source: trunk/src/series/civ_input.m @ 635

Last change on this file since 635 was 635, checked in by sommeria, 11 years ago
File size: 87.5 KB
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1
2%'civ_input': function associated with the interface 'civ_input.fig' for PIV, spline interpolation and stereo PIV (patch)
3%------------------------------------------------------------------------
4%  provides an interface for the software menucivx
5% function varargout = civ_input(varargin)
6% provides an interface for the software menucivx
7%
8%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
10%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11%     This file is part of the toolbox UVMAT.
12%
13%     UVMAT is free software; you can redistribute it and/or modify
14%     it under the terms of the GNU General Public License as published by
15%     the Free Software Foundation; either version 2 of the License, or
16%     (at your option) any later version.
17%
18%     UVMAT is distributed in the hope that it will be useful,
19%     but WITHOUT ANY WARRANTY; without even the implied warranty of
20%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
22%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23function varargout = civ_input(varargin)
24%TODO: search range
25
26
27% Last Modified by GUIDE v2.5 04-Apr-2013 22:08:23
28% Begin initialization code - DO NOT EDIT
29gui_Singleton = 1;
30gui_State = struct('gui_Name',       mfilename, ...
31    'gui_Singleton',  gui_Singleton, ...
32    'gui_OpeningFcn', @civ_input_OpeningFcn, ...
33    'gui_OutputFcn',  @civ_input_OutputFcn, ...
34    'gui_LayoutFcn',  [] , ...
35    'gui_Callback',   []);
36
37if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once'))
38        gui_State.gui_Callback = str2func(varargin{1});
39end
40
41if nargout
42    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
43else
44    gui_mainfcn(gui_State, varargin{:});
45end
46
47% End initialization code - DO NOT EDIT
48
49%------------------------------------------------------------------------
50% --- Executes just before civ_input is made visible.
51function civ_input_OpeningFcn(hObject, eventdata, handles, Param)
52%------------------------------------------------------------------------
53% This function has no output args, see OutputFcn.
54
55%% General settings
56handles.output = Param;
57guidata(hObject, handles); % Update handles structure
58set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
59SeriesData.ParentHandle=gcbf;
60SeriesData=get(gcbf,'UserData');
61% relevant data in gcbf:.FileType,.FileInfo,.Time,.TimeUnit,.GeometryCalib{1};
62
63%% set visibility options: case civ_matlab
64if strcmp(Param.Action.ActionName,'civ_series')
65        set(handles.Program,'String','civ_series')
66        set(handles.num_MaxDiff,'Visible','on')
67        set(handles.num_MaxVel,'Visible','on')
68        set(handles.title_MaxVel,'Visible','on')
69        set(handles.title_MaxDiff,'Visible','on')
70        set(handles.num_Nx,'Visible','off')
71        set(handles.num_Ny,'Visible','off')
72        set(handles.title_Nx,'Visible','off')
73        set(handles.title_Ny,'Visible','off')
74        set(handles.num_CorrSmooth,'Style','popupmenu')
75        set(handles.num_CorrSmooth,'Value',1)
76        set(handles.num_CorrSmooth,'String',{'1';'2'})
77        set(handles.CheckThreshold,'Visible','on')
78        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
79        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
80end
81
82%% input file info
83RootPath=Param.InputTable{1,1};
84set(handles.RootPath,'String',RootPath)
85RootFile=Param.InputTable{1,3};
86SubDir=Param.InputTable{1,2};
87NomTypeInput=Param.InputTable{1,4};
88FileExt=Param.InputTable{1,5};
89FileType=SeriesData.FileType{1};
90FileInfo=SeriesData.FileInfo{1};
91FileInput=SeriesData.RefFile{1};
92
93%% case of netcdf file as input, get the processing stage and look for corresponding images
94% imageinput=fileinput;%default
95% TODO: insert image input in the GUI series
96ind_opening=0;%default
97NomTypeNc='';
98switch FileType
99         case {'image','multimage','video','mmreader'}
100          NomTypeIma=NomTypeInput;
101    case 'civdata'
102        if ~strcmp(Param.Action.ActionName,'civ_series')
103            msgbox_uvmat('ERROR','bad input data file: open an image or a nc file from civ_series')
104            return
105        end
106        NomTypeNc=NomTypeInput;
107        ind_opening=FileInfo.CivStage;
108        if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
109            set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
110            set(handles.RootFile_1,'Visible','On');
111        else
112            set(handles.ListCompareMode,'Value',1)
113            set(handles.RootFile_1,'Visible','Off');
114        end
115        imageinput='';
116        Data=nc2struct(FileInput,'ListGlobalAttribute','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB');
117        [PathCiv1_ImageA,Civ1_ImageA,FileExtA]=fileparts(Data.Civ1_ImageA);
118        [PathCiv1_ImageB,Civ1_ImageB,FileExtA]=fileparts(Data.Civ1_ImageB);
119        [PathCiv2_ImageA,Civ2_ImageA,FileExtA]=fileparts(Data.Civ2_ImageA);
120        [PathCiv2_ImageB,Civ2_ImageB,FileExtA]=fileparts(Data.Civ2_ImageB);
121        set(handles.Civ1_ImageA,'String',Civ1_ImageA)
122        set(handles.Civ1_ImageB,'String',Civ1_ImageB)
123        set(handles.Civ2_ImageA,'String',Civ2_ImageA)
124        set(handles.Civ2_ImageB,'String',Civ2_ImageB)
125    if isfield(Data,'Txt')
126        errormsg=Data.Txt;
127        return
128        %TODO: introduce the image in the input table of series
129    end
130        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA);
131        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ1_ImageB);
132    case 'civxdata'% case of  civx data,
133        NomTypeNc=NomTypeInput;
134        ind_opening=FileInfo.CivStage;
135        set(handles.Program,'Value',3) %select Cix by default
136        msgbox_uvmat('ERROR','old civX convention, use the GUI civ')
137        return
138     
139end
140
141%% TODO: get corresponding image in nc case
142
143%% reinitialise menus
144set(handles.ListPairMode,'Value',1)
145set(handles.ListPairMode,'String',{''})
146set(handles.ListPairCiv1,'Value',1)
147set(handles.ListPairCiv1,'String',{''})
148set(handles.ListPairCiv2,'Value',1)
149set(handles.ListPairCiv2,'String',{''})
150fill_GUI(Param,hObject);%fill the GUI with the parameters retrieved from the input Param
151
152       
153%% prepare the GUI with input parameters
154set(handles.ListCompareMode,'Visible','on')
155
156%display the parameters stored on the GUI series
157% set(handles.first_i,'String',num2str(Param.IndexRange.first_i))
158% set(handles.incr_i,'String',num2str(Param.IndexRange.incr_i))
159% set(handles.last_i,'String',num2str(Param.IndexRange.last_i))
160set(handles.ref_i,'String',num2str(Param.IndexRange.first_i))
161if isfield(Param.IndexRange,'first_j')
162%     set(handles.first_j,'String',num2str(Param.IndexRange.first_j))
163%     set(handles.incr_j,'String',num2str(Param.IndexRange.incr_j))
164%     set(handles.last_j,'String',num2str(Param.IndexRange.last_j))
165    set(handles.ref_j,'String',num2str(Param.IndexRange.first_j))
166end
167
168%% set the civ_input options depending on the input file content when a nc file has been opened
169ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
170checkbox=zeros(size(ListOptions));%default
171if ind_opening==0%case of image opening, start with Civ1
172    for index=1:numel(ListOptions)
173        checkbox(index)=get(handles.(ListOptions{index}),'Value');
174    end
175    index_max=find(checkbox, 1, 'last' );
176    if isempty(index_max),index_max=1;end
177    for index=1:index_max
178        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
179    end
180else
181    for index = 1:min(ind_opening,5)
182        set(handles.(ListOptions{index}),'value',0)
183    end
184    set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
185    for index = ind_opening+2:6
186        set(handles.(ListOptions{index}),'value',0)
187    end
188end
189%list_operation={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2'};
190
191%set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
192
193
194%%  set the menus of image pairs and default selection for civ_input   %%%%%%%%%%%%%%%%%%%
195%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
196%if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
197MaxIndex_i=Param.IndexRange.MaxIndex_i(1);
198MinIndex_i=Param.IndexRange.MinIndex_i(1);
199MaxIndex_j=1;%default
200MinIndex_j=1;
201if isfield(Param.IndexRange,'MaxIndex_j')&&isfield(Param.IndexRange,'MinIndex_j')
202MaxIndex_j=Param.IndexRange.MaxIndex_j(1);
203MinIndex_j=Param.IndexRange.MinIndex_j(1);
204end
205CivInputData.MaxIndex_i=MaxIndex_i;
206CivInputData.MaxIndex_j=MaxIndex_j;
207CivInputData.MinIndex_i=MinIndex_i;
208CivInputData.MinIndex_j=MinIndex_j;
209if ~isfield(Param.IndexRange,'first_j')
210    set(handles.ListPairMode,'Value',1)
211    set(handles.ListPairMode,'String',{'series(Di)'})
212elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
213    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
214    if  MaxIndex_j <= 10
215        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
216    end
217%elseif ~(strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
218else
219    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
220    if strcmp(NomTypeNc,'_1-2_1')
221        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
222    elseif  MaxIndex_j <= 10
223        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
224    end
225end
226
227%%  transfer the time from the GUI series, or use file index by default
228time=[];
229TimeUnit='frame'; %default
230CoordUnit='';%default
231pxcm_search=1;
232if isfield(SeriesData,'Time') && ~isempty(SeriesData.Time{1})
233    time=SeriesData.Time{1};
234    %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
235%     if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
236%         if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
237%             time=time';
238%             MaxIndex_i=MaxIndex_j;
239%             MaxIndex_j=1;
240%         end
241%     end
242end
243if isfield(Param.IndexRange,'TimeUnit')&&~isempty(Param.IndexRange.TimeUnit)
244    TimeUnit=Param.IndexRange.TimeUnit;
245end
246if isfield(SeriesData,'TimeSource')
247    set(handles.ImaDoc,'String',SeriesData.TimeSource)
248end 
249if isfield(SeriesData,'GeometryCalib')
250    tsai=SeriesData.GeometryCalib;
251    if isfield(tsai,'fx_fy')
252        pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
253    end
254    if isfield(tsai,'CoordUnit')
255        CoordUnit=tsai.CoordUnit;
256    end
257end
258% timing set by video input
259% if isempty(time) && (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
260%     set(handles.ListPairMode,'Value',1);
261%     dt=1/get(MovieObject,'FrameRate');%time interval between successive frames
262%     if strcmp(NomTypeIma,'*')
263%         set(handles.ListPairMode,'String',{'series(Di)'})
264%         time=(dt*(0:MaxIndex_i-1))';%list of image times
