source: trunk/src/series/civ_input.m @ 860

Last change on this file since 860 was 860, checked in by sommeria, 6 years ago

Testpatch_fixed

File size: 93.4 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 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
13%   http://www.legi.grenoble-inp.fr
14%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.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
62%set(hObject,'KeyPressFcn',{@KeyPressFcn,handles})%set keyboard action function
63set(handles.ref_i,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function
64set(handles.ref_j,'KeyPressFcn',{@ref_i_KeyPressFcn,handles})%set keyboard action function
65%set(hObject,'WindowKeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
66hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
67hhseries=guidata(hseries); %handles of the elements in 'series'
68SeriesData=get(hseries,'UserData');% info stored in the GUI series
69
70%% set visibility options depending on the calling function (Param.Action.ActionName):
71if strcmp(Param.Action.ActionName,'civ_series')||strcmp(Param.Action.ActionName,'stereo_civ')
72     set(handles.num_MaxDiff,'Visible','on')
73    set(handles.num_MaxVel,'Visible','on')
74    set(handles.title_MaxVel,'Visible','on')
75    set(handles.title_MaxDiff,'Visible','on')
76    set(handles.num_Nx,'Visible','off')
77    set(handles.num_Ny,'Visible','off')
78    set(handles.title_Nx,'Visible','off')
79    set(handles.title_Ny,'Visible','off')
80    set(handles.num_CorrSmooth,'Style','popupmenu')
81    set(handles.num_CorrSmooth,'Value',1)
82    set(handles.num_CorrSmooth,'String',{'1';'2'})
83    set(handles.CheckThreshold,'Visible','on')
84    set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
85    %set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
86end
87switch Param.Action.ActionName
88    case 'stereo_civ'
89        set(handles.ListCompareMode,'Visible','off')
90        set(handles.PairIndices,'Visible','off')
91    case 'civ_series'
92        set(handles.ListCompareMode,'Visible','on')
93        set(handles.PairIndices,'Visible','on')
94end
95
96%% input file info
97NomTypeInput=Param.InputTable{1,4};
98FileType='image';%fdefault
99FileInfo=[];
100if isfield(SeriesData,'FileType')&&isfield(SeriesData,'FileInfo')
101    FileType=SeriesData.FileType{1};%type of the first input file series
102    FileInfo=SeriesData.FileInfo{1};% info on the first input file series
103else
104    set(hhseries.REFRESH,'BackgroundColor',[1 0 1])% indicate that the file input in series needs to be refreshed
105end
106
107%% case of netcdf file as input, read the processing stage and look for corresponding images
108ind_opening=0;%default
109NomTypeNc='';
110NomTypeImaA=NomTypeInput;
111iview_image=1;%line # for the input images
112switch FileType
113    case {'image','multimage','video','mmreader','netcdf'}
114%         NomTypeImaA=NomTypeInput;
115%         iview_image=1;%line # for the input images
116    case 'civdata'
117        if ~strcmp(Param.Action.ActionName,'civ_series')
118            msgbox_uvmat('ERROR','bad input data file: open an image or a nc file from civ_series')
119            return
120        end
121        NomTypeNc=NomTypeInput;
122        ind_opening=FileInfo.CivStage;
123        if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
124            set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
125        else
126            set(handles.ListCompareMode,'Value',1)
127        end
128        [Data,tild,tild,errormsg]=nc2struct(FileInfo.FileName,[]);
129        if ~isempty(errormsg)
130            msgbox_uvmat('ERROR',['error in netcdf input file: ' errormsg])
131            return
132        end
133        [PathCiv1_ImageA,Civ1_ImageA,FileExtA]=fileparts(Data.Civ1_ImageA);%look for the source image A
134        [PathCiv1_ImageB,Civ1_ImageB,FileExtA]=fileparts(Data.Civ1_ImageB);%look for the source image B
135        if isfield(Data,'Civ2_ImageA')
136            [PathCiv2_ImageA,Civ2_ImageA,FileExtA]=fileparts(Data.Civ2_ImageA);
137            [PathCiv2_ImageB,Civ2_ImageB,FileExtA]=fileparts(Data.Civ2_ImageB);
138        end
139        if size(Param.InputTable,1)==1
140            series('display_file_name',hhseries,Data.Civ1_ImageA,'append');%append the image series to the input list
141        end
142        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA);
143        [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ1_ImageB);
144        iview_image=2;%line # for the input images
145    case 'civxdata'% case of  civx data,
146        msgbox_uvmat('ERROR','old civX convention, use the GUI civ')
147        return
148    otherwise
149        msgbox_uvmat('ERROR','civ_series needs images, scalar fields in netcdf format, or civ data as input')
150        return
151end
152
153%% reinitialise menus
154set(handles.ListPairMode,'Value',1)
155set(handles.ListPairMode,'String',{''})
156set(handles.ListPairCiv1,'Value',1)
157set(handles.ListPairCiv1,'String',{''})
158set(handles.ListPairCiv2,'Value',1)
159set(handles.ListPairCiv2,'String',{''})
160       
161%% prepare the GUI with input parameters
162%
163set(handles.ref_i,'String',num2str(Param.IndexRange.first_i))
164if isfield(Param.IndexRange,'first_j')
165    set(handles.ref_j,'String',num2str(Param.IndexRange.first_j))
166end
167set(handles.ConfigSource,'String','\default')
168
169%%  set the menus of image pairs and default selection for civ_input   %%%%%%%%%%%%%%%%%%%
170
171%% display the min and max indices for the whole file series
172if isempty(Param.IndexRange.MaxIndex_i)|| isempty(Param.IndexRange.MinIndex_i)
173    msgbox_uvmat('ERROR','REFRESH the input files in the GUI series')
174     return
175end
176MaxIndex_i=Param.IndexRange.MaxIndex_i(iview_image);
177MinIndex_i=Param.IndexRange.MinIndex_i(iview_image);
178MaxIndex_j=1;%default
179MinIndex_j=1;
180if isfield(Param.IndexRange,'MaxIndex_j')&&isfield(Param.IndexRange,'MinIndex_j')...
