source: trunk/src/series/civ_input.m @ 1152

Last change on this file since 1152 was 1152, checked in by sommeria, 3 months ago

update_xml simlified, bug on civ_series corrected

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):
69switch Param.Action.ActionName
70    case 'stereo_civ'
71        set(handles.ListCompareMode,'Visible','off')
72        set(handles.PairIndices,'Visible','off')
73    case 'civ_series'
74        set(handles.ListCompareMode,'Visible','on')
75        set(handles.PairIndices,'Visible','on')
76    case 'civ_3D'
77        set(handles.ListCompareMode,'Visible','on')
78        set(handles.PairIndices,'Visible','on')
79        set(handles.title_z,'Visible','on')
80        set(handles.num_CorrBoxSize_3,'Visible','on')
81        set(handles.num_SearchBoxSize_3,'Visible','on')
82        set(handles.num_SearchBoxShift_3,'Visible','on')
83        set(handles.num_Dz,'Visible','on')
84        set(handles.title_Dz,'Visible','on')
85end
86
87%% input file info
88NomTypeInput=Param.InputTable{1,4};
89FileType='image';%fdefault
90FileInfo=[];
91if isfield(SeriesData,'FileInfo')
92    FileType=SeriesData.FileInfo{1}.FileType;% info on the first input file series
93    FieldType=SeriesData.FileInfo{1}.FieldType;% info on the first input file series
94else
95    set(hhseries.REFRESH,'BackgroundColor',[1 0 1])% indicate that the file input in series needs to be refreshed
96end
97
98%% case of netcdf file as input, read the processing stage and look for corresponding images
99ind_opening=0;%default
100NomTypeNc='';
101NomTypeImaA=NomTypeInput;
102iview_image=1;%line # for the input images
103switch FileType
104    case 'civdata'
105        if ~strcmp(Param.Action.ActionName,'civ_series')
106            msgbox_uvmat('ERROR','bad input data file: open an image or a nc file from civ_series')
107            return
108        end
109        NomTypeNc=NomTypeInput;
110        ind_opening=SeriesData.FileInfo{1}.CivStage;
111        if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
112            set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
113        else
114            set(handles.ListCompareMode,'Value',1)
115        end
116        [Data,tild,tild,errormsg]=nc2struct(SeriesData.FileInfo{1}.FileName,[]);
117        if ~isempty(errormsg)
118            msgbox_uvmat('ERROR',['error in netcdf input file: ' errormsg])
119            return
120        end
121        if isfield(Data,'.Civ1_ImageA')
122        [PathCiv1_ImageA,Civ1_ImageA,FileExtA]=fileparts(Data.Civ1_ImageA);%look for the source image A
123        [PathCiv1_ImageB,Civ1_ImageB,FileExtA]=fileparts(Data.Civ1_ImageB);%look for the source image B
124        end
125        if isfield(Data,'Civ2_ImageA')
126            [PathCiv2_ImageA,Civ2_ImageA,FileExtA]=fileparts(Data.Civ2_ImageA);
127            [PathCiv2_ImageB,Civ2_ImageB,FileExtA]=fileparts(Data.Civ2_ImageB);
128        end
129        if size(Param.InputTable,1)==1
130             if isfield(Data,'.Civ1_ImageA')
131            series('display_file_name',hhseries,Data.Civ1_ImageA,'append');%append the image series to the input list
132                    [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA);
133        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ1_ImageB);
134             else
135                 series('display_file_name',hhseries,Data.Civ2_ImageA,'append');%append the image series to the input list
136                         [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ2_ImageA);
137        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ2_ImageB);
138             end
139        end
140
141        iview_image=2;%line # for the input images
142    case 'civxdata'% case of  civx data,
143        msgbox_uvmat('ERROR','old civX convention, use the GUI civ')
144        return
145    otherwise
146        if ~strcmp(FieldType,'image')
147        msgbox_uvmat('ERROR','civ_series needs images, scalar fields in netcdf format, or civ data as input')
148        return
149        end
150end
151       
152%% prepare the GUI with input parameters
153%
154set(handles.ref_i,'String',num2str(Param.IndexRange.first_i))
155if isfield(Param.IndexRange,'first_j')
156    set(handles.ref_j,'String',num2str(Param.IndexRange.first_j))
157end
158set(handles.ConfigSource,'String','\default')
159
160%%  set the menus of image pairs and default selection for civ_input   %%%%%%%%%%%%%%%%%%%
161
162%% display the min and max indices for the whole file series
163if isempty(Param.IndexRange.MaxIndex_i)|| isempty(Param.IndexRange.MinIndex_i)
164    msgbox_uvmat('ERROR','REFRESH the input files in the GUI series')
165     return
166end
167MaxIndex_i=Param.IndexRange.MaxIndex_i(iview_image);
168MinIndex_i=Param.IndexRange.MinIndex_i(iview_image);
169MaxIndex_j=1;%default
170MinIndex_j=1;
171if isfield(Param.IndexRange,'MaxIndex_j')&&isfield(Param.IndexRange,'MinIndex_j')...
172        && numel(Param.IndexRange.MaxIndex_j')>=iview_image &&numel(Param.IndexRange.MinIndex_j')>=iview_image
173    MaxIndex_j=Param.IndexRange.MaxIndex_j(iview_image);
174    MinIndex_j=Param.IndexRange.MinIndex_j(iview_image);
175end
176%update the bounds if possible
177if isfield(SeriesData,'i1_series')&&numel(SeriesData.i1_series)>=iview_image
178    if size(SeriesData.i1_series{iview_image},2)==2 && min(min(SeriesData.i1_series{iview_image}(:,1,:)))==0
179        MinIndex_j=1;% index j set to 1 by default
180        MaxIndex_j=1;
181        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)
182        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)
183    else
184        ref_i=squeeze(max(SeriesData.i1_series{iview_image}(1,:,:),[],2));% select ref_j index for each ref_i
185        ref_j=squeeze(max(SeriesData.j1_series{iview_image}(1,:,:),[],3));% select ref_i index for each ref_j
186        MinIndex_i=min(find(ref_i))-1;
187        MaxIndex_i=max(find(ref_i))-1;
188        MaxIndex_j=max(find(ref_j))-1;
189        MinIndex_j=min(find(ref_j))-1;
190    end
191end
192
193
194%%  transfer the time from the GUI series, or use file index by default
195time=[];
196TimeUnit='frame'; %default
197CoordUnit='';%default
198pxcm_search=1;
199if isfield(SeriesData,'Time') &&numel(SeriesData.Time')>=1 && ~isempty(SeriesData.Time{1})
200    time=SeriesData.Time{1};
201end
202if isfield(Param.IndexRange,'TimeUnit')&&~isempty(Param.IndexRange.TimeUnit)
203    TimeUnit=Param.IndexRange.TimeUnit;
204end
205if isfield(SeriesData,'GeometryCalib')
206    tsai=SeriesData.GeometryCalib;
207    if isfield(tsai,'fx_fy')
208        pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
209    end
210    if isfield(tsai,'CoordUnit')
211        CoordUnit=tsai.CoordUnit;
212    end
213end
214
215%% timing display
216%show the reference image edit box if relevant (not needed for movies or in the absence of time information
217if numel(time)>=2 % if there are at least two time values to define dt
218    if size(time,1)<MaxIndex_i;
219        msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
220    elseif size(time,2)<MaxIndex_j
221        msgbox_uvmat('WARNING','maximum j index restricted by the timing of the xml file');
222    end
223    MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data
224    MaxIndex_j=min(size(time,2),MaxIndex_j);
225    set(handles.TimeSource,'String',Param.IndexRange.TimeSource);
226else
227    set(handles.TimeSource,'String',''); %xml file not used for timing
228    TimeUnit='frame';
229    time=ones(MaxIndex_j-MinIndex_j+1,1)*(MinIndex_i:MaxIndex_i);
230    time=time+0.001*(MinIndex_j:MaxIndex_j)'*ones(1,MaxIndex_i-MinIndex_i+1);
231end
232CivInputData.Time=time;
233CivInputData.NomTypeIma=NomTypeImaA;
234set(handles.civ_input,'UserData',CivInputData)
235set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
236set(handles.TimeUnit,'String',TimeUnit);
237set(handles.SearchRange,'UserData', pxcm_search);
238
239
240%% set the civ_input options, depending on the input file content if a nc file has been opened
241ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
242checkbox=zeros(size(ListOptions));%default
243checkrefresh=0;
244if ind_opening==0  %case of image opening, start with Civ1
245    for index=1:numel(ListOptions)
246        checkbox(index)=get(handles.(ListOptions{index}),'Value');
247    end
248    index_max=find(checkbox, 1, 'last' );
249    if isempty(index_max),index_max=1;end
250    for index=1:index_max
251        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
252    end
253else  %case of netcdf file opening, start with the stage read in the file if the input file is being refreshed
254%     if isequal(get(hhseries.REFRESH,'BackgroundColor'),[1 1 0]) &&...
255%             ~(isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ConfigSource'))
256            for index = 1:min(ind_opening,5)
257                set(handles.(ListOptions{index}),'value',0)
258                fill_civ_input(Data,handles); %fill civ_input with the parameters retrieved from an input Civ file
259            end
260            if isempty(FileInfo)
261            FileInfo.FileName='';
262end
263            set(handles.ConfigSource,'String',FileInfo.FileName);
264            set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
265            for index = ind_opening+2:6
266                set(handles.(ListOptions{index}),'value',0)
267            end
268            checkrefresh=1;
269%     end
270    if ind_opening>=3
271        set(handles.CheckCiv3,'Visible','on')% make visible the switch 'iterate/repet' for Civ2.
272    else
273        set(handles.CheckCiv3,'Visible','off')
274    end
275end
276
277%% introduce the stored Civ parameters  if available (from previous input or ImportConfig in series)
278if ~checkrefresh && isfield(Param,'ActionInput')&& strcmp(Param.ActionInput.Program,Param.Action.ActionName)% the program fits with the stored data
279    fill_GUI(Param.ActionInput,hObject);%fill the GUI with the parameters retrieved from the input Param
280    hcheckgrid=findobj(handles.civ_input,'Tag','CheckGrid');
281    for ilist=1:numel(hcheckgrid)
282        if get(hcheckgrid(ilist),'Value')% if a grid is used, do not show Dx and Dy for an automatic grid
283            hparent=get(hcheckgrid(ilist),'parent');%handles of the parent panel
284            hchildren=get(hparent,'children');
285            handle_dx=findobj(hchildren,'tag','num_Dx');
286            handle_dy=findobj(hchildren,'tag','num_Dy');
287            handle_title_dx=findobj(hchildren,'tag','title_Dx');
288            handle_title_dy=findobj(hchildren,'tag','title_Dy');
289            set(handle_dx,'Visible','off');
290            set(handle_dy,'Visible','off');
291            set(handle_title_dy,'Visible','off');
292            set(handle_title_dx,'Visible','off');
293        end
294    end
295    if isfield(Param.ActionInput,'Civ2')
296        CheckDeformation_Callback(hObject, eventdata, handles)
297    end
298end
299if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ListCompareMode')&&...