265%     else
266%         set(handles.ListPairMode,'String',[{'series(Dj)'};{'series(Di)'}])
267%         time=ones(MaxIndex_i,1)*(dt*(0:MaxIndex_j-1));%list of image times
268%         enable_j(handles,'on')
269%     end
270%     TimeUnit='s';
271%     set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
272% end
273
274%% timing display
275%show the reference image edit box if relevant (not needed for movies or in the absence of time information
276if numel(time)>=2 % if there are at least two time values to define dt
277    if size(time,1)<MaxIndex_i;
278        msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
279    elseif size(time,2)<MaxIndex_j
280        msgbox_uvmat('WARNING','maximum j index restricted by the timing of the xml file');
281    end
282    MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data
283    MaxIndex_j=min(size(time,2),MaxIndex_j);
284else
285    set(handles.ImaDoc,'String',''); %xml file not used for timing
286    TimeUnit='frame';
287    time=ones(MaxIndex_j-MinIndex_j+1,1)*(MinIndex_i:MaxIndex_i);
288    time=time+0.001*(MinIndex_j:MaxIndex_j)'*ones(1,MaxIndex_i-MinIndex_i+1);
289end
290% time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
291% time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
292CivInputData.Time=time;
293CivInputData.NomTypeIma=NomTypeIma;
294set(handles.civ_input,'UserData',CivInputData)
295set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
296set(handles.TimeUnit,'String',TimeUnit);
297% set(handles.nb_field,'String',num2str(MaxIndex_i));
298% set(handles.nb_field2,'String',num2str(MaxIndex_j));
299
300set(handles.CoordUnit,'String',CoordUnit)
301set(handles.SearchRange,'UserData', pxcm_search);
302
303%% set the reference indices from the input file indices
304num_ref_i=str2num(get(handles.ref_i,'String'));
305num_ref_j=str2num(get(handles.ref_j,'String'));
306
307update_CivOptions(handles,ind_opening)
308
309%% list the possible index pairs, depending on the option set in ListPairMode
310ListPairMode_Callback([], [], handles)
311
312% for movies don't modify except if the current ref is outside index bounds
313%if strcmp(ExtInput,'.nc')|| ~(strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader') && num_ref_i<=MaxIndex_i && num_ref_j<=MaxIndex_j)
314% if ~isempty(i1)% if i1 has been selected by the input
315%     num_ref_i=i1;%default ref index
316%     if ~isempty(i2)
317%         num_ref_i=floor((num_ref_i+i2)/2);
318%     end
319%     if ~isempty(j1)
320%         num_ref_j=j1;
321%         if ~isempty(j2)
322%             num_ref_j=floor((num_ref_j+j2)/2);
323%         end
324%     end
325% end
326% if num_ref_i>MaxIndex_i||num_ref_i<MinIndex_i
327%     num_ref_i=round((MinIndex_i+MaxIndex_i)/2);
328% end
329% if ~isempty(num_ref_j)&&~isempty(MaxIndex_j)&& ~isempty(MinIndex_j)
330%     if (num_ref_j>MaxIndex_j||num_ref_j<MinIndex_j)
331%         num_ref_j=round((MinIndex_j+MaxIndex_j)/2);
332%     end
333% end
334% if isempty(num_ref_j)
335%     num_ref_j=1;
336% end
337%
338%% set the GUI to modal: wait for OK to close
339set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal
340drawnow
341uiwait(handles.civ_input);
342
343
344
345%Program_Callback([],[], handles)
346
347%------------------------------------------------------------------------
348% --- Outputs from this function are returned to the command line.
349function varargout = civ_input_OutputFcn(hObject, eventdata, handles)
350%------------------------------------------------------------------------
351% Get default command line output from handles structure
352varargout{1} = handles.output;
353delete(handles.civ_input)
354
355% --- Executes when user attempts to close get_field.
356function civ_input_CloseRequestFcn(hObject, eventdata, handles)
357if isequal(get(handles.get_field, 'waitstatus'), 'waiting')
358    % The GUI is still in UIWAIT, us UIRESUME
359    uiresume(handles.civ_input);
360else
361    % The GUI is no longer waiting, just close it
362    delete(handles.civ_input);
363end
364
365
366
367% -----------------------------------------------------------------------
368% -----------------------------------------------------------------------
369% --- Open the help html file
370function MenuHelp_Callback(hObject, eventdata, handles)
371% -----------------------------------------------------------------------
372path_civ=fileparts(which ('civ'));
373helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
374if isempty(dir(helpfile))
375    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
376else
377    addpath (fullfile(path_civ,'uvmat_doc'))
378    web([helpfile '#civ'])
379end
380
381
382%------------------------------------------------------------------------
383% --- general function activated for an input file series
384function errormsg=display_file_name(handles,fileinput)
385%------------------------------------------------------------------------
386
387
388%% enable OK, BATCH button and 'status' display
389% set(handles.OK, 'Enable','On')
390% set(handles.OK,'BackgroundColor',[1 0 0])%set RUN button to red color
391% if isfield(handles,'status')
392%     set(handles.status,'Value',0);       %suppress the 'status' display
393%     status_Callback([], [], handles)
394% end
395
396%% determine nomenclature types and extension of the input files
397% [RootPath,SubDir,Civ2_ImageB,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
398% NomTypeNc='';%default
399
400
401
402%% scan the image file series
403[FilePath,FileName,ImaExt]=fileparts(imageinput);
404% detect the file type, get the movie object if relevant, and look for the corresponding file series:
405% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
406%[RootPath,Civ1_ImageA,Civ2_ImageB,i1_series,tild,j1_series,tild,NomTypeIma,FileType,MovieObject]=find_file_series(FilePath,[FileName ImaExt]);
407switch Param.FileType{1}
408    case {'image','multimage','video','mmreader'}
409    otherwise
410        errormsg='invalid input file: enter an image, a movie or civ .nc file';
411        return
412end
413set(handles.RootPath,'String',RootPath)
414set(handles.Civ1_ImageA,'String',SubDirImages)
415set(handles.Civ2_ImageB,'String',RootFile)
416if strcmp(ExtInput,'.nc')
417    SubDirCiv=regexprep(SubDir,['^' SubDirImages],'');%suppress the root  SuddirImages;
418else
419    SubDirCiv= '.civ';
420end
421set(handles.Civ1_ImageB,'String',SubDirCiv)
422set(handles.Civ2_ImageA,'String',SubDirCiv)
423browse=get(handles.RootPath,'UserData');
424browse.incr_pair=[0 0];%default
425
426%% scan the images if a civ_input file has been opened
427MinIndex_i=min(i1_series(i1_series>0));
428MinIndex_j=min(j1_series(j1_series>0));
429MaxIndex_i=max(i1_series(i1_series>0));
430MaxIndex_j=max(j1_series(j1_series>0));
431
432%% look for an image documentation file
433XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt);
434if isempty(XmlFileName)
435    if (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
436        ext_imadoc=ImaExt;% the timing from the video movie is used
437    else
438        ext_imadoc='';
439    end
440else
441    [tild,tild,ext_imadoc]=fileparts(XmlFileName);
442end
443set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
444
445
446
447%% update i and j index range if a nc file has been opened or pb withmin max image indices:
448% then set first and last to the inputfile index by default
449first_i=str2num(get(handles.first_i,'String'));
450last_i=str2num(get(handles.last_i,'String'));
451if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)||ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
452    first_i=num_ref_i;
453    last_i=num_ref_i;
454    set(handles.first_i,'String',num2str(first_i));
455    set(handles.last_i,'String',num2str(last_i));%
456end
457
458%j index range
459first_j=str2num(get(handles.first_j,'String'));
460last_j=str2num(get(handles.last_j,'String'));
461if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)||ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
462    first_j=num_ref_j;
463    last_j=num_ref_j;
464    set(handles.first_j,'String',num2str(first_j));
465    set(handles.last_j,'String',num2str(last_j));%
466end
467if num_ref_i>last_i || num_ref_i<first_i
468    num_ref_i=round((first_i+last_i)/2);
469end
470if num_ref_j>last_j || num_ref_j<first_j
471    num_ref_j=round((first_j+last_j)/2);
472end
473set(handles.ref_i,'String',num2str(num_ref_i))
474set(handles.ref_j,'String',num2str(num_ref_j))
475
476
477
478%% scan files to update the subdirectory list display
479listot=dir(RootPath);%directory of RootPath
480idir=0;
481listdir={''};%default
482% get the list of existing civ_input subdirectories in the path of theinput root  file
483for ilist=1:length(listot)
484    if listot(ilist).isdir
485        name=listot(ilist).name;
486        if ~isequal(name,'.') && ~isequal(name,'..')
487            idir=idir+1;
488            listdir{idir,1}=listot(ilist).name;
489        end
490    end
491end
492
493%% store info
494%set(handles.RootPath,'UserData',browse)% store the nomenclature type
495
496%% list the possible index pairs, depending on the option set in ListPairMode
497ListPairMode_Callback([], [], handles)
498
499%------------------------------------------------------------------------
500% --- Executes on carriage return on the subdir checkciv1 edit window
501function Civ1_ImageB_Callback(hObject, eventdata, handles)
502%------------------------------------------------------------------------
503SubDir=get(handles.Civ1_ImageB,'String');
504menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
505ichoice=find(strcmp(SubDir,menu_str),1);
506if isempty(ichoice)
507    ilist=numel(menu_str); %select 'new...' in the menu
508else
509    ilist=ichoice;
510end
511set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
512if get(handles.CheckCiv1,'Value')% if Civ1 is performed
513    set(handles.Civ2_ImageA,'String',SubDir);% set by default civ2 directory the same as civ1
514%     set(handles.ListSubdirCiv2,'Value',ilist)
515else % if Civ1 data already exist
516    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
517    if ~isempty(errormsg)
518    msgbox_uvmat('ERROR',errormsg)
519    end
520end
521
522%------------------------------------------------------------------------
523% --- Executes on carriage return on the SubDir checkciv1 edit window
524function Civ2_ImageA_Callback(hObject, eventdata, handles)
525%------------------------------------------------------------------------
526SubDir=get(handles.Civ1_ImageB,'String');
527menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
528ichoice=find(strcmp(SubDir,menu_str),1);
529if isempty(ichoice)
530    ilist=numel(menu_str); %select 'new...' in the menu
531else
532    ilist=ichoice;
533end
534set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
535%update the list of available pairs from netcdf files in the new directory
536if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
537    errormsg=find_netcpair_civ(handles,2);
538        if ~isempty(errormsg)
539    msgbox_uvmat('ERROR',errormsg)
540    end
541end
542
543%------------------------------------------------------------------------
544% --- Executes on button press in CheckCiv1.