181        && numel(Param.IndexRange.MaxIndex_j')>=iview_image &&numel(Param.IndexRange.MinIndex_j')>=iview_image
182    MaxIndex_j=Param.IndexRange.MaxIndex_j(iview_image);
183    MinIndex_j=Param.IndexRange.MinIndex_j(iview_image);
184end
185%update the bounds if possible
186if isfield(SeriesData,'i1_series')&&numel(SeriesData.i1_series)>=iview_image
187    if size(SeriesData.i1_series{iview_image},2)==2 && min(min(SeriesData.i1_series{iview_image}(:,1,:)))==0
188        MinIndex_j=1;% index j set to 1 by default
189        MaxIndex_j=1;
190        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)
191        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)
192    else
193        ref_i=squeeze(max(SeriesData.i1_series{iview_image}(1,:,:),[],2));% select ref_j index for each ref_i
194        ref_j=squeeze(max(SeriesData.j1_series{iview_image}(1,:,:),[],3));% select ref_i index for each ref_j
195        MinIndex_i=min(find(ref_i))-1;
196        MaxIndex_i=max(find(ref_i))-1;
197        MaxIndex_j=max(find(ref_j))-1;
198        MinIndex_j=min(find(ref_j))-1;
199    end
200end
201if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs
202    set(handles.ListPairMode,'Value',1)
203    set(handles.ListPairMode,'String',{'series(Di)'})
204elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
205    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
206    if  MaxIndex_j <= 10
207        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
208    end
209else
210    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
211    if strcmp(NomTypeNc,'_1-2_1')
212        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
213    elseif  MaxIndex_j <= 10
214        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
215    end
216end
217
218%%  transfer the time from the GUI series, or use file index by default
219time=[];
220TimeUnit='frame'; %default
221CoordUnit='';%default
222pxcm_search=1;
223if isfield(SeriesData,'Time') && ~isempty(SeriesData.Time{1})
224    time=SeriesData.Time{1};
225end
226if isfield(Param.IndexRange,'TimeUnit')&&~isempty(Param.IndexRange.TimeUnit)
227    TimeUnit=Param.IndexRange.TimeUnit;
228end
229% if isfield(SeriesData,'TimeSource')
230%     set(handles.TimeSource,'String',SeriesData.TimeSource)
231% end 
232if isfield(SeriesData,'GeometryCalib')
233    tsai=SeriesData.GeometryCalib;
234    if isfield(tsai,'fx_fy')
235        pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
236    end
237    if isfield(tsai,'CoordUnit')
238        CoordUnit=tsai.CoordUnit;
239    end
240end
241
242%% timing display
243%show the reference image edit box if relevant (not needed for movies or in the absence of time information
244if numel(time)>=2 % if there are at least two time values to define dt
245    if size(time,1)<MaxIndex_i;
246        msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
247    elseif size(time,2)<MaxIndex_j
248        msgbox_uvmat('WARNING','maximum j index restricted by the timing of the xml file');
249    end
250    MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data
251    MaxIndex_j=min(size(time,2),MaxIndex_j);
252    set(handles.TimeSource,'String',Param.IndexRange.TimeSource);
253else
254    set(handles.TimeSource,'String',''); %xml file not used for timing
255    TimeUnit='frame';
256    time=ones(MaxIndex_j-MinIndex_j+1,1)*(MinIndex_i:MaxIndex_i);
257    time=time+0.001*(MinIndex_j:MaxIndex_j)'*ones(1,MaxIndex_i-MinIndex_i+1);
258end
259CivInputData.Time=time;
260CivInputData.NomTypeIma=NomTypeImaA;
261set(handles.civ_input,'UserData',CivInputData)
262set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
263set(handles.TimeUnit,'String',TimeUnit);
264%set(handles.CoordUnit,'String',CoordUnit)
265set(handles.SearchRange,'UserData', pxcm_search);
266
267% indicate the min and max indices i and j on the GUI
268set(handles.MinIndex_i,'String',num2str(MinIndex_i))
269set(handles.MaxIndex_i,'String',num2str(MaxIndex_i))
270set(handles.MinIndex_j,'String',num2str(MinIndex_j))
271set(handles.MaxIndex_j,'String',num2str(MaxIndex_j))
272
273
274%% set the civ_input options, depending on the input file content if a nc file has been opened
275ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
276checkbox=zeros(size(ListOptions));%default
277checkrefresh=0;
278if ind_opening==0  %case of image opening, start with Civ1
279    for index=1:numel(ListOptions)
280        checkbox(index)=get(handles.(ListOptions{index}),'Value');
281    end
282    index_max=find(checkbox, 1, 'last' );
283    if isempty(index_max),index_max=1;end
284    for index=1:index_max
285        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
286    end
287else  %case of netcdf file opening, start with the stage read in the file if the input file is being refreshed
288    if isequal(get(hhseries.REFRESH,'BackgroundColor'),[1 1 0]) &&...
289            ~(isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ConfigSource'))
290%         answer=msgbox_uvmat('INPUT_Y-N',['import the civ parameters from the netcdf file']);
291%         if strcmp(answer,'Yes')
292            for index = 1:min(ind_opening,5)
293                set(handles.(ListOptions{index}),'value',0)
294                fill_civ_input(Data,handles); %fill civ_input with the parameters retrieved from an input Civ file
295            end
296            set(handles.ConfigSource,'String',FileInfo.FileName);
297            set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
298            for index = ind_opening+2:6
299                set(handles.(ListOptions{index}),'value',0)
300            end
301            checkrefresh=1;
302%         end
303    end
304    if ind_opening>=3
305        set(handles.CheckCiv3,'Visible','on')% make visible the switch 'iterate/repet' for Civ2.
