source: trunk/src/series/civ_input.m @ 1141

Last change on this file since 1141 was 1141, checked in by sommeria, 5 months ago

smoothig parameter renormalised in filter_tps

File size: 98.2 KB
Line 
1%'civ_input': function associated with the GUI 'civ_input.fig' to set the input parameters for civ_series
2%------------------------------------------------------------------------
3% function ParamOut = civ_input(Param)
4%
5% OUPUT:
6% ParamOut: Matlab structure containing the parameters set by the GUI civ_input
7%
8% INPUT:
9% Param: Matlab structure containing the input parameters set by the GUI
10
11%=======================================================================
12% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
13%   http://www.legi.grenoble-inp.fr
14%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
15%
16%     This file is part of the toolbox UVMAT.
17%
18%     UVMAT is free software; you can redistribute it and/or modify
19%     it under the terms of the GNU General Public License as published
20%     by the Free Software Foundation; either version 2 of the license,
21%     or (at your option) any later version.
22%
23%     UVMAT is distributed in the hope that it will be useful,
24%     but WITHOUT ANY WARRANTY; without even the implied warranty of
25%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
26%     GNU General Public License (see LICENSE.txt) for more details.
27%=======================================================================
28
29function varargout = civ_input(varargin)
30
31gui_Singleton = 1;
32gui_State = struct('gui_Name',       mfilename, ...
33    'gui_Singleton',  gui_Singleton, ...
34    'gui_OpeningFcn', @civ_input_OpeningFcn, ...
35    'gui_OutputFcn',  @civ_input_OutputFcn, ...
36    'gui_LayoutFcn',  [] , ...
37    'gui_Callback',   []);
38
39if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once'))
40        gui_State.gui_Callback = str2func(varargin{1});
41end
42
43if nargout
44    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
45else
46    gui_mainfcn(gui_State, varargin{:});
47end
48
49% End initialization code - DO NOT EDIT
50
51%------------------------------------------------------------------------
52% --- Executes just before civ_input is made visible.
53function civ_input_OpeningFcn(hObject, eventdata, handles, Param)
54%------------------------------------------------------------------------
55% This function has no output args, see OutputFcn.
56
57%% General settings
58handles.output = Param;
59guidata(hObject, handles); % Update handles structure
60set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
61set(hObject,'WindowKeyPressFcn',{@keyboard_callback,handles})%set keyboard action function
62set(handles.ref_i,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function
63set(handles.ref_j,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function
64hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
65hhseries=guidata(hseries); %handles of the elements in 'series'
66SeriesData=get(hseries,'UserData');% info stored in the GUI series
67
68%% set visibility options depending on the calling function (Param.Action.ActionName):
69if strcmp(Param.Action.ActionName,'civ_series')||strcmp(Param.Action.ActionName,'stereo_civ')
70     set(handles.num_MaxDiff,'Visible','on')
71    set(handles.num_MaxVel,'Visible','on')
72    set(handles.title_MaxVel,'Visible','on')
73    set(handles.title_MaxDiff,'Visible','on')
74    set(handles.num_Nx,'Visible','off')
75    set(handles.num_Ny,'Visible','off')
76    set(handles.title_Nx,'Visible','off')
77    set(handles.title_Ny,'Visible','off')
78    set(handles.num_CorrSmooth,'Style','popupmenu')
79    set(handles.num_CorrSmooth,'Value',1)
80    set(handles.num_CorrSmooth,'String',{'1';'2'})
81    set(handles.CheckThreshold,'Visible','on')
82    set(handles.CheckDeformation,'Value',0)% desactivate
83    set(handles.num_SubDomainSize(1),'String','250')
84    set(handles.num_SubDomainSize(2),'String','500')
85end
86switch Param.Action.ActionName
87    case 'stereo_civ'
88        set(handles.ListCompareMode,'Visible','off')
89        set(handles.PairIndices,'Visible','off')
90    case 'civ_series'
91        set(handles.ListCompareMode,'Visible','on')
92        set(handles.PairIndices,'Visible','on')
93end
94
95%% input file info
96NomTypeInput=Param.InputTable{1,4};
97FileType='image';%fdefault
98FileInfo=[];
99if isfield(SeriesData,'FileInfo')...
100    FileType=SeriesData.FileInfo{1}.FileType;% info on the first input file series
101    FieldType=SeriesData.FileInfo{1}.FieldType;% info on the first input file series
102else
103    set(hhseries.REFRESH,'BackgroundColor',[1 0 1])% indicate that the file input in series needs to be refreshed
104end
105
106%% case of netcdf file as input, read the processing stage and look for corresponding images
107ind_opening=0;%default
108NomTypeNc='';
109NomTypeImaA=NomTypeInput;
110iview_image=1;%line # for the input images
111switch FileType
112    case 'civdata'
113        if ~strcmp(Param.Action.ActionName,'civ_series')
114            msgbox_uvmat('ERROR','bad input data file: open an image or a nc file from civ_series')
115            return
116        end
117        NomTypeNc=NomTypeInput;
118        ind_opening=SeriesData.FileInfo{1}.CivStage;
119        if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
120            set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
121        else
122            set(handles.ListCompareMode,'Value',1)
123        end
124        [Data,tild,tild,errormsg]=nc2struct(SeriesData.FileInfo{1}.FileName,[]);
125        if ~isempty(errormsg)
126            msgbox_uvmat('ERROR',['error in netcdf input file: ' errormsg])
127            return
128        end
129        if isfield(Data,'.Civ1_ImageA')
130        [PathCiv1_ImageA,Civ1_ImageA,FileExtA]=fileparts(Data.Civ1_ImageA);%look for the source image A
131        [PathCiv1_ImageB,Civ1_ImageB,FileExtA]=fileparts(Data.Civ1_ImageB);%look for the source image B
132        end
133        if isfield(Data,'Civ2_ImageA')
134            [PathCiv2_ImageA,Civ2_ImageA,FileExtA]=fileparts(Data.Civ2_ImageA);
135            [PathCiv2_ImageB,Civ2_ImageB,FileExtA]=fileparts(Data.Civ2_ImageB);
136        end
137        if size(Param.InputTable,1)==1
138             if isfield(Data,'.Civ1_ImageA')
139            series('display_file_name',hhseries,Data.Civ1_ImageA,'append');%append the image series to the input list
140                    [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA);
141        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ1_ImageB);
142             else
143                 series('display_file_name',hhseries,Data.Civ2_ImageA,'append');%append the image series to the input list
144                         [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ2_ImageA);
145        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ2_ImageB);
146             end
147        end
148
149        iview_image=2;%line # for the input images
150    case 'civxdata'% case of  civx data,
151        msgbox_uvmat('ERROR','old civX convention, use the GUI civ')
152        return
153    otherwise
154        if ~strcmp(FieldType,'image')
155        msgbox_uvmat('ERROR','civ_series needs images, scalar fields in netcdf format, or civ data as input')
156        return
157        end
158end
159
160%% reinitialise menus
161set(handles.ListPairMode,'Value',1)
162set(handles.ListPairMode,'String',{''})
163set(handles.ListPairCiv1,'Value',1)
164set(handles.ListPairCiv1,'String',{''})
165set(handles.ListPairCiv2,'Value',1)
166set(handles.ListPairCiv2,'String',{''})
167       
168%% prepare the GUI with input parameters
169%
170set(handles.ref_i,'String',num2str(Param.IndexRange.first_i))
171if isfield(Param.IndexRange,'first_j')
172    set(handles.ref_j,'String',num2str(Param.IndexRange.first_j))
173end
174set(handles.ConfigSource,'String','\default')
175
176%%  set the menus of image pairs and default selection for civ_input   %%%%%%%%%%%%%%%%%%%
177
178%% display the min and max indices for the whole file series
179if isempty(Param.IndexRange.MaxIndex_i)|| isempty(Param.IndexRange.MinIndex_i)
180    msgbox_uvmat('ERROR','REFRESH the input files in the GUI series')
181     return
182end
183MaxIndex_i=Param.IndexRange.MaxIndex_i(iview_image);
184MinIndex_i=Param.IndexRange.MinIndex_i(iview_image);
185MaxIndex_j=1;%default
186MinIndex_j=1;
187if isfield(Param.IndexRange,'MaxIndex_j')&&isfield(Param.IndexRange,'MinIndex_j')...
188        && numel(Param.IndexRange.MaxIndex_j')>=iview_image &&numel(Param.IndexRange.MinIndex_j')>=iview_image
189    MaxIndex_j=Param.IndexRange.MaxIndex_j(iview_image);
190    MinIndex_j=Param.IndexRange.MinIndex_j(iview_image);
191end
192%update the bounds if possible
193if isfield(SeriesData,'i1_series')&&numel(SeriesData.i1_series)>=iview_image
194    if size(SeriesData.i1_series{iview_image},2)==2 && min(min(SeriesData.i1_series{iview_image}(:,1,:)))==0
195        MinIndex_j=1;% index j set to 1 by default
196        MaxIndex_j=1;
197        MinIndex_i=find(SeriesData.i1_series{iview_image}(1,2,:), 1 )-1;% min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index)
198        MaxIndex_i=find(SeriesData.i1_series{iview_image}(1,2,:),1,'last' )-1;%max ref index i detected in the series (corresponding to the last non-zero value of i1_series)
199    else
200        ref_i=squeeze(max(SeriesData.i1_series{iview_image}(1,:,:),[],2));% select ref_j index for each ref_i
201        ref_j=squeeze(max(SeriesData.j1_series{iview_image}(1,:,:),[],3));% select ref_i index for each ref_j
202        MinIndex_i=min(find(ref_i))-1;
203        MaxIndex_i=max(find(ref_i))-1;
204        MaxIndex_j=max(find(ref_j))-1;
205        MinIndex_j=min(find(ref_j))-1;
206    end
207end
208
209
210%%  transfer the time from the GUI series, or use file index by default
211time=[];
212TimeUnit='frame'; %default
213CoordUnit='';%default
214pxcm_search=1;
215if isfield(SeriesData,'Time') &&numel(SeriesData.Time')>=1 && ~isempty(SeriesData.Time{1})
216    time=SeriesData.Time{1};
217end
218if isfield(Param.IndexRange,'TimeUnit')&&~isempty(Param.IndexRange.TimeUnit)
219    TimeUnit=Param.IndexRange.TimeUnit;
220end
221if isfield(SeriesData,'GeometryCalib')
222    tsai=SeriesData.GeometryCalib;
223    if isfield(tsai,'fx_fy')
224        pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
225    end
226    if isfield(tsai,'CoordUnit')
227        CoordUnit=tsai.CoordUnit;
228    end
229end
230
231%% timing display
232%show the reference image edit box if relevant (not needed for movies or in the absence of time information
233if numel(time)>=2 % if there are at least two time values to define dt
234    if size(time,1)<MaxIndex_i;
235        msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
236    elseif size(time,2)<MaxIndex_j
237        msgbox_uvmat('WARNING','maximum j index restricted by the timing of the xml file');
238    end
239    MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data
240    MaxIndex_j=min(size(time,2),MaxIndex_j);
241    set(handles.TimeSource,'String',Param.IndexRange.TimeSource);
242else
243    set(handles.TimeSource,'String',''); %xml file not used for timing
244    TimeUnit='frame';
245    time=ones(MaxIndex_j-MinIndex_j+1,1)*(MinIndex_i:MaxIndex_i);
246    time=time+0.001*(MinIndex_j:MaxIndex_j)'*ones(1,MaxIndex_i-MinIndex_i+1);
247end
248CivInputData.Time=time;
249CivInputData.NomTypeIma=NomTypeImaA;
250set(handles.civ_input,'UserData',CivInputData)
251set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
252set(handles.TimeUnit,'String',TimeUnit);
253set(handles.SearchRange,'UserData', pxcm_search);
254
255
256%% set the civ_input options, depending on the input file content if a nc file has been opened
257ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
258checkbox=zeros(size(ListOptions));%default
259checkrefresh=0;
260if ind_opening==0  %case of image opening, start with Civ1
261    for index=1:numel(ListOptions)
262        checkbox(index)=get(handles.(ListOptions{index}),'Value');
263    end
264    index_max=find(checkbox, 1, 'last' );
265    if isempty(index_max),index_max=1;end
266    for index=1:index_max
267        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
268    end
269else  %case of netcdf file opening, start with the stage read in the file if the input file is being refreshed
270    if isequal(get(hhseries.REFRESH,'BackgroundColor'),[1 1 0]) &&...
271            ~(isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ConfigSource'))
272            for index = 1:min(ind_opening,5)
273                set(handles.(ListOptions{index}),'value',0)
274                fill_civ_input(Data,handles); %fill civ_input with the parameters retrieved from an input Civ file
275            end
276            set(handles.ConfigSource,'String',FileInfo.FileName);
277            set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
278            for index = ind_opening+2:6
279                set(handles.(ListOptions{index}),'value',0)
280            end
281            checkrefresh=1;
282    end
283    if ind_opening>=3
284        set(handles.CheckCiv3,'Visible','on')% make visible the switch 'iterate/repet' for Civ2.