545function CheckCiv1_Callback(hObject, eventdata, handles)
546%------------------------------------------------------------------------
547update_CivOptions(handles,0)
548
549%------------------------------------------------------------------------
550% --- Executes on button press in CheckFix1.
551function CheckFix1_Callback(hObject, eventdata, handles)
552%------------------------------------------------------------------------
553update_CivOptions(handles,0)
554
555%------------------------------------------------------------------------
556% --- Executes on button press in CheckPatch1.
557function CheckPatch1_Callback(hObject, eventdata, handles)
558%------------------------------------------------------------------------
559update_CivOptions(handles,0)
560
561%------------------------------------------------------------------------
562% --- Executes on button press in CheckCiv2.
563function CheckCiv2_Callback(hObject, eventdata, handles)
564%------------------------------------------------------------------------
565update_CivOptions(handles,0)
566
567%------------------------------------------------------------------------
568% --- Executes on button press in CheckFix2.
569function CheckFix2_Callback(hObject, eventdata, handles)
570%------------------------------------------------------------------------
571update_CivOptions(handles,0)
572
573%------------------------------------------------------------------------
574% --- Executes on button press in CheckPatch2.
575function CheckPatch2_Callback(hObject, eventdata, handles)
576%------------------------------------------------------------------------
577update_CivOptions(handles,0)
578
579%------------------------------------------------------------------------
580% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
581function update_CivOptions(handles,opening)
582%------------------------------------------------------------------------
583checkbox=zeros(1,6);
584checkbox(1)=get(handles.CheckCiv1,'Value');
585checkbox(2)=get(handles.CheckFix1,'Value');
586checkbox(3)=get(handles.CheckPatch1,'Value');
587checkbox(4)=get(handles.CheckCiv2,'Value');
588checkbox(5)=get(handles.CheckFix2,'Value');
589checkbox(6)=get(handles.CheckPatch2,'Value');
590ind_selected=find(checkbox,1);
591% if ~isempty(ind_selected)
592%     RootPath=get(handles.RootPath,'String');
593%     if isempty(RootPath)
594%         msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
595%         return
596%     end
597% end
598set(handles.PairIndices,'Visible','on')
599set(handles.Civ1_ImageB,'Visible','on')
600set(handles.TitleSubdirCiv1,'Visible','on')
601if opening==0
602    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
603    if ~isempty(errormsg)
604        msgbox_uvmat('ERROR',errormsg)
605    end
606end
607if max(checkbox(4:6))% case of civ2 pair choice needed
608    set(handles.TitlePairCiv2,'Visible','on')
609    set(handles.TitleSubdirCiv2,'Visible','on')
610    set(handles.Civ2_ImageA,'Visible','on')
611    %set(handles.ListSubdirCiv2,'Visible','on')
612    set(handles.ListPairCiv2,'Visible','on')
613    if ~opening
614        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
615        if ~isempty(errormsg)
616            msgbox_uvmat('ERROR',errormsg)
617        end
618    end
619else
620    set(handles.TitleSubdirCiv2,'Visible','off')
621    set(handles.Civ2_ImageA,'Visible','off')
622    set(handles.ListPairCiv2,'Visible','off')
623end
624options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
625for ilist=1:length(options)
626    if checkbox(ilist)
627        set(handles.(options{ilist}),'Visible','on')
628    else
629        set(handles.(options{ilist}),'Visible','off')
630    end
631end
632
633%------------------------------------------------------------------------
634% --- Executes on button press in OK: processing on local computer
635function OK_Callback(hObject, eventdata, handles)
636%------------------------------------------------------------------------
637
638handles.output.ActionInput=read_GUI(handles.civ_input);
639guidata(hObject, handles);% Update handles structure
640uiresume(handles.civ_input);
641drawnow
642
643return
644
645
646set(handles.OK, 'Enable','Off')
647set(handles.OK,'BackgroundColor',[0.831 0.816 0.784])
648set(handles.OK,'UserData',now)% record the time of launch
649
650errormsg=launch_jobs(hObject, eventdata, handles);
651set(handles.OK, 'Enable','On')
652set(handles.OK,'BackgroundColor',[1 0 0])
653
654% display errors or start status callback to visualise results
655if ~isempty(errormsg)
656    display(errormsg)
657    msgbox_uvmat('ERROR',errormsg)
658elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
659    set(handles.status,'Value',1);%suppress status display
660    status_Callback(hObject, eventdata, handles)
661end
662
663
664
665%------------------------------------------------------------------------
666% --- determine the list of index pairs of processing file
667function [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
668    find_pair_indices(handles,ref_i,ref_j,mode)
669%------------------------------------------------------------------------
670
671list_civ1=get(handles.ListPairCiv1,'String');
672index_civ1=get(handles.ListPairCiv1,'Value');
673str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
674if isempty(str_civ1)||isequal(str_civ1,'')
675    msgbox_uvmat('ERROR','no image pair selected for civ1')
676    return
677end
678list_civ2=get(handles.ListPairCiv2,'String');
679index_civ2=get(handles.ListPairCiv2,'Value');
680if index_civ2>length(list_civ2)
681    list_civ2=list_civ1;
682    index_civ2=index_civ1;
683end
684str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
685
686if isequal (mode,'series(Di)')
687    lastfield=str2double(get(handles.nb_field,'String'));
688    i1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
689    i2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
690    j1_civ1=ref_j;
691    j2_civ1=ref_j;
692    i1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
693    i2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
694    j1_civ2=ref_j;
695    j2_civ2=ref_j;
696   
697    % adjust the first and last field number
698    lastfield=str2double(get(handles.nb_field,'String'));
699    if isnan(lastfield)
700        indsel=find((i1_civ1 >= 1)&(i1_civ2 >= 1));
701    else
702        indsel=find((i2_civ1 <= lastfield)&(i2_civ2 <= lastfield)&(i1_civ1 >= 1)&(i1_civ2 >= 1));
703    end
704    if length(indsel)>=1
705        firstind=indsel(1);
706        lastind=indsel(end);
707        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
708        set(handles.last_i,'String',num2str(ref_i(lastind)))
709        ref_i=ref_i(indsel);
710        i1_civ1=i1_civ1(indsel);
711        i1_civ2=i1_civ2(indsel);
712        i2_civ1=i2_civ1(indsel);
713        i2_civ2=i2_civ2(indsel);
714    end
715elseif isequal (mode,'series(Dj)')
716    lastfield_j=str2double(get(handles.nb_field2,'String'));
717    i1_civ1=ref_i;% set of first image numbers
718    i2_civ1=ref_i;
719    j1_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
720    j2_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
721    i1_civ2=ref_i;
722    i2_civ2=ref_i;
723    j1_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
724    j2_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
725    % adjust the first and last field number
726    if isnan(lastfield_j)
727        indsel=find((j1_civ1 >= 1)&(j1_civ2 >= 1));
728    else
729        indsel=find((j2_civ1 <= lastfield_j)&(j2_civ2 <= lastfield_j)&(j1_civ1 >= 1)&(j1_civ2 >= 1));
730    end
731    if length(indsel)>=1
732        firstind=indsel(1);
733        lastind=indsel(end);
734        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
735        set(handles.last_j,'String',num2str(ref_j(lastind)))
736        ref_j=ref_j(indsel);
737        j1_civ1=j1_civ1(indsel);
738        j2_civ1=j2_civ1(indsel);
739        j1_civ2=j1_civ2(indsel);
740        j2_civ2=j2_civ2(indsel);
741    end
742elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
743    displ_num=get(handles.ListPairCiv1,'UserData');
744    i1_civ1=ref_i;
745    i2_civ1=ref_i;
746    j1_civ1=displ_num(1,index_civ1);
747    j2_civ1=displ_num(2,index_civ1);
748    i1_civ2=ref_i;
749    i2_civ2=ref_i;
750    j1_civ2=displ_num(1,index_civ2);
751    j2_civ2=displ_num(2,index_civ2);
752elseif isequal(mode,'displacement')
753    i1_civ1=ref_i;
754    i2_civ1=ref_i;
755    j1_civ1=ref_j;
756    j2_civ1=ref_j;
757    i1_civ2=ref_i;
758    i2_civ2=ref_i;
759    j1_civ2=ref_j;
760    j2_civ2=ref_j;
761end
762
763%------------------------------------------------------------------------
764% --- Executes on button press in ListCompareMode.
765function ListCompareMode_Callback(hObject, eventdata, handles)
766%------------------------------------------------------------------------
767ListCompareMode=get(handles.ListCompareMode,'String');
768option=ListCompareMode{get(handles.ListCompareMode,'Value')};
769switch option
770    case 'PIV'
771        set(handles.RootFile_1,'Visible','Off');
772        set(handles.sub_txt,'Visible','off')
773        set(handles.RootFile_1,'String',[]);
774        mode_store=get(handles.ListCompareMode,'UserData');
775        set(handles.ListPairMode,'Visible','on')
776        set(handles.ListPairMode,'Value',1)
777        set(handles.ListPairMode,'String',mode_store)
778        set(handles.CheckStereo,'Value',0)     
779    case 'PIV volume'     
780        set(handles.RootFile_1,'Visible','Off');
781        set(handles.sub_txt,'Visible','off')
782        set(handles.RootFile_1,'String',[]);
783        mode_store=get(handles.ListCompareMode,'UserData');
784        set(handles.ListPairMode,'Visible','on')
785        set(handles.ListPairMode,'Value',1)
786        set(handles.ListPairMode,'String',{'series(Di)'})
787        set(handles.CheckStereo,'Value',0)
788        set(handles.last_j,'String',get(handles.nb_field2,'String'))% select the whole volume scan by default
789        set(handles.incr_i,'String',num2str(2))%
790    otherwise
791        filebase=get(handles.RootPath,'String');
792        set(handles.sub_txt,'Visible','on')
793        set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
794        mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
795        set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
796        set(handles.ListPairMode,'Visible','off')
797       
798        %% open an image file with the browser
799        ind_opening=1;%default
800        browse.incr_pair=[0 0]; %default
801        oldfile=get(handles.RootPath,'String');
802        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
803            '*.png','.png image files'; ...