300        strcmp(Param.ActionInput.ListCompareMode,'displacement')
301    set(handles.PairIndices,'Visible','off')
302        set(handles.CheckRefFile,'Visible','on')
303else
304    set(handles.CheckRefFile,'Visible','off')
305end
306
307%% reinitialise pair menus
308set(handles.ListPairMode,'Value',1)
309set(handles.ListPairMode,'String',{''})
310set(handles.ListPairCiv1,'Value',1)
311set(handles.ListPairCiv1,'String',{''})
312set(handles.ListPairCiv2,'Value',1)
313set(handles.ListPairCiv2,'String',{''})
314
315%% set the menu and default choice of civ pairs
316if isequal(MaxIndex_j,MinIndex_j)|| strcmp(Param.Action.ActionName,'civ_3D')% no possibility of j pairs
317    PairMenu={'series(Di)'};
318elseif MaxIndex_j-MinIndex_j==1
319    PairMenu={'pair j1-j2'};
320elseif  MaxIndex_i==MinIndex_i && MaxIndex_j-MinIndex_j>2% simple series in j
321    PairMenu={'pair j1-j2';'series(Dj)'};
322else
323    PairMenu={'pair j1-j2';'series(Dj)';'series(Di)'};%multiple choice
324end
325set(handles.ListPairMode,'String',PairMenu)
326
327%% set default choice of pair mode
328PairIndex=[];
329if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'PairIndices')
330    PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu));%retrieve the previous option
331end
332if strcmp(Param.Action.ActionName,'civ_3D')
333    PairIndex=1
334else
335    if isempty(PairIndex)
336        if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs
337            PairIndex=1;
338        elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
339            if  MaxIndex_j <= 10
340                PairIndex=1;% advice 'pair j1-j2' except in MaxIndex_j is large
341            end
342        else
343            if strcmp(NomTypeNc,'_1-2_1')
344                PairIndex=3;% advise 'series(Di)'
345            elseif  MaxIndex_j <= 10
346                PairIndex=1;% advice 'pair j1-j2' except in MaxIndex_j is large
347            else
348                PairIndex=2;% advice 'Dj'
349            end
350        end
351    end
352end
353set(handles.ListPairMode,'Value',PairIndex);
354
355%% indicate the min and max indices i and j on the GUI
356set(handles.MinIndex_i,'String',num2str(MinIndex_i))
357set(handles.MaxIndex_i,'String',num2str(MaxIndex_i))
358set(handles.MinIndex_j,'String',num2str(MinIndex_j))
359set(handles.MaxIndex_j,'String',num2str(MaxIndex_j))
360
361%% set the reference indices from the input file indices
362if ~(isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ConfigSource'))
363update_CivOptions(handles,ind_opening)% fill the menu of possible pairs
364end
365
366%% list the possible index pairs, depending on the option set in ListPairMode
367ListPairMode_Callback([], [], handles)
368
369%% set the GUI to modal: wait for OK to close
370set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal
371drawnow
372uiwait(handles.civ_input);% wait for OK action to end the function
373
374
375%------------------------------------------------------------------------
376% --- Outputs from this function are returned to the command line.
377function varargout = civ_input_OutputFcn(hObject, eventdata, handles)
378%------------------------------------------------------------------------
379% Get default command line output from handles structure
380varargout{1}=[];% default output when civ_input is canceled (no 'OK')
381if ~isempty(handles)
382    varargout{1} = handles.output;
383    delete(handles.civ_input)
384end
385
386% --- Executes when user attempts to close get_field.
387function civ_input_CloseRequestFcn(hObject, eventdata, handles)
388if isequal(get(handles.get_field, 'waitstatus'), 'waiting')
389    % The GUI is still in UIWAIT, us UIRESUME
390    uiresume(handles.civ_input);
391else
392    % The GUI is no longer waiting, just close it
393    delete(handles.civ_input);
394end
395
396%------------------------------------------------------------------------
397% --- Executes on button press in SetDefaultParam.
398%------------------------------------------------------------------------
399function SetDefaultParam_Callback(hObject, eventdata, handles)
400
401Param.ConfigSource='\default';
402
403%% Civ1 parameters
404%Param.CheckCiv1=1;
405Param.Civ1.CorrBoxSize=[25 25 1];
406Param.Civ1.SearchBoxSize=[55 55 5];
407Param.Civ1.SearchBoxShift=[0 0];
408Param.Civ1.CorrSmooth=1;
409Param.Civ1.Dx=20;
410Param.Civ1.Dy=20;
411Param.Civ1.CheckGrid=0;
412Param.Civ1.CheckMask=0;
413Param.Civ1.Mask='';
414Param.Civ1.CheckThreshold=0;
415Param.Civ1.TestCiv1=0;
416
417%% Fix1 parameters
418Param.Fix1.MinCorr=0.2000;
419
420%% Patch1 parameters
421%Param.CheckPatch1=1;
422Param.Patch1.FieldSmooth=20;
423Param.Patch1.MaxDiff=2;
424Param.Patch1.SubDomainSize=125;
425
426%% Civ2 parameters
427%Param.CheckCiv2=1;
428Param.Civ2.CorrBoxSize=[21 21];
429Param.Civ2.SearchBoxSize=[27 27];
430Param.Civ2.CorrSmooth=1;
431Param.Civ2.Dx=10;
432Param.Civ2.Dy=10;
433Param.Civ2.CheckGrid=0;
434Param.Civ2.CheckMask=0;
435Param.Civ2.Mask='';
436Param.Civ2.CheckThreshold=0;
437
438%% Fix2 parameters
439Param.Fix2.MinCorr=0.2000;
440
441%% Patch2 parameters
442Param.Patch2.FieldSmooth=5;
443Param.Patch2.MaxDiff=1.5000;
444Param.Patch2.SubDomainSize=250;
445Param.Patch2.TestPatch2=0;
446
447fill_GUI(Param,handles.civ_input)% fill the elements of the GUI series with the input parameters
448update_CivOptions(handles,0)
449
450% -----------------------------------------------------------------------
451% -----------------------------------------------------------------------
452% --- Open the help html file
453function MenuHelp_Callback(hObject, eventdata, handles)
454% -----------------------------------------------------------------------
455web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#Civ')
456
457%------------------------------------------------------------------------
458% --- Executes on carriage return on the subdir checkciv1 edit window
459function Civ1_ImageB_Callback(hObject, eventdata, handles)
460%------------------------------------------------------------------------
461SubDir=get(handles.Civ1_ImageB,'String');
462menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
463ichoice=find(strcmp(SubDir,menu_str),1);
464if isempty(ichoice)
465    ilist=numel(menu_str); %select 'new...' in the menu
466else
467    ilist=ichoice;
468end
469set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
470if get(handles.CheckCiv1,'Value')% if Civ1 is performed
471    set(handles.Civ2_ImageA,'String',SubDir);% set by default civ2 directory the same as civ1
472%     set(handles.ListSubdirCiv2,'Value',ilist)
473else % if Civ1 data already exist
474    errormsg=find_netcpair_civ(handles,1); %update the list of available index pairs in the new directory
475    if ~isempty(errormsg)
476    msgbox_uvmat('ERROR',errormsg)
477    end
478end
479
480%------------------------------------------------------------------------
481% --- Executes on carriage return on the SubDir checkciv1 edit window
482function Civ2_ImageA_Callback(hObject, eventdata, handles)
483%------------------------------------------------------------------------
484SubDir=get(handles.Civ1_ImageB,'String');
485menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
486ichoice=find(strcmp(SubDir,menu_str),1);
487if isempty(ichoice)
488    ilist=numel(menu_str); %select 'new...' in the menu
489else
490    ilist=ichoice;
491end
492set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
493%update the list of available pairs from netcdf files in the new directory
494if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
495    errormsg=find_netcpair_civ(handles,2);
496        if ~isempty(errormsg)
497    msgbox_uvmat('ERROR',errormsg)
498    end
499end
500
501%------------------------------------------------------------------------
502% --- Executes on button press in CheckCiv1.
503function CheckCiv1_Callback(hObject, eventdata, handles)
504%------------------------------------------------------------------------
505update_CivOptions(handles,0)
506
507%------------------------------------------------------------------------
508% --- Executes on button press in CheckFix1.
509function CheckFix1_Callback(hObject, eventdata, handles)
510%------------------------------------------------------------------------
511update_CivOptions(handles,0)
512
513%------------------------------------------------------------------------
514% --- Executes on button press in CheckPatch1.
515function CheckPatch1_Callback(hObject, eventdata, handles)
516%------------------------------------------------------------------------
517update_CivOptions(handles,0)
518
519%------------------------------------------------------------------------
520% --- Executes on button press in CheckCiv2.
521function CheckCiv2_Callback(hObject, eventdata, handles)
522%------------------------------------------------------------------------
523update_CivOptions(handles,0)
524
525%------------------------------------------------------------------------
526% --- Executes on button press in CheckFix2.
527function CheckFix2_Callback(hObject, eventdata, handles)
528%------------------------------------------------------------------------
529update_CivOptions(handles,0)
530
531%------------------------------------------------------------------------
532% --- Executes on button press in CheckPatch2.
533function CheckPatch2_Callback(hObject, eventdata, handles)
534%------------------------------------------------------------------------
535update_CivOptions(handles,0)
536
537%------------------------------------------------------------------------
538% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
539function update_CivOptions(handles,opening)
540%------------------------------------------------------------------------
541if opening>0
542    set(handles.CheckCiv2,'UserData',opening)% store the info on the current status of the civ processing
543end
544checkbox=zeros(1,6);
545checkbox(1)=get(handles.CheckCiv1,'Value');
546checkbox(2)=get(handles.CheckFix1,'Value');
547checkbox(3)=get(handles.CheckPatch1,'Value');
548checkbox(4)=get(handles.CheckCiv2,'Value');
549checkbox(5)=get(handles.CheckFix2,'Value');
550checkbox(6)=get(handles.CheckPatch2,'Value');
551if opening==0
552    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
553    if ~isempty(errormsg)
554        msgbox_uvmat('ERROR',errormsg)
555    end
556end
557if max(checkbox(4:6))>0% case of civ2 pair choice needed
558    set(handles.TitlePairCiv2,'Visible','on')
559    set(handles.ListPairCiv2,'Visible','on')
560    if ~opening
561        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
562        if ~isempty(errormsg)
563            msgbox_uvmat('ERROR',errormsg)
564        end
565    end
566else
567    set(handles.ListPairCiv2,'Visible','off')
568end
569hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
570hhseries=guidata(hseries); %handles of the elements in 'series'
571InputTable=get(hhseries.InputTable,'Data');
572if 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
573    set(handles.CheckCiv3,'Visible','on')
574else
575    set(handles.CheckCiv3,'Visible','off')
576end
577
578%% set the visibility of the different panels
579options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
580for ilist=1:length(options)
581    if checkbox(ilist)
582        set(handles.(options{ilist}),'Visible','on')
583    else
584        set(handles.(options{ilist}),'Visible','off')
585    end
586end
587
588%------------------------------------------------------------------------
589% --- Executes on button press in OK: processing on local computer
590function OK_Callback(hObject, eventdata, handles)
591%------------------------------------------------------------------------
592
593ActionInput=read_GUI(handles.civ_input);% read the infos on the GUI civ_input
594
595%% correct input inconsistencies
596if isfield(ActionInput,'Civ1')
597    checkeven=(mod(ActionInput.Civ1.CorrBoxSize,2)==0);
598    ActionInput.Civ1.CorrBoxSize(checkeven)=ActionInput.Civ1.CorrBoxSize(checkeven)+1;% set correlation box sizes to odd values
599    ActionInput.Civ1.SearchBoxSize(1:2)=max(ActionInput.Civ1.SearchBoxSize(1:2),ActionInput.Civ1.CorrBoxSize(1:2)+8);% insure that the search box size is large enough
600    checkeven=(mod(ActionInput.Civ1.SearchBoxSize,2)==0);
601    ActionInput.Civ1.SearchBoxSize(checkeven)=ActionInput.Civ1.SearchBoxSize(checkeven)+1;% set search box sizes to odd values
602end
603if isfield(ActionInput,'Civ2')
604    checkeven=(mod(ActionInput.Civ2.CorrBoxSize,2)==0);
605    ActionInput.Civ2.CorrBoxSize(checkeven)=ActionInput.Civ2.CorrBoxSize(checkeven)+1;% set correlation box sizes to odd values
606    ActionInput.Civ2.SearchBoxSize=max(ActionInput.Civ2.SearchBoxSize,ActionInput.Civ2.CorrBoxSize+4);
607    checkeven=(mod(ActionInput.Civ2.SearchBoxSize,2)==0);
608    ActionInput.Civ2.SearchBoxSize(checkeven)=ActionInput.Civ2.SearchBoxSize(checkeven)+1;% set search box sizes to odd values
609end
610
611%% correct mask or grid name for Windows system (replace '\' by '/')
612if isfield(ActionInput,'Civ1')
613    if isfield(ActionInput.Civ1,'Mask')
614        ActionInput.Civ1.Mask=regexprep(ActionInput.Civ1.Mask,'\','/');
615    end
616    if isfield(ActionInput.Civ1,'Grid')
617        ActionInput.Civ1.Grid=regexprep(ActionInput.Civ1.Grid,'\','/');
618    end
619end
620if isfield(ActionInput,'Civ2')
621    if isfield(ActionInput.Civ2,'Mask')
622        ActionInput.Civ2.Mask=regexprep(ActionInput.Civ2.Mask,'\','/');
623    end
624    if isfield(ActionInput.Civ2,'Grid')
625        ActionInput.Civ2.Grid=regexprep(ActionInput.Civ2.Grid,'\','/');
626    end
627end
628
629%% exit the GUI and close it
630handles.output.ActionInput=ActionInput;
631guidata(hObject, handles);% Update handles structure
632uiresume(handles.civ_input);
633
634
635%------------------------------------------------------------------------
636% --- Executes on button press in ListCompareMode.