285    else
286        set(handles.CheckCiv3,'Visible','off')
287    end
288end
289
290%% introduce the stored Civ parameters  if available (from previous input or ImportConfig in series)
291if ~checkrefresh && isfield(Param,'ActionInput')&& strcmp(Param.ActionInput.Program,Param.Action.ActionName)% the program fits with the stored data
292    fill_GUI(Param.ActionInput,hObject);%fill the GUI with the parameters retrieved from the input Param
293    hcheckgrid=findobj(handles.civ_input,'Tag','CheckGrid');
294    for ilist=1:numel(hcheckgrid)
295        if get(hcheckgrid(ilist),'Value')% if a grid is used, do not show Dx and Dy for an automatic grid
296            hparent=get(hcheckgrid(ilist),'parent');%handles of the parent panel
297            hchildren=get(hparent,'children');
298            handle_dx=findobj(hchildren,'tag','num_Dx');
299            handle_dy=findobj(hchildren,'tag','num_Dy');
300            handle_title_dx=findobj(hchildren,'tag','title_Dx');
301            handle_title_dy=findobj(hchildren,'tag','title_Dy');
302            set(handle_dx,'Visible','off');
303            set(handle_dy,'Visible','off');
304            set(handle_title_dy,'Visible','off');
305            set(handle_title_dx,'Visible','off');
306        end
307    end
308    if isfield(Param.ActionInput,'Civ2')
309        CheckDeformation_Callback(hObject, eventdata, handles)
310    end
311end
312if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ListCompareMode')&&...
313        strcmp(Param.ActionInput.ListCompareMode,'displacement')
314    set(handles.PairIndices,'Visible','off')
315        set(handles.CheckRefFile,'Visible','on')
316else
317    set(handles.CheckRefFile,'Visible','off')
318end
319
320%% set the menu and default choice of civ pairs
321if isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs
322    PairMenu={'series(Di)'};
323elseif MaxIndex_j-MinIndex_j==1
324    PairMenu={'pair j1-j2'};
325elseif  MaxIndex_i==MinIndex_i && MaxIndex_j-MinIndex_j>2% simple series in j
326    PairMenu={'pair j1-j2';'series(Dj)'};
327else
328    PairMenu={'pair j1-j2';'series(Dj)';'series(Di)'};%multiple choice
329end
330set(handles.ListPairMode,'String',PairMenu)
331
332%% set default choice of pair mode
333PairIndex=[];
334if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'PairIndices')
335    PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu));%retrieve the previous option
336end
337if isempty(PairIndex)
338    if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs
339        PairIndex=1;
340    elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
341        if  MaxIndex_j <= 10
342            PairIndex=1;% advice 'pair j1-j2' except in MaxIndex_j is large
343        end
344    else
345        if strcmp(NomTypeNc,'_1-2_1')
346            PairIndex=3;% advise 'series(Di)'
347        elseif  MaxIndex_j <= 10
348            PairIndex=1;% advice 'pair j1-j2' except in MaxIndex_j is large
349        else
350            PairIndex=2;% advice 'Dj'
351        end
352    end
353end
354set(handles.ListPairMode,'Value',PairIndex); 
355
356%% indicate the min and max indices i and j on the GUI
357set(handles.MinIndex_i,'String',num2str(MinIndex_i))
358set(handles.MaxIndex_i,'String',num2str(MaxIndex_i))
359set(handles.MinIndex_j,'String',num2str(MinIndex_j))
360set(handles.MaxIndex_j,'String',num2str(MaxIndex_j))
361
362%% set the reference indices from the input file indices
363if ~(isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ConfigSource'))
364update_CivOptions(handles,ind_opening)% fill the menu of possible pairs
365end
366
367%% list the possible index pairs, depending on the option set in ListPairMode
368ListPairMode_Callback([], [], handles)
369
370%% set the GUI to modal: wait for OK to close
371set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal
372drawnow
373uiwait(handles.civ_input);% wait for OK action to end the function
374
375
376%------------------------------------------------------------------------
377% --- Outputs from this function are returned to the command line.
378function varargout = civ_input_OutputFcn(hObject, eventdata, handles)
379%------------------------------------------------------------------------
380% Get default command line output from handles structure
381varargout{1}=[];% default output when civ_input is canceled (no 'OK')
382if ~isempty(handles)
383    varargout{1} = handles.output;
384    delete(handles.civ_input)
385end
386
387% --- Executes when user attempts to close get_field.
388function civ_input_CloseRequestFcn(hObject, eventdata, handles)
389if isequal(get(handles.get_field, 'waitstatus'), 'waiting')
390    % The GUI is still in UIWAIT, us UIRESUME
391    uiresume(handles.civ_input);
392else
393    % The GUI is no longer waiting, just close it
394    delete(handles.civ_input);
395end
396
397%------------------------------------------------------------------------
398% --- Executes on button press in SetDefaultParam.
399%------------------------------------------------------------------------
400function SetDefaultParam_Callback(hObject, eventdata, handles)
401
402Param.ConfigSource='\default';
403
404%% Civ1 parameters
405%Param.CheckCiv1=1;
406Param.Civ1.CorrBoxSize=[25 25];
407Param.Civ1.SearchBoxSize=[55 55];
408Param.Civ1.SearchBoxShift=[0 0];
409Param.Civ1.CorrSmooth=1;
410Param.Civ1.Dx=20;
411Param.Civ1.Dy=20;
412Param.Civ1.CheckGrid=0;
413Param.Civ1.CheckMask=0;
414Param.Civ1.Mask='';
415Param.Civ1.CheckThreshold=0;
416Param.Civ1.TestCiv1=0;
417
418%% Fix1 parameters
419%Param.CheckFix1=1;
420Param.Fix1.CheckFmin2=1;
421Param.Fix1.CheckF3=1;
422Param.Fix1.MinCorr=0.2000;
423
424%% Patch1 parameters
425%Param.CheckPatch1=1;
426Param.Patch1.FieldSmooth=10;
427Param.Patch1.MaxDiff=1.5000;
428Param.Patch1.SubDomainSize=250;
429Param.Patch1.TestPatch1=0;
430
431%% Civ2 parameters
432%Param.CheckCiv2=1;
433Param.Civ2.CorrBoxSize=[21 21];
434Param.Civ2.SearchBoxSize=[27 27];
435Param.Civ2.CorrSmooth=1;
436Param.Civ2.Dx=10;
437Param.Civ2.Dy=10;
438Param.Civ2.CheckGrid=0;
439Param.Civ2.CheckMask=0;
440Param.Civ2.Mask='';
441Param.Civ2.CheckThreshold=0;
442Param.Civ2.TestCiv2=0;
443
444%% Fix2 parameters
445%Param.CheckFix2=1;
446Param.Fix2.CheckFmin2=1;
447Param.Fix2.CheckF4=1;
448Param.Fix2.CheckF3=1;
449Param.Fix2.MinCorr=0.2000;
450
451%% Patch2 parameters
452%Param.CheckPatch2=1;
453Param.Patch2.FieldSmooth=2;
454Param.Patch2.MaxDiff=1.5000;
455Param.Patch2.SubDomainSize=500;
456Param.Patch2.TestPatch2=0;
457
458fill_GUI(Param,handles.civ_input)% fill the elements of the GUI series with the input parameters
459update_CivOptions(handles,0)
460
461% -----------------------------------------------------------------------
462% -----------------------------------------------------------------------
463% --- Open the help html file
464function MenuHelp_Callback(hObject, eventdata, handles)
465% -----------------------------------------------------------------------
466web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#Civ')
467
468%------------------------------------------------------------------------
469% --- Executes on carriage return on the subdir checkciv1 edit window
470function Civ1_ImageB_Callback(hObject, eventdata, handles)
471%------------------------------------------------------------------------
472SubDir=get(handles.Civ1_ImageB,'String');
473menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
474ichoice=find(strcmp(SubDir,menu_str),1);
475if isempty(ichoice)
476    ilist=numel(menu_str); %select 'new...' in the menu
477else
478    ilist=ichoice;
479end
480set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
481if get(handles.CheckCiv1,'Value')% if Civ1 is performed
482    set(handles.Civ2_ImageA,'String',SubDir);% set by default civ2 directory the same as civ1
483%     set(handles.ListSubdirCiv2,'Value',ilist)
484else % if Civ1 data already exist
485    errormsg=find_netcpair_civ(handles,1); %update the list of available index pairs in the new directory
486    if ~isempty(errormsg)
487    msgbox_uvmat('ERROR',errormsg)
488    end
489end
490
491%------------------------------------------------------------------------
492% --- Executes on carriage return on the SubDir checkciv1 edit window
493function Civ2_ImageA_Callback(hObject, eventdata, handles)
494%------------------------------------------------------------------------
495SubDir=get(handles.Civ1_ImageB,'String');
496menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
497ichoice=find(strcmp(SubDir,menu_str),1);
498if isempty(ichoice)
499    ilist=numel(menu_str); %select 'new...' in the menu
500else
501    ilist=ichoice;
502end
503set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
504%update the list of available pairs from netcdf files in the new directory
505if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
506    errormsg=find_netcpair_civ(handles,2);
507        if ~isempty(errormsg)
508    msgbox_uvmat('ERROR',errormsg)
509    end
510end
511
512%------------------------------------------------------------------------
513% --- Executes on button press in CheckCiv1.
514function CheckCiv1_Callback(hObject, eventdata, handles)
515%------------------------------------------------------------------------
516update_CivOptions(handles,0)
517
518%------------------------------------------------------------------------
519% --- Executes on button press in CheckFix1.
520function CheckFix1_Callback(hObject, eventdata, handles)
521%------------------------------------------------------------------------
522update_CivOptions(handles,0)
523
524%------------------------------------------------------------------------
525% --- Executes on button press in CheckPatch1.
526function CheckPatch1_Callback(hObject, eventdata, handles)
527%------------------------------------------------------------------------
528update_CivOptions(handles,0)
529
530%------------------------------------------------------------------------
531% --- Executes on button press in CheckCiv2.
532function CheckCiv2_Callback(hObject, eventdata, handles)
533%------------------------------------------------------------------------
534update_CivOptions(handles,0)
535
536%------------------------------------------------------------------------
537% --- Executes on button press in CheckFix2.
538function CheckFix2_Callback(hObject, eventdata, handles)
539%------------------------------------------------------------------------
540update_CivOptions(handles,0)
541
542%------------------------------------------------------------------------
543% --- Executes on button press in CheckPatch2.