306    else
307        set(handles.CheckCiv3,'Visible','off')
308    end
309end
310
311%% introduce the stored Civ parameters  if available (from previous input or ImportConfig in series)
312if ~checkrefresh && isfield(Param,'ActionInput')&& strcmp(Param.ActionInput.Program,Param.Action.ActionName)% the program fits with the stored data
313    fill_GUI(Param.ActionInput,hObject);%fill the GUI with the parameters retrieved from the input Param
314    hcheckgrid=findobj(handles.civ_input,'Tag','CheckGrid');
315    for ilist=1:numel(hcheckgrid)
316        if get(hcheckgrid(ilist),'Value')% if a grid is used, do not show Dx and Dy for an automatic grid
317            hparent=get(hcheckgrid(ilist),'parent');%handles of the parent panel
318            hchildren=get(hparent,'children');
319            handle_dx=findobj(hchildren,'tag','num_Dx');
320            handle_dy=findobj(hchildren,'tag','num_Dy');
321            handle_title_dx=findobj(hchildren,'tag','title_Dx');
322            handle_title_dy=findobj(hchildren,'tag','title_Dy');
323            set(handle_dx,'Visible','off');
324            set(handle_dy,'Visible','off');
325            set(handle_title_dy,'Visible','off');
326            set(handle_title_dx,'Visible','off');
327        end
328    end
329end
330
331%% set the reference indices from the input file indices
332if ~(isfield(Param,'ActionInput') && isfield(Param.ActionInput,'ConfigSource'))
333update_CivOptions(handles,ind_opening)% fill the menu of possible pairs
334end
335
336%% list the possible index pairs, depending on the option set in ListPairMode
337ListPairMode_Callback([], [], handles)
338ListPairCiv1_Callback(hObject, eventdata, handles)
339
340%% set the GUI to modal: wait for OK to close
341set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal
342drawnow
343uiwait(handles.civ_input);% wait for OK action to end the function
344
345
346%------------------------------------------------------------------------
347% --- Outputs from this function are returned to the command line.
348function varargout = civ_input_OutputFcn(hObject, eventdata, handles)
349%------------------------------------------------------------------------
350% Get default command line output from handles structure
351varargout{1}=[];% default output when civ_input is canceled (no 'OK')
352if ~isempty(handles)
353    varargout{1} = handles.output;
354    delete(handles.civ_input)
355end
356
357% --- Executes when user attempts to close get_field.
358function civ_input_CloseRequestFcn(hObject, eventdata, handles)
359if isequal(get(handles.get_field, 'waitstatus'), 'waiting')
360    % The GUI is still in UIWAIT, us UIRESUME
361    uiresume(handles.civ_input);
362else
363    % The GUI is no longer waiting, just close it
364    delete(handles.civ_input);
365end
366
367%------------------------------------------------------------------------
368% --- Executes on button press in SetDefaultParam.
369%------------------------------------------------------------------------
370function SetDefaultParam_Callback(hObject, eventdata, handles)
371
372Param.ConfigSource='\default';
373
374%% Civ1 parameters
375Param.Civ1.CorrBoxSize=[25 25];
376Param.Civ1.SearchBoxSize=[55 55];
377Param.Civ1.SearchBoxShift=[0 0];
378Param.Civ1.CorrSmooth=1;
379Param.Civ1.Dx=20;
380Param.Civ1.Dy=20;
381Param.Civ1.CheckGrid=0;
382Param.Civ1.CheckMask=0;
383Param.Civ1.CheckThreshold=0;
384Param.Civ1.TestCiv1=0;
385
386%% Fix1 parameters
387Param.Fix1.CheckFmin2=1;
388Param.Fix1.CheckF3=1;
389Param.Fix1.MinCorr=0.2000;
390
391%% Patch1 parameters
392Param.Patch1.FieldSmooth=10;
393Param.Patch1.MaxDiff=1.5000;
394Param.Patch1.SubDomainSize=1000;
395Param.Patch1.TestPatch1=0;
396
397%% Civ2 parameters
398Param.Civ2.CorrBoxSize=[21 21];
399Param.Civ2.SearchBoxSize=[31 31];
400Param.Civ2.CorrSmooth=1;
401Param.Civ2.Dx=10;
402Param.Civ2.Dy=10;
403Param.Civ2.CheckGrid=0;
404Param.Civ2.CheckMask=0;
405Param.Civ2.CheckThreshold=0;
406Param.Civ2.TestCiv2=0;
407
408%% Fix2 parameters
409Param.Fix2.CheckFmin2=1;
410Param.Fix2.CheckF4=1;
411Param.Fix2.CheckF3=1;
412Param.Fix2.MinCorr=0.2000;
413
414%% Patch2 parameters
415Param.Patch2.FieldSmooth=2;
416Param.Patch2.MaxDiff=1.5000;
417Param.Patch2.SubDomainSize=1000;
418Param.Patch2.TestPatch2=0;
419
420fill_GUI(Param,handles.civ_input)% fill the elements of the GUI series with the input parameters
421
422% -----------------------------------------------------------------------
423% -----------------------------------------------------------------------
424% --- Open the help html file
425function MenuHelp_Callback(hObject, eventdata, handles)
426% -----------------------------------------------------------------------
427web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#Civ')
428
429%------------------------------------------------------------------------
430% --- Executes on carriage return on the subdir checkciv1 edit window
431function Civ1_ImageB_Callback(hObject, eventdata, handles)
432%------------------------------------------------------------------------
433SubDir=get(handles.Civ1_ImageB,'String');
434menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
435ichoice=find(strcmp(SubDir,menu_str),1);
436if isempty(ichoice)
437    ilist=numel(menu_str); %select 'new...' in the menu
438else
439    ilist=ichoice;
440end
441set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
442if get(handles.CheckCiv1,'Value')% if Civ1 is performed
443    set(handles.Civ2_ImageA,'String',SubDir);% set by default civ2 directory the same as civ1
444%     set(handles.ListSubdirCiv2,'Value',ilist)
445else % if Civ1 data already exist
446    errormsg=find_netcpair_civ(handles,1); %update the list of available index pairs in the new directory
447    if ~isempty(errormsg)
448    msgbox_uvmat('ERROR',errormsg)
449    end
450end
451
452%------------------------------------------------------------------------
453% --- Executes on carriage return on the SubDir checkciv1 edit window
454function Civ2_ImageA_Callback(hObject, eventdata, handles)
455%------------------------------------------------------------------------
456SubDir=get(handles.Civ1_ImageB,'String');
457menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
458ichoice=find(strcmp(SubDir,menu_str),1);
459if isempty(ichoice)
460    ilist=numel(menu_str); %select 'new...' in the menu
461else
462    ilist=ichoice;
463end
464set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
465%update the list of available pairs from netcdf files in the new directory
466if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
467    errormsg=find_netcpair_civ(handles,2);
468        if ~isempty(errormsg)
469    msgbox_uvmat('ERROR',errormsg)
470    end
471end
472
473%------------------------------------------------------------------------
474% --- Executes on button press in CheckCiv1.