637function ListCompareMode_Callback(hObject, eventdata, handles)
638%------------------------------------------------------------------------
639ListCompareMode=get(handles.ListCompareMode,'String');
640option=ListCompareMode{get(handles.ListCompareMode,'Value')};
641hseries=findobj(allchild(0),'Tag','series');
642SeriesData=get(hseries,'UserData');
643check_nc=strcmp(SeriesData.FileType{1},'.nc');
644ImageType=SeriesData.FileType(2:end);
645if check_nc
646    ImageType=SeriesData.FileType(2:end);
647else
648    ImageType=SeriesData.FileType;
649end
650hhseries=guidata(hseries);
651InputTable=get(hhseries.InputTable,'Data');
652OriginIndex='off';
653PairIndices='off';
654switch option
655    case 'PIV'
656        PairIndices='on';% needs to define index pairs for PIV       
657    % case 'PIV volume'
658    %     PairIndices='on';% needs to define index pairs for PIV
659    %     set(handles.ListPairMode,'Value',1)
660    %     set(handles.ListPairMode,'String',{'series(Di)'})
661    %     ListPairMode_Callback(hObject, eventdata, handles)
662    case 'displacement'
663        OriginIndex='on';%define a frame origin for displacement
664end
665set(handles.num_OriginIndex,'Visible',OriginIndex)
666set(handles.OriginIndex_title,'Visible',OriginIndex)
667set(handles.CheckRefFile,'Visible',OriginIndex)
668set(handles.RefFile,'Visible',OriginIndex)
669set(handles.PairIndices,'Visible',PairIndices)
670ListPairMode_Callback(hObject,eventdata,handles)
671if strcmp(OriginIndex,'on')
672    set(handles.CheckRefFile,'Value',1)
673    CheckRefFile_Callback(hObject,eventdata,handles)
674end
675       
676
677
678%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
679% Callbacks in the uipanel Pair Indices
680%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
681%------------------------------------------------------------------------
682% --- Executes on button press in ListPairMode.
683function ListPairMode_Callback(hObject, eventdata, handles)
684%------------------------------------------------------------------------
685compare_list=get(handles.ListCompareMode,'String');
686val=get(handles.ListCompareMode,'Value');
687compare=compare_list{val};
688if strcmp(compare,'displacement')||strcmp(compare,'shift')
689    mode_selected='displacement';
690else
691    mode_list=get(handles.ListPairMode,'String');
692    if ischar(mode_list)
693        mode_list={mode_list};
694    end 
695    mode_value=get(handles.ListPairMode,'Value');
696    if isempty(mode_value)
697        mode_value=1;
698    end
699    mode_selected=mode_list{mode_value};
700end
701ref_i=str2double(get(handles.ref_i,'String'));
702CivInputData=get(handles.civ_input,'UserData');
703TimeUnit=get(handles.TimeUnit,'String');
704checkframe=strcmp(TimeUnit,'frame');
705time=CivInputData.Time;
706siztime=size(CivInputData.Time);
707nbfield=siztime(1)-1;
708nbfield2=siztime(2)-1;
709%indchosen=1;  %%first pair selected by default
710% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
711% are relative to the reference indices ref_i and ref_j respectively.
712if isequal(mode_selected,'pair j1-j2')
713    dt=1;
714    index=0;
715    numlist_a=[];
716    numlist_B=[];
717    %get all the time intervals in bursts
718    displ_dt=1;%default
719    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
720    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
721        for numod_b=(numod_a+1):nbfield2
722            index=index+1;
723            numlist_a(index)=numod_a;
724            numlist_b(index)=numod_b;
725            if size(time,2)>1 && ~checkframe && size(CivInputData.Time,1)>ref_i && size(CivInputData.Time,2)>numod_b
726                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
727                displ_dt(index)=dt(numod_a,numod_b);
728            else
729                displ_dt(index)=1;
730            end
731        end
732    end
733    [dtsort,indsort]=sort(displ_dt);
734    enable_j(handles, 'off')
735elseif isequal(mode_selected,'series(Dj)') %| isequal(mode,'st_series(Dj)')
736    enable_j(handles, 'on')
737elseif isequal(mode_selected,'series(Di)') %| isequal(mode,'st_series(Di)')
738    enable_i(handles, 'on')
739    if nbfield2 > 1
740        enable_j(handles, 'on')
741    else
742        enable_j(handles, 'off')
743    end
744elseif isequal(mode_selected,'displacement')%the pairs have the same indices
745    if nbfield > 1 || nbfield==0
746        enable_i(handles, 'on')
747    else
748        enable_j(handles, 'off')
749    end
750    if nbfield2 > 1
751        enable_j(handles, 'on')
752    else
753        enable_j(handles, 'off')
754    end
755end
756errormsg=find_netcpair_civ( handles,1);
757if ~isempty(errormsg)
758    msgbox_uvmat('ERROR',errormsg)
759end
760
761%------------------------------------------------------------------------
762function enable_i(handles, state)
763set(handles.itext,'Visible',state)
764set(handles.MaxIndex_i,'Visible',state)
765set(handles.ref_i,'Visible',state)
766
767%------------------------------------------------------------------------
768function enable_j(handles, state)
769set(handles.jtext,'Visible',state)
770set(handles.MinIndex_j,'Visible',state)
771set(handles.MaxIndex_j,'Visible',state)
772set(handles.ref_j,'Visible',state)
773
774%------------------------------------------------------------------------
775% --- Executes on selection change in ListPairCiv1.
776function ListPairCiv1_Callback(hObject, eventdata, handles)
777%------------------------------------------------------------------------
778%reproduce by default the chosen pair in the checkciv2 menu
779list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
780PairString=list_pair{get(handles.ListPairCiv1,'Value')};
781
782[ind1,ind2]=...
783    find_pair_indices(PairString);
784hseries=findobj(allchild(0),'Tag','series');
785hhseries=guidata(hseries);
786set(hhseries.num_first_j,'String',num2str(ind1));
787set(hhseries.num_last_j,'String',num2str(ind2));
788set(hhseries.num_incr_j,'String',num2str(ind2-ind1));
789set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))%civ2 selection the same as civ& by default
790
791
792%------------------------------------------------------------------------
793% --- Executes on selection change in ListPairCiv2.
794function ListPairCiv2_Callback(hObject, eventdata, handles)
795%------------------------------------------------------------------------
796
797
798%------------------------------------------------------------------------
799function ref_i_Callback(hObject, eventdata, handles)
800%------------------------------------------------------------------------
801mode_list=get(handles.ListPairMode,'String');
802mode_value=get(handles.ListPairMode,'Value');
803mode_selected=mode_list{mode_value};
804errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
805if isequal(mode_selected,'series(Di)') || ...% we do patch2 only
806        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
807    errormsg=find_netcpair_civ( handles,2);
808end
809if isempty(errormsg)
810    set(handles.ref_i,'BackgroundColor',[1 1 1])
811    set(handles.ref_j,'BackgroundColor',[1 1 1])
812else
813    msgbox_uvmat('ERROR',errormsg)
814end
815
816function ref_i_KeyPressFcn(hObject, eventdata, handles)
817set(hObject,'BackgroundColor',[1 0 1])
818       
819% %------------------------------------------------------------------------
820
821function errormsg=find_netcpair_civ(handles,index)
822%------------------------------------------------------------------------
823set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
824
825%% initialisation
826errormsg='';
827CivInputData=get(handles.civ_input,'UserData');
828compare_list=get(handles.ListCompareMode,'String');
829val=get(handles.ListCompareMode,'Value');
830compare=compare_list{val};
831mode_selected='displacement';
832if ~strcmp(compare,'displacement')%||strcmp(compare,'shift')
833 
834    mode_list=get(handles.ListPairMode,'String');
835    mode_value=get(handles.ListPairMode,'Value');
836    if isempty(mode_value)
837        mode_value=1;
838    end
839    if isempty(mode_list)
840        return
841    end
842    mode_selected=mode_list{mode_value};
843end
844nom_type_ima=CivInputData.NomTypeIma;
845menu_pair=get(handles.ListPairCiv1,'String');%previous menu of ListPairCiv1
846PairCiv1Init=menu_pair{get(handles.ListPairCiv1,'Value')};%previous choice of pair
847menu_pair=get(handles.ListPairCiv2,'String');%previous menu of ListPairCiv1
848PairCiv2Init=menu_pair{get(handles.ListPairCiv2,'Value')};%previous choice of pair
849
850%% reads .nc subdirectoy and image numbers from the interface
851%SubDirImages=get(handles.Civ1_ImageA,'String');
852%TODO: determine
853%subdir_civ1=[SubDirImages get(handles.Civ1_ImageB,'String')];%subdirectory subdir_civ1 for the netcdf data
854%subdir_civ2=[SubDirImages get(handles.Civ2_ImageA,'String')];%subdirectory subdir_civ2 for the netcdf data
855ref_i=str2double(get(handles.ref_i,'String'));
856ref_j=[];
857if isequal(mode_selected,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
858    ref_j=0;
859elseif strcmp(get(handles.ref_j,'Visible'),'on')
860    ref_j=str2double(get(handles.ref_j,'String'));
861end
862if isempty(ref_j)
863    ref_j=1;
864end
865CivInputData=get(handles.civ_input,'UserData');
866TimeUnit=get(handles.TimeUnit,'String');
867Time=CivInputData.Time;
868checkframe=strcmp(TimeUnit,'frame');
869
870%% case with no Civ1 operation, netcdf files need to exist for reading
871displ_pair={''};
872nbpair=200;%default
873select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
874
875%% determine the menu display in .ListPairCiv1
876switch mode_selected
877    case 'series(Di)'
878        for ipair=1:nbpair
879            if select(ipair)
880                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
881                displ_pair_dt{ipair}=displ_pair{ipair};
882                if ~checkframe
883                    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
884                        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
885                        displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(dt*1000)];
886                    end
887                else
888                    dt=ipair/1000;
889                    displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(ipair)];
890                end
891            else
892                displ_pair{ipair}='...';
893                displ_pair_dt{ipair}='...'; %pair not displayed in the menu
894            end
895        end
896    case 'series(Dj)'
897        for ipair=1:nbpair
898            if select(ipair)
899                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
900                displ_pair_dt{ipair}=displ_pair{ipair};
901                if ~checkframe
902                    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
903                        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
904                        displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(dt*1000)];
905                    end
906                else
907                    dt=ipair/1000;
908                    displ_pair_dt{ipair}=[displ_pair_dt{ipair} ' :dt= ' num2str(dt*1000)];
909                end
910            else
911                displ_pair{ipair}='...'; %pair not displayed in the menu
912                displ_pair_dt{ipair}='...'; %pair not displayed in the menu
913            end
914        end
915    case 'pair j1-j2'%case of pairs
916        MinIndex_j=str2num(get(handles.MinIndex_j,'String'));
917        MaxIndex_j=str2num(get(handles.MaxIndex_j,'String'));
918        index_pair=0;
919        %get all the Time intervals in bursts
920        displ_pair_dt='';
921        for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode
922            for numod_b=(numod_a+1):MaxIndex_j
923                index_pair=index_pair+1;
924                displ_pair{index_pair}=['j= ' num2stra(numod_a,nom_type_ima) '-' num2stra(numod_b,nom_type_ima)];
925                displ_pair_dt{index_pair}=displ_pair{index_pair};
926                dt(index_pair)=numod_b-numod_a;%default dt
927                if size(Time,1)>ref_i && size(Time,2)>numod_b  % && ~checkframe
928                    dt(index_pair)=Time(ref_i+1,numod_b+1)-Time(ref_i+1,numod_a+1);% Time interval dt
929                    displ_pair_dt{index_pair}=[displ_pair_dt{index_pair} ' :dt= ' num2str(dt(index_pair)*1000)];
930                end
931            end
932           
933        end
934        if index_pair ~=0
935        [tild,indsort]=sort(dt);
936        displ_pair=displ_pair(indsort);
937        displ_pair_dt=displ_pair_dt(indsort);
938        end
939    case 'displacement'
940%         displ_pair={'Di=Dj=0'};
941%         displ_pair_dt={'Di=Dj=0'};
942        set(handles.PairIndices,'Visible','off')
943end
944if index==1 && ~strcmp(mode_selected,'displacement')
945    set(handles.ListPairCiv1,'String',displ_pair_dt');
946end
947
948%% determine the default selection in the pair menu for Civ1
949%ichoice=find(select,1);% index of first selected pair
950%if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
951end_pair=regexp(PairCiv1Init,' :dt=');
952if ~isempty(end_pair)
953    PairCiv1Init=PairCiv1Init(1:end_pair-1);
954end
955ichoice=find(strcmp(PairCiv1Init,displ_pair'),1);
956if ~isempty(ichoice)
957    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
958else
959   set(handles.ListPairCiv1,'Value',1)
960end
961
962%% determine the default selection in the pair menu for Civ2
963if ~strcmp(mode_selected,'displacement')
964if strcmp(get(handles.ListPairCiv2,'Visible'),'on')
965    end_pair=regexp(PairCiv2Init,' :dt=');
966    if ~isempty(end_pair)
967        PairCiv2Init=PairCiv2Init(1:end_pair-1);
