)
3311    set(handles.mask_fix2,'String','')
3312else
[12]3313    mask_displ='no mask'; %default
[71]3314    filebase=get(handles.RootName,'String');
[12]3315    [nbslice, flag_mask]=get_mask(filebase,handles);
3316    if isequal(flag_mask,1)
[112]3317        mask_displ=[num2str(nbslice) 'mask'];
[12]3318    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
[112]3319        filebase_a=get(handles.RootName_1,'String');
3320        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3321        if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
3322            mask_displ='no mask';
3323        end
[12]3324    end
3325    if isequal(mask_displ,'no mask')
3326        [FileName, PathName, filterindex] = uigetfile( ...
[112]3327            {'*.png', ' (*.png)';
3328            '*.png',  '.png files '; ...
3329            '*.*', 'All Files (*.*)'}, ...
3330            'Pick a mask file *.png',filebase);
3331        mask_displ=fullfile(PathName,FileName);
[12]3332        if ~exist(mask_displ,'file')
[2]3333            mask_displ='no mask';
3334        end
[12]3335    end
3336    if isequal(mask_displ,'no mask')
3337        set(handles.get_mask_fix2,'Value',0)
[112]3338    end
[12]3339    set(handles.mask_fix2,'String',mask_displ)
[2]3340end
3341
[12]3342%------------------------------------------------------------------------
3343% --- function called to look for mask files
[2]3344function [nbslice, flag_mask]=get_mask(filebase,handles)
[12]3345%------------------------------------------------------------------------
[112]3346%detect mask files, images with appropriate file base
[2]3347%[filebase '_' xx 'mask'], xx=nbslice
3348%flag_mask=1 indicates detection
3349
3350flag_mask=0;%default
3351nbslice=1;
3352
3353% subdir=get(handles.subdir_civ1,'String');
3354[Path,Name]=fileparts(filebase);
[12]3355if ~isdir(Path)
3356    msgbox_uvmat('ERROR','no path for input files')
3357    return
3358end
[2]3359currentdir=pwd;
3360cd(Path);%move in the dir of the root name filebase
3361maskfiles=dir([Name '_*mask_*.png']);%look for mask files
3362cd(currentdir);%come back to the current working directory
[12]3363if ~isempty(maskfiles)
[112]3364    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3365    % else
[2]3366    flag_mask=1;
3367    maskname=maskfiles(1).name;% take the first mask file in the list
3368    [Path2,Name,ext]=fileparts(maskname);
3369    Namedouble=double(Name);
3370    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3371    ind_mask=findstr('mask',Name);
3372    i=ind_mask-1;
[137]3373    while val(i)==0 && i>0
[112]3374        i=i-1;
[2]3375    end
[137]3376    nbslice=str2double(Name(i+1:ind_mask-1));
3377    if ~isnan(nbslice) && Name(i)=='_'
[112]3378        flag_mask=1;
[2]3379    else
[112]3380        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3381        return
3382        nbslice=1;
[2]3383    end
[112]3384end
[2]3385
[12]3386%------------------------------------------------------------------------
3387% --- function called to look for grid files
[2]3388function [nbslice, flag_mask]=get_grid(filebase,handles)
[12]3389%------------------------------------------------------------------------
[2]3390flag_mask=0;%default
3391nbslice=1;
3392[Path,Name]=fileparts(filebase);
3393currentdir=pwd;
3394cd(Path);%move in the dir of the root name filebase
3395maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3396cd(currentdir);%come back to the current working directory
3397if ~isempty(maskfiles)
3398    flag_mask=1;
3399    maskname=maskfiles(1).name;% take the first mask file in the list
3400    [Path2,Name,ext]=fileparts(maskname);
3401    Namedouble=double(Name);
3402    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3403    ind_mask=findstr('grid',Name);
3404    i=ind_mask-1;
[137]3405    while val(i)==0 && i>0
[112]3406        i=i-1;
[2]3407    end
[137]3408    nbslice=str2double(Name(i+1:ind_mask-1));
3409    if ~isnan(nbslice) && Name(i)=='_'
[112]3410        flag_mask=1;
[2]3411    else
[112]3412        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3413        return
3414        nbslice=1;
[2]3415    end
[12]3416end
[2]3417
[12]3418%------------------------------------------------------------------------
3419% --- transform numbers to letters
[122]3420function str=num2stra(num,nom_type)
[12]3421%------------------------------------------------------------------------
[122]3422if isempty(nom_type)
3423    str='';
3424elseif strcmp(nom_type(end),'a')
[2]3425    str=char(96+num);
[122]3426elseif strcmp(nom_type(end),'A')
3427    str=char(96+num);
3428elseif isempty(nom_type(2:end))%a single index
[2]3429    str='';
3430else
3431    str=num2str(num);
3432end
[12]3433
3434%------------------------------------------------------------------------
[2]3435function mask_civ1_Callback(hObject, eventdata, handles)
[12]3436%------------------------------------------------------------------------
[2]3437set(handles.mask_civ1,'UserData',[])
3438set(handles.mask_civ1,'String','')
[12]3439
3440%------------------------------------------------------------------------
[2]3441function mask_civ2_Callback(hObject, eventdata, handles)
[12]3442%------------------------------------------------------------------------
[2]3443set(handles.mask_civ2,'UserData',[])
3444set(handles.mask_civ2,'String','')
[12]3445
3446%------------------------------------------------------------------------
[2]3447function mask_fix1_Callback(hObject, eventdata, handles)
[12]3448%------------------------------------------------------------------------
[2]3449set(handles.mask_fix1,'UserData',[])
3450set(handles.mask_fix1,'String','')
[12]3451
3452%------------------------------------------------------------------------
[2]3453function mask_fix2_Callback(hObject, eventdata, handles)
[12]3454%------------------------------------------------------------------------
[2]3455set(handles.mask_fix2,'UserData',[])
3456set(handles.mask_fix2,'String','')
3457
[12]3458%------------------------------------------------------------------------
[2]3459% --- Executes on button press in list_subdir_civ1.