475function CheckCiv1_Callback(hObject, eventdata, handles)
476%------------------------------------------------------------------------
477update_CivOptions(handles,0)
478
479%------------------------------------------------------------------------
480% --- Executes on button press in CheckFix1.
481function CheckFix1_Callback(hObject, eventdata, handles)
482%------------------------------------------------------------------------
483update_CivOptions(handles,0)
484
485%------------------------------------------------------------------------
486% --- Executes on button press in CheckPatch1.
487function CheckPatch1_Callback(hObject, eventdata, handles)
488%------------------------------------------------------------------------
489update_CivOptions(handles,0)
490
491%------------------------------------------------------------------------
492% --- Executes on button press in CheckCiv2.
493function CheckCiv2_Callback(hObject, eventdata, handles)
494%------------------------------------------------------------------------
495update_CivOptions(handles,0)
496
497%------------------------------------------------------------------------
498% --- Executes on button press in CheckFix2.
499function CheckFix2_Callback(hObject, eventdata, handles)
500%------------------------------------------------------------------------
501update_CivOptions(handles,0)
502
503%------------------------------------------------------------------------
504% --- Executes on button press in CheckPatch2.
505function CheckPatch2_Callback(hObject, eventdata, handles)
506%------------------------------------------------------------------------
507update_CivOptions(handles,0)
508
509%------------------------------------------------------------------------
510% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
511function update_CivOptions(handles,opening)
512%------------------------------------------------------------------------
513if opening>0
514    set(handles.CheckCiv2,'UserData',opening)% store the info on the current status of the civ processing
515end
516checkbox=zeros(1,6);
517checkbox(1)=get(handles.CheckCiv1,'Value');
518checkbox(2)=get(handles.CheckFix1,'Value');
519checkbox(3)=get(handles.CheckPatch1,'Value');
520checkbox(4)=get(handles.CheckCiv2,'Value');
521checkbox(5)=get(handles.CheckFix2,'Value');
522checkbox(6)=get(handles.CheckPatch2,'Value');
523if opening==0
524    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
525    if ~isempty(errormsg)
526        msgbox_uvmat('ERROR',errormsg)
527    end
528end
529if max(checkbox(4:6))>0% case of civ2 pair choice needed
530    set(handles.TitlePairCiv2,'Visible','on')
531    set(handles.ListPairCiv2,'Visible','on')
532    if ~opening
533        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
534        if ~isempty(errormsg)
535            msgbox_uvmat('ERROR',errormsg)
536        end
537    end
538else
539    set(handles.ListPairCiv2,'Visible','off')
540end
541if max(checkbox(1:3))==0 && get(handles.CheckCiv2,'UserData')==6,% no operation asked before Civ2 and input file ready for civ3
542    set(handles.CheckCiv3,'Visible','on')
543else
544    set(handles.CheckCiv3,'Visible','off')
545end
546
547%% set the visibility of the different panels
548options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
549for ilist=1:length(options)
550    if checkbox(ilist)
551        set(handles.(options{ilist}),'Visible','on')
552    else
553        set(handles.(options{ilist}),'Visible','off')
554    end
555end
556
557%------------------------------------------------------------------------
558% --- Executes on button press in OK: processing on local computer
559function OK_Callback(hObject, eventdata, handles)
560%------------------------------------------------------------------------
561
562ActionInput=read_GUI(handles.civ_input);% read the infos on the GUI civ_input
563
564%% correct input inconsistencies
565if isfield(ActionInput,'Civ1')
566    checkeven=(mod(ActionInput.Civ1.CorrBoxSize,2)==0);
567    ActionInput.Civ1.CorrBoxSize(checkeven)=ActionInput.Civ1.CorrBoxSize(checkeven)+1;% set correlation box sizes to odd values
568    ActionInput.Civ1.SearchBoxSize=max(ActionInput.Civ1.SearchBoxSize,ActionInput.Civ1.CorrBoxSize+8);% insure that the search box size is large enough
569    checkeven=(mod(ActionInput.Civ1.SearchBoxSize,2)==0);
570    ActionInput.Civ1.SearchBoxSize(checkeven)=ActionInput.Civ1.SearchBoxSize(checkeven)+1;% set search box sizes to odd values
571end
572if isfield(ActionInput,'Civ2')
573    checkeven=(mod(ActionInput.Civ2.CorrBoxSize,2)==0);
574    ActionInput.Civ2.CorrBoxSize(checkeven)=ActionInput.Civ2.CorrBoxSize(checkeven)+1;% set correlation box sizes to odd values
575    ActionInput.Civ2.SearchBoxSize=max(ActionInput.Civ2.SearchBoxSize,ActionInput.Civ2.CorrBoxSize+6);
576    checkeven=(mod(ActionInput.Civ2.SearchBoxSize,2)==0);
577    ActionInput.Civ2.SearchBoxSize(checkeven)=ActionInput.Civ2.SearchBoxSize(checkeven)+1;% set search box sizes to odd values
578end
579
580%% correct mask or grid name for Windows system (replace '\' by '/')
581if isfield(ActionInput,'Civ1')
582    if isfield(ActionInput.Civ1,'Mask')
583        ActionInput.Civ1.Mask=regexprep(ActionInput.Civ1.Mask,'\','/');
584    end
585    if isfield(ActionInput.Civ1,'Grid')
586        ActionInput.Civ1.Grid=regexprep(ActionInput.Civ1.Grid,'\','/');
587    end
588end
589if isfield(ActionInput,'Civ2')
590    if isfield(ActionInput.Civ2,'Mask')
591        ActionInput.Civ2.Mask=regexprep(ActionInput.Civ2.Mask,'\','/');
592    end
593    if isfield(ActionInput.Civ2,'Grid')
594        ActionInput.Civ2.Grid=regexprep(ActionInput.Civ2.Grid,'\','/');
595    end
596end
597
598%% exit the GUI and close it
599handles.output.ActionInput=ActionInput;
600guidata(hObject, handles);% Update handles structure
601uiresume(handles.civ_input);
602
603
604%------------------------------------------------------------------------
605% --- Executes on button press in ListCompareMode.