544function CheckPatch2_Callback(hObject, eventdata, handles)
545%------------------------------------------------------------------------
546update_CivOptions(handles,0)
547
548%------------------------------------------------------------------------
549% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
550function update_CivOptions(handles,opening)
551%------------------------------------------------------------------------
552if opening>0
553    set(handles.CheckCiv2,'UserData',opening)% store the info on the current status of the civ processing
554end
555checkbox=zeros(1,6);
556checkbox(1)=get(handles.CheckCiv1,'Value');
557checkbox(2)=get(handles.CheckFix1,'Value');
558checkbox(3)=get(handles.CheckPatch1,'Value');
559checkbox(4)=get(handles.CheckCiv2,'Value');
560checkbox(5)=get(handles.CheckFix2,'Value');
561checkbox(6)=get(handles.CheckPatch2,'Value');
562if opening==0
563    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
564    if ~isempty(errormsg)
565        msgbox_uvmat('ERROR',errormsg)
566    end
567end
568if max(checkbox(4:6))>0% case of civ2 pair choice needed
569    set(handles.TitlePairCiv2,'Visible','on')
570    set(handles.ListPairCiv2,'Visible','on')
571    if ~opening
572        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
573        if ~isempty(errormsg)
574            msgbox_uvmat('ERROR',errormsg)
575        end
576    end
577else
578    set(handles.ListPairCiv2,'Visible','off')
579end
580hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
581hhseries=guidata(hseries); %handles of the elements in 'series'
582InputTable=get(hhseries.InputTable,'Data');
583if size(InputTable,1)>=1 && strcmp(InputTable{1,5},'.nc') && max(checkbox(1:3))==0 %&& get(handles.CheckCiv2,'UserData')==6,% no operation asked before Civ2 and input file ready for civ3
584    set(handles.CheckCiv3,'Visible','on')
585else
586    set(handles.CheckCiv3,'Visible','off')
587end
588
589%% set the visibility of the different panels
590options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
591for ilist=1:length(options)
592    if checkbox(ilist)
593        set(handles.(options{ilist}),'Visible','on')
594    else
595        set(handles.(options{ilist}),'Visible','off')
596    end
597end
598
599%------------------------------------------------------------------------
600% --- Executes on button press in OK: processing on local computer
601function OK_Callback(hObject, eventdata, handles)
602%------------------------------------------------------------------------
603
604ActionInput=read_GUI(handles.civ_input);% read the infos on the GUI civ_input
605
606%% correct input inconsistencies
607if isfield(ActionInput,'Civ1')
608    checkeven=(mod(ActionInput.Civ1.CorrBoxSize,2)==0);
609    ActionInput.Civ1.CorrBoxSize(checkeven)=ActionInput.Civ1.CorrBoxSize(checkeven)+1;% set correlation box sizes to odd values
610    ActionInput.Civ1.SearchBoxSize=max(ActionInput.Civ1.SearchBoxSize,ActionInput.Civ1.CorrBoxSize+8);% insure that the search box size is large enough
611    checkeven=(mod(ActionInput.Civ1.SearchBoxSize,2)==0);
612    ActionInput.Civ1.SearchBoxSize(checkeven)=ActionInput.Civ1.SearchBoxSize(checkeven)+1;% set search box sizes to odd values
613end
614if isfield(ActionInput,'Civ2')
615    checkeven=(mod(ActionInput.Civ2.CorrBoxSize,2)==0);
616    ActionInput.Civ2.CorrBoxSize(checkeven)=ActionInput.Civ2.CorrBoxSize(checkeven)+1;% set correlation box sizes to odd values
617    ActionInput.Civ2.SearchBoxSize=max(ActionInput.Civ2.SearchBoxSize,ActionInput.Civ2.CorrBoxSize+4);
618    checkeven=(mod(ActionInput.Civ2.SearchBoxSize,2)==0);
619    ActionInput.Civ2.SearchBoxSize(checkeven)=ActionInput.Civ2.SearchBoxSize(checkeven)+1;% set search box sizes to odd values
620end
621
622%% correct mask or grid name for Windows system (replace '\' by '/')
623if isfield(ActionInput,'Civ1')
624    if isfield(ActionInput.Civ1,'Mask')
625        ActionInput.Civ1.Mask=regexprep(ActionInput.Civ1.Mask,'\','/');
626    end
627    if isfield(ActionInput.Civ1,'Grid')
628        ActionInput.Civ1.Grid=regexprep(ActionInput.Civ1.Grid,'\','/');
629    end
630end
631if isfield(ActionInput,'Civ2')
632    if isfield(ActionInput.Civ2,'Mask')
633        ActionInput.Civ2.Mask=regexprep(ActionInput.Civ2.Mask,'\','/');
634    end
635    if isfield(ActionInput.Civ2,'Grid')
636        ActionInput.Civ2.Grid=regexprep(ActionInput.Civ2.Grid,'\','/');
637    end
638end
639
640%% exit the GUI and close it
641handles.output.ActionInput=ActionInput;
642guidata(hObject, handles);% Update handles structure
643uiresume(handles.civ_input);
644
645
646%------------------------------------------------------------------------
647% --- Executes on button press in ListCompareMode.
648function ListCompareMode_Callback(hObject, eventdata, handles)
649%------------------------------------------------------------------------
650ListCompareMode=get(handles.ListCompareMode,'String');
651option=ListCompareMode{get(handles.ListCompareMode,'Value')};
652hseries=findobj(allchild(0),'Tag','series');
653SeriesData=get(hseries,'UserData');
654check_nc=strcmp(SeriesData.FileType{1},'.nc');
655ImageType=SeriesData.FileType(2:end);
656if check_nc
657    ImageType=SeriesData.FileType(2:end);
658else
659    ImageType=SeriesData.FileType;
660end
661hhseries=guidata(hseries);
662InputTable=get(hhseries.InputTable,'Data');
663OriginIndex='off';
664PairIndices='off';
665switch option
666    case 'PIV'
667        PairIndices='on';% needs to define index pairs for PIV       
668    case 'PIV volume'
669        PairIndices='on';% needs to define index pairs for PIV
670        set(handles.ListPairMode,'Value',1)
671        set(handles.ListPairMode,'String',{'series(Di)'})
672        ListPairMode_Callback(hObject, eventdata, handles)
673    case 'displacement'
674        OriginIndex='on';%define a frame origin for displacement
675end
676set(handles.num_OriginIndex,'Visible',OriginIndex)
677set(handles.OriginIndex_title,'Visible',OriginIndex)
678set(handles.CheckRefFile,'Visible',OriginIndex)
679set(handles.RefFile,'Visible',OriginIndex)
680set(handles.PairIndices,'Visible',PairIndices)
681ListPairMode_Callback(hObject,eventdata,handles)
682if strcmp(OriginIndex,'on')
683    set(handles.CheckRefFile,'Value',1)
684    CheckRefFile_Callback(hObject,eventdata,handles)
685end
686       
687
688
689%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
690% Callbacks in the uipanel Pair Indices
691%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
692%------------------------------------------------------------------------
693% --- Executes on button press in ListPairMode.
694function ListPairMode_Callback(hObject, eventdata, handles)
695%------------------------------------------------------------------------
696compare_list=get(handles.ListCompareMode,'String');
697val=get(handles.ListCompareMode,'Value');
698compare=compare_list{val};
699if strcmp(compare,'displacement')||strcmp(compare,'shift')
700    mode_selected='displacement';
701else
702    mode_list=get(handles.ListPairMode,'String');
703    if ischar(mode_list)
704        mode_list={mode_list};
705    end 
706    mode_value=get(handles.ListPairMode,'Value');
707    if isempty(mode_value)
708        mode_value=1;
709    end
710    mode_selected=mode_list{mode_value};
711end
712ref_i=str2double(get(handles.ref_i,'String'));
713CivInputData=get(handles.civ_input,'UserData');
714TimeUnit=get(handles.TimeUnit,'String');
715checkframe=strcmp(TimeUnit,'frame');
716time=CivInputData.Time;
717siztime=size(CivInputData.Time);
718nbfield=siztime(1)-1;
719nbfield2=siztime(2)-1;
720%indchosen=1;  %%first pair selected by default
721% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
722% are relative to the reference indices ref_i and ref_j respectively.
723if isequal(mode_selected,'pair j1-j2')
724    dt=1;
725    index=0;
726    numlist_a=[];
727    numlist_B=[];
728    %get all the time intervals in bursts
729    displ_dt=1;%default
730    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
731    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
732        for numod_b=(numod_a+1):nbfield2
733            index=index+1;
734            numlist_a(index)=numod_a;
735            numlist_b(index)=numod_b;
736            if size(time,2)>1 && ~checkframe && size(CivInputData.Time,1)>ref_i && size(CivInputData.Time,2)>numod_b
737                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
738                displ_dt(index)=dt(numod_a,numod_b);
739            else
740                displ_dt(index)=1;
741            end
742        end
743    end
744    [dtsort,indsort]=sort(displ_dt);
745    enable_j(handles, 'off')
746elseif isequal(mode_selected,'series(Dj)') %| isequal(mode,'st_series(Dj)')
747    enable_j(handles, 'on')
748elseif isequal(mode_selected,'series(Di)') %| isequal(mode,'st_series(Di)')
749    enable_i(handles, 'on')
750    if nbfield2 > 1
751        enable_j(handles, 'on')
752    else
753        enable_j(handles, 'off')
754    end
755elseif isequal(mode_selected,'displacement')%the pairs have the same indices
756    if nbfield > 1 || nbfield==0
757        enable_i(handles, 'on')
758    else
759        enable_j(handles, 'off')
760    end
761    if nbfield2 > 1
762        enable_j(handles, 'on')
763    else
764        enable_j(handles, 'off')
765    end
766end
767errormsg=find_netcpair_civ( handles,1);
768if ~isempty(errormsg)
769    msgbox_uvmat('ERROR',errormsg)
770end
771
772%------------------------------------------------------------------------
773function enable_i(handles, state)
774set(handles.itext,'Visible',state)
775set(handles.MaxIndex_i,'Visible',state)
776set(handles.ref_i,'Visible',state)
777
778%------------------------------------------------------------------------
779function enable_j(handles, state)
780set(handles.jtext,'Visible',state)
781set(handles.MinIndex_j,'Visible',state)
782set(handles.MaxIndex_j,'Visible',state)
783set(handles.ref_j,'Visible',state)
784
785%------------------------------------------------------------------------
786% --- Executes on selection change in ListPairCiv1.
787function ListPairCiv1_Callback(hObject, eventdata, handles)
788%------------------------------------------------------------------------
789%reproduce by default the chosen pair in the checkciv2 menu
790list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
791PairString=list_pair{get(handles.ListPairCiv1,'Value')};
792
793[ind1,ind2]=...
794    find_pair_indices(PairString);
795hseries=findobj(allchild(0),'Tag','series');
796hhseries=guidata(hseries);
797set(hhseries.num_first_j,'String',num2str(ind1));
798set(hhseries.num_last_j,'String',num2str(ind2));
799set(hhseries.num_incr_j,'String',num2str(ind2-ind1));
800set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))%civ2 selection the same as civ& by default
801
802
803%------------------------------------------------------------------------
804% --- Executes on selection change in ListPairCiv2.