804            '*.jpg',' jpeg image files'; ...
805            '*.tif','.tif image files'; ...
806            '*.avi;*.AVI','.avi movie files'; ...
807            '*.*',  'All Files (*.*)'};
808        if strcmp(option,'displacement')
809            comment='Pick the reference file for displacements';
810        else
811            comment='Pick a file of the second series';
812        end
813        [FileName, PathName] = uigetfile( menu, comment,oldfile);
814        fileinput=[PathName FileName];%complete file name
815        sizf=size(fileinput);
816        if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
817        [path,name,ext]=fileparts(fileinput);
818        [path1]=fileparts(filebase);
819        if isunix
820            [status,path]=system(['readlink ' path]);
821            [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
822        end
823        if ~strcmp(path1,path)
824            msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
825            return
826        end
827        if strcmp(option,'displacement')
828            [tild,RootFile_1]=fileparts(name);
829        else
830            [FilePath,FileName,Ext]=fileparts(fileinput);
831            % detect the file type, get the movie object if relevant, and look for the corresponding file series:
832            % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
833            [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,FileInfo,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]);
834           
835            %check image nom type
836            if ~strcmp(nom_type_1,get(handles.NomType,'String'))
837                msgbox_uvmat('ERROR','The second image series must have the same indexing type as the first one, or use the option displacement for a fixed image')
838                return
839            end
840        end
841        %check image  extension
842        if ~strcmp(ext,get(handles.ImaExt,'String'))
843            msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
844            return
845        end
846        set(handles.RootFile_1,'String',RootFile_1);
847       
848end
849ListPairMode_Callback(hObject, eventdata, handles)
850
851
852%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
853% Callbacks in the uipanel Pair Indices
854%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
855%------------------------------------------------------------------------
856% --- Executes on button press in ListPairMode.
857function ListPairMode_Callback(hObject, eventdata, handles)
858%------------------------------------------------------------------------
859compare_list=get(handles.ListCompareMode,'String');
860val=get(handles.ListCompareMode,'Value');
861compare=compare_list{val};
862if strcmp(compare,'displacement')||strcmp(compare,'shift')
863    mode='displacement';
864else
865    mode_list=get(handles.ListPairMode,'String');
866    if ischar(mode_list)
867        mode_list={mode_list};
868    end
869    mode_value=get(handles.ListPairMode,'Value');
870    mode=mode_list{mode_value};
871end
872% displ_num=[];%default
873ref_i=str2double(get(handles.ref_i,'String'));
874% last_i=str2num(get(handles.last_i,'String'));
875CivInputData=get(handles.civ_input,'UserData');
876TimeUnit=get(handles.TimeUnit,'String');
877checkframe=strcmp(TimeUnit,'frame');
878time=CivInputData.Time;
879siztime=size(CivInputData.Time);
880nbfield=siztime(1)-1;
881nbfield2=siztime(2)-1;
882indchosen=1;  %%first pair selected by default
883%displ_num used to define the indices of the civ_input pairs
884% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
885% are relative to the reference indices ref_i and ref_j respectively.
886if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
887    dt=1;
888    displ='';
889    index=0;
890    numlist_a=[];
891    numlist_B=[];
892    %get all the time intervals in bursts
893    displ_dt=1;%default
894    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
895    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
896        for numod_b=(numod_a+1):nbfield2
897            index=index+1;
898            numlist_a(index)=numod_a;
899            numlist_b(index)=numod_b;
900            if size(time,2)>1 && ~checkframe
901                dt(numod_a,numod_b)=CivInputData.Time(ref_i+1,numod_b+1)-CivInputData.Time(ref_i+1,numod_a+1);%first time interval dt
902                displ_dt(index)=dt(numod_a,numod_b);
903            else
904                displ_dt(index)=1;
905            end
906        end
907    end
908    [dtsort,indsort]=sort(displ_dt);
909    if ~isempty(numlist_a)
910        displ_num(1,:)=numlist_a(indsort);
911        displ_num(2,:)=numlist_b(indsort);
912    end
913    displ_num(3,:)=0;
914    displ_num(4,:)=0;
915    enable_j(handles, 'off')
916elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
917    index=1:200;
918    displ_num(1,index)=-floor(index/2);
919    displ_num(2,index)=ceil(index/2);
920    displ_num(3:4,index)=zeros(2,200);
921    enable_j(handles, 'on')
922elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
923%     index=1:200;
924%     displ_num(1:2,index)=zeros(2,200);
925%     displ_num(3,index)=-floor(index/2);
926%     displ_num(4,index)=ceil(index/2);
927    enable_i(handles, 'on')
928    if nbfield2 > 1
929        enable_j(handles, 'on')
930    else
931        enable_j(handles, 'off')
932    end
933elseif isequal(mode,'displacement')%the pairs have the same indices
934    displ_num(1,1)=0;
935    displ_num(2,1)=0;
936    displ_num(3,1)=0;
937    displ_num(4,1)=0;
938    if nbfield > 1 || nbfield==0
939        enable_i(handles, 'on')
940    else
941        enable_j(handles, 'off')
942    end
943    if nbfield2 > 1
944        enable_j(handles, 'on')
945    else
946        enable_j(handles, 'off')
947    end
948end
949%set(handles.ListPairCiv1,'UserData',displ_num);
950errormsg=find_netcpair_civ( handles,1);
951    if ~isempty(errormsg)
952    msgbox_uvmat('ERROR',errormsg)
953    end
954% find_netcpair_civ2(handles)
955
956function enable_i(handles, state)
957set(handles.itext,'Visible',state)
958% set(handles.first_i,'Visible',state)
959% set(handles.last_i,'Visible',state)
960% set(handles.incr_i,'Visible',state)
961set(handles.nb_field,'Visible',state)
962set(handles.ref_i,'Visible',state)
963
964function enable_j(handles, state)
965set(handles.jtext,'Visible',state)
966% set(handles.first_j,'Visible',state)
967% set(handles.last_j,'Visible',state)
968% set(handles.incr_j,'Visible',state)
969set(handles.nb_field2,'Visible',state)
970set(handles.ref_j,'Visible',state)
971
972
973%------------------------------------------------------------------------
974% --- Executes on selection change in ListPairCiv1.
975function ListPairCiv1_Callback(hObject, eventdata, handles)
976%------------------------------------------------------------------------
977%reproduce by default the chosen pair in the checkciv2 menu
978list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
979index_pair=get(handles.ListPairCiv1,'Value');
980displ_num=get(handles.ListPairCiv1,'UserData');
981list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
982if index_pair<=length(list_pair2)
983    set(handles.ListPairCiv2,'Value',index_pair);
984end
985
986%update first_i and last_i according to the chosen image pairs
987% mode_list=get(handles.ListPairMode,'String');
988% mode_value=get(handles.ListPairMode,'Value');
989% mode=mode_list{mode_value};
990% if isequal(mode,'series(Di)')
991%     first_i=str2double(get(handles.first_i,'String'));
992%     last_i=str2double(get(handles.last_i,'String'));
993%     incr_i=str2double(get(handles.incr_i,'String'));
994%     num_i=first_i:incr_i:last_i;
995%     lastfield=str2double(get(handles.nb_field,'String'));
996%     if ~isnan(lastfield)
997%         test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ...
998%             (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield);
999%         num_i=num_i(test_find);
1000%     end
1001%     set(handles.first_i,'String',num2str(num_i(1)));
1002%     set(handles.last_i,'String',num2str(num_i(end)));
1003% elseif isequal(mode,'series(Dj)')
1004%     first_j=str2double(get(handles.first_j,'String'));
1005%     last_j=str2double(get(handles.last_j,'String'));
1006%     incr_j=str2double(get(handles.incr_j,'String'));
1007%     num_j=first_j:incr_j:last_j;
1008%     lastfield2=str2double(get(handles.nb_field2,'String'));
1009%     if ~isnan(lastfield2)
1010%         test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1011%             (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
1012%         num_j=num_j(test_find);
1013%     end
1014%     set(handles.first_j,'String',num2str(num_j(1)));
1015%     set(handles.last_j,'String',num2str(num_j(end)));
1016% end
1017
1018%------------------------------------------------------------------------
1019% --- Executes on selection change in ListPairCiv2.
1020function ListPairCiv2_Callback(hObject, eventdata, handles)
1021%------------------------------------------------------------------------
1022index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
1023
1024%update first_i and last_i according to the chosen image pairs
1025mode_list=get(handles.ListPairMode,'String');
1026mode_value=get(handles.ListPairMode,'Value');
1027mode=mode_list{mode_value};
1028if isequal(mode,'series(Di)')
1029    first_i=str2double(get(handles.first_i,'String'));
1030    last_i=str2double(get(handles.last_i,'String'));
1031    incr_i=str2double(get(handles.incr_i,'String'));
1032    num_i=first_i:incr_i:last_i;
1033    lastfield=str2double(get(handles.nb_field,'String'));
1034    if ~isnan(lastfield)
1035        test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ...
1036            (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield);
1037        num_i=num_i(test_find);
1038    end
1039    set(handles.first_i,'String',num2str(num_i(1)));
1040    set(handles.last_i,'String',num2str(num_i(end)));
1041elseif isequal(mode,'series(Dj)')
1042    first_j=str2double(get(handles.first_j,'String'));
1043    last_j=str2double(get(handles.last_j,'String'));
1044    incr_j=str2double(get(handles.incr_j,'String'));
1045    num_j=first_j:incr_j:last_j;
1046    lastfield2=str2double(get(handles.nb_field2,'String'));
1047    if ~isnan(lastfield2)
1048        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1049            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
1050        num_j=num_j(test_find);
1051    end
1052    set(handles.first_j,'String',num2str(num_j(1)));
1053    set(handles.last_j,'String',num2str(num_j(end)));
1054end
1055
1056%------------------------------------------------------------------------
1057function ref_i_Callback(hObject, eventdata, handles)
1058%------------------------------------------------------------------------
1059mode_list=get(handles.ListPairMode,'String');
1060mode_value=get(handles.ListPairMode,'Value');
1061mode=mode_list{mode_value};
1062errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
1063if isequal(mode,'series(Di)') || ...% we do patch2 only
1064        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
1065    errormsg=find_netcpair_civ( handles,2);
1066end
1067    if ~isempty(errormsg)
1068    msgbox_uvmat('ERROR',errormsg)
1069    end
1070
1071%------------------------------------------------------------------------
1072function ref_j_Callback(hObject, eventdata, handles)
1073%------------------------------------------------------------------------
1074mode_list=get(handles.ListPairMode,'String');
1075mode_value=get(handles.ListPairMode,'Value');
1076mode=mode_list{mode_value};
1077if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
1078    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
1079end
1080if isequal(mode,'series(Dj)') || ...