3460function list_subdir_civ1_Callback(hObject, eventdata, handles)
[12]3461%------------------------------------------------------------------------
[2]3462list_subdir_civ1=get(handles.list_subdir_civ1,'String');
3463val=get(handles.list_subdir_civ1,'Value');
3464if val>1
3465    subdir=list_subdir_civ1{val};
3466    set(handles.subdir_civ1,'String',subdir);
3467    set(handles.list_subdir_civ1,'Value',1);
3468end
3469
[12]3470%------------------------------------------------------------------------
[2]3471% --- Executes on button press in list_subdir_civ2.
3472function list_subdir_civ2_Callback(hObject, eventdata, handles)
[12]3473%------------------------------------------------------------------------
[2]3474list_subdir_civ2=get(handles.list_subdir_civ2,'String');
3475val=get(handles.list_subdir_civ2,'Value');
3476if val>1
3477    subdir=list_subdir_civ2{val};
3478    set(handles.subdir_civ2,'String',subdir);
3479    set(handles.list_subdir_civ2,'Value',1);
3480end
3481
[12]3482%------------------------------------------------------------------------
[2]3483% --- Executes on button press in browse_gridciv1.
3484function browse_gridciv1_Callback(hObject, eventdata, handles)
[12]3485%------------------------------------------------------------------------
[2]3486value=get(handles.browse_gridciv1,'Value');
3487testgrid=0;
3488if value
[112]3489    filebase=get(handles.RootName,'String');
[39]3490    [nbslice, flag_grid]=get_grid(filebase,handles);
[2]3491    if isequal(flag_grid,1)
[112]3492        filegrid=[num2str(nbslice) 'grid'];
3493        testgrid=1;
3494    else
[2]3495        [FileName, PathName, filterindex] = uigetfile( ...
[112]3496            {'*.grid', ' (*.grid)';
3497            '*.grid',  '.grid files '; ...
3498            '*.*', 'All Files (*.*)'}, ...
3499            'Pick a file',filebase);
[2]3500        filegrid=fullfile(PathName,FileName);
3501        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3502            testgrid=1;
3503        end
[112]3504    end
[2]3505end
3506if testgrid
[112]3507    set(handles.browse_gridciv2,'Value',1)
3508    set(handles.get_gridpatch1,'Value',1)
3509    set(handles.get_gridpatch2,'Value',1)
3510    set(handles.dx_civ1,'Visible','off');
3511    set(handles.dy_civ1,'Visible','off');
3512    set(handles.dx_civ2,'Visible','off');
3513    set(handles.dy_civ2,'Visible','off');
3514    set(handles.grid_civ1,'String',filegrid)
3515    set(handles.grid_patch1,'String',filegrid)
3516    set(handles.grid_civ2,'String',filegrid)
3517    set(handles.grid_patch2,'String',filegrid)
3518else
3519    set(handles.browse_gridciv1,'Value',0);
3520    set(handles.browse_gridciv2,'Value',0);
3521    set(handles.get_gridpatch1,'Value',0)
3522    set(handles.get_gridpatch2,'Value',0)
3523    set(handles.dx_civ1,'Visible','on');
3524    set(handles.dy_civ1,'Visible','on');
3525    set(handles.dx_civ2,'Visible','on');
3526    set(handles.dy_civ2,'Visible','on');
3527    set(handles.grid_civ1,'String','')
3528    set(handles.grid_patch1,'String','')
3529    set(handles.grid_civ2,'String','')
3530    set(handles.grid_patch2,'String','')
[2]3531end
3532
[12]3533%------------------------------------------------------------------------
[2]3534% --- Executes on button press in browse_gridciv1.
3535function browse_gridciv2_Callback(hObject, eventdata, handles)
[12]3536%------------------------------------------------------------------------
[2]3537value=get(handles.browse_gridciv2,'Value');
3538if value
[112]3539    filebase=get(handles.RootName,'String');
[39]3540    [nbslice, flag_grid]=get_grid(filebase,handles);
[2]3541    if isequal(flag_grid,1)
3542        mask_displ=[num2str(nbslice) 'grid'];
3543        set(handles.grid_civ2,'String',mask_displ)
3544        set(handles.dx_civ2,'Visible','off');
3545        set(handles.dy_civ2,'Visible','off');
[112]3546    else
[2]3547        [FileName, PathName, filterindex] = uigetfile( ...
[112]3548            {'*.grid', ' (*.grid)';
3549            '*.grid',  '.grid files '; ...
3550            '*.*', 'All Files (*.*)'}, ...
3551            'Pick a file',filebase);
[2]3552        filegrid=fullfile(PathName,FileName);
3553        if isempty(FileName)|isempty(PathName)|isequal(FileName,0)|~exist(filegrid,'file')
3554            set(handles.browse_gridciv2,'Value',0);
3555            set(handles.grid_civ2,'string','');
3556            set(handles.dx_civ2,'Visible','on');
3557            set(handles.dy_civ2,'Visible','on');
3558            set(handles.grid_civ2,'string','');
3559        else
3560            set(handles.grid_civ2,'string',filegrid);
3561            set(handles.dx_civ2,'Visible','off');
3562            set(handles.dy_civ2,'Visible','off');
3563            set(handles.grid_civ2,'string',filegrid);
3564        end
3565    end
3566else
3567    set(handles.grid_civ2,'string','');
[112]3568    set(handles.dx_civ2,'Visible','on');
3569    set(handles.dy_civ2,'Visible','on');
3570    set(handles.grid_civ2,'string','');
[2]3571end
3572
3573% % --- Executes on button press in browse_gridciv2.