805function ListPairCiv2_Callback(hObject, eventdata, handles)
806%------------------------------------------------------------------------
807
808
809%------------------------------------------------------------------------
810function ref_i_Callback(hObject, eventdata, handles)
811%------------------------------------------------------------------------
812mode_list=get(handles.ListPairMode,'String');
813mode_value=get(handles.ListPairMode,'Value');
814mode_selected=mode_list{mode_value};
815errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
816if isequal(mode_selected,'series(Di)') || ...% we do patch2 only
817        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
818    errormsg=find_netcpair_civ( handles,2);
819end
820if isempty(errormsg)
821    set(handles.ref_i,'BackgroundColor',[1 1 1])
822    set(handles.ref_j,'BackgroundColor',[1 1 1])
823else
824    msgbox_uvmat('ERROR',errormsg)
825end
826
827function ref_i_KeyPressFcn(hObject, eventdata, handles)
828set(hObject,'BackgroundColor',[1 0 1])
829       
830% %------------------------------------------------------------------------
831
832function errormsg=find_netcpair_civ(handles,index)
833%------------------------------------------------------------------------
834set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
835
836%% initialisation
837errormsg='';
838CivInputData=get(handles.civ_input,'UserData');
839compare_list=get(handles.ListCompareMode,'String');
840val=get(handles.ListCompareMode,'Value');
841compare=compare_list{val};
842mode_selected='displacement';
843if ~strcmp(compare,'displacement')%||strcmp(compare,'shift')
844 
845    mode_list=get(handles.ListPairMode,'String');
846    mode_value=get(handles.ListPairMode,'Value');
847    if isempty(mode_value)
848        mode_value=1;
849    end
850    if isempty(mode_list)
851        return
852    end
853    mode_selected=mode_list{mode_value};
854end
855nom_type_ima=CivInputData.NomTypeIma;
856menu_pair=get(handles.ListPairCiv1,'String');%previous menu of ListPairCiv1
857PairCiv1Init=menu_pair{get(handles.ListPairCiv1,'Value')};%previous choice of pair
858menu_pair=get(handles.ListPairCiv2,'String');%previous menu of ListPairCiv1
859PairCiv2Init=menu_pair{get(handles.ListPairCiv2,'Value')};%previous choice of pair
860
861%% reads .nc subdirectoy and image numbers from the interface
862%SubDirImages=get(handles.Civ1_ImageA,'String');
863%TODO: determine
864%subdir_civ1=[SubDirImages get(handles.Civ1_ImageB,'String')];%subdirectory subdir_civ1 for the netcdf data
865%subdir_civ2=[SubDirImages get(handles.Civ2_ImageA,'String')];%subdirectory subdir_civ2 for the netcdf data
866ref_i=str2double(get(handles.ref_i,'String'));
867ref_j=[];
868if isequal(mode_selected,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
869    ref_j=0;
870elseif strcmp(get(handles.ref_j,'Visible'),'on')
871    ref_j=str2double(get(handles.ref_j,'String'));
872end
873if isempty(ref_j)
874    ref_j=1;
875end
876CivInputData=get(handles.civ_input,'UserData');
877TimeUnit=get(handles.TimeUnit,'String');
878Time=CivInputData.Time;
879checkframe=strcmp(TimeUnit,'frame');
880
881%% case with no Civ1 operation, netcdf files need to exist for reading
882displ_pair={''};
883nbpair=200;%default
884select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
885
886%% determine the menu display in .ListPairCiv1
887switch mode_selected
888    case 'series(Di)'
889        for ipair=1:nbpair
890            if select(ipair)
891                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
892                displ_pair_dt{ipair}=displ_pair{ipair};
893                if ~checkframe
894                    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
895                        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
896                        displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(dt*1000)];
897                    end
898                else
899                    dt=ipair/1000;
900                    displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(ipair)];
901                end
902            else
903                displ_pair{ipair}='...';
904                displ_pair_dt{ipair}='...'; %pair not displayed in the menu
905            end
906        end
907    case 'series(Dj)'
908        for ipair=1:nbpair
909            if select(ipair)
910                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
911                displ_pair_dt{ipair}=displ_pair{ipair};
912                if ~checkframe
913                    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
914                        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
915                        displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(dt*1000)];
916                    end
917                else
918                    dt=ipair/1000;
919                    displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(dt*1000)];
920                end
921            else
922                displ_pair{ipair}='...'; %pair not displayed in the menu
923                displ_pair_dt{ipair}='...'; %pair not displayed in the menu
924            end
925        end
926    case 'pair j1-j2'%case of pairs
927        MinIndex_j=str2num(get(handles.MinIndex_j,'String'));
928        MaxIndex_j=str2num(get(handles.MaxIndex_j,'String'));
929        index_pair=0;
930        %get all the Time intervals in bursts
931        displ_pair_dt='';
932        for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode
933            for numod_b=(numod_a+1):MaxIndex_j
934                index_pair=index_pair+1;
935                displ_pair{index_pair}=['j= ' num2stra(numod_a,nom_type_ima) '-' num2stra(numod_b,nom_type_ima)];
936                displ_pair_dt{index_pair}=displ_pair{index_pair};
937                dt(index_pair)=numod_b-numod_a;%default dt
938                if size(Time,1)>ref_i && size(Time,2)>numod_b  % && ~checkframe
939                    dt(index_pair)=Time(ref_i+1,numod_b+1)-Time(ref_i+1,numod_a+1);% Time interval dt
940                    displ_pair_dt{index_pair}=[displ_pair_dt{index_pair} ' :dt= ' num2str(dt(index_pair)*1000)];
941                end
942            end
943           
944        end
945        if index_pair ~=0
946        [tild,indsort]=sort(dt);
947        displ_pair=displ_pair(indsort);
948        displ_pair_dt=displ_pair_dt(indsort);
949        end
950    case 'displacement'
951%         displ_pair={'Di=Dj=0'};
952%         displ_pair_dt={'Di=Dj=0'};
953        set(handles.PairIndices,'Visible','off')
954end
955if index==1 && ~strcmp(mode_selected,'displacement')
956    set(handles.ListPairCiv1,'String',displ_pair_dt');
957end
958
959%% determine the default selection in the pair menu for Civ1
960%ichoice=find(select,1);% index of first selected pair
961%if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
962end_pair=regexp(PairCiv1Init,' :dt=');
963if ~isempty(end_pair)
964    PairCiv1Init=PairCiv1Init(1:end_pair-1);
965end
966ichoice=find(strcmp(PairCiv1Init,displ_pair'),1);
967if ~isempty(ichoice)
968    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
969else
970   set(handles.ListPairCiv1,'Value',1)
971end
972
973%% determine the default selection in the pair menu for Civ2
974if ~strcmp(mode_selected,'displacement')
975if strcmp(get(handles.ListPairCiv2,'Visible'),'on')
976    end_pair=regexp(PairCiv2Init,' :dt=');
977    if ~isempty(end_pair)
978        PairCiv2Init=PairCiv2Init(1:end_pair-1);
979    end
980    ichoice=find(strcmp(PairCiv2Init,displ_pair'),1);
981    if ~isempty(ichoice)
982        set(handles.ListPairCiv2,'Value',ichoice);% first valid pair proposed by default in the menu
983    else
984        set(handles.ListPairCiv2,'Value',1)
985    end
986else
987    set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))% initiate the choice of Civ2 as a reproduction of if civ1
988end
989set(handles.ListPairCiv2,'String',displ_pair_dt');
990end
991set(gcf,'Pointer','arrow')% Indicate that the process is finished
992
993
994%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
995% Callbacks in the uipanel Reference Indices
996%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
997%------------------------------------------------------------------------
998function MinIndex_i_Callback(hObject, eventdata, handles)
999%------------------------------------------------------------------------
1000first_i=str2double(get(handles.MinIndex_i,'String'));
1001set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
1002ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
1003
1004% %------------------------------------------------------------------------
1005% function MinIndex_j_Callback(hObject, eventdata, handles)
1006% %------------------------------------------------------------------------
1007% first_j=str2num(get(handles.MinIndex_j,'String'));
1008% set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
1009% ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
1010
1011%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1012% Callbacks in the uipanel Civ1
1013%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1014%------------------------------------------------------------------------
1015% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
1016function SearchRange_Callback(hObject, eventdata, handles)
1017%------------------------------------------------------------------------
1018%determine pair numbers
1019if strcmp(get(handles.num_UMin,'Visible'),'off')
1020    set(handles.u_title,'Visible','on')
1021    set(handles.v_title,'Visible','on')
1022    set(handles.num_UMin,'Visible','on')
1023    set(handles.num_UMax,'Visible','on')
1024    set(handles.num_VMin,'Visible','on')
1025    set(handles.num_VMax,'Visible','on')
1026    %set(handles.CoordUnit,'Visible','on')
1027    %set(handles.TimeUnit,'Visible','on')
1028    %set(handles.slash_title,'Visible','on')
1029    set(handles.min_title,'Visible','on')
1030    set(handles.max_title,'Visible','on')
1031    set(handles.unit_title,'Visible','on')
1032else
1033    get_search_range(hObject, eventdata, handles)
1034end
1035
1036%------------------------------------------------------------------------
1037% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
1038function get_search_range(hObject, eventdata, handles)
1039%------------------------------------------------------------------------
1040param_civ1=read_GUI(handles.Civ1);
1041umin=param_civ1.UMin;
1042umax=param_civ1.UMax;
1043vmin=param_civ1.VMin;
1044vmax=param_civ1.VMax;
1045%switch min_title and max_title in case of error
1046if umax<=umin
1047    umin_old=umin;
1048    umin=umax;
1049    umax=umin_old;
1050    set(handles.num_UMin,'String', num2str(umin))
1051    set(handles.num_UMax,'String', num2str(umax))
1052end
1053if vmax<=vmin
1054    vmin_old=vmin;
1055    vmin=vmax;
1056    vmax=vmin_old;
1057    set(handles.num_VMin,'String', num2str(vmin))
1058    set(handles.num_VMax,'String', num2str(vmax))
1059end   
1060if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
1061    shiftx=round((umin+umax)/2);
1062    shifty=round((vmin+vmax)/2);
1063    isx=(umax+2-shiftx)*2+param_civ1.CorrBoxSize(1);
1064    isx=2*ceil(isx/2)+1;
1065    isy=(vmax+2-shifty)*2+param_civ1.CorrBoxSize(2);
1066    isy=2*ceil(isy/2)+1;
1067    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
1068    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
1069    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
1070    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
1071end
1072
1073%------------------------------------------------------------------------
1074% --- Executes on selection in menu CorrSmooth.
1075function num_CorrSmooth_Callback(hObject, eventdata, handles)
1076set(handles.ConfigSource,'String','NEW')
1077set(handles.OK,'BackgroundColor',[1 0 1])
1078%------------------------------------------------------------------------
1079
1080% --- Executes on button press in CheckDeformation.
1081function CheckDeformation_Callback(hObject, eventdata, handles)
1082set(handles.ConfigSource,'String','NEW')
1083set(handles.OK,'BackgroundColor',[1 0 1])
1084handles_CoorSmooth=findobj(get(handles.Civ2,'children'),'Tag','num_CorrSmooth');
1085if get(handles.CheckDeformation,'Value')   
1086    set(handles_CoorSmooth,'Visible','off')
1087else
1088    set(handles_CoorSmooth,'Visible','on')
1089end
1090
1091%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1092% Callbacks in the uipanel Fix1
1093%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1094%------------------------------------------------------------------------
1095% % --- Executes on button press in CheckMask.
1096% function get_mask_fix1_Callback(hObject, eventdata, handles)
1097% %------------------------------------------------------------------------
1098% maskval=get(handles.CheckMask,'Value');
1099% if isequal(maskval,0)
1100%     set(handles.Mask,'String','')
1101% else
1102%     mask_displ='no mask'; %default
1103%     filebase=get(handles.RootPath,'String');
1104%     [nbslice, flag_mask]=get_mask(filebase,handles);
1105%     if isequal(flag_mask,1)
1106%         mask_displ=[num2str(nbslice) 'mask'];
1107%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1108%         filebase_a=get(handles.RootFile_1,'String');
1109%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1110%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1111%             mask_displ='no mask';
1112%         end
1113%     end
1114%     if isequal(mask_displ,'no mask')
1115%         [FileName, PathName, filterindex] = uigetfile( ...
1116%             {'*.png', ' (*.png)';
1117%             '*.png',  '.png files '; ...
1118%             '*.*', 'All Files (*.*)'}, ...
1119%             'Pick a mask file *.png',filebase);
1120%         mask_displ=fullfile(PathName,FileName);
1121%         if ~exist(mask_displ,'file')
1122%             mask_displ='no mask';
1123%         end
1124%     end
1125%     if isequal(mask_displ,'no mask')
1126%         set(handles.CheckMask,'Value',0)
1127%         set(handles.CheckMask,'Value',0)
1128%         set(handles.CheckMask,'Value',0)
1129%     else
1130%         %set(handles.CheckMask,'Value',1)
1131%         set(handles.CheckMask,'Value',1)
1132%     end
1133%     set(handles.Mask,'String',mask_displ)
1134%     set(handles.Mask,'String',mask_displ)
1135%     set(handles.Mask,'String',mask_displ)
1136% end
1137
1138%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1139% Callbacks in the uipanel Civ2
1140%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1141%------------------------------------------------------------------------
1142% --- Executes on button press in CheckMask: select box for mask option
1143function get_mask_civ2_Callback(hObject, eventdata, handles)
1144%------------------------------------------------------------------------
1145maskval=get(handles.CheckMask,'Value');
1146if isequal(maskval,0)
1147    set(handles.Mask,'String','')
1148else
1149    mask_displ='no mask'; %default
1150    filebase=get(handles.RootPath,'String');
1151    [nbslice, flag_mask]=get_mask(filebase,handles);
1152    if isequal(flag_mask,1)
1153        mask_displ=[num2str(nbslice) 'mask'];
1154    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1155        filebase_a=get(handles.RootFile_1,'String');
1156        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1157        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1158            mask_displ='no mask';
1159        end
1160    end
1161    if isequal(mask_displ,'no mask')
1162        [FileName, PathName, filterindex] = uigetfile( ...
1163            {'*.png', ' (*.png)';
1164            '*.png',  '.png files '; ...
1165            '*.*', 'All Files (*.*)'}, ...
1166            'Pick a mask file *.png',filebase);
1167        mask_displ=fullfile(PathName,FileName);
1168        if ~exist(mask_displ,'file')
1169            mask_displ='no mask';
1170        end
1171    end
1172    if isequal(mask_displ,'no mask')
1173        set(handles.CheckMask,'Value',0)
1174        set(handles.CheckMask,'Value',0)
1175    else
1176        set(handles.CheckMask,'Value',1)
1177    end
1178    set(handles.Mask,'String',mask_displ)
1179end
1180
1181% %------------------------------------------------------------------------
1182% % --- Executes on button press in CheckMask.
1183% function get_mask_fix2_Callback(hObject, eventdata, handles)
1184% %------------------------------------------------------------------------
1185% maskval=get(handles.CheckMask,'Value');
1186% if isequal(maskval,0)
1187%     set(handles.Mask,'String','')
1188% else
1189%     mask_displ='no mask'; %default
1190%     filebase=get(handles.RootPath,'String');
1191%     [nbslice, flag_mask]=get_mask(filebase,handles);
1192%     if isequal(flag_mask,1)
1193%         mask_displ=[num2str(nbslice) 'mask'];
1194%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1195%         filebase_a=get(handles.RootFile_1,'String');
1196%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1197%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1198%             mask_displ='no mask';
1199%         end
1200%     end
1201%     if isequal(mask_displ,'no mask')
1202%         [FileName, PathName, filterindex] = uigetfile( ...
1203%             {'*.png', ' (*.png)';
1204%             '*.png',  '.png files '; ...
1205%             '*.*', 'All Files (*.*)'}, ...