1081        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
1082    errormsg=find_netcpair_civ(handles,2);
1083end
1084    if ~isempty(errormsg)
1085    msgbox_uvmat('ERROR',errormsg)
1086    end
1087
1088%------------------------------------------------------------------------
1089% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
1090% the field series set by first_i, incr, last_i
1091% index=1: look for pairs for civ1
1092% index=2: look for pairs for civ2
1093function errormsg=find_netcpair_civ(handles,index)
1094%------------------------------------------------------------------------
1095set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
1096
1097%% initialisation
1098errormsg='';
1099CivInputData=get(handles.civ_input,'UserData');
1100%browse=get(handles.RootPath,'UserData');
1101compare_list=get(handles.ListCompareMode,'String');
1102val=get(handles.ListCompareMode,'Value');
1103compare=compare_list{val};
1104if strcmp(compare,'displacement')||strcmp(compare,'shift')
1105    mode='displacement';
1106else
1107    mode_list=get(handles.ListPairMode,'String');
1108    mode_value=get(handles.ListPairMode,'Value');
1109    if isempty(mode_list)
1110        return
1111    end
1112    mode=mode_list{mode_value};
1113end
1114nom_type_ima=CivInputData.NomTypeIma;
1115
1116%% determine nom_type_nc, nomenclature type of the .nc files:
1117[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
1118
1119%% reads .nc subdirectoy and image numbers from the interface
1120SubDirImages=get(handles.Civ1_ImageA,'String');
1121%TODO: determine
1122subdir_civ1=[SubDirImages get(handles.Civ1_ImageB,'String')];%subdirectory subdir_civ1 for the netcdf data
1123subdir_civ2=[SubDirImages get(handles.Civ2_ImageA,'String')];%subdirectory subdir_civ2 for the netcdf data
1124ref_i=str2double(get(handles.ref_i,'String'));
1125ref_j=[];
1126if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1127    ref_j=0;
1128elseif strcmp(get(handles.ref_j,'Visible'),'on')
1129    ref_j=str2double(get(handles.ref_j,'String'));
1130end
1131if isempty(ref_j)
1132    ref_j=1;
1133end
1134CivInputData=get(handles.civ_input,'UserData');
1135TimeUnit=get(handles.TimeUnit,'String');
1136Time=CivInputData.Time;
1137checkframe=strcmp(TimeUnit,'frame');
1138
1139%% case with no Civ1 operation, netcdf files need to exist for reading
1140displ_pair={''};
1141nbpair=200;%default
1142select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
1143testpair=0;
1144RootPath=get(handles.RootPath,'String');
1145RootFile=get(handles.Civ2_ImageB,'String');
1146nbpair=200; %default
1147if index==1 % case civ1
1148    if ~get(handles.CheckCiv1,'Value') %
1149        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
1150            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
1151            set(handles.ListPairCiv1,'String',{});
1152            return
1153        end
1154        for ipair=1:nbpair
1155            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
1156                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
1157            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
1158        end
1159        % case of no displayed pair
1160        if isequal(select,zeros(size(1:nbpair)))
1161            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
1162                num_i1=ref_i-floor(browse.incr_pair(1)/2);
1163                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
1164                num_j1=ref_j-floor(browse.incr_pair(2)/2);
1165                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
1166                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
1167                select(1)=exist(filename,'file')==2;
1168                testpair=1;
1169            else
1170%                 if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1171%                     errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
1172%                 else
1173                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
1174%                 end
1175                set(handles.ListPairCiv1,'String',{''});
1176                %COMPLETER CAS STEREO
1177                return
1178            end
1179        end
1180    end
1181else %case civ2 alone
1182    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
1183        if ~exist(fullfile(RootPath,subdir_civ2),'dir')
1184            msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
1185            set(handles.ListPairCiv2,'Value',1);
1186            set(handles.ListPairCiv2,'String',{''});
1187            return
1188        end
1189        for ipair=1:nbpair
1190            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
1191                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
1192            select(ipair)=exist(filename,'file')==2;
1193        end
1194        if  isequal(select,zeros(size(1:nbpair)))
1195            if isfield(browse,'incr_pair')
1196                num_i1=ref_i-floor(browse.incr_pair(1)/2);
1197                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
1198                num_j1=ref_j-floor(browse.incr_pair(2)/2);
1199                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
1200                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
1201                select(1)=exist(filename,'file')==2;
1202            else
1203                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1204                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
1205                else
1206                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
1207                end
1208                set(handles.ListPairCiv2,'Value',1);
1209                set(handles.ListPairCiv2,'String',{''});
1210                return
1211            end
1212        end
1213    end
1214end
1215
1216%% determine the menu display in .ListPairCiv1
1217testpair=0; %TODO: check
1218if isequal(mode,'series(Di)')
1219    if testpair
1220        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1221    else
1222        for ipair=1:nbpair
1223            if select(ipair)
1224                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
1225               if ~checkframe
1226                   if size(Time,1)>=ref_i+1+ceil(ipair/2) && size(Time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0
1227                 dt=Time(ref_i+1+ceil(ipair/2),ref_j+1)-Time(ref_i+1-floor(ipair/2),ref_j+1);%Time interval dtref_j+1
1228                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
1229                   end
1230                else
1231                    dt=ipair/1000;
1232                      displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(ipair)];
1233               end             
1234            else
1235                displ_pair{ipair}='...'; %pair not displayed in the menu
1236            end
1237        end
1238    end
1239elseif isequal(mode,'series(Dj)')
1240    if testpair
1241        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1242    else
1243        for ipair=1:nbpair
1244            if select(ipair)
1245                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
1246               if ~checkframe
1247                   if size(Time,2)>=ref_j+1+ceil(ipair/2) && size(Time,1)>=ref_i+1 && ref_j-floor(ipair/2)>=0 && ref_i>=0
1248                 dt=Time(ref_i+1,ref_j+1+ceil(ipair/2))-Time(ref_i+1,ref_j+1-floor(ipair/2));%Time interval dtref_j+1
1249                  displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
1250                   end
1251                else
1252                    dt=ipair/1000;
1253                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
1254               end                 
1255            else
1256                displ_pair{ipair}='...'; %pair not displayed in the menu
1257            end
1258        end
1259    end
1260elseif isequal(mode,'pair j1-j2')%case of pairs
1261    MinIndex_j=CivInputData.MinIndex_j;
1262    MaxIndex_j=min(CivInputData.MaxIndex_j,10);%limitate the number of pairs to 10x10
1263    index_pair=0;
1264    %get all the Time intervals in bursts   
1265   for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode
1266        for numod_b=(numod_a+1):MaxIndex_j
1267            index_pair=index_pair+1;
1268            displ_pair{index_pair}=['j= ' num2stra(numod_a,nom_type_ima) '-' num2stra(numod_b,nom_type_ima)];
1269            dt(index_pair)=numod_b-numod_a;%default dt
1270            if size(Time,1)>ref_i && size(Time,2)>numod_b  % && ~checkframe
1271                dt(index_pair)=Time(ref_i+1,numod_b+1)-Time(ref_i+1,numod_a+1);% Time interval dt
1272                 displ_pair{index_pair}=[displ_pair{index_pair} ' :dt= ' num2str(dt(index_pair)*1000)];
1273            end
1274        end
1275    end
1276    [dtsort,indsort]=sort(dt);
1277    displ_pair=displ_pair(indsort);
1278elseif isequal(mode,'displacement')
1279    displ_pair={'Di=Dj=0'};
1280end
1281if index==1
1282set(handles.ListPairCiv1,'String',displ_pair');
1283end
1284
1285%% determine the default selection in the pair menu
1286ichoice=find(select,1);% index of selected pair
1287if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1288initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
1289if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
1290    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
1291end
1292initial=get(handles.ListPairCiv2,'Value');
1293if initial>length(displ_pair')%|~isequal(select(initial),1)
1294    if ichoice <= length(displ_pair')
1295        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
1296    else
1297        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
1298    end
1299end
1300set(handles.ListPairCiv2,'String',displ_pair');
1301set(gcf,'Pointer','arrow')
1302
1303
1304   
1305% %------------------------------------------------------------------------   
1306% % call 'view_field.fig' to display the  field selected in the list of 'status'
1307% function open_view_field(hObject, eventdata)
1308% %------------------------------------------------------------------------
1309% list=get(hObject,'String');
1310% index=get(hObject,'Value');
1311% rootroot=get(hObject,'UserData');
1312% filename=list{index};
1313% ind_dot=strfind(filename,'...');
1314% filename=filename(1:ind_dot-1);
1315% filename=fullfile(rootroot,filename);
1316% delete(get(hObject,'parent'))%delete the display figure to stop the check process
1317% if exist(filename,'file')%visualise the vel field if it exists
1318%     uvmat(filename)
1319%     set(gcbo,'Value',1)
1320% end
1321
1322
1323%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1324% Callbacks in the uipanel Reference Indices
1325%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1326%------------------------------------------------------------------------
1327function first_i_Callback(hObject, eventdata, handles)
1328%------------------------------------------------------------------------
1329first_i=str2double(get(handles.first_i,'String'));
1330set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
1331ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
1332
1333%------------------------------------------------------------------------
1334function first_j_Callback(hObject, eventdata, handles)
1335%------------------------------------------------------------------------
1336first_j=str2num(get(handles.first_j,'String'));
1337set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
1338ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
1339
1340%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1341% Callbacks in the uipanel Civ1
1342%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1343%------------------------------------------------------------------------
1344% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
1345function SearchRange_Callback(hObject, eventdata, handles)
1346%------------------------------------------------------------------------
1347%determine pair numbers
1348if strcmp(get(handles.num_UMin,'Visible'),'off')
1349    set(handles.u_title,'Visible','on')
1350    set(handles.v_title,'Visible','on')