3574% function browse_gridciv2_Callback(hObject, eventdata, handles)
[112]3575%
[71]3576% filebase=get(handles.RootName,'String');
[2]3577% [FileName, PathName, filterindex] = uigetfile( ...
3578%        {'*.grid', ' (*.grid)';
3579%         '*.grid',  '.grid files '; ...
3580%         '*.*', 'All Files (*.*)'}, ...
3581%         'Pick a file',filebase);
3582% filegrid=fullfile(PathName,FileName);
3583% set(handles.grid_civ2,'string',filegrid);
3584% set(handles.dx_civ2,'String',' ');
3585% set(handles.dy_civ2,'String',' ');
3586% % set(handles.grid_patch2,'string',filegrid);
3587
3588% --- Executes on button press in get_gridpatch1.
3589function get_gridpatch1_Callback(hObject, eventdata, handles)
3590% hObject    handle to get_gridpatch1 (see GCBO)
3591% eventdata  reserved - to be defined in a future version of MATLAB
3592% handles    structure with handles and user data (see GUIDATA)
3593
[71]3594filebase=get(handles.RootName,'String');
[2]3595[FileName, PathName, filterindex] = uigetfile( ...
[112]3596    {'*.grid', ' (*.grid)';
3597    '*.grid',  '.grid files '; ...
3598    '*.*', 'All Files (*.*)'}, ...
3599    'Pick a file',filebase);
[2]3600filegrid=fullfile(PathName,FileName);
3601set(handles.grid_patch1,'string',filegrid);
3602% set(handles.grid_patch2,'string',filegrid
3603
[12]3604%------------------------------------------------------------------------
[2]3605% --- Executes on button press in get_gridpatch2.
3606function get_gridpatch2_Callback(hObject, eventdata, handles)
[12]3607%------------------------------------------------------------------------
[2]3608
[12]3609%------------------------------------------------------------------------
[2]3610function enable_civ1(handles,state)
[12]3611%------------------------------------------------------------------------
[2]3612if isequal(state,0)
3613    state='off';
3614end
3615if isequal(state,1)
3616    state='on';
3617end
3618if isequal(state,'on')
3619    set(handles.frame_civ1,'BackgroundColor',[1 1 0])
3620    set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
3621    set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
3622else
3623    set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
3624    set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
3625    set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
3626end
3627set(handles.ibx,'Visible',state)
3628set(handles.iby,'Visible',state)
3629set(handles.isx,'Visible',state)
3630set(handles.isy,'Visible',state)
3631set(handles.shiftx,'Visible',state)
3632set(handles.shifty,'Visible',state)
3633set(handles.rho,'Visible',state)
3634set(handles.dx_civ1,'Visible',state)
3635set(handles.dy_civ1,'Visible',state)
3636set(handles.calcul_search,'Visible',state)
3637set(handles.u_text,'Visible',state)
3638set(handles.v_text,'Visible',state)
3639set(handles.min,'Visible',state)
3640set(handles.max,'Visible',state)
3641set(handles.umin,'Visible',state)
3642set(handles.umax,'Visible',state)
3643set(handles.vmin,'Visible',state)
3644set(handles.vmax,'Visible',state)
3645set(handles.grid_civ1,'Visible',state)
3646set(handles.mask_civ1,'Visible',state)
3647set(handles.browse_gridciv1,'Visible',state)
3648set(handles.get_mask_civ1,'Visible',state)
3649set(handles.parameters,'Visible',state)
3650set(handles.grid,'Visible',state)
3651set(handles.dx_civ1,'Visible',state)
3652set(handles.dy_civ1,'Visible',state)
3653set(handles.ImaThreshold,'Visible',state)
3654if isequal(state,'off')
3655    set(handles.MinIma,'Visible','off')
3656    set(handles.MaxIma,'Visible','off')
3657    set(handles.ImaThreshold,'Value',0)
3658end
3659set(handles.dx_civ1_title,'Visible',state)
3660set(handles.dy_civ1_title,'Visible',state)
3661set(handles.ImaThreshold_title,'Visible',state)
3662set(handles.ib_title,'Visible',state)
3663set(handles.is_title,'Visible',state)
3664set(handles.shift_title,'Visible',state)
3665set(handles.rho_title,'Visible',state)
3666
[12]3667%------------------------------------------------------------------------
[2]3668function enable_fix1(handles,state)
[12]3669%------------------------------------------------------------------------
[2]3670if isequal(state,0)
3671    state='off';
3672end
3673if isequal(state,1)
3674    state='on';
3675end
3676if isequal(state,'on')
3677    set(handles.frame_fix1,'BackgroundColor',[1 1 0])
3678else
3679    set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7])
3680end
3681set(handles.REMOVE,'Visible',state)
3682set(handles.vec_Fmin2,'Visible',state)
3683set(handles.vec_F2,'Visible',state)
3684set(handles.vec_F3,'Visible',state)
3685set(handles.thresh_vecC,'Visible',state)
3686set(handles.thresh_vecC_title,'Visible',state)
3687set(handles.thresh_vel,'Visible',state)
3688set(handles.thresh_vel_text,'Visible',state)
3689set(handles.mask_fix1,'Visible',state)
3690set(handles.get_mask_fix1,'Visible',state)
3691set(handles.get_ref_fix1,'Visible',state)
3692set(handles.ref_fix1,'Visible',state)
3693set(handles.inf_sup1,'Visible',state)
3694set(handles.field_ref1,'Visible',state)
3695
[12]3696%------------------------------------------------------------------------
[2]3697function enable_patch1(handles)