968    end
969    ichoice=find(strcmp(PairCiv2Init,displ_pair'),1);
970    if ~isempty(ichoice)
971        set(handles.ListPairCiv2,'Value',ichoice);% first valid pair proposed by default in the menu
972    else
973        set(handles.ListPairCiv2,'Value',1)
974    end
975else
976    set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))% initiate the choice of Civ2 as a reproduction of if civ1
977end
978set(handles.ListPairCiv2,'String',displ_pair_dt');
979end
980set(gcf,'Pointer','arrow')% Indicate that the process is finished
981
982
983%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
984% Callbacks in the uipanel Reference Indices
985%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
986%------------------------------------------------------------------------
987function MinIndex_i_Callback(hObject, eventdata, handles)
988%------------------------------------------------------------------------
989first_i=str2double(get(handles.MinIndex_i,'String'));
990set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
991ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
992
993% %------------------------------------------------------------------------
994% function MinIndex_j_Callback(hObject, eventdata, handles)
995% %------------------------------------------------------------------------
996% first_j=str2num(get(handles.MinIndex_j,'String'));
997% set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
998% ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
999
1000%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1001% Callbacks in the uipanel Civ1
1002%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1003%------------------------------------------------------------------------
1004% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
1005function SearchRange_Callback(hObject, eventdata, handles)
1006%------------------------------------------------------------------------
1007%determine pair numbers
1008if strcmp(get(handles.num_UMin,'Visible'),'off')
1009    set(handles.u_title,'Visible','on')
1010    set(handles.v_title,'Visible','on')
1011    set(handles.num_UMin,'Visible','on')
1012    set(handles.num_UMax,'Visible','on')
1013    set(handles.num_VMin,'Visible','on')
1014    set(handles.num_VMax,'Visible','on')
1015    %set(handles.CoordUnit,'Visible','on')
1016    %set(handles.TimeUnit,'Visible','on')
1017    %set(handles.slash_title,'Visible','on')
1018    set(handles.min_title,'Visible','on')
1019    set(handles.max_title,'Visible','on')
1020    set(handles.unit_title,'Visible','on')
1021else
1022    get_search_range(hObject, eventdata, handles)
1023end
1024
1025%------------------------------------------------------------------------
1026% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
1027function get_search_range(hObject, eventdata, handles)
1028%------------------------------------------------------------------------
1029param_civ1=read_GUI(handles.Civ1);
1030umin=param_civ1.UMin;
1031umax=param_civ1.UMax;
1032vmin=param_civ1.VMin;
1033vmax=param_civ1.VMax;
1034%switch min_title and max_title in case of error
1035if umax<=umin
1036    umin_old=umin;
1037    umin=umax;
1038    umax=umin_old;
1039    set(handles.num_UMin,'String', num2str(umin))
1040    set(handles.num_UMax,'String', num2str(umax))
1041end
1042if vmax<=vmin
1043    vmin_old=vmin;
1044    vmin=vmax;
1045    vmax=vmin_old;
1046    set(handles.num_VMin,'String', num2str(vmin))
1047    set(handles.num_VMax,'String', num2str(vmax))
1048end   
1049if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
1050    shiftx=round((umin+umax)/2);
1051    shifty=round((vmin+vmax)/2);
1052    isx=(umax+2-shiftx)*2+param_civ1.CorrBoxSize(1);
1053    isx=2*ceil(isx/2)+1;
1054    isy=(vmax+2-shifty)*2+param_civ1.CorrBoxSize(2);
1055    isy=2*ceil(isy/2)+1;
1056    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
1057    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
1058    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
1059    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
1060end
1061
1062%------------------------------------------------------------------------
1063% --- Executes on selection in menu CorrSmooth.
1064function num_CorrSmooth_Callback(hObject, eventdata, handles)
1065set(handles.ConfigSource,'String','NEW')
1066set(handles.OK,'BackgroundColor',[1 0 1])
1067%------------------------------------------------------------------------
1068
1069% --- Executes on button press in CheckDeformation.
1070function CheckDeformation_Callback(hObject, eventdata, handles)
1071set(handles.ConfigSource,'String','NEW')
1072set(handles.OK,'BackgroundColor',[1 0 1])
1073handles_CoorSmooth=findobj(get(handles.Civ2,'children'),'Tag','num_CorrSmooth');
1074if get(handles.CheckDeformation,'Value')   
1075    set(handles_CoorSmooth,'Visible','off')
1076else
1077    set(handles_CoorSmooth,'Visible','on')
1078end
1079
1080%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1081% Callbacks in the uipanel Fix1
1082%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1083%------------------------------------------------------------------------
1084% % --- Executes on button press in CheckMask.
1085% function get_mask_fix1_Callback(hObject, eventdata, handles)
1086% %------------------------------------------------------------------------
1087% maskval=get(handles.CheckMask,'Value');
1088% if isequal(maskval,0)
1089%     set(handles.Mask,'String','')
1090% else
1091%     mask_displ='no mask'; %default
1092%     filebase=get(handles.RootPath,'String');
1093%     [nbslice, flag_mask]=get_mask(filebase,handles);
1094%     if isequal(flag_mask,1)
1095%         mask_displ=[num2str(nbslice) 'mask'];
1096%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1097%         filebase_a=get(handles.RootFile_1,'String');
1098%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1099%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1100%             mask_displ='no mask';
1101%         end
1102%     end
1103%     if isequal(mask_displ,'no mask')
1104%         [FileName, PathName, filterindex] = uigetfile( ...
1105%             {'*.png', ' (*.png)';
1106%             '*.png',  '.png files '; ...
1107%             '*.*', 'All Files (*.*)'}, ...
1108%             'Pick a mask file *.png',filebase);
1109%         mask_displ=fullfile(PathName,FileName);
1110%         if ~exist(mask_displ,'file')
1111%             mask_displ='no mask';
1112%         end
1113%     end
1114%     if isequal(mask_displ,'no mask')
1115%         set(handles.CheckMask,'Value',0)
1116%         set(handles.CheckMask,'Value',0)
1117%         set(handles.CheckMask,'Value',0)
1118%     else
1119%         %set(handles.CheckMask,'Value',1)
1120%         set(handles.CheckMask,'Value',1)
1121%     end
1122%     set(handles.Mask,'String',mask_displ)
1123%     set(handles.Mask,'String',mask_displ)
1124%     set(handles.Mask,'String',mask_displ)
1125% end
1126
1127%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1128% Callbacks in the uipanel Civ2
1129%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1130%------------------------------------------------------------------------
1131% --- Executes on button press in CheckMask: select box for mask option
1132function get_mask_civ2_Callback(hObject, eventdata, handles)
1133%------------------------------------------------------------------------
1134maskval=get(handles.CheckMask,'Value');
1135if isequal(maskval,0)
1136    set(handles.Mask,'String','')
1137else
1138    mask_displ='no mask'; %default
1139    filebase=get(handles.RootPath,'String');
1140    [nbslice, flag_mask]=get_mask(filebase,handles);
1141    if isequal(flag_mask,1)
1142        mask_displ=[num2str(nbslice) 'mask'];
1143    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1144        filebase_a=get(handles.RootFile_1,'String');
1145        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1146        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1147            mask_displ='no mask';
1148        end
1149    end
1150    if isequal(mask_displ,'no mask')
1151        [FileName, PathName, filterindex] = uigetfile( ...
1152            {'*.png', ' (*.png)';
1153            '*.png',  '.png files '; ...
1154            '*.*', 'All Files (*.*)'}, ...
1155            'Pick a mask file *.png',filebase);
1156        mask_displ=fullfile(PathName,FileName);
1157        if ~exist(mask_displ,'file')
1158            mask_displ='no mask';
1159        end
1160    end
1161    if isequal(mask_displ,'no mask')
1162        set(handles.CheckMask,'Value',0)
1163        set(handles.CheckMask,'Value',0)
1164    else
1165        set(handles.CheckMask,'Value',1)
1166    end
1167    set(handles.Mask,'String',mask_displ)
1168end
1169
1170% %------------------------------------------------------------------------
1171% % --- Executes on button press in CheckMask.
1172% function get_mask_fix2_Callback(hObject, eventdata, handles)
1173% %------------------------------------------------------------------------
1174% maskval=get(handles.CheckMask,'Value');
1175% if isequal(maskval,0)
1176%     set(handles.Mask,'String','')
1177% else
1178%     mask_displ='no mask'; %default
1179%     filebase=get(handles.RootPath,'String');
1180%     [nbslice, flag_mask]=get_mask(filebase,handles);
1181%     if isequal(flag_mask,1)
1182%         mask_displ=[num2str(nbslice) 'mask'];
1183%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1184%         filebase_a=get(handles.RootFile_1,'String');
1185%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1186%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1187%             mask_displ='no mask';
1188%         end
1189%     end
1190%     if isequal(mask_displ,'no mask')
1191%         [FileName, PathName, filterindex] = uigetfile( ...
1192%             {'*.png', ' (*.png)';
1193%             '*.png',  '.png files '; ...
1194%             '*.*', 'All Files (*.*)'}, ...
1195%             'Pick a mask file *.png',filebase);
1196%         mask_displ=fullfile(PathName,FileName);
1197%         if ~exist(mask_displ,'file')
1198%             mask_displ='no mask';
1199%         end
1200%     end
1201%     if isequal(mask_displ,'no mask')
1202%         set(handles.CheckMask,'Value',0)
1203%     end
1204%     set(handles.Mask,'String',mask_displ)
1205% end
1206
1207%------------------------------------------------------------------------
1208% --- function called to look for mask files
1209function [nbslice, flag_mask]=get_mask(filebase,handles)
1210%------------------------------------------------------------------------
1211%detect mask files, images with appropriate file base
1212%[filebase '_' xx 'mask'], xx=nbslice
1213%flag_mask=1 indicates detection
1214
1215flag_mask=0;%default
1216nbslice=1;
1217
1218% subdir=get(handles.Civ1_ImageB,'String');
1219[Path,Name]=fileparts(filebase);
1220if ~isdir(Path)
1221    msgbox_uvmat('ERROR','no path for input files')
1222    return
1223end
1224% currentdir=pwd;
1225% cd(Path);%move in the dir of the root name filebase
1226maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
1227% cd(currentdir);%come back to the current working directory
1228if ~isempty(maskfiles)
1229    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
1230    % else
1231    flag_mask=1;
1232    maskname=maskfiles(1).name;% take the first mask file in the list
1233    [Path2,Name,ext]=fileparts(maskname);
1234    Namedouble=double(Name);
1235    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1236    ind_mask=findstr('mask',Name);
1237    i=ind_mask-1;
1238    while val(i)==0 && i>0
1239        i=i-1;
1240    end
1241    nbslice=str2double(Name(i+1:ind_mask-1));
1242    if ~isnan(nbslice) && Name(i)=='_'
1243        flag_mask=1;
1244    else
1245        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
1246        return
1247        nbslice=1;
1248    end
1249end
1250
1251%------------------------------------------------------------------------
1252% --- function called to look for grid files
1253function [nbslice, flag_grid]=get_grid(filebase,handles)
1254%------------------------------------------------------------------------
1255flag_grid=0;%default
1256nbslice=1;
1257[Path,Name]=fileparts(filebase);
1258currentdir=pwd;
1259cd(Path);%move in the dir of the root name filebase
1260gridfiles=dir([Name '_*grid_*.grid']);%look for grid files
1261cd(currentdir);%come back to the current working directory
1262if ~isempty(gridfiles)
1263    flag_grid=1;
1264    gridname=gridfiles(1).name;% take the first grid file in the list
1265    [Path2,Name,ext]=fileparts(gridname);
1266    Namedouble=double(Name);
1267    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1268    ind_grid=findstr('grid',Name);
1269    i=ind_grid-1;
1270    while val(i)==0 && i>0
1271        i=i-1;
1272    end
1273    nbslice=str2double(Name(i+1:ind_grid-1));
1274    if ~isnan(nbslice) && Name(i)=='_'
1275        flag_grid=1;
1276    else
1277        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
1278        return
1279        nbslice=1;
1280    end
1281end
1282
1283%------------------------------------------------------------------------
1284% --- transform numbers to letters
1285function str=num2stra(num,nom_type)
1286%------------------------------------------------------------------------
1287if isempty(nom_type)
1288    str='';
1289elseif strcmp(nom_type(end),'a')
1290    str=char(96+num);
1291elseif strcmp(nom_type(end),'A')
1292    str=char(96+num);
1293elseif isempty(nom_type(2:end))%a single index
1294    str='';
1295else
1296    str=num2str(num);
1297end
1298
1299% %------------------------------------------------------------------------
1300% % --- Executes on button press in ListSubdirCiv1.