1351    set(handles.num_UMin,'Visible','on')
1352    set(handles.num_UMax,'Visible','on')
1353    set(handles.num_VMin,'Visible','on')
1354    set(handles.num_VMax,'Visible','on')
1355    set(handles.CoordUnit,'Visible','on')
1356    set(handles.TimeUnit,'Visible','on')
1357    set(handles.slash_title,'Visible','on')
1358    set(handles.min_title,'Visible','on')
1359    set(handles.max_title,'Visible','on')
1360    set(handles.unit_title,'Visible','on')
1361else
1362    get_search_range(hObject, eventdata, handles)
1363end
1364
1365%------------------------------------------------------------------------
1366% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
1367function get_search_range(hObject, eventdata, handles)
1368%------------------------------------------------------------------------
1369param_civ1=read_GUI(handles.Civ1);
1370umin=param_civ1.UMin;
1371umax=param_civ1.UMax;
1372vmin=param_civ1.VMin;
1373vmax=param_civ1.VMax;
1374%switch min_title and max_title in case of error
1375if umax<=umin
1376    umin_old=umin;
1377    umin=umax;
1378    umax=umin_old;
1379    set(handles.num_UMin,'String', num2str(umin))
1380    set(handles.num_UMax,'String', num2str(umax))
1381end
1382if vmax<=vmin
1383    vmin_old=vmin;
1384    vmin=vmax;
1385    vmax=vmin_old;
1386    set(handles.num_VMin,'String', num2str(vmin))
1387    set(handles.num_VMax,'String', num2str(vmax))
1388end   
1389if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
1390    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
1391    index=get(handles.ListPairCiv1,'Value');
1392    pair_string=list_pair{index};
1393    time=get(handles.ImaDoc,'UserData'); %get the set of times
1394    pxcm=get(handles.SearchRange,'UserData');
1395    mode_list=get(handles.ListPairMode,'String');
1396    mode_value=get(handles.ListPairMode,'Value');
1397    mode=mode_list{mode_value};     
1398    if isequal (mode, 'series(Di)' )
1399        ref_i=str2double(get(handles.ref_i,'String'));
1400        num1=ref_i-floor(index/2);%  first image numbers
1401        num2=ref_i+ceil(index/2);
1402        num_a=1;
1403        num_b=1;
1404    elseif isequal (mode, 'series(Dj)')
1405        num1=1;
1406        num2=1;
1407        ref_j=str2double(get(handles.ref_j,'String'));
1408        num_a=ref_j-floor(index/2);%  first image numbers
1409        num_b=ref_j+ceil(index/2);
1410    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
1411        ref_i=str2double(get(handles.ref_i,'String'));
1412        num1=ref_i;
1413        num2=ref_i;
1414                r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
1415        if isempty(r)
1416            r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
1417        end 
1418        num_a=str2num(r.num1);
1419        num_b=str2num(r.num2);
1420    end
1421    dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
1422    ibx=str2double(get(handles.num_CorrBoxSize_1,'String'));
1423    iby=str2double(get(handles.num_CorrBoxSize_2,'String'));
1424    umin=dt*pxcm*umin;
1425    umax=dt*pxcm*umax;
1426    vmin=dt*pxcm*vmin;
1427    vmax=dt*pxcm*vmax;
1428    shiftx=round((umin+umax)/2);
1429    shifty=round((vmin+vmax)/2);
1430    isx=(umax+2-shiftx)*2+param_civ1.Bx;
1431    isx=2*ceil(isx/2)+1;
1432    isy=(vmax+2-shifty)*2+param_civ1.Bx;
1433    isy=2*ceil(isy/2)+1;
1434    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
1435    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
1436    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
1437    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
1438end
1439
1440%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1441% Callbacks in the uipanel Fix1
1442%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1443%------------------------------------------------------------------------
1444% --- Executes on button press in CheckMask.
1445function get_mask_fix1_Callback(hObject, eventdata, handles)
1446%------------------------------------------------------------------------
1447maskval=get(handles.CheckMask,'Value');
1448if isequal(maskval,0)
1449    set(handles.Mask,'String','')
1450else
1451    mask_displ='no mask'; %default
1452    filebase=get(handles.RootPath,'String');
1453    [nbslice, flag_mask]=get_mask(filebase,handles);
1454    if isequal(flag_mask,1)
1455        mask_displ=[num2str(nbslice) 'mask'];
1456    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1457        filebase_a=get(handles.RootFile_1,'String');
1458        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1459        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1460            mask_displ='no mask';
1461        end
1462    end
1463    if isequal(mask_displ,'no mask')
1464        [FileName, PathName, filterindex] = uigetfile( ...
1465            {'*.png', ' (*.png)';
1466            '*.png',  '.png files '; ...
1467            '*.*', 'All Files (*.*)'}, ...
1468            'Pick a mask file *.png',filebase);
1469        mask_displ=fullfile(PathName,FileName);
1470        if ~exist(mask_displ,'file')
1471            mask_displ='no mask';
1472        end
1473    end
1474    if isequal(mask_displ,'no mask')
1475        set(handles.CheckMask,'Value',0)
1476        set(handles.CheckMask,'Value',0)
1477        set(handles.CheckMask,'Value',0)
1478    else
1479        %set(handles.CheckMask,'Value',1)
1480        set(handles.CheckMask,'Value',1)
1481    end
1482    set(handles.Mask,'String',mask_displ)
1483    set(handles.Mask,'String',mask_displ)
1484    set(handles.Mask,'String',mask_displ)
1485end
1486
1487%------------------------------------------------------------------------
1488% --- Executes on button press in CheckMask: select box for mask option
1489function get_mask_civ2_Callback(hObject, eventdata, handles)
1490%------------------------------------------------------------------------
1491maskval=get(handles.CheckMask,'Value');
1492if isequal(maskval,0)
1493    set(handles.Mask,'String','')
1494else
1495    mask_displ='no mask'; %default
1496    filebase=get(handles.RootPath,'String');
1497    [nbslice, flag_mask]=get_mask(filebase,handles);
1498    if isequal(flag_mask,1)
1499        mask_displ=[num2str(nbslice) 'mask'];
1500    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1501        filebase_a=get(handles.RootFile_1,'String');
1502        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1503        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1504            mask_displ='no mask';
1505        end
1506    end
1507    if isequal(mask_displ,'no mask')
1508        [FileName, PathName, filterindex] = uigetfile( ...
1509            {'*.png', ' (*.png)';
1510            '*.png',  '.png files '; ...
1511            '*.*', 'All Files (*.*)'}, ...
1512            'Pick a mask file *.png',filebase);
1513        mask_displ=fullfile(PathName,FileName);
1514        if ~exist(mask_displ,'file')
1515            mask_displ='no mask';
1516        end
1517    end
1518    if isequal(mask_displ,'no mask')
1519        set(handles.CheckMask,'Value',0)
1520        set(handles.CheckMask,'Value',0)
1521    else
1522        set(handles.CheckMask,'Value',1)
1523    end
1524    set(handles.Mask,'String',mask_displ)
1525    set(handles.Mask,'String',mask_displ)
1526end
1527
1528%------------------------------------------------------------------------
1529% --- Executes on button press in CheckMask.
1530function get_mask_fix2_Callback(hObject, eventdata, handles)
1531%------------------------------------------------------------------------
1532maskval=get(handles.CheckMask,'Value');
1533if isequal(maskval,0)
1534    set(handles.Mask,'String','')
1535else
1536    mask_displ='no mask'; %default
1537    filebase=get(handles.RootPath,'String');
1538    [nbslice, flag_mask]=get_mask(filebase,handles);
1539    if isequal(flag_mask,1)
1540        mask_displ=[num2str(nbslice) 'mask'];
1541    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1542        filebase_a=get(handles.RootFile_1,'String');
1543        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1544        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1545            mask_displ='no mask';
1546        end
1547    end
1548    if isequal(mask_displ,'no mask')
1549        [FileName, PathName, filterindex] = uigetfile( ...
1550            {'*.png', ' (*.png)';
1551            '*.png',  '.png files '; ...
1552            '*.*', 'All Files (*.*)'}, ...
1553            'Pick a mask file *.png',filebase);
1554        mask_displ=fullfile(PathName,FileName);
1555        if ~exist(mask_displ,'file')
1556            mask_displ='no mask';
1557        end
1558    end
1559    if isequal(mask_displ,'no mask')
1560        set(handles.CheckMask,'Value',0)
1561    end
1562    set(handles.Mask,'String',mask_displ)
1563end
1564
1565%------------------------------------------------------------------------
1566% --- function called to look for mask files
1567function [nbslice, flag_mask]=get_mask(filebase,handles)
1568%------------------------------------------------------------------------
1569%detect mask files, images with appropriate file base
1570%[filebase '_' xx 'mask'], xx=nbslice
1571%flag_mask=1 indicates detection
1572
1573flag_mask=0;%default
1574nbslice=1;
1575
1576% subdir=get(handles.Civ1_ImageB,'String');
1577[Path,Name]=fileparts(filebase);
1578if ~isdir(Path)
1579    msgbox_uvmat('ERROR','no path for input files')
1580    return
1581end
1582% currentdir=pwd;
1583% cd(Path);%move in the dir of the root name filebase
1584maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
1585% cd(currentdir);%come back to the current working directory
1586if ~isempty(maskfiles)
1587    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
1588    % else
1589    flag_mask=1;
1590    maskname=maskfiles(1).name;% take the first mask file in the list
1591    [Path2,Name,ext]=fileparts(maskname);
1592    Namedouble=double(Name);
1593    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1594    ind_mask=findstr('mask',Name);
1595    i=ind_mask-1;
1596    while val(i)==0 && i>0
1597        i=i-1;
1598    end
1599    nbslice=str2double(Name(i+1:ind_mask-1));
1600    if ~isnan(nbslice) && Name(i)=='_'
1601        flag_mask=1;
1602    else
1603        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
1604        return
1605        nbslice=1;
1606    end
1607end
1608
1609%------------------------------------------------------------------------
1610% --- function called to look for grid files
1611function [nbslice, flag_grid]=get_grid(filebase,handles)
1612%------------------------------------------------------------------------
1613flag_grid=0;%default
1614nbslice=1;
1615[Path,Name]=fileparts(filebase);
1616currentdir=pwd;
1617cd(Path);%move in the dir of the root name filebase
1618gridfiles=dir([Name '_*grid_*.grid']);%look for grid files
1619cd(currentdir);%come back to the current working directory
1620if ~isempty(gridfiles)
1621    flag_grid=1;
1622    gridname=gridfiles(1).name;% take the first grid file in the list
1623    [Path2,Name,ext]=fileparts(gridname);
1624    Namedouble=double(Name);
1625    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1626    ind_grid=findstr('grid',Name);
1627    i=ind_grid-1;
1628    while val(i)==0 && i>0
1629        i=i-1;
1630    end
1631    nbslice=str2double(Name(i+1:ind_grid-1));
1632    if ~isnan(nbslice) && Name(i)=='_'
1633        flag_grid=1;
1634    else
1635        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
1636        return
1637        nbslice=1;
1638    end
1639end
1640
1641%------------------------------------------------------------------------
1642% --- transform numbers to letters
1643function str=num2stra(num,nom_type)
1644%------------------------------------------------------------------------
1645if isempty(nom_type)
1646    str='';
1647elseif strcmp(nom_type(end),'a')
1648    str=char(96+num);
1649elseif strcmp(nom_type(end),'A')
1650    str=char(96+num);
1651elseif isempty(nom_type(2:end))%a single index
1652    str='';
1653else
1654    str=num2str(num);
1655end
1656
1657% %------------------------------------------------------------------------
1658% % --- Executes on button press in ListSubdirCiv1.