1206%             'Pick a mask file *.png',filebase);
1207%         mask_displ=fullfile(PathName,FileName);
1208%         if ~exist(mask_displ,'file')
1209%             mask_displ='no mask';
1210%         end
1211%     end
1212%     if isequal(mask_displ,'no mask')
1213%         set(handles.CheckMask,'Value',0)
1214%     end
1215%     set(handles.Mask,'String',mask_displ)
1216% end
1217
1218%------------------------------------------------------------------------
1219% --- function called to look for mask files
1220function [nbslice, flag_mask]=get_mask(filebase,handles)
1221%------------------------------------------------------------------------
1222%detect mask files, images with appropriate file base
1223%[filebase '_' xx 'mask'], xx=nbslice
1224%flag_mask=1 indicates detection
1225
1226flag_mask=0;%default
1227nbslice=1;
1228
1229% subdir=get(handles.Civ1_ImageB,'String');
1230[Path,Name]=fileparts(filebase);
1231if ~isdir(Path)
1232    msgbox_uvmat('ERROR','no path for input files')
1233    return
1234end
1235% currentdir=pwd;
1236% cd(Path);%move in the dir of the root name filebase
1237maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
1238% cd(currentdir);%come back to the current working directory
1239if ~isempty(maskfiles)
1240    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
1241    % else
1242    flag_mask=1;
1243    maskname=maskfiles(1).name;% take the first mask file in the list
1244    [Path2,Name,ext]=fileparts(maskname);
1245    Namedouble=double(Name);
1246    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1247    ind_mask=findstr('mask',Name);
1248    i=ind_mask-1;
1249    while val(i)==0 && i>0
1250        i=i-1;
1251    end
1252    nbslice=str2double(Name(i+1:ind_mask-1));
1253    if ~isnan(nbslice) && Name(i)=='_'
1254        flag_mask=1;
1255    else
1256        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
1257        return
1258        nbslice=1;
1259    end
1260end
1261
1262%------------------------------------------------------------------------
1263% --- function called to look for grid files
1264function [nbslice, flag_grid]=get_grid(filebase,handles)
1265%------------------------------------------------------------------------
1266flag_grid=0;%default
1267nbslice=1;
1268[Path,Name]=fileparts(filebase);
1269currentdir=pwd;
1270cd(Path);%move in the dir of the root name filebase
1271gridfiles=dir([Name '_*grid_*.grid']);%look for grid files
1272cd(currentdir);%come back to the current working directory
1273if ~isempty(gridfiles)
1274    flag_grid=1;
1275    gridname=gridfiles(1).name;% take the first grid file in the list
1276    [Path2,Name,ext]=fileparts(gridname);
1277    Namedouble=double(Name);
1278    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1279    ind_grid=findstr('grid',Name);
1280    i=ind_grid-1;
1281    while val(i)==0 && i>0
1282        i=i-1;
1283    end
1284    nbslice=str2double(Name(i+1:ind_grid-1));
1285    if ~isnan(nbslice) && Name(i)=='_'
1286        flag_grid=1;
1287    else
1288        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
1289        return
1290        nbslice=1;
1291    end
1292end
1293
1294%------------------------------------------------------------------------
1295% --- transform numbers to letters
1296function str=num2stra(num,nom_type)
1297%------------------------------------------------------------------------
1298if isempty(nom_type)
1299    str='';
1300elseif strcmp(nom_type(end),'a')
1301    str=char(96+num);
1302elseif strcmp(nom_type(end),'A')
1303    str=char(96+num);
1304elseif isempty(nom_type(2:end))%a single index
1305    str='';
1306else
1307    str=num2str(num);
1308end
1309
1310% %------------------------------------------------------------------------
1311% % --- Executes on button press in ListSubdirCiv1.
1312% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
1313% %------------------------------------------------------------------------
1314% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
1315% val=get(handles.ListSubdirCiv1,'Value');
1316% SubDir=list_subdir_civ1{val};
1317% if strcmp(SubDir,'new...')
1318%     if get(handles.CheckCiv1,'Value')
1319%         SubDir='CIV_INPUT'; %default subdirectory
1320%     else
1321%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new civ_input operation')
1322%         return
1323%     end   
1324% end
1325% set(handles.Civ1_ImageB,'String',SubDir);
1326% errormsg=find_netcpair_civ(handles,1);
1327% if ~isempty(errormsg)
1328%     msgbox_uvmat('ERROR',errormsg)
1329% end
1330%     
1331%------------------------------------------------------------------------
1332% % --- Executes on button press in ListSubdirCiv2.
1333% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
1334% %------------------------------------------------------------------------
1335% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
1336% val=get(handles.ListSubdirCiv2,'Value');
1337% SubDir=list_subdir_civ2{val};
1338% if strcmp(SubDir,'new...')
1339%     if get(handles.CheckCiv2,'Value')
1340%         SubDir='CIV_INPUT'; %default subdirectory
1341%     else
1342%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new civ_input operation')
1343%         return
1344%     end
1345% end
1346% set(handles.Civ2_ImageA,'String',SubDir);
1347
1348%------------------------------------------------------------------------
1349% --- Executes on button press in CheckGrid.
1350function CheckGrid_Callback(hObject, eventdata, handles)
1351%------------------------------------------------------------------------
1352value=get(hObject,'Value');
1353hparent=get(hObject,'parent');%handles of the parent panel
1354hchildren=get(hparent,'children');
1355handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
1356handle_dx=findobj(hchildren,'tag','num_Dx');
1357handle_dy=findobj(hchildren,'tag','num_Dy');
1358handle_title_dx=findobj(hchildren,'tag','title_Dx');
1359handle_title_dy=findobj(hchildren,'tag','title_Dy');
1360testgrid=0;
1361filegrid='';
1362if value
1363        hseries=findobj(allchild(0),'Tag','series');
1364    hhseries=guidata(hseries);
1365    InputTable=get(hhseries.InputTable,'Data');
1366     ind_A=1;% line index of the (first) image series
1367    if strcmp(InputTable{1,5},'.nc');
1368        ind_A=2;
1369    end
1370    filebase=InputTable{ind_A,1};
1371    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
1372    if isequal(flag_grid,1)
1373        filegrid=[num2str(nbslice) 'grid'];
1374        testgrid=1;
1375    else % browse for a grid
1376        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
1377        if exist(filegrid,'file')
1378            filebase=filegrid;
1379        end
1380       filegrid = uigetfile_uvmat('pick a grid file .grid:',filebase,'.grid');
1381        set(hObject,'UserData',filegrid);%store for future use
1382        if ~isempty(filegrid)
1383            testgrid=1;
1384        end
1385        set(hObject,'UserData',filegrid);%store for future use
1386    end
1387end
1388if testgrid
1389    set(handle_dx,'Visible','off');
1390    set(handle_dy,'Visible','off');
1391    set(handle_title_dy,'Visible','off');
1392    set(handle_title_dx,'Visible','off');
1393    set(handle_txtbox,'Visible','on')
1394    set(handle_txtbox,'String',filegrid)
1395else
1396    set(hObject,'Value',0);
1397    set(handle_dx,'Visible','on');
1398    set(handle_dy,'Visible','on');
1399    set(handle_title_dy,'Visible','on');
1400    set(handle_title_dx,'Visible','on');
1401    set(handle_txtbox,'Visible','off')
1402end
1403
1404%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
1405PanelName=get(hparent,'tag');
1406if strcmp(PanelName,'Civ1')
1407    hchildren=get(handles.Civ2,'children');
1408    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
1409    handle_txtbox=findobj(hchildren,'tag','Grid');
1410    handle_dx=findobj(hchildren,'tag','num_Dx');
1411    handle_dy=findobj(hchildren,'tag','num_Dy');
1412    handle_title_dx=findobj(hchildren,'tag','title_Dx');
1413    handle_title_dy=findobj(hchildren,'tag','title_Dy');
1414    set(handle_checkbox,'UserData',filegrid);%store for future use
1415    if testgrid
1416        set(handle_checkbox,'Value',1);
1417        set(handle_dx,'Visible','off');
1418        set(handle_dy,'Visible','off');
1419        set(handle_title_dx,'Visible','off');
1420        set(handle_title_dy,'Visible','off');
1421        set(handle_txtbox,'Visible','on')
1422        set(handle_txtbox,'String',filegrid)
1423    end
1424end
1425set(handles.ConfigSource,'String','NEW')
1426set(handles.OK,'BackgroundColor',[1 0 1])
1427
1428%------------------------------------------------------------------------
1429% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
1430function CheckMask_Callback(hObject, eventdata, handles)
1431%------------------------------------------------------------------------
1432value=get(hObject,'Value');
1433hparent=get(hObject,'parent');
1434parent_tag=get(hparent,'Tag');
1435hchildren=get(hparent,'children');
1436handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
1437handle_NbSlice=findobj(hchildren,'tag','num_NbSlice');% look for the mask name box in the same panel
1438testmask=0;
1439if value
1440    hseries=findobj(allchild(0),'Tag','series');
1441    hhseries=guidata(hseries);
1442    InputTable=get(hhseries.InputTable,'Data');
1443    ind_A=1;% line index of the (first) image series
1444    if strcmp(InputTable{1,5},'.nc');
1445        ind_A=2;
1446    end
1447 % browse for a mask
1448        filemask= uigetfile_uvmat('pick a mask image file:',InputTable{ind_A,1},'image');
1449        [FilePath,FileName,Ext]=fileparts(filemask);   
1450        [RootPath,SubDir,RootFile,i1_series,i2,j1,j2,NomType]=find_file_series(FilePath,[FileName,Ext]);
1451        if strcmp(NomType,'_1')
1452           NbSlice=i1_series(1,2,end);
1453           set(handles.num_NbSlice,'String',num2str(NbSlice))
1454        end
1455        set(hObject,'UserData',filemask);%store for future use
1456        if ~isempty(filemask)
1457            testmask=1;
1458        end
1459end
1460if testmask
1461    set(handles.Mask,'Visible','on')
1462    set(handles.Mask,'String',filemask)
1463    set(handles.CheckMask,'Value',1)
1464    if strcmp(NomType,'_1')
1465        set(handles.num_NbSlice,'Visible','on')
1466    end
1467else
1468    set(hObject,'Value',0);
1469    set(handle_txtbox,'Visible','off')
1470    set(handles.num_NbSlice,'Visible','off')
1471end
1472set(handles.ConfigSource,'String','NEW')
1473set(handles.ConfigSource,'BackgroundColor',[1 0 1])
1474
1475% %------------------------------------------------------------------------
1476% % --- Executes on button press in get_gridpatch1.
1477% function get_gridpatch1_Callback(hObject, eventdata, handles)
1478% %------------------------------------------------------------------------
1479% filebase=get(handles.RootPath,'String');
1480% [FileName, PathName, filterindex] = uigetfile( ...
1481%     {'*.grid', ' (*.grid)';
1482%     '*.grid',  '.grid files '; ...
1483%     '*.*', 'All Files (*.*)'}, ...
1484%     'Pick a file',filebase);
1485% filegrid=fullfile(PathName,FileName);
1486% set(handles.grid_patch1,'string',filegrid);
1487% set(hObject,'BackgroundColor',[1 0 1])
1488
1489%------------------------------------------------------------------------
1490% --- STEREO Interp
1491function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
1492%------------------------------------------------------------------------
1493namelog=[filename_nc(1:end-3) '_stinterp.log'];
1494cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
1495    ' -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
1496
1497% %------------------------------------------------------------------------
1498% %--read images and convert them to the uint16 format used for PIV
1499% function A=read_image(filename,type_ima,num,movieobject)
1500% %------------------------------------------------------------------------
1501% %num is the view number needed for an avi movie
1502% switch type_ima
1503%     case 'movie'
1504%         A=read(movieobject,num);
1505%     case 'avi'
1506%         mov=aviread(filename,num);
1507%         A=frame2im(mov(1));
1508%     case 'multimage'
1509%         A=imread(filename,num);
1510%     case 'image'
1511%         A=imread(filename);
1512% end
1513% siz=size(A);
1514% if length(siz)==3;%color images
1515%     A=sum(double(A),3);
1516%     A=uint16(A);
1517% end
1518
1519
1520%------------------------------------------------------------------------
1521% --- Executes on button press in get_ref_fix1.
1522function get_ref_fix1_Callback(hObject, eventdata, handles)
1523%------------------------------------------------------------------------
1524filebase=get(handles.RootPath,'String');
1525[FileName, PathName, filterindex] = uigetfile( ...
1526    {'*.nc', ' (*.nc)';
1527    '*.nc',  'netcdf files '; ...
1528    '*.*', 'All Files (*.*)'}, ...