1301% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
1302% %------------------------------------------------------------------------
1303% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
1304% val=get(handles.ListSubdirCiv1,'Value');
1305% SubDir=list_subdir_civ1{val};
1306% if strcmp(SubDir,'new...')
1307%     if get(handles.CheckCiv1,'Value')
1308%         SubDir='CIV_INPUT'; %default subdirectory
1309%     else
1310%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new civ_input operation')
1311%         return
1312%     end   
1313% end
1314% set(handles.Civ1_ImageB,'String',SubDir);
1315% errormsg=find_netcpair_civ(handles,1);
1316% if ~isempty(errormsg)
1317%     msgbox_uvmat('ERROR',errormsg)
1318% end
1319%     
1320%------------------------------------------------------------------------
1321% % --- Executes on button press in ListSubdirCiv2.
1322% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
1323% %------------------------------------------------------------------------
1324% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
1325% val=get(handles.ListSubdirCiv2,'Value');
1326% SubDir=list_subdir_civ2{val};
1327% if strcmp(SubDir,'new...')
1328%     if get(handles.CheckCiv2,'Value')
1329%         SubDir='CIV_INPUT'; %default subdirectory
1330%     else
1331%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new civ_input operation')
1332%         return
1333%     end
1334% end
1335% set(handles.Civ2_ImageA,'String',SubDir);
1336
1337%------------------------------------------------------------------------
1338% --- Executes on button press in CheckGrid.
1339function CheckGrid_Callback(hObject, eventdata, handles)
1340%------------------------------------------------------------------------
1341value=get(hObject,'Value');
1342hparent=get(hObject,'parent');%handles of the parent panel
1343hchildren=get(hparent,'children');
1344handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
1345handle_dx=findobj(hchildren,'tag','num_Dx');
1346handle_dy=findobj(hchildren,'tag','num_Dy');
1347handle_title_dx=findobj(hchildren,'tag','title_Dx');
1348handle_title_dy=findobj(hchildren,'tag','title_Dy');
1349testgrid=0;
1350filegrid='';
1351if value
1352        hseries=findobj(allchild(0),'Tag','series');
1353    hhseries=guidata(hseries);
1354    InputTable=get(hhseries.InputTable,'Data');
1355     ind_A=1;% line index of the (first) image series
1356    if strcmp(InputTable{1,5},'.nc');
1357        ind_A=2;
1358    end
1359    filebase=InputTable{ind_A,1};
1360    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
1361    if isequal(flag_grid,1)
1362        filegrid=[num2str(nbslice) 'grid'];
1363        testgrid=1;
1364    else % browse for a grid
1365        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
1366        if exist(filegrid,'file')
1367            filebase=filegrid;
1368        end
1369       filegrid = uigetfile_uvmat('pick a grid file .grid:',filebase,'.grid');
1370        set(hObject,'UserData',filegrid);%store for future use
1371        if ~isempty(filegrid)
1372            testgrid=1;
1373        end
1374        set(hObject,'UserData',filegrid);%store for future use
1375    end
1376end
1377if testgrid
1378    set(handle_dx,'Visible','off');
1379    set(handle_dy,'Visible','off');
1380    set(handle_title_dy,'Visible','off');
1381    set(handle_title_dx,'Visible','off');
1382    set(handle_txtbox,'Visible','on')
1383    set(handle_txtbox,'String',filegrid)
1384else
1385    set(hObject,'Value',0);
1386    set(handle_dx,'Visible','on');
1387    set(handle_dy,'Visible','on');
1388    set(handle_title_dy,'Visible','on');
1389    set(handle_title_dx,'Visible','on');
1390    set(handle_txtbox,'Visible','off')
1391end
1392
1393%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
1394PanelName=get(hparent,'tag');
1395if strcmp(PanelName,'Civ1')
1396    hchildren=get(handles.Civ2,'children');
1397    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
1398    handle_txtbox=findobj(hchildren,'tag','Grid');
1399    handle_dx=findobj(hchildren,'tag','num_Dx');
1400    handle_dy=findobj(hchildren,'tag','num_Dy');
1401    handle_title_dx=findobj(hchildren,'tag','title_Dx');
1402    handle_title_dy=findobj(hchildren,'tag','title_Dy');
1403    set(handle_checkbox,'UserData',filegrid);%store for future use
1404    if testgrid
1405        set(handle_checkbox,'Value',1);
1406        set(handle_dx,'Visible','off');
1407        set(handle_dy,'Visible','off');
1408        set(handle_title_dx,'Visible','off');
1409        set(handle_title_dy,'Visible','off');
1410        set(handle_txtbox,'Visible','on')
1411        set(handle_txtbox,'String',filegrid)
1412    end
1413end
1414set(handles.ConfigSource,'String','NEW')
1415set(handles.OK,'BackgroundColor',[1 0 1])
1416
1417%------------------------------------------------------------------------
1418% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
1419function CheckMask_Callback(hObject, eventdata, handles)
1420%------------------------------------------------------------------------
1421value=get(hObject,'Value');
1422hparent=get(hObject,'parent');
1423parent_tag=get(hparent,'Tag');
1424hchildren=get(hparent,'children');
1425handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
1426handle_NbSlice=findobj(hchildren,'tag','num_NbSlice');% look for the mask name box in the same panel
1427testmask=0;
1428if value
1429    hseries=findobj(allchild(0),'Tag','series');
1430    hhseries=guidata(hseries);
1431    InputTable=get(hhseries.InputTable,'Data');
1432    ind_A=1;% line index of the (first) image series
1433    if strcmp(InputTable{1,5},'.nc');
1434        ind_A=2;
1435    end
1436 % browse for a mask
1437        filemask= uigetfile_uvmat('pick a mask image file:',InputTable{ind_A,1},'image');
1438        [FilePath,FileName,Ext]=fileparts(filemask);   
1439        [RootPath,SubDir,RootFile,i1_series,i2,j1,j2,NomType]=find_file_series(FilePath,[FileName,Ext]);
1440        if strcmp(NomType,'_1')
1441           NbSlice=i1_series(1,2,end);
1442           set(handles.num_NbSlice,'String',num2str(NbSlice))
1443        end
1444        set(hObject,'UserData',filemask);%store for future use
1445        if ~isempty(filemask)
1446            testmask=1;
1447        end
1448end
1449if testmask
1450    set(handles.Mask,'Visible','on')
1451    set(handles.Mask,'String',filemask)
1452    set(handles.CheckMask,'Value',1)
1453    if strcmp(NomType,'_1')
1454        set(handles.num_NbSlice,'Visible','on')
1455    end
1456else
1457    set(hObject,'Value',0);
1458    set(handle_txtbox,'Visible','off')
1459    set(handles.num_NbSlice,'Visible','off')
1460end
1461set(handles.ConfigSource,'String','NEW')
1462set(handles.ConfigSource,'BackgroundColor',[1 0 1])
1463
1464% %------------------------------------------------------------------------
1465% % --- Executes on button press in get_gridpatch1.
1466% function get_gridpatch1_Callback(hObject, eventdata, handles)
1467% %------------------------------------------------------------------------
1468% filebase=get(handles.RootPath,'String');
1469% [FileName, PathName, filterindex] = uigetfile( ...
1470%     {'*.grid', ' (*.grid)';
1471%     '*.grid',  '.grid files '; ...
1472%     '*.*', 'All Files (*.*)'}, ...
1473%     'Pick a file',filebase);
1474% filegrid=fullfile(PathName,FileName);
1475% set(handles.grid_patch1,'string',filegrid);
1476% set(hObject,'BackgroundColor',[1 0 1])
1477
1478%------------------------------------------------------------------------
1479% --- STEREO Interp
1480function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
1481%------------------------------------------------------------------------
1482namelog=[filename_nc(1:end-3) '_stinterp.log'];
1483cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
1484    ' -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
1485
1486% %------------------------------------------------------------------------
1487% %--read images and convert them to the uint16 format used for PIV
1488% function A=read_image(filename,type_ima,num,movieobject)
1489% %------------------------------------------------------------------------
1490% %num is the view number needed for an avi movie
1491% switch type_ima
1492%     case 'movie'
1493%         A=read(movieobject,num);
1494%     case 'avi'
1495%         mov=aviread(filename,num);
1496%         A=frame2im(mov(1));
1497%     case 'multimage'
1498%         A=imread(filename,num);
1499%     case 'image'
1500%         A=imread(filename);
1501% end
1502% siz=size(A);
1503% if length(siz)==3;%color images
1504%     A=sum(double(A),3);
1505%     A=uint16(A);
1506% end
1507
1508
1509%------------------------------------------------------------------------
1510% --- Executes on button press in get_ref_fix1.
1511function get_ref_fix1_Callback(hObject, eventdata, handles)
1512%------------------------------------------------------------------------
1513filebase=get(handles.RootPath,'String');
1514[FileName, PathName, filterindex] = uigetfile( ...
1515    {'*.nc', ' (*.nc)';
1516    '*.nc',  'netcdf files '; ...
1517    '*.*', 'All Files (*.*)'}, ...
1518    'Pick a file',filebase);
1519
1520fileinput=[PathName FileName];
1521sizf=size(fileinput);
1522if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1523%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1524[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1525ref.filebase=fullfile(Path,File);
1526% ref.num_a=stra2num(str_a);
1527% ref.num_b=stra2num(str_b);
1528% ref.num1=str2double(field_count);
1529% ref.num2=str2double(str2);
1530browse=[];%initialisation
1531if ~isequal(ref.ext,'.nc')
1532    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1533    return
1534end
1535set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
1536set(handles.ref_fix1,'UserData',ref)
1537menu_field{1}='civ1';
1538Data=nc2struct(fileinput,[]);
1539if isfield(Data,'patch') && isequal(Data.patch,1)
1540    menu_field{2}='filter1';
1541end
1542if isfield(Data,'civ2') && isequal(Data.civ2,1)
1543    menu_field{3}='civ2';
1544end
1545if isfield(Data,'patch2') && isequal(Data.patch2,1)
1546    menu_field{4}='filter2';
1547end
1548set(handles.field_ref1,'String',menu_field);
1549set(handles.field_ref1,'Value',length(menu_field));
1550set(handles.num_MinVel,'Value',2);
1551set(handles.num_MinVel,'String','1');%default threshold
1552set(handles.ref_fix1,'Enable','on')
1553
1554%------------------------------------------------------------------------
1555% --- Executes on button press in get_ref_fix2.
1556function get_ref_fix2_Callback(hObject, eventdata, handles)
1557%------------------------------------------------------------------------
1558if isequal(get(handles.get_ref_fix2,'Value'),1)
1559    filebase=get(handles.RootPath,'String');
1560    [FileName, PathName, filterindex] = uigetfile( ...
1561        {'*.nc', ' (*.nc)';
1562        '*.nc',  'netcdf files '; ...
1563        '*.*', 'All Files (*.*)'}, ...