[12]3698%------------------------------------------------------------------------
[67]3699global patch_newBin
[2]3700set(handles.frame_patch1,'BackgroundColor',[1 1 0])
3701set(handles.rho_patch1,'Visible','on')
3702set(handles.rho_text1,'Visible','on')
3703set(handles.thresh_patch1,'Visible','on')
3704set(handles.thresh_text1,'Visible','on')
3705set(handles.subdomain_patch1,'Visible','on')
3706set(handles.subdomain_text1,'Visible','on')
3707set(handles.nx_patch1,'Visible','on')
3708set(handles.ny_patch1,'Visible','on')
3709set(handles.nx_patch1_title,'Visible','on')
3710set(handles.ny_patch1_title,'Visible','on')
[112]3711% if ~isempty(patch_newBin)
[100]3712%     set(handles.test_interp,'Visible','on');
3713% end
[2]3714set(handles.get_gridpatch1,'Visible','on')
3715set(handles.grid_patch1,'string','none');
3716set(handles.grid_patch1,'Visible','on')
3717
[12]3718%------------------------------------------------------------------------
[2]3719function desable_patch1(handles)
[12]3720%------------------------------------------------------------------------
[2]3721set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
3722set(handles.rho_patch1,'Visible','off')
3723set(handles.rho_text1,'Visible','off')
3724set(handles.thresh_patch1,'Visible','off')
3725set(handles.thresh_text1,'Visible','off')
3726set(handles.subdomain_patch1,'Visible','off')
3727set(handles.subdomain_text1,'Visible','off')
3728set(handles.nx_patch1,'Visible','off')
3729set(handles.ny_patch1,'Visible','off')
3730set(handles.nx_patch1_title,'Visible','off')
3731set(handles.ny_patch1_title,'Visible','off')
[100]3732%set(handles.test_interp,'Visible','off')
[2]3733set(handles.get_gridpatch1,'Visible','off')
3734set(handles.grid_patch1,'Visible','off')
3735
[12]3736%------------------------------------------------------------------------
[2]3737function enable_civ2(handles,state)
[12]3738%------------------------------------------------------------------------
[2]3739if isequal(state,0)
3740    state='off';
3741end
3742if isequal(state,1)
3743    state='on';
3744end
3745if isequal(state,'on')
3746    set(handles.frame_civ2,'BackgroundColor',[1 1 0])
3747    set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
3748    set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
3749    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
3750else
3751    set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784])
3752    set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784])
3753    set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784])
3754    set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
3755end
3756set(handles.ibx_civ2,'Visible',state)
3757set(handles.iby_civ2,'Visible',state)
3758set(handles.decimal,'Visible',state)
3759set(handles.deformation,'Visible',state)
3760set(handles.rho_civ2,'Visible',state)
3761set(handles.dx_civ2,'Visible',state)
3762set(handles.dy_civ2,'Visible',state)
3763set(handles.browse_gridciv2,'Visible',state)
3764set(handles.get_mask_civ2,'Visible',state)
3765set(handles.parameters,'Visible',state)
3766set(handles.grid,'Visible',state)
3767set(handles.parameters_text,'Visible',state)
3768set(handles.grid_text,'Visible',state)
3769set(handles.grid_civ2,'Visible',state)
3770set(handles.mask_civ2,'Visible',state)
3771set(handles.dx_civ2_title,'Visible',state)
3772set(handles.dy_civ2_title,'Visible',state)
3773set(handles.ibx_civ2_text,'Visible',state)
3774set(handles.rho_civ2_title,'Visible',state)
3775set(handles.ImaThreshold2,'Visible',state)
3776set(handles.ImaThreshold_title2,'Visible',state)
3777if isequal(state,'off')
3778    set(handles.MinIma2,'Visible','off')
3779    set(handles.MaxIma2,'Visible','off')
3780    set(handles.ImaThreshold2,'Value',0)
[112]3781    if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
[2]3782        set(handles.list_pair_civ2,'Visible','off')
3783        set(handles.subdir_civ2,'Visible','off')
3784        set(handles.subdir_civ2_text,'Visible','off')
[71]3785        set(handles.dt_unit_civ2,'Visible','off')
3786        set(handles.ref_i_civ2,'Visible','off')
3787        set(handles.i_ref_civ2_title,'Visible','off')
3788        set(handles.j_ref_civ2_title,'Visible','off')
3789        set(handles.ref_j_civ2,'Visible','off')
[2]3790    end
3791else
3792    set(handles.list_pair_civ2,'Visible','on')
3793    set(handles.subdir_civ2,'Visible','on')
3794    set(handles.subdir_civ2_text,'Visible','on')
[71]3795    set(handles.dt_unit_civ2,'Visible','on')
3796    set(handles.ref_i_civ2,'Visible','on')
3797    set(handles.i_ref_civ2_title,'Visible','on')
3798    set(handles.j_ref_civ2_title,'Visible','on')
3799    set(handles.ref_j_civ2,'Visible','on')
[2]3800end
[71]3801set(handles.rho_civ2_title,'Visible',state)
[2]3802
[12]3803%------------------------------------------------------------------------
[2]3804function enable_fix2(handles)
[12]3805%------------------------------------------------------------------------
[2]3806set(handles.frame_fix2,'BackgroundColor',[1 1 0])
3807set(handles.REMOVE2,'Visible','on')
3808set(handles.vec_Fmin2_2,'Visible','on')
3809set(handles.vec_F4,'Visible','on')
3810set(handles.vec_F3_2,'Visible','on')