606function ListCompareMode_Callback(hObject, eventdata, handles)
607%------------------------------------------------------------------------
608ListCompareMode=get(handles.ListCompareMode,'String');
609option=ListCompareMode{get(handles.ListCompareMode,'Value')};
610hseries=findobj(allchild(0),'Tag','series');
611SeriesData=get(hseries,'UserData');
612check_nc=strcmp(SeriesData.FileType{1},'.nc');
613ImageType=SeriesData.FileType(2:end);
614if check_nc
615    ImageType=SeriesData.FileType(2:end);
616else
617    ImageType=SeriesData.FileType;
618end
619hhseries=guidata(hseries);
620InputTable=get(hhseries.InputTable,'Data');
621OriginIndex='off';
622PairIndices='off';
623DoubleInputSeries='off';
624switch option
625    case 'PIV'
626        PairIndices='on';% needs to define index pairs for PIV
627       
628    case 'PIV volume'
629        PairIndices='on';% needs to define index pairs for PIV
630        set(handles.ListPairMode,'Value',1)
631        set(handles.ListPairMode,'String',{'series(Di)'})
632        ListPairMode_Callback(hObject, eventdata, handles)
633    case 'displacement'
634        OriginIndex='on';%define a frame origin for displacement
635%     case 'shift'
636%         if numel(ImageType)==1
637%             fileinput=uigetfile_uvmat('pick a second file series for synchronous shift',InputTable{check_nc+1});
638%             if ~isempty(fileinput)
639%                 series( 'display_file_name',hhseries,fileinput,'append')
640%             end
641%             
642%             
643%         end
644end
645set(handles.num_OriginIndex,'Visible',OriginIndex)
646set(handles.OriginIndex_title,'Visible',OriginIndex)
647set(handles.PairIndices,'Visible',PairIndices)
648ListPairMode_Callback(hObject, eventdata, handles)
649       
650
651
652%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
653% Callbacks in the uipanel Pair Indices
654%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
655%------------------------------------------------------------------------
656% --- Executes on button press in ListPairMode.
657function ListPairMode_Callback(hObject, eventdata, handles)
658%------------------------------------------------------------------------
659compare_list=get(handles.ListCompareMode,'String');
660val=get(handles.ListCompareMode,'Value');
661compare=compare_list{val};
662if strcmp(compare,'displacement')||strcmp(compare,'shift')
663    mode='displacement';
664else
665    mode_list=get(handles.ListPairMode,'String');
666    if ischar(mode_list)
667        mode_list={mode_list};
668    end
669    mode_value=get(handles.ListPairMode,'Value');
670    mode=mode_list{mode_value};
671end
672% displ_num=[];%default
673ref_i=str2double(get(handles.ref_i,'String'));
674% last_i=str2num(get(handles.last_i,'String'));
675CivInputData=get(handles.civ_input,'UserData');
676TimeUnit=get(handles.TimeUnit,'String');
677checkframe=strcmp(TimeUnit,'frame');
678time=CivInputData.Time;
679siztime=size(CivInputData.Time);
680nbfield=siztime(1)-1;
681nbfield2=siztime(2)-1;
682indchosen=1;  %%first pair selected by default
683%displ_num used to define the indices of the civ_input pairs
684% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
685% are relative to the reference indices ref_i and ref_j respectively.
686if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
687    dt=1;
688    displ='';
689    index=0;
690    numlist_a=[];
691    numlist_B=[];
692    %get all the time intervals in bursts
693    displ_dt=1;%default
694    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
695    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
696        for numod_b=(numod_a+1):nbfield2
697            index=index+1;
698            numlist_a(index)=numod_a;
699            numlist_b(index)=numod_b;
700            if size(time,2)>1 && ~checkframe
701                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
702                displ_dt(index)=dt(numod_a,numod_b);
703            else
704                displ_dt(index)=1;
705            end
706        end
707    end
708    [dtsort,indsort]=sort(displ_dt);
709    if ~isempty(numlist_a)
710        displ_num(1,:)=numlist_a(indsort);
711        displ_num(2,:)=numlist_b(indsort);
712    end
713    displ_num(3,:)=0;
714    displ_num(4,:)=0;
715    enable_j(handles, 'off')
716elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
717    index=1:200;
718    displ_num(1,index)=-floor(index/2);
719    displ_num(2,index)=ceil(index/2);
720    displ_num(3:4,index)=zeros(2,200);
721    enable_j(handles, 'on')
722elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
723%     index=1:200;
724%     displ_num(1:2,index)=zeros(2,200);
725%     displ_num(3,index)=-floor(index/2);
726%     displ_num(4,index)=ceil(index/2);
727    enable_i(handles, 'on')
728    if nbfield2 > 1
729        enable_j(handles, 'on')
730    else
731        enable_j(handles, 'off')
732    end
733elseif isequal(mode,'displacement')%the pairs have the same indices
734    displ_num(1,1)=0;
735    displ_num(2,1)=0;
736    displ_num(3,1)=0;
737    displ_num(4,1)=0;
738    if nbfield > 1 || nbfield==0
739        enable_i(handles, 'on')
740    else
741        enable_j(handles, 'off')
742    end
743    if nbfield2 > 1
744        enable_j(handles, 'on')
745    else
746        enable_j(handles, 'off')
747    end
748end
749%set(handles.ListPairCiv1,'UserData',displ_num);
750errormsg=find_netcpair_civ( handles,1);
751    if ~isempty(errormsg)
752    msgbox_uvmat('ERROR',errormsg)
753    end
754% find_netcpair_civ2(handles)
755
756function enable_i(handles, state)
757set(handles.itext,'Visible',state)
758% set(handles.MinIndex_i,'Visible',state)
759% set(handles.last_i,'Visible',state)
760% set(handles.incr_i,'Visible',state)
761set(handles.MaxIndex_i,'Visible',state)
762set(handles.ref_i,'Visible',state)
763
764function enable_j(handles, state)
765set(handles.jtext,'Visible',state)
766% set(handles.MinIndex_j,'Visible',state)
767% set(handles.last_j,'Visible',state)
768% set(handles.incr_j,'Visible',state)
769set(handles.MinIndex_j,'Visible',state)
770set(handles.MaxIndex_j,'Visible',state)
771set(handles.ref_j,'Visible',state)
772%hseries=findobj(allchild(0),'Tag','series');
773%hhseries=guidata(hseries);
774%series('enable_j',hhseries,state); %file input with xml reading  in uvmat, show the image in phys coordinates
775
776
777
778%------------------------------------------------------------------------
779% --- Executes on selection change in ListPairCiv1.