1564        'Pick a file',filebase);
1565    fileinput=[PathName FileName];
1566    sizf=size(fileinput);
1567    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1568    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1569    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1570    ref.filebase=fullfile(Path,File);
1571    %     ref.num_a=stra2num(str_a);
1572    %     ref.num_b=stra2num(str_b);
1573    %     ref.num1=str2num(field_count);
1574    %     ref.num2=str2num(str2);
1575    browse=[];%initialisation
1576    if ~isequal(ref.ext,'.nc')
1577        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1578        return
1579    end
1580    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
1581    set(handles.ref_fix2,'UserData',ref)
1582    menu_field{1}='civ1';
1583    Data=nc2struct(fileinput,[]);
1584    if isfield(Data,'patch') && isequal(Data.patch,1)
1585        menu_field{2}='filter1';
1586    end
1587    if isfield(Data,'civ2') && isequal(Data.civ2,1)
1588        menu_field{3}='civ2';
1589    end
1590    if isfield(Data,'patch2') && isequal(Data.patch2,1)
1591        menu_field{4}='filter2';
1592    end
1593    set(handles.field_ref2,'String',menu_field);
1594    set(handles.field_ref2,'Value',length(menu_field));
1595    set(handles.num_MinVel,'Value',2);
1596    set(handles.num_MinVel,'String','1');%default threshold
1597    set(handles.ref_fix2,'Enable','on')
1598    set(handles.ref_fix2,'Visible','on')
1599    set(handles.field_ref2,'Visible','on')
1600else
1601    set(handles.ref_fix2,'Visible','off')
1602    set(handles.field_ref2,'Visible','off')
1603end
1604
1605%------------------------------------------------------------------------
1606function ref_fix1_Callback(hObject, eventdata, handles)
1607%------------------------------------------------------------------------
1608set(handles.num_MinVel,'Value',1);
1609set(handles.field_ref1,'Value',1)
1610set(handles.field_ref1,'String',{' '})
1611set(handles.ref_fix1,'UserData',[]);
1612set(handles.ref_fix1,'String','');
1613set(handles.thresh_vel1,'String','0');
1614
1615%------------------------------------------------------------------------
1616function ref_fix2_Callback(hObject, eventdata, handles)
1617%------------------------------------------------------------------------
1618set(handles.num_MinVel,'Value',1);
1619set(handles.field_ref2,'Value',1)
1620set(handles.field_ref2,'String',{' '})
1621set(handles.ref_fix2,'UserData',[]);
1622set(handles.ref_fix2,'String','');
1623set(handles.num_MinVel,'String','0');
1624
1625%------------------------------------------------------------------------
1626% --- TO ABANDON Executes on button press in test_stereo1.
1627function CheckStereo_Callback(hObject, eventdata, handles)
1628%------------------------------------------------------------------------
1629hparent=get(hObject,'parent');
1630parent_tag=get(hparent,'Tag');
1631hchildren=get(hparent,'children');
1632handle_txtbox=findobj(hchildren,'tag','txt_Mask');
1633if isequal(get(hObject,'Value'),0)
1634    set(handles.num_SubDomainSize,'Visible','on')
1635    set(handles.num_FieldSmooth,'Visible','on')
1636else
1637    set(handles.num_SubDomainSize,'Visible','off')
1638    set(handles.num_FieldSmooth,'Visible','off')
1639end
1640
1641% %------------------------------------------------------------------------
1642% % --- Executes on button press in CheckStereo.
1643% function StereoCheck_Callback(hObject, eventdata, handles)
1644% %------------------------------------------------------------------------
1645% if isequal(get(handles.CheckStereo,'Value'),0)
1646%     set(handles.num_subdomainsize,'Visible','on')
1647%     set(handles.num_FieldSmooth,'Visible','on')
1648% else
1649
1650%     set(handles.num_subdomainsize,'Visible','off')
1651%     set(handles.num_FieldSmooth,'Visible','off')
1652% end
1653
1654
1655
1656%------------------------------------------------------------------------
1657%----function introduced for the correlation window figure, activated by deleting this window
1658function closeview_field(gcbo,eventdata)
1659%------------------------------------------------------------------------
1660hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1661if ~isempty(hview_field)
1662    delete(hview_field)
1663end
1664
1665%------------------------------------------------------------------------
1666% --- Executes on button press in CheckThreshold.
1667function CheckThreshold_Callback(hObject, eventdata, handles)
1668%------------------------------------------------------------------------
1669huipanel=get(hObject,'parent');
1670obj(1)=findobj(huipanel,'Tag','num_MinIma');
1671obj(2)=findobj(huipanel,'Tag','num_MaxIma');
1672obj(3)=findobj(huipanel,'Tag','title_Threshold');
1673if get(hObject,'Value')
1674    set(obj,'Visible','on')
1675else
1676    set(obj,'Visible','off')
1677end
1678set(handles.ConfigSource,'String','NEW')
1679set(handles.OK,'BackgroundColor',[1 0 1])
1680%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1681%%%%%%%%%%%%%%   TEST functions
1682%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1683%------------------------------------------------------------------------
1684% --- Executes on button press in TestCiv1: prepare the image correlation function
1685%     activated by mouse motion
1686function TestCiv1_Callback(hObject, eventdata, handles)
1687%------------------------------------------------------------------------
1688drawnow
1689if get(handles.TestCiv1,'Value')
1690    set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch 
1691    set(handles.CheckFix1,'value',0)% desactivate next step
1692    set(handles.CheckPatch1,'value',0)% desactivate next step
1693    set(handles.CheckCiv2,'value',0)% desactivate next step
1694    set(handles.CheckFix2,'value',0)% desactivate next step
1695    set(handles.CheckPatch2,'value',0)% desactivate next step
1696    update_CivOptions(handles,0)
1697      hseries=findobj(allchild(0),'Tag','series');
1698     Param=read_GUI(hseries);
1699     Param.Action.RUN=1;
1700     Param.ActionInput=read_GUI(handles.civ_input);
1701     if isfield(Param.ActionInput,'Fix1')
1702         Param.ActionInput=rmfield(Param.ActionInput,'Fix1');
1703     end
1704     if isfield(Param.ActionInput,'Patch1')
1705         Param.ActionInput=rmfield(Param.ActionInput,'Patch1');
1706     end
1707     if isfield(Param.ActionInput,'Civ2')%remove options that may be selected beyond Patch1
1708         Param.ActionInput=rmfield(Param.ActionInput,'Civ2');
1709     end
1710     if isfield(Param.ActionInput,'Fix2')
1711         Param.ActionInput=rmfield(Param.ActionInput,'Fix2');
1712     end
1713     if isfield(Param.ActionInput,'Patch2')
1714         Param.ActionInput=rmfield(Param.ActionInput,'Patch2');
1715     end
1716     if isfield(Param,'OutputSubDir')
1717     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1718     end
1719     Param.ActionInput.Civ1.CorrSmooth=0;% launch Civ1 with no data point (to get the image names for A and B)
1720     Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
1721     Param.IndexRange.last_i=str2num(get(handles.ref_i,'String'));
1722     if strcmp(get(handles.ref_j,'Visible'),'on')
1723         Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
1724         Param.IndexRange.last_j=Param.IndexRange.first_j;
1725     else
1726         Param.IndexRange.first_j=1;
1727         Param.IndexRange.last_j=1;
1728     end
1729     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1730     if ~isempty(errormsg), return, end % rmq: error msg displayed in civ_series
1731     
1732 %% create image data ImageData for display
1733     ImageData.ListVarName={'ny','nx','A'};
1734     ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
1735     ImageData.VarAttribute{1}.Role='coord_y';
1736     ImageData.VarAttribute{2}.Role='coord_x';
1737     ImageData.VarAttribute{3}.Role='scalar';
1738     ImageData.A=imread(Data.Civ1_ImageA); % read the first image
1739     if ndims(ImageData.A)==3 %case of color image
1740         ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
1741     end
1742     ImageData.ny=[size(ImageData.A,1) 1];
1743     ImageData.nx=[1 size(ImageData.A,2)];
1744     ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
1745
1746     %% create the figure view_field for image visualization
1747     hview_field=view_field(ImageData); %view the image in the GUI view_field
1748     set(0,'CurrentFigure',hview_field)
1749     hhview_field=guihandles(hview_field);
1750     set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
1751     ViewData=get(hview_field,'UserData');
1752     ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
1753     ViewData.PlotAxes.X=Data.Civ1_X';
1754     ViewData.PlotAxes.Y=Data.Civ1_Y';
1755     ViewData.PlotAxes.B=imread(Data.Civ1_ImageB);%store the second image in the UserData of the GUI view_field
1756     set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field
1757   
1758    %% look for a current figure for image correlation display
1759    corrfig=findobj(allchild(0),'tag','corrfig');
1760    if isempty(corrfig)
1761        corrfig=figure;
1762        set(corrfig,'tag','corrfig')
1763        set(corrfig,'name','image correlation')
1764        set(corrfig,'DeleteFcn',{@closeview_field})%
1765        set(handles.TestCiv1,'BackgroundColor',[1 0 0])
1766    else
1767        set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
1768        corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1769        if ~isempty(corrfig)
1770            delete(corrfig)
1771        end
1772        hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1773        if ~isempty(hview_field)
1774            delete(hview_field)
1775        end
1776    end
1777else
1778    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
1779    if ~isempty(hview_field)
1780        delete(hview_field)
1781    end     
1782end
1783
1784% --------------------------------------------------------------------
1785% --- Executes on button press in TestPatch1.
1786% --------------------------------------------------------------------
1787function TestPatch1_Callback(hObject, eventdata, handles)
1788msgbox_uvmat('WARNING','open the civ file and run "series/test_patch_tps" ')
1789
1790% if get(handles.TestPatch1,'Value')% if TestPatch1 is activated
1791%     hseries=findobj(allchild(0),'Tag','series');
1792%     Param=read_GUI(hseries);
1793%     CivDir=fullfile(Param.OutputPath,Param.Experiment,Param.Device,[Param.OutputSubDir Param.OutputDirExt]);
1794%     % ListXml=dir(CivXmlDir);
1795%     if exist(CivDir,'dir')
1796%         CivFile=uigetfile_uvmat('pick .nc file with civ1-fix1 data',CivDir,'.nc');
1797%         [Field,VelTypeOut,errormsg]=read_civdata(CivFile)
1798%         for ilist=1:numel(Field.ListGlobalAttribute)
1799%             r=regexp(Field.ListGlobalAttribute{ilist},'Civ1_(?<field>.+)','names');% \D = not a digit, \d =digi
1800%             if ~isempty(r)
1801%                 ParamTest.Civ1.(r.field)=(Field.(['Civ1_' r.field]));
1802%             end
1803%             r=regexp(Field.ListGlobalAttribute{ilist},'Fix1_(?<field>.+)','names');% \D = not a digit, \d =digi
1804%             if ~isempty(r)
1805%                 ParamTest.Fix1.(r.field)=(Field.(['Fix1_' r.field]));
1806%             end
1807%         end
1808%         fill_GUI(ParamTest,handles.civ_input)% fill the elements of the GUI series with the input parameters
1809%         drawnow
1810%         update_CivOptions(handles,0)
1811%
1812%         set(handles.TestPatch1,'BackgroundColor',[1 1 0])%paint TestPatch1 button in yellow to indicate activation
1813% %         set(handles.Civ1,'BackgroundColor',[1 1 0])% indicate civ1 calculation is performed
1814%         Param.Action.RUN=1;
1815%          Param.ActionInput=read_GUI(handles.civ_input);
1816%          Param.ActionInput.CheckCiv1=0;% do not repeat Civ1 computation       
1817%         if isfield(Param.ActionInput,'Civ2')%remove options that may be selected beyond Patch1
1818%             Param.ActionInput=rmfield(Param.ActionInput,'Civ2');
1819%         end
1820%         if isfield(Param.ActionInput,'Fix2')
1821%             Param.ActionInput=rmfield(Param.ActionInput,'Fix2');
1822%         end
1823%         if isfield(Param.ActionInput,'Patch2')
1824%             Param.ActionInput=rmfield(Param.ActionInput,'Patch2');
1825%         end
1826%         if isfield(Param,'OutputSubDir')
1827%             Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1828%         end
1829%         ParamPatch1=Param.ActionInput.Patch1; %store the patch1 parameters
1830%         Param.ActionInput=rmfield(Param.ActionInput,'Patch1');% does not execute Patch
1831%         Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
1832%         Param.IndexRange.last_i=Param.IndexRange.first_i;
1833%         if strcmp(get(handles.ref_j,'Visible'),'on')
1834%             Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
1835%             Param.IndexRange.last_j=Param.IndexRange.first_j;
1836%         else
1837%             Param.IndexRange.first_j=1;
1838%             Param.IndexRange.last_j=1;
1839%         end
1840%         [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1841%         bckcolor=get(handles.civ_input,'Color');
1842%         set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calculation is finished
1843%
1844%         %% prepare Param for iterative Patch processing without input file reading
1845%         Param.Civ1_X=Data.Civ1_X;
1846%         Param.Civ1_Y=Data.Civ1_Y;
1847%         Param.Civ1_U=Data.Civ1_U;
1848%         Param.Civ1_V=Data.Civ1_V;
1849%         Param.Civ1_FF=Data.Civ1_FF;
1850%         Param=rmfield(Param,'InputTable');%desactivate input file reading
1851%         if isfield(Param.ActionInput,'Civ1')
1852%             Param.ActionInput=rmfield(Param.ActionInput,'Civ1');%desactivate civ1: remove civ1 input param if relevant
1853%         end
1854%         if isfield(Param.ActionInput,'Fix1')
1855%             Param.ActionInput=rmfield(Param.ActionInput,'Fix1');%desactivate fix1:remove fix1 input param if relevant
1856%         end
1857%         SmoothingParam=(ParamPatch1.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
1858%         NbGood=numel(find(Data.Civ1_FF==0));
1859%         NbExclude=zeros(1,7);% initialize the set of smoothing parameters
1860%         DiffVel=zeros(1,7);% initialize the rms difference between patch and civ
1861%         Param.ActionInput.Patch1=ParamPatch1;% retrieve Patch1 parameters
1862%         for irho=1:7
1863%             Param.ActionInput.Patch1.FieldSmooth=SmoothingParam(irho);
1864%             [Data,errormsg]= civ_series(Param);%apply the processing fct
1865%             if ~isempty(errormsg)
1866%                 msgbox_uvmat('ERROR',errormsg)
1867%                 return
1868%             end
1869%             ind_good=find(Data.Civ1_FF==0);
1870%             Civ1_U_Diff=Data.Civ1_U(ind_good)-Data.Civ1_U_smooth(ind_good);
1871%             Civ1_V_Diff=Data.Civ1_V(ind_good)-Data.Civ1_V_smooth(ind_good);
1872%             DiffVel(irho)=sqrt(mean(Civ1_U_Diff.*Civ1_U_Diff+Civ1_V_Diff.*Civ1_V_Diff));
1873%             NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
1874%         end
1875%         figure(1)
1876%         semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r',SmoothingParam,0.2*ones(size(SmoothingParam)),'m')
1877%         grid on
1878%         legend('rms velocity diff. Patch1-Civ1 (pixels)','proportion of excluded vectors (between 0 to 1)','recommended diff Patch1-Civ1')
1879%         xlabel('smoothing parameter')
1880%         ylabel('smoothing effect')
1881%         set(handles.TestPatch1,'BackgroundColor',[0 1 0])
1882%     else
1883%         corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1884%         if ~isempty(corrfig)
1885%             delete(corrfig)
1886%         end
1887%         hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1888%         if ~isempty(hview_field)
1889%             delete(hview_field)
1890%         end
1891%     end
1892% else
1893%     msgbox_uvmat('ERROR','no output file: first perform a civ1-fix1 computation')
1894%     return
1895% end
1896 
1897%------------------------------------------------------------------------
1898% --- Executes on button press in TestCiv2.