1659% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
1660% %------------------------------------------------------------------------
1661% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
1662% val=get(handles.ListSubdirCiv1,'Value');
1663% SubDir=list_subdir_civ1{val};
1664% if strcmp(SubDir,'new...')
1665%     if get(handles.CheckCiv1,'Value')
1666%         SubDir='CIV_INPUT'; %default subdirectory
1667%     else
1668%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new civ_input operation')
1669%         return
1670%     end   
1671% end
1672% set(handles.Civ1_ImageB,'String',SubDir);
1673% errormsg=find_netcpair_civ(handles,1);
1674% if ~isempty(errormsg)
1675%     msgbox_uvmat('ERROR',errormsg)
1676% end
1677%     
1678%------------------------------------------------------------------------
1679% % --- Executes on button press in ListSubdirCiv2.
1680% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
1681% %------------------------------------------------------------------------
1682% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
1683% val=get(handles.ListSubdirCiv2,'Value');
1684% SubDir=list_subdir_civ2{val};
1685% if strcmp(SubDir,'new...')
1686%     if get(handles.CheckCiv2,'Value')
1687%         SubDir='CIV_INPUT'; %default subdirectory
1688%     else
1689%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new civ_input operation')
1690%         return
1691%     end
1692% end
1693% set(handles.Civ2_ImageA,'String',SubDir);
1694
1695%------------------------------------------------------------------------
1696% --- Executes on button press in CheckGrid.
1697function CheckGrid_Callback(hObject, eventdata, handles)
1698%------------------------------------------------------------------------
1699value=get(hObject,'Value');
1700hparent=get(hObject,'parent');%handles of the parent panel
1701hchildren=get(hparent,'children');
1702handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
1703handle_dx=findobj(hchildren,'tag','num_Dx');
1704handle_dy=findobj(hchildren,'tag','num_Dy');
1705handle_title_dx=findobj(hchildren,'tag','title_Dx');
1706handle_title_dy=findobj(hchildren,'tag','title_Dy');
1707testgrid=0;
1708filegrid='';
1709if value
1710    filebase=get(handles.RootPath,'String');
1711    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
1712    if isequal(flag_grid,1)
1713        filegrid=[num2str(nbslice) 'grid'];
1714        testgrid=1;
1715    else % browse for a grid
1716        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
1717        if exist(filegrid,'file')
1718            filebase=filegrid;
1719        end
1720        [FileName, PathName] = uigetfile( ...
1721            {'*.grid', ' (*.grid)';
1722            '*.grid',  '.grid files '; ...
1723            '*.*', 'All Files (*.*)'}, ...
1724            'Pick a file',filebase);
1725        filegrid=fullfile(PathName,FileName);
1726        set(hObject,'UserData',filegrid);%store for future use
1727        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
1728            testgrid=1;
1729        end
1730    end
1731end
1732if testgrid
1733    set(handle_dx,'Visible','off');
1734    set(handle_dy,'Visible','off');
1735    set(handle_title_dy,'Visible','off');
1736    set(handle_title_dx,'Visible','off');
1737    set(handle_txtbox,'Visible','on')
1738    set(handle_txtbox,'String',filegrid)
1739else
1740    set(hObject,'Value',0);
1741    set(handle_dx,'Visible','on');
1742    set(handle_dy,'Visible','on');
1743    set(handle_title_dy,'Visible','on');
1744    set(handle_title_dx,'Visible','on');
1745    set(handle_txtbox,'Visible','off')
1746end
1747
1748%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
1749PanelName=get(hparent,'tag');
1750if strcmp(PanelName,'Civ1')
1751    hchildren=get(handles.Civ2,'children');
1752    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
1753    handle_txtbox=findobj(hchildren,'tag','Grid');
1754    handle_dx=findobj(hchildren,'tag','num_Dx');
1755    handle_dy=findobj(hchildren,'tag','num_Dy');
1756    handle_title_dx=findobj(hchildren,'tag','title_Dx');
1757    handle_title_dy=findobj(hchildren,'tag','title_Dy');
1758    set(handle_checkbox,'UserData',filegrid);%store for future use
1759    if testgrid
1760        set(handle_checkbox,'Value',1);
1761        set(handle_dx,'Visible','off');
1762        set(handle_dy,'Visible','off');
1763        set(handle_title_dx,'Visible','off');
1764        set(handle_title_dy,'Visible','off');
1765        set(handle_txtbox,'Visible','on')
1766        set(handle_txtbox,'String',filegrid)
1767    end
1768end
1769
1770%------------------------------------------------------------------------
1771% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
1772function CheckMask_Callback(hObject, eventdata, handles)
1773%------------------------------------------------------------------------
1774value=get(hObject,'Value');
1775hparent=get(hObject,'parent');
1776parent_tag=get(hparent,'Tag');
1777hchildren=get(hparent,'children');
1778handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
1779testmask=0;
1780if value
1781    filebase=get(handles.RootPath,'String');
1782    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
1783    if isequal(flag_mask,1)
1784        filemask=[num2str(nbslice) 'mask'];
1785        testmask=1;
1786    else % browse for a mask
1787        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
1788        if exist(filemask,'file')
1789            filebase=filemask;
1790        end
1791        [FileName, PathName] = uigetfile( ...
1792            {'*.png', ' (*.png)';
1793            '*.png',  '.png files '; ...
1794            '*.*', 'All Files (*.*)'}, ...
1795            'Pick a mask file *.png',filebase);
1796        filemask=fullfile(PathName,FileName);
1797        set(hObject,'UserData',filemask);%store for future use
1798        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
1799            testmask=1;
1800        end
1801    end
1802end
1803if testmask
1804    if strcmp(parent_tag,'Civ1')
1805        set(handles.Mask,'Visible','on')
1806        set(handles.Mask,'String',filemask)
1807    set(handles.CheckMask,'Value',1)
1808    end
1809else
1810    set(hObject,'Value',0);
1811    set(handle_txtbox,'Visible','off')
1812end
1813
1814%------------------------------------------------------------------------
1815% --- Executes on button press in get_gridpatch1.
1816function get_gridpatch1_Callback(hObject, eventdata, handles)
1817%------------------------------------------------------------------------
1818filebase=get(handles.RootPath,'String');
1819[FileName, PathName, filterindex] = uigetfile( ...
1820    {'*.grid', ' (*.grid)';
1821    '*.grid',  '.grid files '; ...
1822    '*.*', 'All Files (*.*)'}, ...
1823    'Pick a file',filebase);
1824filegrid=fullfile(PathName,FileName);
1825set(handles.grid_patch1,'string',filegrid);
1826
1827
1828%------------------------------------------------------------------------
1829% --- Executes on button press in get_gridpatch2.
1830function get_gridpatch2_Callback(hObject, eventdata, handles)
1831%------------------------------------------------------------------------
1832
1833
1834%------------------------------------------------------------------------
1835% --- STEREO Interp
1836function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
1837%------------------------------------------------------------------------
1838namelog=[filename_nc(1:end-3) '_stinterp.log'];
1839cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
1840    ' -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
1841
1842% %------------------------------------------------------------------------
1843% %--read images and convert them to the uint16 format used for PIV
1844% function A=read_image(filename,type_ima,num,movieobject)
1845% %------------------------------------------------------------------------
1846% %num is the view number needed for an avi movie
1847% switch type_ima
1848%     case 'movie'
1849%         A=read(movieobject,num);
1850%     case 'avi'
1851%         mov=aviread(filename,num);
1852%         A=frame2im(mov(1));
1853%     case 'multimage'
1854%         A=imread(filename,num);
1855%     case 'image'
1856%         A=imread(filename);
1857% end
1858% siz=size(A);
1859% if length(siz)==3;%color images
1860%     A=sum(double(A),3);
1861%     A=uint16(A);
1862% end
1863
1864
1865%------------------------------------------------------------------------
1866% --- Executes on button press in get_ref_fix1.
1867function get_ref_fix1_Callback(hObject, eventdata, handles)
1868%------------------------------------------------------------------------
1869filebase=get(handles.RootPath,'String');
1870[FileName, PathName, filterindex] = uigetfile( ...
1871    {'*.nc', ' (*.nc)';
1872    '*.nc',  'netcdf files '; ...
1873    '*.*', 'All Files (*.*)'}, ...
1874    'Pick a file',filebase);
1875
1876fileinput=[PathName FileName];
1877sizf=size(fileinput);
1878if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1879%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1880[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1881ref.filebase=fullfile(Path,File);
1882% ref.num_a=stra2num(str_a);
1883% ref.num_b=stra2num(str_b);
1884% ref.num1=str2double(field_count);
1885% ref.num2=str2double(str2);
1886browse=[];%initialisation
1887if ~isequal(ref.ext,'.nc')
1888    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1889    return
1890end
1891set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
1892set(handles.ref_fix1,'UserData',ref)
1893menu_field{1}='civ1';
1894Data=nc2struct(fileinput,[]);
1895if isfield(Data,'patch') && isequal(Data.patch,1)
1896    menu_field{2}='filter1';
1897end
1898if isfield(Data,'civ2') && isequal(Data.civ2,1)
1899    menu_field{3}='civ2';
1900end
1901if isfield(Data,'patch2') && isequal(Data.patch2,1)
1902    menu_field{4}='filter2';
1903end
1904set(handles.field_ref1,'String',menu_field);
1905set(handles.field_ref1,'Value',length(menu_field));
1906set(handles.num_MinVel,'Value',2);
1907set(handles.num_MinVel,'String','1');%default threshold
1908set(handles.ref_fix1,'Enable','on')
1909
1910%------------------------------------------------------------------------
1911% --- Executes on button press in get_ref_fix2.