1529    'Pick a file',filebase);
1530
1531fileinput=[PathName FileName];
1532sizf=size(fileinput);
1533if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1534%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1535[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1536ref.filebase=fullfile(Path,File);
1537% ref.num_a=stra2num(str_a);
1538% ref.num_b=stra2num(str_b);
1539% ref.num1=str2double(field_count);
1540% ref.num2=str2double(str2);
1541browse=[];%initialisation
1542if ~isequal(ref.ext,'.nc')
1543    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1544    return
1545end
1546set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
1547set(handles.ref_fix1,'UserData',ref)
1548menu_field{1}='civ1';
1549Data=nc2struct(fileinput,[]);
1550if isfield(Data,'patch') && isequal(Data.patch,1)
1551    menu_field{2}='filter1';
1552end
1553if isfield(Data,'civ2') && isequal(Data.civ2,1)
1554    menu_field{3}='civ2';
1555end
1556if isfield(Data,'patch2') && isequal(Data.patch2,1)
1557    menu_field{4}='filter2';
1558end
1559set(handles.field_ref1,'String',menu_field);
1560set(handles.field_ref1,'Value',length(menu_field));
1561set(handles.num_MinVel,'Value',2);
1562set(handles.num_MinVel,'String','1');%default threshold
1563set(handles.ref_fix1,'Enable','on')
1564
1565%------------------------------------------------------------------------
1566% --- Executes on button press in get_ref_fix2.
1567function get_ref_fix2_Callback(hObject, eventdata, handles)
1568%------------------------------------------------------------------------
1569if isequal(get(handles.get_ref_fix2,'Value'),1)
1570    filebase=get(handles.RootPath,'String');
1571    [FileName, PathName, filterindex] = uigetfile( ...
1572        {'*.nc', ' (*.nc)';
1573        '*.nc',  'netcdf files '; ...
1574        '*.*', 'All Files (*.*)'}, ...
1575        'Pick a file',filebase);
1576    fileinput=[PathName FileName];
1577    sizf=size(fileinput);
1578    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1579    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1580    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1581    ref.filebase=fullfile(Path,File);
1582    %     ref.num_a=stra2num(str_a);
1583    %     ref.num_b=stra2num(str_b);
1584    %     ref.num1=str2num(field_count);
1585    %     ref.num2=str2num(str2);
1586    browse=[];%initialisation
1587    if ~isequal(ref.ext,'.nc')
1588        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1589        return
1590    end
1591    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
1592    set(handles.ref_fix2,'UserData',ref)
1593    menu_field{1}='civ1';
1594    Data=nc2struct(fileinput,[]);
1595    if isfield(Data,'patch') && isequal(Data.patch,1)
1596        menu_field{2}='filter1';
1597    end
1598    if isfield(Data,'civ2') && isequal(Data.civ2,1)
1599        menu_field{3}='civ2';
1600    end
1601    if isfield(Data,'patch2') && isequal(Data.patch2,1)
1602        menu_field{4}='filter2';
1603    end
1604    set(handles.field_ref2,'String',menu_field);
1605    set(handles.field_ref2,'Value',length(menu_field));
1606    set(handles.num_MinVel,'Value',2);
1607    set(handles.num_MinVel,'String','1');%default threshold
1608    set(handles.ref_fix2,'Enable','on')
1609    set(handles.ref_fix2,'Visible','on')
1610    set(handles.field_ref2,'Visible','on')
1611else
1612    set(handles.ref_fix2,'Visible','off')
1613    set(handles.field_ref2,'Visible','off')
1614end
1615
1616%------------------------------------------------------------------------
1617function ref_fix1_Callback(hObject, eventdata, handles)
1618%------------------------------------------------------------------------
1619set(handles.num_MinVel,'Value',1);
1620set(handles.field_ref1,'Value',1)
1621set(handles.field_ref1,'String',{' '})
1622set(handles.ref_fix1,'UserData',[]);
1623set(handles.ref_fix1,'String','');
1624set(handles.thresh_vel1,'String','0');
1625
1626%------------------------------------------------------------------------
1627function ref_fix2_Callback(hObject, eventdata, handles)
1628%------------------------------------------------------------------------
1629set(handles.num_MinVel,'Value',1);
1630set(handles.field_ref2,'Value',1)
1631set(handles.field_ref2,'String',{' '})
1632set(handles.ref_fix2,'UserData',[]);
1633set(handles.ref_fix2,'String','');
1634set(handles.num_MinVel,'String','0');
1635
1636%------------------------------------------------------------------------
1637% --- TO ABANDON Executes on button press in test_stereo1.
1638function CheckStereo_Callback(hObject, eventdata, handles)
1639%------------------------------------------------------------------------
1640hparent=get(hObject,'parent');
1641parent_tag=get(hparent,'Tag');
1642hchildren=get(hparent,'children');
1643handle_txtbox=findobj(hchildren,'tag','txt_Mask');
1644if isequal(get(hObject,'Value'),0)
1645    set(handles.num_SubDomainSize,'Visible','on')
1646    set(handles.num_FieldSmooth,'Visible','on')
1647else
1648    set(handles.num_SubDomainSize,'Visible','off')
1649    set(handles.num_FieldSmooth,'Visible','off')
1650end
1651
1652% %------------------------------------------------------------------------
1653% % --- Executes on button press in CheckStereo.
1654% function StereoCheck_Callback(hObject, eventdata, handles)
1655% %------------------------------------------------------------------------
1656% if isequal(get(handles.CheckStereo,'Value'),0)
1657%     set(handles.num_subdomainsize,'Visible','on')
1658%     set(handles.num_FieldSmooth,'Visible','on')
1659% else
1660
1661%     set(handles.num_subdomainsize,'Visible','off')
1662%     set(handles.num_FieldSmooth,'Visible','off')
1663% end
1664
1665
1666
1667%------------------------------------------------------------------------
1668%----function introduced for the correlation window figure, activated by deleting this window
1669function closeview_field(gcbo,eventdata)
1670%------------------------------------------------------------------------
1671hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1672if ~isempty(hview_field)
1673    delete(hview_field)
1674end
1675
1676%------------------------------------------------------------------------
1677% --- Executes on button press in CheckThreshold.
1678function CheckThreshold_Callback(hObject, eventdata, handles)
1679%------------------------------------------------------------------------
1680huipanel=get(hObject,'parent');
1681obj(1)=findobj(huipanel,'Tag','num_MinIma');
1682obj(2)=findobj(huipanel,'Tag','num_MaxIma');
1683obj(3)=findobj(huipanel,'Tag','title_Threshold');
1684if get(hObject,'Value')
1685    set(obj,'Visible','on')
1686else
1687    set(obj,'Visible','off')
1688end
1689set(handles.ConfigSource,'String','NEW')
1690set(handles.OK,'BackgroundColor',[1 0 1])
1691%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1692%%%%%%%%%%%%%%   TEST functions
1693%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1694%------------------------------------------------------------------------
1695% --- Executes on button press in TestCiv1: prepare the image correlation function
1696%     activated by mouse motion
1697function TestCiv1_Callback(hObject, eventdata, handles)
1698%------------------------------------------------------------------------
1699drawnow
1700if get(handles.TestCiv1,'Value')
1701    set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch 
1702    set(handles.CheckFix1,'value',0)% desactivate next step
1703    set(handles.CheckPatch1,'value',0)% desactivate next step
1704    set(handles.CheckCiv2,'value',0)% desactivate next step
1705    set(handles.CheckFix2,'value',0)% desactivate next step
1706    set(handles.CheckPatch2,'value',0)% desactivate next step
1707    update_CivOptions(handles,0)
1708      hseries=findobj(allchild(0),'Tag','series');
1709     Param=read_GUI(hseries);
1710     Param.Action.RUN=1;
1711     Param.ActionInput=read_GUI(handles.civ_input);
1712     if isfield(Param.ActionInput,'Fix1')
1713         Param.ActionInput=rmfield(Param.ActionInput,'Fix1');
1714     end
1715     if isfield(Param.ActionInput,'Patch1')
1716         Param.ActionInput=rmfield(Param.ActionInput,'Patch1');
1717     end
1718     if isfield(Param.ActionInput,'Civ2')%remove options that may be selected beyond Patch1
1719         Param.ActionInput=rmfield(Param.ActionInput,'Civ2');
1720     end
1721     if isfield(Param.ActionInput,'Fix2')
1722         Param.ActionInput=rmfield(Param.ActionInput,'Fix2');
1723     end
1724     if isfield(Param.ActionInput,'Patch2')
1725         Param.ActionInput=rmfield(Param.ActionInput,'Patch2');
1726     end
1727     if isfield(Param,'OutputSubDir')
1728     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1729     end
1730     Param.ActionInput.Civ1.CorrSmooth=0;% launch Civ1 with no data point (to get the image names for A and B)
1731     Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
1732     Param.IndexRange.last_i=str2num(get(handles.ref_i,'String'));
1733     if strcmp(get(handles.ref_j,'Visible'),'on')
1734         Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
1735         Param.IndexRange.last_j=Param.IndexRange.first_j;
1736     else
1737         Param.IndexRange.first_j=1;
1738         Param.IndexRange.last_j=1;
1739     end
1740     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1741     if ~isempty(errormsg), return, end % rmq: error msg displayed in civ_series
1742     
1743 %% create image data ImageData for display
1744     ImageData.ListVarName={'ny','nx','A'};
1745     ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
1746     ImageData.VarAttribute{1}.Role='coord_y';
1747     ImageData.VarAttribute{2}.Role='coord_x';
1748     ImageData.VarAttribute{3}.Role='scalar';
1749     ImageData.A=imread(Data.Civ1_ImageA); % read the first image
1750     if ndims(ImageData.A)==3 %case of color image
1751         ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
1752     end
1753     ImageData.ny=[size(ImageData.A,1) 1];
1754     ImageData.nx=[1 size(ImageData.A,2)];
1755     ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
1756
1757     %% create the figure view_field for image visualization
1758     hview_field=view_field(ImageData); %view the image in the GUI view_field
1759     set(0,'CurrentFigure',hview_field)
1760     hhview_field=guihandles(hview_field);
1761     set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
1762     ViewData=get(hview_field,'UserData');
1763     ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
1764     ViewData.PlotAxes.X=Data.Civ1_X';
1765     ViewData.PlotAxes.Y=Data.Civ1_Y';
1766     ViewData.PlotAxes.B=imread(Data.Civ1_ImageB);%store the second image in the UserData of the GUI view_field
1767     set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field
1768   
1769    %% look for a current figure for image correlation display
1770    corrfig=findobj(allchild(0),'tag','corrfig');
1771    if isempty(corrfig)
1772        corrfig=figure;
1773        set(corrfig,'tag','corrfig')
1774        set(corrfig,'name','image correlation')
1775        set(corrfig,'DeleteFcn',{@closeview_field})%
1776        set(handles.TestCiv1,'BackgroundColor',[1 0 0])
1777    else
1778        set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
1779        corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1780        if ~isempty(corrfig)
1781            delete(corrfig)
1782        end
1783        hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1784        if ~isempty(hview_field)
1785            delete(hview_field)
1786        end
1787    end
1788else
1789    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
1790    if ~isempty(hview_field)
1791        delete(hview_field)
1792    end     
1793end
1794
1795% --------------------------------------------------------------------
1796% --- Executes on button press in TestPatch1.