1899%------------------------------------------------------------------------
1900function TestCiv2_Callback(hObject, eventdata, handles)
1901drawnow
1902if get(handles.TestCiv2,'Value')
1903    set(handles.TestCiv2,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch
1904    set(handles.CheckFix2,'value',0)% desactivate next step
1905    set(handles.CheckPatch2,'value',0)% desactivate next step
1906    update_CivOptions(handles,0)
1907      hseries=findobj(allchild(0),'Tag','series');
1908     Param=read_GUI(hseries);
1909     Param.Action.RUN=1;
1910     Param.ActionInput=read_GUI(handles.civ_input);
1911     if isfield(Param,'OutputSubDir')
1912     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1913     end
1914     Param.ActionInput.Civ2.CorrSmooth=0;% launch Civ2 with no data point (to get the image names for A and B)
1915     set(handles.Civ1,'BackgroundColor',[1 1 0])
1916     set(handles.Fix1,'BackgroundColor',[1 1 0])
1917     set(handles.Patch1,'BackgroundColor',[1 1 0])
1918     Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
1919     Param.IndexRange.last_i=Param.IndexRange.first_i;
1920     if strcmp(get(handles.ref_j,'Visible'),'on')
1921         Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
1922         Param.IndexRange.last_j=Param.IndexRange.first_j;
1923     else
1924         Param.IndexRange.first_j=1;
1925         Param.IndexRange.last_j=1;
1926     end
1927     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1928     
1929     %% create image data ImageData for display
1930     ImageData.ListVarName={'ny','nx','A'};
1931     ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
1932     ImageData.A=imread(Data.Civ2_ImageA); % read the first image
1933     if ndims(ImageData.A)==3 %case of color image
1934         ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
1935     end
1936     ImageData.ny=[size(ImageData.A,1) 1];
1937     ImageData.nx=[1 size(ImageData.A,2)];
1938     ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
1939
1940     %% create the figure view_field for image visualization
1941    hview_field=view_field(ImageData); %view the image in the GUI view_field
1942    set(0,'CurrentFigure',hview_field)
1943    % plot the boundaries of the subdomains used for patch
1944    for isub=1:size(Data.Civ1_SubRange,3);
1945        pos_x=Data.Civ1_SubRange(1,1,isub);
1946        pos_y=Data.Civ1_SubRange(2,1,isub);
1947        width=Data.Civ1_SubRange(1,2,isub)-Data.Civ1_SubRange(1,1,isub);
1948        height=Data.Civ1_SubRange(2,2,isub)-Data.Civ1_SubRange(2,1,isub);
1949        rectangle('Position',[pos_x pos_y width height],'EdgeColor',[0 0 1])
1950    end
1951    hhview_field=guihandles(hview_field);%
1952    set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
1953    ViewData=get(hview_field,'UserData'); % get the currently plotted field (the image A)
1954    % store info in the UserData of view-field
1955    ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
1956    ViewData.PlotAxes.B=imread(Data.Civ2_ImageB);%store the second image in the UserData of the GUI view_field
1957    ViewData.PlotAxes.X=Data.Civ2_X';
1958    ViewData.PlotAxes.Y=Data.Civ2_Y';
1959    ViewData.PlotAxes.ShiftX=Data.Civ2_U';% shift at each point (from patch1) estimated by the preliminary run of civ2
1960    ViewData.PlotAxes.ShiftY=Data.Civ2_V';
1961    ViewData.PlotAxes.Civ1_SubRange=Data.Civ1_SubRange;
1962    ViewData.PlotAxes.Civ1_NbCentres=Data.Civ1_NbCentres;
1963    ViewData.PlotAxes.Civ1_Coord_tps=Data.Civ1_Coord_tps;
1964    ViewData.PlotAxes.Civ1_U_tps=Data.Civ1_U_tps;
1965    ViewData.PlotAxes.Civ1_V_tps=Data.Civ1_V_tps;
1966    ViewData.PlotAxes.Civ1_Dt=Data.Civ1_Dt;
1967    ViewData.PlotAxes.Civ2_Dt=Data.Civ2_Dt;
1968    set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field
1969    bckcolor=get(handles.civ_input,'Color');
1970    set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calmculation is finished
1971    set(handles.Fix1,'BackgroundColor',bckcolor)
1972    set(handles.Patch1,'BackgroundColor',bckcolor)
1973    drawnow
1974   
1975    %% look for a current figure for image correlation display
1976    corrfig=findobj(allchild(0),'tag','corrfig');
1977    if isempty(corrfig)
1978        corrfig=figure;
1979        set(corrfig,'tag','corrfig')
1980        set(corrfig,'name','image correlation')
1981        set(corrfig,'DeleteFcn',{@closeview_field})%
1982        set(handles.TestCiv1,'BackgroundColor',[1 0 0])
1983    else
1984        set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
1985        corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1986        if ~isempty(corrfig)
1987            delete(corrfig)
1988        end
1989        hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1990        if ~isempty(hview_field)
1991            delete(hview_field)
1992        end
1993    end   
1994else
1995    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
1996    if ~isempty(hview_field)
1997        delete(hview_field)
1998    end     
1999end
2000
2001
2002% --- Executes on button press in TestPatch2.
2003function TestPatch2_Callback(hObject, eventdata, handles)
2004if get(handles.TestPatch2,'Value')% if TestPatch2 is activated
2005    msgbox_uvmat('WARNING','open the civ file and run "series/test_patch_tps" ')
2006end
2007%      set(handles.TestPatch2,'BackgroundColor',[1 1 0])%paint TestPatch2 button in yellow to indicate activation
2008%      set(handles.Civ1,'BackgroundColor',[1 1 0])% indicate civ1 calculation is activated
2009%      set(handles.Fix1,'BackgroundColor',[1 1 0])% indicate fix1 calculation is activated
2010%      set(handles.Patch1,'BackgroundColor',[1 1 0])% indicate Patch1 calculation is activated
2011%      set(handles.Civ2,'BackgroundColor',[1 1 0])% indicate civ2 calculation is activated
2012%      set(handles.Fix2,'BackgroundColor',[1 1 0])% indicate fix2 calculation is activated
2013%      hseries=findobj(allchild(0),'Tag','series');
2014%      Param=read_GUI(hseries);
2015%      Param.Action.RUN=1;
2016%      Param.ActionInput=read_GUI(handles.civ_input);
2017%      if isfield(Param,'OutputSubDir')
2018%      Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
2019%      end
2020%      ParamPatch2=Param.ActionInput.Patch2; %store the patch1 parameters
2021%      Param.ActionInput=rmfield(Param.ActionInput,'Patch2');% does not execute Patch
2022%      Param.IndexRange.first_i=str2num(get(handles.ref_i,'String'));
2023%      Param.IndexRange.last_i=Param.IndexRange.first_i;
2024%      if strcmp(get(handles.ref_j,'Visible'),'on')
2025%          Param.IndexRange.first_j=str2num(get(handles.ref_j,'String'));
2026%          Param.IndexRange.last_j=Param.IndexRange.first_j;
2027%      else
2028%          Param.IndexRange.first_j=1;
2029%          Param.IndexRange.last_j=1;
2030%      end
2031%      [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
2032%      bckcolor=get(handles.civ_input,'Color');
2033%      set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calculation is finished
2034%      set(handles.Fix1,'BackgroundColor',bckcolor)% indicate fix1 calculation is finished
2035%      set(handles.Patch1,'BackgroundColor',bckcolor)% indicate Patch1 calculation is finished
2036%      set(handles.Civ2,'BackgroundColor',bckcolor)% indicate civ2 calculation is finished
2037%      set(handles.Fix2,'BackgroundColor',bckcolor)% indicate fix2 calculation is finished
2038%
2039%      %% prepare Param for iterative Patch processing without input file reading
2040%      Param.Civ2_X=Data.Civ2_X;
2041%      Param.Civ2_Y=Data.Civ2_Y;
2042%      Param.Civ2_U=Data.Civ2_U;
2043%      Param.Civ2_V=Data.Civ2_V;
2044%      Param.Civ2_FF=Data.Civ2_FF;
2045%      Param=rmfield(Param,'InputTable');%desactivate input file reading
2046%     if isfield(Param.ActionInput,'Civ1')
2047%         Param.ActionInput=rmfield(Param.ActionInput,'Civ1');%desactivate civ1: remove civ1 input param if relevant
2048%     end
2049%     if isfield(Param.ActionInput,'Fix1')
2050%         Param.ActionInput=rmfield(Param.ActionInput,'Fix1');%desactivate fix1:remove fix1 input param if relevant
2051%     end
2052%     if isfield(Param.ActionInput,'Patch1')
2053%         Param.ActionInput=rmfield(Param.ActionInput,'Patch1');%desactivate fix1:remove fix1 input param if relevant
2054%     end
2055%     if isfield(Param.ActionInput,'Civ2')
2056%         Param.ActionInput=rmfield(Param.ActionInput,'Civ2');%desactivate civ2: remove civ2 input param if relevant
2057%     end
2058%     if isfield(Param.ActionInput,'Fix2')
2059%         Param.ActionInput=rmfield(Param.ActionInput,'Fix2');%desactivate fix1:remove fix1 input param if relevant
2060%     end
2061%     SmoothingParam=(ParamPatch2.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
2062%     NbGood=numel(find(Data.Civ2_FF==0));
2063%     NbExclude=zeros(1,7);% initialize the set of smoothing parameters
2064%     DiffVel=zeros(1,7);% initialize the rms difference between patch and civ
2065%     Param.ActionInput.Patch2=ParamPatch2;% retrieve Patch2 parameters
2066%     for irho=1:7
2067%         Param.ActionInput.Patch2.FieldSmooth=SmoothingParam(irho);
2068%         [Data,errormsg]= civ_series(Param);%apply the processing fct
2069%         if ~isempty(errormsg)
2070%             msgbox_uvmat('ERROR',errormsg)
2071%             return
2072%         end
2073%         ind_good=find(Data.Civ2_FF==0);
2074%         Civ2_U_Diff=Data.Civ2_U(ind_good)-Data.Civ2_U_smooth(ind_good);
2075%         Civ2_V_Diff=Data.Civ2_V(ind_good)-Data.Civ2_V_smooth(ind_good);
2076%         DiffVel(irho)=sqrt(mean(Civ2_U_Diff.*Civ2_U_Diff+Civ2_V_Diff.*Civ2_V_Diff));
2077%         NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
2078%     end
2079%     figure(1)
2080%     semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r',SmoothingParam,0.1*ones(size(SmoothingParam)),'m')
2081%     grid on
2082%     legend('rms velocity diff. Patch2-Civ2 (pixels)','proportion of excluded vectors (between 0 to 1)','recommended value diff. Patch2-Civ2')
2083%     xlabel('smoothing parameter')
2084%     ylabel('smoothing effect')
2085%     set(handles.TestPatch2,'BackgroundColor',[0 1 0])
2086% else
2087%     corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
2088%     if ~isempty(corrfig)
2089%         delete(corrfig)
2090%     end
2091%     hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
2092%     if ~isempty(hview_field)
2093%         delete(hview_field)
2094%     end
2095% end
2096%
2097
2098%'nomtype2pair': creates nomenclature for index pairs knowing the image nomenclature
2099%---------------------------------------------------------------------
2100function NomTypeNc=nomtype2pair(NomTypeIma,mode_selected)
2101%---------------------------------------------------------------------           
2102% OUTPUT:
2103% NomTypeNc
2104%---------------------------------------------------------------------
2105% INPUT:
2106% 'NomTypeIma': string defining the kind of nomenclature used for images
2107
2108NomTypeNc=NomTypeIma;%default
2109switch mode_selected
2110    case 'pair j1-j2'     
2111    if ~isempty(regexp(NomTypeIma,'a$'))
2112        NomTypeNc=[NomTypeIma 'b'];
2113    elseif ~isempty(regexp(NomTypeIma,'A$'))
2114        NomTypeNc=[NomTypeIma 'B'];
2115    else
2116        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2117        if ~isempty(r)
2118            NomTypeNc='_1_1-2';
2119        end
2120    end
2121    case 'series(Dj)' 
2122%         r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2123%         if ~isempty(r)
2124            NomTypeNc='_1_1-2';
2125%         end
2126   case 'series(Di)'
2127        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2128        if ~isempty(r)
2129            NomTypeNc='_1-2_1';
2130        else
2131            NomTypeNc='_1-2';
2132        end
2133end
2134
2135
2136%------------------------------------------------------------------------
2137% --- determine the list of index pairs of processing file
2138function [ind1,ind2,mode_selected]=...