780function ListPairCiv1_Callback(hObject, eventdata, handles)
781%------------------------------------------------------------------------
782%reproduce by default the chosen pair in the checkciv2 menu
783list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
784PairString=list_pair{get(handles.ListPairCiv1,'Value')};
785
786[ind1,ind2]=...
787    find_pair_indices(PairString);
788hseries=findobj(allchild(0),'Tag','series');
789hhseries=guidata(hseries);
790set(hhseries.num_first_j,'String',num2str(ind1));
791set(hhseries.num_last_j,'String',num2str(ind2));
792set(hhseries.num_incr_j,'String',num2str(ind2-ind1));
793set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))%civ2 selection the same as civ& by default
794
795
796%------------------------------------------------------------------------
797% --- Executes on selection change in ListPairCiv2.
798function ListPairCiv2_Callback(hObject, eventdata, handles)
799%------------------------------------------------------------------------
800
801
802%------------------------------------------------------------------------
803function ref_i_Callback(hObject, eventdata, handles)
804%------------------------------------------------------------------------
805mode_list=get(handles.ListPairMode,'String');
806mode_value=get(handles.ListPairMode,'Value');
807mode=mode_list{mode_value};
808errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
809if isequal(mode,'series(Di)') || ...% we do patch2 only
810        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
811    errormsg=find_netcpair_civ( handles,2);
812end
813if isempty(errormsg)
814    set(handles.ref_i,'BackgroundColor',[1 1 1])
815    set(handles.ref_j,'BackgroundColor',[1 1 1])
816else
817    msgbox_uvmat('ERROR',errormsg)
818end
819
820function ref_i_KeyPressFcn(hObject, eventdata, handles)
821set(hObject,'BackgroundColor',[1 0 1])
822       
823% %------------------------------------------------------------------------
824% function ref_j_Callback(hObject, eventdata, handles)
825% %------------------------------------------------------------------------
826% mode_list=get(handles.ListPairMode,'String');
827% mode_value=get(handles.ListPairMode,'Value');
828% mode=mode_list{mode_value};
829% errormsg='';
830% if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
831%     errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
832% end
833% if isequal(mode,'series(Dj)') || ...
834%         (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
835%     errormsg=find_netcpair_civ(handles,2);
836% end
837% if ~isempty(errormsg)
838%     msgbox_uvmat('ERROR',errormsg)
839% end
840%
841% function ref_j_KeyPressFcn(hObject, eventdata, handles)
842% set(handles.ref_j,'BackgroundColor',[1 0 1])
843%------------------------------------------------------------------------
844% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
845% the field series set by MinIndex_i, incr, last_i
846% index=1: look for pairs for civ1
847% index=2: look for pairs for civ2
848function errormsg=find_netcpair_civ(handles,index)
849%------------------------------------------------------------------------
850set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
851
852%% initialisation
853errormsg='';
854CivInputData=get(handles.civ_input,'UserData');
855%browse=get(handles.RootPath,'UserData');
856compare_list=get(handles.ListCompareMode,'String');
857val=get(handles.ListCompareMode,'Value');
858compare=compare_list{val};
859if strcmp(compare,'displacement')||strcmp(compare,'shift')
860    mode='displacement';
861else
862    mode_list=get(handles.ListPairMode,'String');
863    mode_value=get(handles.ListPairMode,'Value');
864    if isempty(mode_list)
865        return
866    end
867    mode=mode_list{mode_value};
868end
869nom_type_ima=CivInputData.NomTypeIma;
870
871%% determine nom_type_nc, nomenclature type of the .nc files:
872%[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
873
874%% reads .nc subdirectoy and image numbers from the interface
875%SubDirImages=get(handles.Civ1_ImageA,'String');
876%TODO: determine
877%subdir_civ1=[SubDirImages get(handles.Civ1_ImageB,'String')];%subdirectory subdir_civ1 for the netcdf data
878%subdir_civ2=[SubDirImages get(handles.Civ2_ImageA,'String')];%subdirectory subdir_civ2 for the netcdf data
879ref_i=str2double(get(handles.ref_i,'String'));
880ref_j=[];
881if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
882    ref_j=0;
883elseif strcmp(get(handles.ref_j,'Visible'),'on')
884    ref_j=str2double(get(handles.ref_j,'String'));
885end
886if isempty(ref_j)
887    ref_j=1;
888end
889CivInputData=get(handles.civ_input,'UserData');
890TimeUnit=get(handles.TimeUnit,'String');
891Time=CivInputData.Time;
892checkframe=strcmp(TimeUnit,'frame');
893
894%% case with no Civ1 operation, netcdf files need to exist for reading
895displ_pair={''};
896nbpair=200;%default
897select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
898nbpair=200; %default
899
900%% determine the menu display in .ListPairCiv1
901switch mode
902    case 'series(Di)'
903        for ipair=1:nbpair
904            if select(ipair)
905                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
906                if ~checkframe
907                    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
908                        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
909                        displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
910                    end
911                else
912                    dt=ipair/1000;
913                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(ipair)];
914                end
915            else
916                displ_pair{ipair}='...'; %pair not displayed in the menu
917            end
918        end
919    case 'series(Dj)'
920        for ipair=1:nbpair
921            if select(ipair)
922                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
923                if ~checkframe
924                    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
925                        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