1797% --------------------------------------------------------------------
1798function TestPatch1_Callback(hObject, eventdata, handles)
1799msgbox_uvmat('WARNING','open the civ file and run "series/test_patch_tps" ')
1800
1801% if get(handles.TestPatch1,'Value')% if TestPatch1 is activated
1802%     hseries=findobj(allchild(0),'Tag','series');
1803%     Param=read_GUI(hseries);
1804%     CivDir=fullfile(Param.OutputPath,Param.Experiment,Param.Device,[Param.OutputSubDir Param.OutputDirExt]);
1805%     % ListXml=dir(CivXmlDir);
1806%     if exist(CivDir,'dir')
1807%         CivFile=uigetfile_uvmat('pick .nc file with civ1-fix1 data',CivDir,'.nc');
1808%         [Field,VelTypeOut,errormsg]=read_civdata(CivFile)
1809%         for ilist=1:numel(Field.ListGlobalAttribute)
1810%             r=regexp(Field.ListGlobalAttribute{ilist},'Civ1_(?<field>.+)','names');% \D = not a digit, \d =digi
1811%             if ~isempty(r)
1812%                 ParamTest.Civ1.(r.field)=(Field.(['Civ1_' r.field]));
1813%             end
1814%             r=regexp(Field.ListGlobalAttribute{ilist},'Fix1_(?<field>.+)','names');% \D = not a digit, \d =digi
1815%             if ~isempty(r)
1816%                 ParamTest.Fix1.(r.field)=(Field.(['Fix1_' r.field]));
1817%             end
1818%         end
1819%         fill_GUI(ParamTest,handles.civ_input)% fill the elements of the GUI series with the input parameters
1820%         drawnow
1821%         update_CivOptions(handles,0)
1822%
1823%         set(handles.TestPatch1,'BackgroundColor',[1 1 0])%paint TestPatch1 button in yellow to indicate activation
1824% %         set(handles.Civ1,'BackgroundColor',[1 1 0])% indicate civ1 calculation is performed
1825%         Param.Action.RUN=1;
1826%          Param.ActionInput=read_GUI(handles.civ_input);
1827%          Param.ActionInput.CheckCiv1=0;% do not repeat Civ1 computation       
1828%         if isfield(Param.ActionInput,'Civ2')%remove options that may be selected beyond Patch1
1829%             Param.ActionInput=rmfield(Param.ActionInput,'Civ2');
1830%         end
1831%         if isfield(Param.ActionInput,'Fix2')
1832%             Param.ActionInput=rmfield(Param.ActionInput,'Fix2');
1833%         end
1834%         if isfield(Param.ActionInput,'Patch2')
1835%             Param.ActionInput=rmfield(Param.ActionInput,'Patch2');
1836%         end
1837%         if isfield(Param,'OutputSubDir')
1838%             Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1839%         end
1840%         ParamPatch1=Param.ActionInput.Patch1; %store the patch1 parameters
1841%         Param.ActionInput=rmfield(Param.ActionInput,'Patch1');% does not execute Patch
1842%         Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
1843%         Param.IndexRange.last_i=Param.IndexRange.first_i;
1844%         if strcmp(get(handles.ref_j,'Visible'),'on')
1845%             Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
1846%             Param.IndexRange.last_j=Param.IndexRange.first_j;
1847%         else
1848%             Param.IndexRange.first_j=1;
1849%             Param.IndexRange.last_j=1;
1850%         end
1851%         [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1852%         bckcolor=get(handles.civ_input,'Color');
1853%         set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calculation is finished
1854%
1855%         %% prepare Param for iterative Patch processing without input file reading
1856%         Param.Civ1_X=Data.Civ1_X;
1857%         Param.Civ1_Y=Data.Civ1_Y;
1858%         Param.Civ1_U=Data.Civ1_U;
1859%         Param.Civ1_V=Data.Civ1_V;
1860%         Param.Civ1_FF=Data.Civ1_FF;
1861%         Param=rmfield(Param,'InputTable');%desactivate input file reading
1862%         if isfield(Param.ActionInput,'Civ1')
1863%             Param.ActionInput=rmfield(Param.ActionInput,'Civ1');%desactivate civ1: remove civ1 input param if relevant
1864%         end
1865%         if isfield(Param.ActionInput,'Fix1')
1866%             Param.ActionInput=rmfield(Param.ActionInput,'Fix1');%desactivate fix1:remove fix1 input param if relevant
1867%         end
1868%         SmoothingParam=(ParamPatch1.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
1869%         NbGood=numel(find(Data.Civ1_FF==0));
1870%         NbExclude=zeros(1,7);% initialize the set of smoothing parameters
1871%         DiffVel=zeros(1,7);% initialize the rms difference between patch and civ
1872%         Param.ActionInput.Patch1=ParamPatch1;% retrieve Patch1 parameters
1873%         for irho=1:7
1874%             Param.ActionInput.Patch1.FieldSmooth=SmoothingParam(irho);
1875%             [Data,errormsg]= civ_series(Param);%apply the processing fct
1876%             if ~isempty(errormsg)
1877%                 msgbox_uvmat('ERROR',errormsg)
1878%                 return
1879%             end
1880%             ind_good=find(Data.Civ1_FF==0);
1881%             Civ1_U_Diff=Data.Civ1_U(ind_good)-Data.Civ1_U_smooth(ind_good);
1882%             Civ1_V_Diff=Data.Civ1_V(ind_good)-Data.Civ1_V_smooth(ind_good);
1883%             DiffVel(irho)=sqrt(mean(Civ1_U_Diff.*Civ1_U_Diff+Civ1_V_Diff.*Civ1_V_Diff));
1884%             NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
1885%         end
1886%         figure(1)
1887%         semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r',SmoothingParam,0.2*ones(size(SmoothingParam)),'m')
1888%         grid on
1889%         legend('rms velocity diff. Patch1-Civ1 (pixels)','proportion of excluded vectors (between 0 to 1)','recommended diff Patch1-Civ1')
1890%         xlabel('smoothing parameter')
1891%         ylabel('smoothing effect')
1892%         set(handles.TestPatch1,'BackgroundColor',[0 1 0])
1893%     else
1894%         corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1895%         if ~isempty(corrfig)
1896%             delete(corrfig)
1897%         end
1898%         hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1899%         if ~isempty(hview_field)
1900%             delete(hview_field)
1901%         end
1902%     end
1903% else
1904%     msgbox_uvmat('ERROR','no output file: first perform a civ1-fix1 computation')
1905%     return
1906% end
1907 
1908%------------------------------------------------------------------------
1909% --- Executes on button press in TestCiv2.
1910%------------------------------------------------------------------------
1911function TestCiv2_Callback(hObject, eventdata, handles)
1912drawnow
1913if get(handles.TestCiv2,'Value')
1914    set(handles.TestCiv2,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch
1915    set(handles.CheckFix2,'value',0)% desactivate next step
1916    set(handles.CheckPatch2,'value',0)% desactivate next step
1917    update_CivOptions(handles,0)
1918      hseries=findobj(allchild(0),'Tag','series');
1919     Param=read_GUI(hseries);
1920     Param.Action.RUN=1;
1921     Param.ActionInput=read_GUI(handles.civ_input);
1922     if isfield(Param,'OutputSubDir')
1923     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1924     end
1925     Param.ActionInput.Civ2.CorrSmooth=0;% launch Civ2 with no data point (to get the image names for A and B)
1926     set(handles.Civ1,'BackgroundColor',[1 1 0])
1927     set(handles.Fix1,'BackgroundColor',[1 1 0])
1928     set(handles.Patch1,'BackgroundColor',[1 1 0])
1929     Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
1930     Param.IndexRange.last_i=Param.IndexRange.first_i;
1931     if strcmp(get(handles.ref_j,'Visible'),'on')
1932         Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
1933         Param.IndexRange.last_j=Param.IndexRange.first_j;
1934     else
1935         Param.IndexRange.first_j=1;
1936         Param.IndexRange.last_j=1;
1937     end
1938     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1939     
1940     %% create image data ImageData for display
1941     ImageData.ListVarName={'ny','nx','A'};
1942     ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
1943     ImageData.A=imread(Data.Civ2_ImageA); % read the first image
1944     if ndims(ImageData.A)==3 %case of color image
1945         ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
1946     end
1947     ImageData.ny=[size(ImageData.A,1) 1];
1948     ImageData.nx=[1 size(ImageData.A,2)];
1949     ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
1950
1951     %% create the figure view_field for image visualization
1952    hview_field=view_field(ImageData); %view the image in the GUI view_field
1953    set(0,'CurrentFigure',hview_field)
1954    % plot the boundaries of the subdomains used for patch
1955    for isub=1:size(Data.Civ1_SubRange,3);
1956        pos_x=Data.Civ1_SubRange(1,1,isub);
1957        pos_y=Data.Civ1_SubRange(2,1,isub);
1958        width=Data.Civ1_SubRange(1,2,isub)-Data.Civ1_SubRange(1,1,isub);
1959        height=Data.Civ1_SubRange(2,2,isub)-Data.Civ1_SubRange(2,1,isub);
1960        rectangle('Position',[pos_x pos_y width height],'EdgeColor',[0 0 1])
1961    end
1962    hhview_field=guihandles(hview_field);%
1963    set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
1964    ViewData=get(hview_field,'UserData'); % get the currently plotted field (the image A)
1965    % store info in the UserData of view-field
1966    ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
1967    ViewData.PlotAxes.B=imread(Data.Civ2_ImageB);%store the second image in the UserData of the GUI view_field
1968    ViewData.PlotAxes.X=Data.Civ2_X';
1969    ViewData.PlotAxes.Y=Data.Civ2_Y';
1970    ViewData.PlotAxes.ShiftX=Data.Civ2_U';% shift at each point (from patch1) estimated by the preliminary run of civ2
1971    ViewData.PlotAxes.ShiftY=Data.Civ2_V';
1972    ViewData.PlotAxes.Civ1_SubRange=Data.Civ1_SubRange;
1973    ViewData.PlotAxes.Civ1_NbCentres=Data.Civ1_NbCentres;
1974    ViewData.PlotAxes.Civ1_Coord_tps=Data.Civ1_Coord_tps;
1975    ViewData.PlotAxes.Civ1_U_tps=Data.Civ1_U_tps;
1976    ViewData.PlotAxes.Civ1_V_tps=Data.Civ1_V_tps;
1977    ViewData.PlotAxes.Civ1_Dt=Data.Civ1_Dt;
1978    ViewData.PlotAxes.Civ2_Dt=Data.Civ2_Dt;
1979    set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field
1980    bckcolor=get(handles.civ_input,'Color');
1981    set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calmculation is finished
1982    set(handles.Fix1,'BackgroundColor',bckcolor)
1983    set(handles.Patch1,'BackgroundColor',bckcolor)
1984    drawnow
1985   
1986    %% look for a current figure for image correlation display
1987    corrfig=findobj(allchild(0),'tag','corrfig');
1988    if isempty(corrfig)
1989        corrfig=figure;
1990        set(corrfig,'tag','corrfig')
1991        set(corrfig,'name','image correlation')
1992        set(corrfig,'DeleteFcn',{@closeview_field})%
1993        set(handles.TestCiv1,'BackgroundColor',[1 0 0])
1994    else
1995        set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
1996        corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1997        if ~isempty(corrfig)
1998            delete(corrfig)
1999        end
2000        hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
2001        if ~isempty(hview_field)
2002            delete(hview_field)
2003        end
2004    end   
2005else
2006    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
2007    if ~isempty(hview_field)
2008        delete(hview_field)
2009    end     
2010end
2011
2012
2013% --- Executes on button press in TestPatch2.