3811set(handles.thresh_vec2C,'Visible','on')
3812set(handles.thresh_vec2C_text,'Visible','on')
3813set(handles.thresh_vel2,'Visible','on')
3814set(handles.thresh_vel2_text,'Visible','on')
3815set(handles.mask_fix2,'Visible','on')
3816set(handles.get_mask_fix2,'Visible','on')
3817set(handles.list_pair_civ2,'Visible','on')
3818set(handles.subdir_civ2,'Visible','on')
3819set(handles.subdir_civ2_text,'Visible','on')
3820set(handles.get_ref_fix2,'Visible','on')
3821set(handles.ref_fix2,'Visible','on')
3822set(handles.inf_sup2,'Visible','on')
3823set(handles.field_ref2,'Visible','on')
3824
[12]3825%------------------------------------------------------------------------
[2]3826function desable_fix2(handles)
[12]3827%------------------------------------------------------------------------
[2]3828set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
3829set(handles.REMOVE2,'Visible','off')
3830set(handles.vec_Fmin2_2,'Visible','off')
3831set(handles.vec_F4,'Visible','off')
3832set(handles.vec_F3_2,'Visible','off')
3833set(handles.thresh_vec2C,'Visible','off')
3834set(handles.thresh_vec2C_text,'Visible','off')
3835set(handles.thresh_vel2,'Visible','off')
3836set(handles.thresh_vel2_text,'Visible','off')
3837set(handles.mask_fix2,'Visible','off')
3838set(handles.get_mask_fix2,'Visible','off')
3839set(handles.get_ref_fix2,'Visible','off')
3840set(handles.ref_fix2,'Visible','off')
3841set(handles.inf_sup2,'Visible','off')
3842set(handles.field_ref2,'Visible','off')
[112]3843if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
[2]3844    set(handles.list_pair_civ2,'Visible','off')
3845    set(handles.subdir_civ2,'Visible','off')
3846    set(handles.subdir_civ2_text,'Visible','off')
3847end
3848
[12]3849%------------------------------------------------------------------------
[2]3850function enable_patch2(handles)
[12]3851%------------------------------------------------------------------------
[2]3852set(handles.frame_patch2,'BackgroundColor',[1 1 0])
[119]3853set(handles.rho_patch2,'Visible','on')
[2]3854set(handles.rho_text2,'Visible','on')
3855set(handles.thresh_patch2,'Visible','on')
3856set(handles.thresh_text2,'Visible','on')
3857set(handles.subdomain_patch2,'Visible','on')
3858set(handles.subdomain_text2,'Visible','on')
3859set(handles.nx_patch2,'Visible','on')
3860set(handles.ny_patch2,'Visible','on')
3861set(handles.nx_patch2_title,'Visible','on')
3862set(handles.ny_patch2_title,'Visible','on')
3863set(handles.get_gridpatch2,'Visible','on')
3864set(handles.grid_patch2,'Visible','on')
3865set(handles.list_pair_civ2,'Visible','on')
3866set(handles.subdir_civ2,'Visible','on')
3867set(handles.subdir_civ2_text,'Visible','on')
3868
[12]3869%------------------------------------------------------------------------
[2]3870function desable_patch2(handles)
[12]3871%------------------------------------------------------------------------
[2]3872set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
3873set(handles.rho_patch2,'Visible','off')
3874set(handles.rho_text2,'Visible','off')
3875set(handles.thresh_patch2,'Visible','off')
3876set(handles.thresh_text2,'Visible','off')
3877set(handles.subdomain_patch2,'Visible','off')
3878set(handles.subdomain_text2,'Visible','off')
3879set(handles.nx_patch2,'Visible','off')
3880set(handles.ny_patch2,'Visible','off')
3881set(handles.nx_patch2_title,'Visible','off')
3882set(handles.ny_patch2_title,'Visible','off')
3883set(handles.get_gridpatch2,'Visible','off')
3884set(handles.grid_patch2,'Visible','off')
[112]3885if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0)
[2]3886    set(handles.list_pair_civ2,'Visible','off')
3887    set(handles.subdir_civ2,'Visible','off')
3888    set(handles.subdir_civ2_text,'Visible','off')
3889end
3890
[12]3891%------------------------------------------------------------------------
[2]3892function enable_pair1(handles,state)
[12]3893%------------------------------------------------------------------------
[2]3894set(handles.subdir_civ1,'Visible',state)
3895set(handles.list_subdir_civ1,'Visible',state)
3896set(handles.SUBDIR_CIV1_txt,'Visible',state)
3897set(handles.frame_subdirciv1,'Visible',state)
3898set(handles.list_pair_civ1,'Visible',state)
3899set(handles.PAIR_txt,'Visible',state)
[71]3900%set(handles.dt_unit,'Visible',state)
[2]3901set(handles.PAIR_frame,'Visible',state)
3902
[12]3903%------------------------------------------------------------------------
3904% --- Read the parameters for civ1 on the interface
[2]3905function par=read_param_civ1(handles,file_ima)
[12]3906%------------------------------------------------------------------------
[127]3907ibx_val=str2double(get(handles.ibx,'String'));
[2]3908par.ibx=num2str(ibx_val);
[127]3909iby_val=str2double(get(handles.iby,'String'));
[2]3910par.iby=num2str(iby_val);
3911isx=get(handles.isx,'String');
[127]3912if isnan(str2double(isx)), isx='41'; set(handles.isx,'String','41'), end; %default
3913if str2double(isx)<ibx_val+8,isx=num2str(ibx_val+8); set(handles.isx,'String',num2str(ibx_val+8)); end
[2]3914isy=get(handles.isy,'String');
[127]3915if isnan(str2double(isy)), isy='41'; set(handles.isy,'String','41'), end;%default