926                        displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
927                    end
928                else
929                    dt=ipair/1000;
930                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
931                end
932            else
933                displ_pair{ipair}='...'; %pair not displayed in the menu
934            end
935        end
936    case 'pair j1-j2'%case of pairs
937%         MinIndex_j=CivInputData.MinIndex_j;
938%         MaxIndex_j=min(CivInputData.MaxIndex_j,10);%limitate the number of pairs to 10x10
939        MinIndex_j=str2num(get(handles.MinIndex_j,'String'));
940        MaxIndex_j=str2num(get(handles.MaxIndex_j,'String'));
941        index_pair=0;
942        %get all the Time intervals in bursts
943        for numod_a=MinIndex_j:MaxIndex_j-1 %nbfield2 always >=2 for 'pair j1-j2' mode
944            for numod_b=(numod_a+1):MaxIndex_j
945                index_pair=index_pair+1;
946                displ_pair{index_pair}=['j= ' num2stra(numod_a,nom_type_ima) '-' num2stra(numod_b,nom_type_ima)];
947                dt(index_pair)=numod_b-numod_a;%default dt
948                if size(Time,1)>ref_i && size(Time,2)>numod_b  % && ~checkframe
949                    dt(index_pair)=Time(ref_i+1,numod_b+1)-Time(ref_i+1,numod_a+1);% Time interval dt
950                    displ_pair{index_pair}=[displ_pair{index_pair} ' :dt= ' num2str(dt(index_pair)*1000)];
951                end
952            end
953           
954        end
955        [tild,indsort]=sort(dt);
956        displ_pair=displ_pair(indsort);
957    case 'displacement'
958        displ_pair={'Di=Dj=0'};
959end
960if index==1
961    set(handles.ListPairCiv1,'String',displ_pair');
962end
963
964%% determine the default selection in the pair menu for Civ1
965ichoice=find(select,1);% index of first selected pair
966if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
967initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
968if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
969    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
970end
971
972%% determine the default selection in the pair menu for Civ2
973if strcmp(get(handles.ListPairCiv2,'Visible'),'on')
974    initial=get(handles.ListPairCiv2,'Value');
975    if initial>length(displ_pair')%|~isequal(select(initial),1)
976        if ichoice <= length(displ_pair')
977            set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
978        else
979            set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
980        end
981    end
982else
983    set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))% initiate the choice of Civ2 as a reproduction of if civ1
984end
985set(handles.ListPairCiv2,'String',displ_pair');
986set(gcf,'Pointer','arrow')% Indicate that the process is finished
987
988
989   
990% %------------------------------------------------------------------------   
991% % call 'view_field.fig' to display the  field selected in the list of 'status'
992% function open_view_field(hObject, eventdata)
993% %------------------------------------------------------------------------
994% list=get(hObject,'String');
995% index=get(hObject,'Value');
996% rootroot=get(hObject,'UserData');
997% filename=list{index};
998% ind_dot=strfind(filename,'...');
999% filename=filename(1:ind_dot-1);
1000% filename=fullfile(rootroot,filename);
1001% delete(get(hObject,'parent'))%delete the display figure to stop the check process
1002% if exist(filename,'file')%visualise the vel field if it exists
1003%     uvmat(filename)
1004%     set(gcbo,'Value',1)
1005% end
1006
1007
1008%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1009% Callbacks in the uipanel Reference Indices
1010%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1011%------------------------------------------------------------------------
1012function MinIndex_i_Callback(hObject, eventdata, handles)
1013%------------------------------------------------------------------------
1014first_i=str2double(get(handles.MinIndex_i,'String'));
1015set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
1016ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
1017
1018% %------------------------------------------------------------------------
1019% function MinIndex_j_Callback(hObject, eventdata, handles)
1020% %------------------------------------------------------------------------
1021% first_j=str2num(get(handles.MinIndex_j,'String'));
1022% set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
1023% ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
1024
1025%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1026% Callbacks in the uipanel Civ1
1027%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1028%------------------------------------------------------------------------
1029% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
1030function SearchRange_Callback(hObject, eventdata, handles)
1031%------------------------------------------------------------------------
1032%determine pair numbers
1033if strcmp(get(handles.num_UMin,'Visible'),'off')
1034    set(handles.u_title,'Visible','on')
1035    set(handles.v_title,'Visible','on')
1036    set(handles.num_UMin,'Visible','on')
1037    set(handles.num_UMax,'Visible','on')
1038    set(handles.num_VMin,'Visible','on')
1039    set(handles.num_VMax,'Visible','on')
1040    %set(handles.CoordUnit,'Visible','on')
1041    %set(handles.TimeUnit,'Visible','on')
1042    %set(handles.slash_title,'Visible','on')
1043    set(handles.min_title,'Visible','on')
1044    set(handles.max_title,'Visible','on')
1045    set(handles.unit_title,'Visible','on')
1046else
1047    get_search_range(hObject, eventdata, handles)
1048end
1049
1050%------------------------------------------------------------------------
1051% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
1052function get_search_range(hObject, eventdata, handles)
1053%------------------------------------------------------------------------
1054param_civ1=read_GUI(handles.Civ1);
1055umin=param_civ1.UMin;
1056umax=param_civ1.UMax;
1057vmin=param_civ1.VMin;
1058vmax=param_civ1.VMax;