1912function get_ref_fix2_Callback(hObject, eventdata, handles)
1913%------------------------------------------------------------------------
1914if isequal(get(handles.get_ref_fix2,'Value'),1)
1915    filebase=get(handles.RootPath,'String');
1916    [FileName, PathName, filterindex] = uigetfile( ...
1917        {'*.nc', ' (*.nc)';
1918        '*.nc',  'netcdf files '; ...
1919        '*.*', 'All Files (*.*)'}, ...
1920        'Pick a file',filebase);
1921    fileinput=[PathName FileName];
1922    sizf=size(fileinput);
1923    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1924    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1925    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1926    ref.filebase=fullfile(Path,File);
1927%     ref.num_a=stra2num(str_a);
1928%     ref.num_b=stra2num(str_b);
1929%     ref.num1=str2num(field_count);
1930%     ref.num2=str2num(str2);
1931    browse=[];%initialisation
1932    if ~isequal(ref.ext,'.nc')
1933        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1934        return
1935    end
1936    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
1937    set(handles.ref_fix2,'UserData',ref)
1938    menu_field{1}='civ1';
1939    Data=nc2struct(fileinput,[]);
1940    if isfield(Data,'patch') && isequal(Data.patch,1)
1941        menu_field{2}='filter1';
1942    end
1943    if isfield(Data,'civ2') && isequal(Data.civ2,1)
1944        menu_field{3}='civ2';
1945    end
1946    if isfield(Data,'patch2') && isequal(Data.patch2,1)
1947        menu_field{4}='filter2';
1948    end
1949    set(handles.field_ref2,'String',menu_field);
1950    set(handles.field_ref2,'Value',length(menu_field));
1951    set(handles.num_MinVel,'Value',2);
1952    set(handles.num_MinVel,'String','1');%default threshold
1953    set(handles.ref_fix2,'Enable','on')
1954    set(handles.ref_fix2,'Visible','on')
1955    set(handles.field_ref2,'Visible','on')
1956else
1957    set(handles.ref_fix2,'Visible','off')
1958    set(handles.field_ref2,'Visible','off')
1959end
1960
1961%------------------------------------------------------------------------
1962function ref_fix1_Callback(hObject, eventdata, handles)
1963%------------------------------------------------------------------------
1964set(handles.num_MinVel,'Value',1);
1965set(handles.field_ref1,'Value',1)
1966set(handles.field_ref1,'String',{' '})
1967set(handles.ref_fix1,'UserData',[]);
1968set(handles.ref_fix1,'String','');
1969set(handles.thresh_vel1,'String','0');
1970
1971%------------------------------------------------------------------------
1972function ref_fix2_Callback(hObject, eventdata, handles)
1973%------------------------------------------------------------------------
1974set(handles.num_MinVel,'Value',1);
1975set(handles.field_ref2,'Value',1)
1976set(handles.field_ref2,'String',{' '})
1977set(handles.ref_fix2,'UserData',[]);
1978set(handles.ref_fix2,'String','');
1979set(handles.num_MinVel,'String','0');
1980
1981%------------------------------------------------------------------------
1982% --- TO ABANDON Executes on button press in test_stereo1.
1983function CheckStereo_Callback(hObject, eventdata, handles)
1984%------------------------------------------------------------------------
1985hparent=get(hObject,'parent');
1986parent_tag=get(hparent,'Tag');
1987hchildren=get(hparent,'children');
1988handle_txtbox=findobj(hchildren,'tag','txt_Mask');
1989if isequal(get(hObject,'Value'),0)
1990    set(handles.num_SubDomainSize,'Visible','on')
1991    set(handles.num_FieldSmooth,'Visible','on')
1992else
1993    set(handles.num_SubDomainSize,'Visible','off')
1994    set(handles.num_FieldSmooth,'Visible','off')
1995end
1996
1997% %------------------------------------------------------------------------
1998% % --- Executes on button press in CheckStereo.
1999% function StereoCheck_Callback(hObject, eventdata, handles)
2000% %------------------------------------------------------------------------
2001% if isequal(get(handles.CheckStereo,'Value'),0)
2002%     set(handles.num_subdomainsize,'Visible','on')
2003%     set(handles.num_FieldSmooth,'Visible','on')
2004% else
2005%     set(handles.num_subdomainsize,'Visible','off')
2006%     set(handles.num_FieldSmooth,'Visible','off')
2007% end
2008
2009%------------------------------------------------------------------------
2010% --- Executes on button press in TestCiv1: prepare the image correlation function
2011% activated by mouse motion
2012function TestCiv1_Callback(hObject, eventdata, handles)
2013%------------------------------------------------------------------------
2014drawnow
2015if get(handles.TestCiv1,'Value')
2016    set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch
2017    ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
2018    if strcmp(get(handles.ref_j,'Visible'),'on')
2019        ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
2020    else
2021        ref_j=1;%default j index
2022    end
2023    [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
2024    Data.ListVarName={'ny','nx','A'};
2025    Data.VarDimName= {'ny','nx',{'ny','nx'}};
2026
2027    Data.A=imread(filecell.ima1.civ1{1}); % read the first image
2028    if ndims(Data.A)==3 %case of color image
2029        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
2030    end
2031    Data.ny=[size(Data.A,1) 1];
2032    Data.nx=[1 size(Data.A,2)];
2033    Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly
2034    par_civ1=read_GUI(handles.Civ1);
2035    par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1});
2036    par_civ1.ImageWidth=size(Data.A,2);
2037    par_civ1.ImageHeight=size(Data.A,1);
2038    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
2039    par_civ1.FrameIndexA=num2str(i1);
2040    par_civ1.FrameIndexB=num2str(i2);
2041    Param.Civ1=par_civ1;
2042    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
2043    hview_field=view_field(Data); %view the image in the GUI view_field
2044    set(0,'CurrentFigure',hview_field)
2045    hhview_field=guihandles(hview_field);
2046    set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
2047    ViewData=get(hview_field,'UserData');
2048    ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
2049    ViewData.PlotAxes.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
2050    ViewData.PlotAxes.X=Grid.Civ1_X; %keep the set of points in memeory
2051    ViewData.PlotAxes.Y=Grid.Civ1_Y;
2052    set(hview_field,'UserData',ViewData)
2053    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
2054    if isempty(corrfig)
2055        corrfig=figure;
2056        set(corrfig,'tag','corrfig')
2057        set(corrfig,'name','image correlation')
2058        set(corrfig,'DeleteFcn',{@closeview_field})%
2059    end
2060    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
2061else
2062    set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
2063    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
2064    if ~isempty(corrfig)
2065        delete(corrfig)
2066    end
2067    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
2068    if ~isempty(hview_field)
2069        delete(hview_field)
2070    end
2071end
2072
2073%------------------------------------------------------------------------
2074%----function introduced for the correlation window figure, activated by deleting this window
2075function closeview_field(gcbo,eventdata)
2076%------------------------------------------------------------------------
2077hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
2078if ~isempty(hview_field)
2079    delete(hview_field)
2080end
2081
2082%------------------------------------------------------------------------
2083% --- Executes on button press in CheckThreshold.
2084function CheckThreshold_Callback(hObject, eventdata, handles)
2085%------------------------------------------------------------------------
2086huipanel=get(hObject,'parent');
2087obj(1)=findobj(huipanel,'Tag','num_MinIma');
2088obj(2)=findobj(huipanel,'Tag','num_MaxIma');
2089obj(3)=findobj(huipanel,'Tag','title_Threshold');
2090if get(hObject,'Value')
2091    set(obj,'Visible','on')
2092else
2093    set(obj,'Visible','off')
2094end
2095
2096
2097
2098
2099%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
2100%---------------------------------------------------------------------
2101function NomTypeNc=nomtype2pair(NomTypeIma,mode)
2102%---------------------------------------------------------------------           
2103% OUTPUT:
2104% NomTypeNc
2105%---------------------------------------------------------------------
2106% INPUT:
2107% 'NomTypeIma': string defining the kind of nomenclature used for images
2108
2109NomTypeNc=NomTypeIma;%default
2110switch mode
2111    case 'pair j1-j2'     
2112    if ~isempty(regexp(NomTypeIma,'a$'))
2113        NomTypeNc=[NomTypeIma 'b'];
2114    elseif ~isempty(regexp(NomTypeIma,'A$'))
2115        NomTypeNc=[NomTypeIma 'B'];
2116    else
2117        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2118        if ~isempty(r)
2119            NomTypeNc='_1_1-2';
2120        end
2121    end
2122    case 'series(Dj)' 
2123%         r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2124%         if ~isempty(r)
2125            NomTypeNc='_1_1-2';
2126%         end
2127   case 'series(Di)'
2128        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2129        if ~isempty(r)
2130            NomTypeNc='_1-2_1';
2131        else
2132            NomTypeNc='_1-2';
2133        end
2134end
2135
2136% --- Executes on button press in TestPatch1.
2137function TestPatch1_Callback(hObject, eventdata, handles)
2138set(handles.TestPatch1,'BackgroundColor',[1 1 0])
2139drawnow
2140if get(handles.TestPatch1,'Value')
2141    ref_i=str2double(get(handles.ref_i,'String'));
2142    if strcmp(get(handles.ref_j,'Visible'),'on')
2143        ref_j=str2double(get(handles.ref_j,'String'));
2144    else
2145        ref_j=1;%default
2146    end
2147    filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);   
2148    Data.ListVarName={'ny','nx','A'};
2149    Data.VarDimName= {'ny','nx',{'ny','nx'}};   
2150    param_patch1=read_GUI(handles.Patch1);
2151    param_patch1.CivFile=filecell.nc.civ1{1};
2152    Param.Patch1=param_patch1;
2153    for irho=1:7
2154        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
2155        if ~isempty(errormsg)
2156            msgbox_uvmat('ERROR',errormsg)
2157            return
2158        end
2159        SmoothingParam(irho)=Param.Patch1.FieldSmooth;
2160        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
2161        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
2162        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
2163        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
2164        Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth;
2165    end
2166    figure
2167    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
2168    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
2169else
2170    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
2171    if ~isempty(corrfig)
2172        delete(corrfig)
2173    end
2174    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
2175    if ~isempty(hview_field)
2176        delete(hview_field)
2177    end
2178end
2179
2180
2181% --- Executes on button press in TestCiv2.
2182function TestCiv2_Callback(hObject, eventdata, handles)
2183
2184
2185
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