2014function TestPatch2_Callback(hObject, eventdata, handles)
2015if get(handles.TestPatch2,'Value')% if TestPatch2 is activated
2016    msgbox_uvmat('WARNING','open the civ file and run "series/test_patch_tps" ')
2017end
2018%      set(handles.TestPatch2,'BackgroundColor',[1 1 0])%paint TestPatch2 button in yellow to indicate activation
2019%      set(handles.Civ1,'BackgroundColor',[1 1 0])% indicate civ1 calculation is activated
2020%      set(handles.Fix1,'BackgroundColor',[1 1 0])% indicate fix1 calculation is activated
2021%      set(handles.Patch1,'BackgroundColor',[1 1 0])% indicate Patch1 calculation is activated
2022%      set(handles.Civ2,'BackgroundColor',[1 1 0])% indicate civ2 calculation is activated
2023%      set(handles.Fix2,'BackgroundColor',[1 1 0])% indicate fix2 calculation is activated
2024%      hseries=findobj(allchild(0),'Tag','series');
2025%      Param=read_GUI(hseries);
2026%      Param.Action.RUN=1;
2027%      Param.ActionInput=read_GUI(handles.civ_input);
2028%      if isfield(Param,'OutputSubDir')
2029%      Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
2030%      end
2031%      ParamPatch2=Param.ActionInput.Patch2; %store the patch1 parameters
2032%      Param.ActionInput=rmfield(Param.ActionInput,'Patch2');% does not execute Patch
2033%      Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
2034%      Param.IndexRange.last_i=Param.IndexRange.first_i;
2035%      if strcmp(get(handles.ref_j,'Visible'),'on')
2036%          Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
2037%          Param.IndexRange.last_j=Param.IndexRange.first_j;
2038%      else
2039%          Param.IndexRange.first_j=1;
2040%          Param.IndexRange.last_j=1;
2041%      end
2042%      [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
2043%      bckcolor=get(handles.civ_input,'Color');
2044%      set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calculation is finished
2045%      set(handles.Fix1,'BackgroundColor',bckcolor)% indicate fix1 calculation is finished
2046%      set(handles.Patch1,'BackgroundColor',bckcolor)% indicate Patch1 calculation is finished
2047%      set(handles.Civ2,'BackgroundColor',bckcolor)% indicate civ2 calculation is finished
2048%      set(handles.Fix2,'BackgroundColor',bckcolor)% indicate fix2 calculation is finished
2049%
2050%      %% prepare Param for iterative Patch processing without input file reading
2051%      Param.Civ2_X=Data.Civ2_X;
2052%      Param.Civ2_Y=Data.Civ2_Y;
2053%      Param.Civ2_U=Data.Civ2_U;
2054%      Param.Civ2_V=Data.Civ2_V;
2055%      Param.Civ2_FF=Data.Civ2_FF;
2056%      Param=rmfield(Param,'InputTable');%desactivate input file reading
2057%     if isfield(Param.ActionInput,'Civ1')
2058%         Param.ActionInput=rmfield(Param.ActionInput,'Civ1');%desactivate civ1: remove civ1 input param if relevant
2059%     end
2060%     if isfield(Param.ActionInput,'Fix1')
2061%         Param.ActionInput=rmfield(Param.ActionInput,'Fix1');%desactivate fix1:remove fix1 input param if relevant
2062%     end
2063%     if isfield(Param.ActionInput,'Patch1')
2064%         Param.ActionInput=rmfield(Param.ActionInput,'Patch1');%desactivate fix1:remove fix1 input param if relevant
2065%     end
2066%     if isfield(Param.ActionInput,'Civ2')
2067%         Param.ActionInput=rmfield(Param.ActionInput,'Civ2');%desactivate civ2: remove civ2 input param if relevant
2068%     end
2069%     if isfield(Param.ActionInput,'Fix2')
2070%         Param.ActionInput=rmfield(Param.ActionInput,'Fix2');%desactivate fix1:remove fix1 input param if relevant
2071%     end
2072%     SmoothingParam=(ParamPatch2.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
2073%     NbGood=numel(find(Data.Civ2_FF==0));
2074%     NbExclude=zeros(1,7);% initialize the set of smoothing parameters
2075%     DiffVel=zeros(1,7);% initialize the rms difference between patch and civ
2076%     Param.ActionInput.Patch2=ParamPatch2;% retrieve Patch2 parameters
2077%     for irho=1:7
2078%         Param.ActionInput.Patch2.FieldSmooth=SmoothingParam(irho);
2079%         [Data,errormsg]= civ_series(Param);%apply the processing fct
2080%         if ~isempty(errormsg)
2081%             msgbox_uvmat('ERROR',errormsg)
2082%             return
2083%         end
2084%         ind_good=find(Data.Civ2_FF==0);
2085%         Civ2_U_Diff=Data.Civ2_U(ind_good)-Data.Civ2_U_smooth(ind_good);
2086%         Civ2_V_Diff=Data.Civ2_V(ind_good)-Data.Civ2_V_smooth(ind_good);
2087%         DiffVel(irho)=sqrt(mean(Civ2_U_Diff.*Civ2_U_Diff+Civ2_V_Diff.*Civ2_V_Diff));
2088%         NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
2089%     end
2090%     figure(1)
2091%     semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r',SmoothingParam,0.1*ones(size(SmoothingParam)),'m')
2092%     grid on
2093%     legend('rms velocity diff. Patch2-Civ2 (pixels)','proportion of excluded vectors (between 0 to 1)','recommended value diff. Patch2-Civ2')
2094%     xlabel('smoothing parameter')
2095%     ylabel('smoothing effect')
2096%     set(handles.TestPatch2,'BackgroundColor',[0 1 0])
2097% else
2098%     corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
2099%     if ~isempty(corrfig)
2100%         delete(corrfig)
2101%     end
2102%     hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
2103%     if ~isempty(hview_field)
2104%         delete(hview_field)
2105%     end
2106% end
2107%
2108
2109%'nomtype2pair': creates nomenclature for index pairs knowing the image nomenclature
2110%---------------------------------------------------------------------
2111function NomTypeNc=nomtype2pair(NomTypeIma,mode_selected)
2112%---------------------------------------------------------------------           
2113% OUTPUT:
2114% NomTypeNc
2115%---------------------------------------------------------------------
2116% INPUT:
2117% 'NomTypeIma': string defining the kind of nomenclature used for images
2118
2119NomTypeNc=NomTypeIma;%default
2120switch mode_selected
2121    case 'pair j1-j2'     
2122    if ~isempty(regexp(NomTypeIma,'a$'))
2123        NomTypeNc=[NomTypeIma 'b'];
2124    elseif ~isempty(regexp(NomTypeIma,'A$'))
2125        NomTypeNc=[NomTypeIma 'B'];
2126    else
2127        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2128        if ~isempty(r)
2129            NomTypeNc='_1_1-2';
2130        end
2131    end
2132    case 'series(Dj)' 
2133%         r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2134%         if ~isempty(r)
2135            NomTypeNc='_1_1-2';
2136%         end
2137   case 'series(Di)'
2138        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2139        if ~isempty(r)
2140            NomTypeNc='_1-2_1';
2141        else
2142            NomTypeNc='_1-2';
2143        end
2144end
2145
2146
2147%------------------------------------------------------------------------
2148% --- determine the list of index pairs of processing file
2149function [ind1,ind2,mode_selected]=...
2150    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
2151%------------------------------------------------------------------------
2152ind1='';
2153ind2='';
2154r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
2155if ~isempty(r)
2156    mode_selected=['D' r.ind];
2157    ind1=stra2num(r.num1);
2158    ind2=stra2num(r.num2);
2159else
2160    mode_selected='burst';
2161    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
2162    if ~isempty(r)
2163        NomTypeNc='_1ab';
2164    else
2165        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
2166        if ~isempty(r)
2167            NomTypeNc='_1AB';
2168        else
2169            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
2170            if ~isempty(r)
2171                NomTypeNc='_1_1-2';
2172            end           
2173        end
2174    end
2175    if isempty(r)
2176        display('wrong pair mode input option')
2177    else
2178    ind1=stra2num(r.num1);
2179    ind2=stra2num(r.num2);
2180    end
2181end
2182
2183%------------------------------------------------------------------------
2184% --- fill civ_input with the parameters retrieved from an input Civ file
2185%------------------------------------------------------------------------
2186function fill_civ_input(Data,handles)
2187
2188%% Civ param
2189% lists of parameters to enter
2190ListParamNum={'CorrBoxSize','SearchBoxSize','SearchBoxShift','Dx','Dy','Dz','MinIma','MaxIma'};% list of numerical values (to transform in strings)
2191ListParamValue={'CorrSmooth','CheckGrid','CheckMask','CheckThreshold'};
2192ListParamString={'Grid','Mask'};
2193% CorrSmooth ??
2194option={'Civ1','Civ2'};
2195for ichoice=1:2
2196    if isfield(Data,[option{ichoice} '_CorrBoxSize'])
2197        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2198    end
2199end
2200
2201%% Fix param
2202option={'Fix1','Fix2'};
2203for ichoice=1:2
2204    if isfield(Data,[option{ichoice} '_CheckFmin2'])
2205        ListParamNum={'MinVel','MaxVel','MinCorr'};% list of numerical values (to transform in strings)
2206        ListParamValue={'CheckFmin2','CheckF3','CheckF4'};
2207        ListParamString={'ref_fix_1'};
2208        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2209    end
2210end
2211
2212%% Patch param
2213option={'Patch1','Patch2'};
2214for ichoice=1:2
2215    if isfield(Data,[option{ichoice} '_FieldSmooth'])
2216        ListParamNum={'FieldSmooth','MaxDiff','SubDomainSize'};% list of numerical values (to transform in strings)
2217        ListParamValue={};
2218        ListParamString={};
2219        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2220    end
2221end
2222%------------------------------------------------------------------------
2223% --- fill a panel of civ_input with the parameters retrieved from an input Civ file
2224%------------------------------------------------------------------------
2225function fill_panel(Data,handles,panel,ListParamNum,ListParamValue,ListParamString)
2226children=get(handles.(panel),'children');%handles of the children of the input GUI with handle 'GUI_handle'
2227handles_panel=[];
2228for ichild=1:numel(children)
2229    if ~isempty(get(children(ichild),'tag'))
2230        handles_panel.(get(children(ichild),'tag'))=children(ichild);
2231    end
2232end
2233for ilist=1:numel(ListParamNum)
2234    ParamName=ListParamNum{ilist};
2235    CivParamName=[panel '_' ParamName];
2236    if isfield(Data,CivParamName)
2237        for icoord=1:numel(Data.(CivParamName))
2238            if numel(Data.(CivParamName))>1
2239                Tag=['num_' ParamName '_' num2str(icoord)];
2240            else
2241                Tag=['num_' ParamName];
2242            end
2243            if isfield(handles_panel,Tag)
2244                set(handles_panel.(Tag),'String',num2str(Data.(CivParamName)(icoord)))
2245                set(handles_panel.(Tag),'Visible','on')
2246            end
2247        end
2248    end
2249end
2250for ilist=1:numel(ListParamValue)
2251    ParamName=ListParamValue{ilist};
2252    CivParamName=[panel '_' ParamName];
2253    if strcmp(ParamName,'CorrSmooth')
2254        ParamName=['num_' ParamName];
2255    end
2256    if isfield(Data,CivParamName)
2257        if isfield(handles_panel,ParamName)
2258            set(handles_panel.(ParamName),'Value',Data.(CivParamName))
2259        end
2260    end
2261end
2262for ilist=1:numel(ListParamString)
2263    ParamName=ListParamString{ilist};
2264    CivParamName=[panel '_' ParamName];
2265    if isfield(Data,CivParamName)
2266        if isfield(handles_panel,ParamName)
2267            set(handles_panel.(ParamName),'String',Data.(CivParamName))
2268        end
2269    end
2270end
2271
2272%------------------------------------------------------------------------
2273% --- Executes on button press in ImportParam.
2274%------------------------------------------------------------------------
2275function ImportParam_Callback(hObject, eventdata, handles)
2276hseries=findobj(allchild(0),'Tag','series');
2277hhseries=guidata(hseries);
2278InputTable=get(hhseries.InputTable,'Data');% read the input file(s) table in the GUI series
2279oldfile=InputTable{1,1};
2280if isempty(oldfile)
2281    % use a file name stored in prefdir
2282    dir_perso=prefdir;
2283    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2284    if exist(profil_perso,'file')
2285        h=load (profil_perso);
2286        if isfield(h,'RootPath') && ischar(h.RootPath)
2287            oldfile=h.RootPath;
2288        end
2289    end
2290end
2291filexml=uigetfile_uvmat('pick a xml parameter file for civ',oldfile,'.xml');% get the xml file containing processing parameters
2292%proceed only if a file has been introduced by the browser
2293if ~isempty(filexml)
2294    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2295    if ~isfield(Param,'InputTable')||~isfield(Param,'IndexRange')
2296        msgbox_uvmat('ERROR','invalid config file: open a file in a folder ''/0_XML''')
2297        return
2298    end
2299    check_input=0;
2300    if isfield(Param,'ActionInput')
2301        if isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'civ_series')
2302            fill_GUI(Param.ActionInput,handles.civ_input)% fill the elements of the GUI series with the input parameters
2303            set(handles.ConfigSource,'String',filexml)
2304            check_input=1;
2305            update_CivOptions(handles,0)             
2306        end
2307    end
2308    if ~check_input
2309        msgbox_uvmat('ERROR','invalid config file (not for civ_series')
2310        return
2311    end
2312end
2313
2314%------------------------------------------------------------------------
2315% --- Executes on selection change in CheckCiv3.
2316%------------------------------------------------------------------------
2317function CheckCiv3_Callback(hObject, eventdata, handles)
2318
2319%------------------------------------------------------------------------
2320% --- Executes on button press in CheckRefFile.
2321%------------------------------------------------------------------------
2322function CheckRefFile_Callback(hObject, eventdata, handles)
2323
2324hseries=findobj(allchild(0),'Tag','series');
2325hhseries=guidata(hseries);
2326InputTable=get(hhseries.InputTable,'Data');
2327i1=str2num(get(hhseries.num_first_i,'String'));
2328j1=str2num(get(hhseries.num_first_j,'String'));
2329InputFile=fullfile_uvmat(InputTable{1,1},InputTable{1,2},InputTable{1,3},InputTable{1,5},InputTable{1,4},i1,[],j1);
2330% browse for a reference file for displacement
2331fileref= uigetfile_uvmat('pick a reference image file:',InputFile);
2332if ~isempty(fileref)
2333    FileInfo=get_file_info(fileref);
2334    CheckImage=strcmp(FileInfo.FieldType,'image');% =1 for images
2335    if ~CheckImage
2336        msgbox_uvmat('ERROR',['invalid file type input for reference image: ' FileInfo.FileType ' not an image'])
2337    else
2338        if isfield (FileInfo,'NumberOfFrames')&& FileInfo.NumberOfFrames>1
2339            set(handles.num_OriginIndex,'Visible','on')
2340            set(handles.OriginIndex_title,'Visible','on')
2341        else
2342            set(handles.num_OriginIndex,'Visible','off')
2343            set(handles.OriginIndex_title,'Visible','off')
2344        end
2345        set(handles.RefFile,'String',fileref)
2346        set(handles.ConfigSource,'String','NEW')
2347        set(handles.ConfigSource,'BackgroundColor',[1 0 1])
2348    end
2349end
2350
2351%------------------------------------------------------------------------
2352% --- Executes on key press with selection of a uicontrol
2353%------------------------------------------------------------------------
2354function keyboard_callback(hObject,eventdata,handles)
2355   
2356ListExclude={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2','ref_i'};
2357if isempty(find(strcmp(get(gco,'Tag'),ListExclude),1))% if the selected uicontrol is not in the Exclude list
2358    set(handles.ConfigSource,'String','NEW')% indicate that the configuration is new
2359    set(handles.OK,'BackgroundColor',[1 0 1])%
2360    drawnow
2361end
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