3916if str2double(isy)<iby_val+8,isy=num2str(iby_val+8); set(handles.isy,'String',num2str(iby_val+8)); end
[2]3917par.isx=get(handles.isx,'String');
3918par.isy=get(handles.isy,'String');
3919par.shiftx=get(handles.shiftx,'String');
3920par.shifty=get(handles.shifty,'String');
[127]3921if isnan(str2double(par.isx))
[112]3922    par.isx='41';%default
3923    set(handles.isx,'String','41');
[2]3924end
[127]3925if isnan(str2double(par.isy))
[112]3926    par.isy='41'; %default
3927    set(handles.isy,'String','41');
[12]3928end
[127]3929if isnan(str2double(par.shiftx))
[112]3930    par.shiftx='0';%default
3931    set(handles.shiftx,'String','0');
3932end
[127]3933if isnan(str2double(par.shifty))
[112]3934    par.shifty='0'; %default
3935    set(handles.shifty,'String','0');
[12]3936end
[112]3937par.rho=get(handles.rho,'String');
3938par.dx=get(handles.dx_civ1,'String');
3939par.dy=get(handles.dy_civ1,'String');
[127]3940if isnan(str2double(par.dx))
[112]3941    if isempty(get(handles.grid_civ1,'String'));
3942        par.dx='0'; %just read by civ program, not used
3943    else
[12]3944        par.dx='20';%default
3945        set(handles.dx_civ1,'String','20');
[112]3946    end
3947end
[127]3948if isnan(str2double(par.dy))
[112]3949    if isempty(get(handles.grid_civ1,'String'));
3950        par.dy='0';%just read by civ program, not used
3951    else
[12]3952        par.dy='20';%default
3953        set(handles.dy_civ1_title,'String','20');
[112]3954    end
3955end
3956par.pxcmx='1'; %velocities are expressed in pixel dispalcement
3957par.pxcmy='1';
[2]3958%      end
[112]3959A=imread(file_ima);%read the first image to get the size
3960sizim=size(A);
3961par.npx=num2str(sizim(2));
3962par.npy=num2str(sizim(1));
[127]3963%time=get(handles.RootName,'UserData'); %get the set of times
[112]3964par.gridname=get(handles.grid_civ1,'String');
3965par.gridflag='y';
[127]3966if strcmp(par.gridname,'')|| isempty(par.gridname)
[112]3967    par.gridname='nogrid';
3968    par.gridflag='n';
3969end
[12]3970
3971%------------------------------------------------------------------------
[2]3972function par=read_param_civ2(handles,file_ima)
[12]3973%------------------------------------------------------------------------
3974par.ibx=get(handles.ibx_civ2,'String');
3975par.iby=get(handles.iby_civ2,'String');
3976par.rho=get(handles.rho_civ2,'String');
3977par.decimal=int2str(get(handles.decimal,'Value'));
3978par.deformation=int2str(get(handles.deformation,'Value'));
3979par.dx=get(handles.dx_civ2,'String');
3980par.dy=get(handles.dy_civ2,'String');
[127]3981if isnan(str2double(par.dx))
[112]3982    if isempty(get(handles.grid_civ2,'String'));
3983        par.dx='0'; %just read by civ program, not used
3984    else
[12]3985        par.dx='20';%default
3986        set(handles.dx_civ2,'String','20');
[112]3987    end
3988end
[127]3989if isnan(str2double(par.dy))
[112]3990    if isempty(get(handles.grid_civ2,'String'));
3991        par.dy='0';%just read by civ program, not used
3992    else
[12]3993        par.dy='20';%default
3994        set(handles.dy_civ2,'String','20');
[112]3995    end
3996end
3997par.pxcmx='1';
3998par.pxcmy='1';
[12]3999A=imread(file_ima);%read the first image to get the size
4000sizim=size(A);
4001par.npx=num2str(sizim(2));
4002par.npy=num2str(sizim(1));
[127]4003%time=get(handles.RootName,'UserData'); %get the set of times
[12]4004par.gridname=get(handles.grid_civ2,'String');
4005par.gridflag='y';
[127]4006if strcmp(par.gridname,'')|| isempty(par.gridname)
[12]4007    par.gridname='nogrid';
4008    par.gridflag='n';
4009end
[2]4010
[12]4011%------------------------------------------------------------------------
4012% --- CIV1  CIV1  CIV1 CIV1
[94]4013function cmd_CIV1=CIV1_CMD(filename,namelog,par,handles,sparam)
[12]4014%------------------------------------------------------------------------
[2]4015%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4016
4017%changes : filename_cmx -> filename ( no extension )
4018
[112]4019if isequal(par.Dt,'0')
4020    par.Dt='1' ;%case of 'displacement' mode
4021end
4022%
[12]4023%     textcmx={'##############   CMX file';...
4024%     ['FirstImage ' par.filename_ima_a];...
4025%     ['LastImage  ' par.filename_ima_b];...
4026%     'XX' ;...
4027%     ['Mask ' par.maskflag] ;...
4028%     ['MaskName ' par.maskname];...
4029%     ['ImageSize ' par.npx ' ' par.npy];...   %VERIFIER CAS GENERAL ?
4030%     ['CorrelationBoxesSize ' par.ibx ' ' par.iby];...
4031%     ['SearchBoxeSize ' par.isx ' ' par.isy];...
4032%     ['RO ' par.rho];...
4033%     ['GridSpacing ' par.dx ' ' par.dy];...
4034%     'XX 1.0';...
4035%     ['Dt_TO ' par.Dt ' ' par.T0];...
4036%     ['PixCmXY ' par.pxcmx ' ' par.pxcmy];...
4037%     'XX 1';...
4038%     ['ShiftXY ' par.shiftx ' '  par.shifty];...
4039%     ['Grid ' par.gridflag];...
4040%     ['GridName ' par.gridname] ;...
4041%     'XX 85';...
4042%     'XX 1.0';...
4043%     'XX 1.0';...
4044%     'Hart 1';...
4045%     'DecimalShift 0';...
4046%     'Deformation 0';...
4047%     'CorrelationMin 0';...
4048%     'IntensityMin 0';...
4049%     'SeuilImage n';...
4050%     'SeuilImageValues 0 4096';...
4051%     ['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ?