2139    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
2140%------------------------------------------------------------------------
2141ind1='';
2142ind2='';
2143r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
2144if ~isempty(r)
2145    mode_selected=['D' r.ind];
2146    ind1=stra2num(r.num1);
2147    ind2=stra2num(r.num2);
2148else
2149    mode_selected='burst';
2150    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
2151    if ~isempty(r)
2152        NomTypeNc='_1ab';
2153    else
2154        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
2155        if ~isempty(r)
2156            NomTypeNc='_1AB';
2157        else
2158            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
2159            if ~isempty(r)
2160                NomTypeNc='_1_1-2';
2161            end           
2162        end
2163    end
2164    if isempty(r)
2165        display('wrong pair mode input option')
2166    else
2167    ind1=stra2num(r.num1);
2168    ind2=stra2num(r.num2);
2169    end
2170end
2171
2172%------------------------------------------------------------------------
2173% --- fill civ_input with the parameters retrieved from an input Civ file
2174%------------------------------------------------------------------------
2175function fill_civ_input(Data,handles)
2176
2177%% Civ param
2178% lists of parameters to enter
2179ListParamNum={'CorrBoxSize','SearchBoxSize','SearchBoxShift','Dx','Dy','Dz','MinIma','MaxIma'};% list of numerical values (to transform in strings)
2180ListParamValue={'CorrSmooth','CheckGrid','CheckMask','CheckThreshold'};
2181ListParamString={'Grid','Mask'};
2182% CorrSmooth ??
2183option={'Civ1','Civ2'};
2184for ichoice=1:2
2185    if isfield(Data,[option{ichoice} '_CorrBoxSize'])
2186        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2187    end
2188end
2189
2190%% Fix param
2191option={'Fix1','Fix2'};
2192for ichoice=1:2
2193    if isfield(Data,[option{ichoice} '_CheckFmin2'])
2194        ListParamNum={'MinVel','MaxVel','MinCorr'};% list of numerical values (to transform in strings)
2195        ListParamValue={'CheckFmin2','CheckF3','CheckF4'};
2196        ListParamString={'ref_fix_1'};
2197        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2198    end
2199end
2200
2201%% Patch param
2202option={'Patch1','Patch2'};
2203for ichoice=1:2
2204    if isfield(Data,[option{ichoice} '_FieldSmooth'])
2205        ListParamNum={'FieldSmooth','MaxDiff','SubDomainSize'};% list of numerical values (to transform in strings)
2206        ListParamValue={};
2207        ListParamString={};
2208        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2209    end
2210end
2211%------------------------------------------------------------------------
2212% --- fill a panel of civ_input with the parameters retrieved from an input Civ file
2213%------------------------------------------------------------------------
2214function fill_panel(Data,handles,panel,ListParamNum,ListParamValue,ListParamString)
2215children=get(handles.(panel),'children');%handles of the children of the input GUI with handle 'GUI_handle'
2216handles_panel=[];
2217for ichild=1:numel(children)
2218    if ~isempty(get(children(ichild),'tag'))
2219        handles_panel.(get(children(ichild),'tag'))=children(ichild);
2220    end
2221end
2222for ilist=1:numel(ListParamNum)
2223    ParamName=ListParamNum{ilist};
2224    CivParamName=[panel '_' ParamName];
2225    if isfield(Data,CivParamName)
2226        for icoord=1:numel(Data.(CivParamName))
2227            if numel(Data.(CivParamName))>1
2228                Tag=['num_' ParamName '_' num2str(icoord)];
2229            else
2230                Tag=['num_' ParamName];
2231            end
2232            if isfield(handles_panel,Tag)
2233                set(handles_panel.(Tag),'String',num2str(Data.(CivParamName)(icoord)))
2234                set(handles_panel.(Tag),'Visible','on')
2235            end
2236        end
2237    end
2238end
2239for ilist=1:numel(ListParamValue)
2240    ParamName=ListParamValue{ilist};
2241    CivParamName=[panel '_' ParamName];
2242    if strcmp(ParamName,'CorrSmooth')
2243        ParamName=['num_' ParamName];
2244    end
2245    if isfield(Data,CivParamName)
2246        if isfield(handles_panel,ParamName)
2247            set(handles_panel.(ParamName),'Value',Data.(CivParamName))
2248        end
2249    end
2250end
2251for ilist=1:numel(ListParamString)
2252    ParamName=ListParamString{ilist};
2253    CivParamName=[panel '_' ParamName];
2254    if isfield(Data,CivParamName)
2255        if isfield(handles_panel,ParamName)
2256            set(handles_panel.(ParamName),'String',Data.(CivParamName))
2257        end
2258    end
2259end
2260
2261%------------------------------------------------------------------------
2262% --- Executes on button press in ImportParam.
2263%------------------------------------------------------------------------
2264function ImportParam_Callback(hObject, eventdata, handles)
2265hseries=findobj(allchild(0),'Tag','series');
2266hhseries=guidata(hseries);
2267InputTable=get(hhseries.InputTable,'Data');% read the input file(s) table in the GUI series
2268oldfile=InputTable{1,1};
2269if isempty(oldfile)
2270    % use a file name stored in prefdir
2271    dir_perso=prefdir;
2272    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2273    if exist(profil_perso,'file')
2274        h=load (profil_perso);
2275        if isfield(h,'RootPath') && ischar(h.RootPath)
2276            oldfile=h.RootPath;
2277        end
2278    end
2279end
2280filexml=uigetfile_uvmat('pick a xml parameter file for civ',oldfile,'.xml');% get the xml file containing processing parameters
2281%proceed only if a file has been introduced by the browser
2282if ~isempty(filexml)
2283    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2284    if ~isfield(Param,'InputTable')||~isfield(Param,'IndexRange')
2285        msgbox_uvmat('ERROR','invalid config file: open a file in a folder ''/0_XML''')
2286        return
2287    end
2288    check_input=0;
2289    if isfield(Param,'ActionInput')
2290        if isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'civ_series')
2291            fill_GUI(Param.ActionInput,handles.civ_input)% fill the elements of the GUI series with the input parameters
2292            set(handles.ConfigSource,'String',filexml)
2293            check_input=1;
2294            update_CivOptions(handles,0)             
2295        end
2296    end
2297    if ~check_input
2298        msgbox_uvmat('ERROR','invalid config file (not for civ_series')
2299        return
2300    end
2301end
2302
2303%------------------------------------------------------------------------
2304% --- Executes on selection change in CheckCiv3.
2305%------------------------------------------------------------------------
2306function CheckCiv3_Callback(hObject, eventdata, handles)
2307
2308%------------------------------------------------------------------------
2309% --- Executes on button press in CheckRefFile.
2310%------------------------------------------------------------------------
2311function CheckRefFile_Callback(hObject, eventdata, handles)
2312
2313hseries=findobj(allchild(0),'Tag','series');
2314hhseries=guidata(hseries);
2315InputTable=get(hhseries.InputTable,'Data');
2316i1=str2num(get(hhseries.num_first_i,'String'));
2317j1=str2num(get(hhseries.num_first_j,'String'));
2318InputFile=fullfile_uvmat(InputTable{1,1},InputTable{1,2},InputTable{1,3},InputTable{1,5},InputTable{1,4},i1,[],j1);
2319% browse for a reference file for displacement
2320fileref= uigetfile_uvmat('pick a reference image file:',InputFile);
2321if ~isempty(fileref)
2322    FileInfo=get_file_info(fileref);
2323    CheckImage=strcmp(FileInfo.FieldType,'image');% =1 for images
2324    if ~CheckImage
2325        msgbox_uvmat('ERROR',['invalid file type input for reference image: ' FileInfo.FileType ' not an image'])
2326    else
2327        if isfield (FileInfo,'NumberOfFrames')&& FileInfo.NumberOfFrames>1
2328            set(handles.num_OriginIndex,'Visible','on')
2329            set(handles.OriginIndex_title,'Visible','on')
2330        else
2331            set(handles.num_OriginIndex,'Visible','off')
2332            set(handles.OriginIndex_title,'Visible','off')
2333        end
2334        set(handles.RefFile,'String',fileref)
2335        set(handles.ConfigSource,'String','NEW')
2336        set(handles.ConfigSource,'BackgroundColor',[1 0 1])
2337    end
2338end
2339
2340%------------------------------------------------------------------------
2341% --- Executes on key press with selection of a uicontrol
2342%------------------------------------------------------------------------
2343function keyboard_callback(hObject,eventdata,handles)
2344   
2345ListExclude={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2','ref_i'};
2346if isempty(find(strcmp(get(gco,'Tag'),ListExclude),1))% if the selected uicontrol is not in the Exclude list
2347    set(handles.ConfigSource,'String','NEW')% indicate that the configuration is new
2348    set(handles.OK,'BackgroundColor',[1 0 1])%
2349    drawnow
2350end
2351
2352
2353function num_CorrBoxSize_3_Callback(hObject, eventdata, handles)
2354
2355
2356function num_SearchBoxSize_3_Callback(hObject, eventdata, handles)
2357
2358
2359function MinIndex_j_Callback(hObject, eventdata, handles)
2360
2361
2362% --- Executes on selection change in field_ref2.
2363function field_ref2_Callback(hObject, eventdata, handles)
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