4052%     'ImageUsedBefore null null'};
[112]4053%
[12]4054%             textout=char(textcmx);
[90]4055par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
[94]4056par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');
4057fid=fopen([filename '.cmx'],'w');
[12]4058fprintf(fid,['##############   CMX file' '\n' ]);
[112]4059fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4060fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4061fprintf(fid,  ['XX' '\n' ]);
4062fprintf(fid,  ['Mask ' par.maskflag '\n' ]);
4063fprintf(fid,  ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);
4064fprintf(fid,   ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4065fprintf(fid,   ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4066fprintf(fid,   ['SearchBoxeSize ' par.isx ' ' par.isy '\n' ]);
4067fprintf(fid,   ['RO ' par.rho '\n' ]);
4068fprintf(fid,   ['GridSpacing ' par.dx ' ' par.dy '\n' ]);
4069fprintf(fid,   ['XX 1.0' '\n' ]);
4070fprintf(fid,   ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4071fprintf(fid,  ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4072fprintf(fid,  ['XX 1' '\n' ]);
4073fprintf(fid,   ['ShiftXY ' par.shiftx ' '  par.shifty '\n' ]);
4074fprintf(fid,  ['Grid ' par.gridflag '\n' ]);
4075fprintf(fid,   ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n' ]);
4076fprintf(fid,   ['XX 85' '\n' ]);
4077fprintf(fid,   ['XX 1.0' '\n' ]);
4078fprintf(fid,   ['XX 1.0' '\n' ]);
4079fprintf(fid,   ['Hart 1' '\n' ]);
4080fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4081fprintf(fid,   ['Deformation 0' '\n' ]);
4082fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4083fprintf(fid,   ['IntensityMin 0' '\n' ]);
4084fprintf(fid,  ['SeuilImage n' '\n' ]);
4085fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4086fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4087fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
[12]4088fclose(fid);
[112]4089
[120]4090cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
[90]4091cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4092namelog=regexprep(namelog,'\\','\\\\');
4093
[12]4094if(isunix)
4095    [Rootbat,Filebat,extbat]=fileparts(namelog);
4096    ncName=fullfile(Rootbat,[ Filebat '.nc']);
[67]4097    cmd_CIV1=[cmd_CIV1 '\n' 'mv ' namelog  ' ' regexprep(namelog,'\.log','') '.civ1.log' '\n' 'chmod g+w ' ncName];
[12]4098else
[67]4099    cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y ' namelog ' ' regexprep(namelog,'\.log','') '.civ1.log'];
[12]4100end
[2]4101
[12]4102%------------------------------------------------------------------------
4103% --- CIV1  Unified
[94]4104function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
[12]4105%------------------------------------------------------------------------
[2]4106%pixels per cm and matrix of the image times, read from the .civ file by uvmat
[73]4107%global CivBin%name of the executable for civ1 calculation
[2]4108
[112]4109civ1.image1=par.filename_ima_a;
4110civ1.image2=par.filename_ima_b;
4111civ1.imageSize_X=par.npx;
4112civ1.imageSize_Y=par.npy;
4113civ1.outputFileName=[filename '.nc'];
4114civ1.correlationBoxesSize_X=par.ibx;
4115civ1.correlationBoxesSize_Y=par.iby;
4116civ1.searchBoxesSize_X=par.isx;
4117civ1.searchBoxesSize_Y=par.isy;
4118civ1.globalShift_X=par.shiftx;
4119civ1.globalShift_Y=par.shifty;
4120civ1.ro=par.rho;
4121civ1.hart='y';
4122if isequal(par.gridflag,'y')
4123    civ1.grid=par.gridname;
4124else
4125    civ1.grid='n';
4126    civ1.gridSpacing_X=par.dx;
4127    civ1.gridSpacing_Y=par.dy;
4128end
4129if isequal(par.maskflag,'y')
4130    civ1.mask=par.maskname;
4131end
4132civ1.dt=par.Dt;
4133civ1.unit='pixel';
4134civ1.absolut_time_T0=par.T0;
4135civ1.pixcmx=par.pxcmx;
4136civ1.pixcmy=par.pxcmy;
4137civ1.convectFlow='n';
[12]4138
[112]4139xml_civ1_parameters=civ1;
4140
[12]4141%------------------------------------------------------------------------
4142% --- CIV2  Unified
[94]4143function civ2=CIV2_CMD_Unified(filename,namelog,par)
[12]4144%------------------------------------------------------------------------
[2]4145%pixels per cm and matrix of the image times, read from the .civ file by uvmat
[73]4146%global CivBin%name of the executable for civ1 calculation
[2]4147
4148civ2.image1=par.filename_ima_a;
4149civ2.image2=par.filename_ima_b;
[112]4150civ2.imageSize_X=par.npx;
[2]4151civ2.imageSize_Y=par.npy;
4152civ2.inputFileName=[par.filename_nc1 '.nc'];
4153civ2.outputFileName=[filename '.nc'];
4154civ2.correlationBoxesSize_X=par.ibx;
4155civ2.correlationBoxesSize_Y=par.iby;
4156civ2.ro=par.rho;
4157%civ2.decimalShift=par.decimal;
4158%civ2.deformation=par.deformation;
4159if isequal(par.decimal,'1')
4160    civ2.decimalShift='y';
4161else
4162    civ2.decimalShift='n';
4163end
4164if isequal(par.deformation,'1')
4165    civ2.deformation='y';
4166else
4167    civ2.deformation='n';
4168end
4169if isequal(par.gridflag,'y')
4170    civ2.grid=par.gridname;
4171else
4172    civ2.grid='n';
4173    civ2.gridSpacing_X=par.dx;
4174    civ2.gridSpacing_Y=par.dy;
4175end
4176civ2.gridSpacing_X='10';
4177civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4178if isequal(par.maskflag,'y')
4179    civ2.mask=par.maskname;
4180else
4181    civ2.mask='n';
4182end
4183civ2.dt=par.Dt;
4184civ2.unit='pixel';
4185civ2.absolut_time_T0=par.T0;
4186civ2.pixcmx=par.pxcmx;
4187civ2.pixcmy=par.pxcmy;
4188civ2.convectFlow='n';
4189civ2.pixcmx=par.pxcmx;
4190civ2.pixcmy=par.pxcmy;
4191civ2.convectFlow='n';
4192
[12]4193%------------------------------------------------------------------------
4194% --- CIV2  CIV2  CIV2 CIV2
[134]4195function cmd_CIV2=CIV2_CMD(filename,namelog,par,sparam)
[12]4196%------------------------------------------------------------------------
[2]4197%pixels per cm and matrix of the image times, read from the .civ file by uvmat
[67]4198% global civ2Bin sge%name of the executable for civ1 calculation
[112]4199if isequal(par.Dt,'0')
4200    par.Dt='1' ;%case of 'displacement' mode
4201end
[94]4202% textcmx=['##############   CMX file'  '\n'...
4203% ['FirstImage ' par.filename_ima_a]  '\n'...
4204% ['LastImage  ' par.filename_ima_b]  '\n'...
4205% 'XX'   '\n'...
4206% ['Mask ' par.maskflag]  '\n'...
4207% ['MaskName ' par.maskname]  '\n'...
[112]4208% ['ImageSize ' par.npx ' ' par.npy]  '\n'...
[94]4209% ['CorrelationBoxesSize ' par.ibx ' ' par.iby]  '\n'...
4210% ['SearchBoxeSize ' par.ibx ' ' par.iby]  '\n'...
4211% ['RO ' par.rho]  '\n'...
4212% ['GridSpacing ' par.dx ' ' par.dy]  '\n'...
4213% 'XX 1.0'  '\n'...
4214% ['Dt_TO ' par.Dt ' ' par.T0]  '\n'...
4215% ['PixCmXY ' par.pxcmx ' ' par.pxcmy]  '\n'...
4216% 'XX 1'  '\n'...
4217% ['ShiftXY 0 0']  '\n'...
4218% ['Grid ' par.gridflag]  '\n'...
4219% ['GridName ' par.gridname]  '\n'...
4220% 'XX 85'  '\n'...
4221% 'XX 1.0'  '\n'...
4222% 'XX 1.0'  '\n'...
4223% 'Hart 1'  '\n'...
4224% ['DecimalShift ' par.decimal]  '\n'...
4225% ['Deformation ' par.deformation]  '\n'...
4226% 'CorrelationMin 0'  '\n'...
4227% 'IntensityMin 0'  '\n'...
4228% 'SeuilImage n'  '\n'...
4229% 'SeuilImageValues 0 4096'  '\n'...
4230% ['ImageToUse ' par.term_a ' ' par.term_b]  '\n'... % VERIFIER ?
4231% ['ImageUsedBefore ' par.filename_nc1]];
4232% textout=char(textcmx);
4233% fid=fopen([filename_cmx '2'],'w');
[112]4234% fprintf(fid,textout);
[94]4235% fclose(fid)
[2]4236
[94]4237par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4238par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');% bug : .png appears two times ?
[134]4239fid=fopen([filename '.cmx2'],'w');
[94]4240fprintf(fid,['##############   CMX file' '\n' ]);
4241fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4242fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4243fprintf(fid,  ['XX' '\n' ]);
4244fprintf(fid, ['Mask ' par.maskflag '\n' ]);
4245fprintf(fid, ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);% for windows compatibility
4246fprintf(fid, ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4247fprintf(fid, ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4248fprintf(fid, ['SearchBoxeSize ' par.ibx ' ' par.iby '\n']);
4249fprintf(fid, ['RO ' par.rho '\n']);
4250fprintf(fid, ['GridSpacing ' par.dx ' ' par.dy '\n']);
4251fprintf(fid, ['XX 1.0' '\n' ]);
4252fprintf(fid, ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4253fprintf(fid, ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4254fprintf(fid, ['XX 1' '\n' ]);
[122]4255fprintf(fid, 'ShiftXY 0 0\n');
[94]4256fprintf(fid, ['Grid ' par.gridflag '\n' ]);
4257fprintf(fid, ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n']);
4258fprintf(fid, ['XX 85' '\n' ]);
4259fprintf(fid, ['XX 1.0' '\n' ]);
4260fprintf(fid, ['XX 1.0' '\n' ]);
4261fprintf(fid, ['Hart 1' '\n' ]);
4262fprintf(fid, ['DecimalShift ' par.decimal '\n']);
4263fprintf(fid, ['Deformation ' par.deformation '\n']);
4264fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4265fprintf(fid,   ['IntensityMin 0' '\n' ]);
4266fprintf(fid,  ['SeuilImage n' '\n' ]);
4267fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4268fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4269fprintf(fid, ['ImageUsedBefore ' regexprep(par.filename_nc1,'\\','\\\\') '\n']);
4270fclose(fid);
4271
[134]4272cmd_CIV2=[sparam.Civ2Bin ' -f ' filename  '.cmx >' filename '.log' ]; % redirect standard output to the log file
[94]4273cmd_CIV2=regexprep(cmd_CIV2,'\\','\\\\');
[134]4274namelog=regexprep(namelog,'\\','\\\\');
[94]4275
[134]4276if(isunix)
4277    [Rootbat,Filebat,extbat]=fileparts(namelog);
4278    ncName=fullfile(Rootbat,[ Filebat '.nc']);
4279    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' namelog  ' ' regexprep(namelog,'\.log','') '.civ2.log' '\n' 'chmod g+w ' ncName];
4280else
4281    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y ' namelog ' ' regexprep(namelog,'\.log','') '.civ2.log'];
4282end
428