1059%switch min_title and max_title in case of error
1060if umax<=umin
1061    umin_old=umin;
1062    umin=umax;
1063    umax=umin_old;
1064    set(handles.num_UMin,'String', num2str(umin))
1065    set(handles.num_UMax,'String', num2str(umax))
1066end
1067if vmax<=vmin
1068    vmin_old=vmin;
1069    vmin=vmax;
1070    vmax=vmin_old;
1071    set(handles.num_VMin,'String', num2str(vmin))
1072    set(handles.num_VMax,'String', num2str(vmax))
1073end   
1074if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
1075%     list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
1076%     index=get(handles.ListPairCiv1,'Value');
1077%     pair_string=list_pair{index};
1078%     time=get(handles.TimeSource,'UserData'); %get the set of times
1079%     pxcm=get(handles.SearchRange,'UserData');
1080%     mode_list=get(handles.ListPairMode,'String');
1081%     mode_value=get(handles.ListPairMode,'Value');
1082%     mode=mode_list{mode_value};     
1083%     if isequal (mode, 'series(Di)' )
1084%         ref_i=str2double(get(handles.ref_i,'String'));
1085%         num1=ref_i-floor(index/2);%  first image numbers
1086%         num2=ref_i+ceil(index/2);
1087%         num_a=1;
1088%         num_b=1;
1089%     elseif isequal (mode, 'series(Dj)')
1090%         num1=1;
1091%         num2=1;
1092%         ref_j=str2double(get(handles.ref_j,'String'));
1093%         num_a=ref_j-floor(index/2);%  first image numbers
1094%         num_b=ref_j+ceil(index/2);
1095%     elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
1096%         ref_i=str2double(get(handles.ref_i,'String'));
1097%         num1=ref_i;
1098%         num2=ref_i;
1099%                 r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
1100%         if isempty(r)
1101%             r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
1102%         end 
1103%         num_a=str2num(r.num1);
1104%         num_b=str2num(r.num2);
1105%     end
1106%     dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
1107%     ibx=str2double(get(handles.num_CorrBoxSize_1,'String'));
1108%     iby=str2double(get(handles.num_CorrBoxSize_2,'String'));
1109%     umin=dt*pxcm*umin;
1110%     umax=dt*pxcm*umax;
1111%     vmin=dt*pxcm*vmin;
1112%     vmax=dt*pxcm*vmax;
1113    shiftx=round((umin+umax)/2);
1114    shifty=round((vmin+vmax)/2);
1115    isx=(umax+2-shiftx)*2+param_civ1.CorrBoxSize(1);
1116    isx=2*ceil(isx/2)+1;
1117    isy=(vmax+2-shifty)*2+param_civ1.CorrBoxSize(2);
1118    isy=2*ceil(isy/2)+1;
1119    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
1120    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
1121    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
1122    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
1123end
1124
1125%------------------------------------------------------------------------
1126% --- Executes on selection in menu CorrSmooth.
1127function num_CorrSmooth_Callback(hObject, eventdata, handles)
1128set(handles.configSource,'String','NEW')
1129set(handles.OK,'BackgroundColor',[1 0 1])
1130%------------------------------------------------------------------------
1131
1132% --- Executes on button press in CheckDeformation.
1133function CheckDeformation_Callback(hObject, eventdata, handles)
1134set(handles.configSource,'String','NEW')
1135set(handles.OK,'BackgroundColor',[1 0 1])
1136
1137%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1138% Callbacks in the uipanel Fix1
1139%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1140%------------------------------------------------------------------------
1141% % --- Executes on button press in CheckMask.
1142% function get_mask_fix1_Callback(hObject, eventdata, handles)
1143% %------------------------------------------------------------------------
1144% maskval=get(handles.CheckMask,'Value');
1145% if isequal(maskval,0)
1146%     set(handles.Mask,'String','')
1147% else
1148%     mask_displ='no mask'; %default
1149%     filebase=get(handles.RootPath,'String');
1150%     [nbslice, flag_mask]=get_mask(filebase,handles);
1151%     if isequal(flag_mask,1)
1152%         mask_displ=[num2str(nbslice) 'mask'];
1153%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1154%         filebase_a=get(handles.RootFile_1,'String');
1155%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1156%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1157%             mask_displ='no mask';
1158%         end
1159%     end
1160%     if isequal(mask_displ,'no mask')
1161%         [FileName, PathName, filterindex] = uigetfile( ...
1162%             {'*.png', ' (*.png)';
1163%             '*.png',  '.png files '; ...
1164%             '*.*', 'All Files (*.*)'}, ...
1165%             'Pick a mask file *.png',filebase);
1166%         mask_displ=fullfile(PathName,FileName);
1167%         if ~exist(mask_displ,'file')
1168%             mask_displ='no mask';
1169%         end
1170%     end
1171%     if isequal(mask_displ,'no mask')
1172%         set(handles.CheckMask,'Value',0)
1173%         set(handles.CheckMask,'Value',0)
1174%         set(handles.CheckMask,'Value',0)
1175%     else
1176%         %set(handles.CheckMask,'Value',1)
1177%         set(handles.CheckMask,'Value',1)
1178%     end
1179%     set(handles.Mask,'String',mask_displ)
1180%     set(handles.Mask,'String',mask_displ)
1181%     set(handles.Mask,'String',mask_displ)
1182% end
1183
1184%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1185% Callbacks in the uipanel Civ2
1186%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1187%------------------------------------------------------------------------
1188% --- Executes on button press in CheckMask: select box for mask option
1189function get_mask_civ2_Callback(hObject, eventdata, handles)
1190%------------------------------------------------------------------------
1191maskval=get(handles.CheckMask,'Value');
1192if isequal(maskval,0)
1193    set(handles.Mask,'String','')
1194else
1195    mask_displ='no mask'; %default
1196    filebase=get(handles.RootPath,'String');
1197    [nbslice, flag_mask]=get_mask(filebase,handles);
1198    if isequal(flag_mask,1)
1199        mask_displ=[num2str(nbslice) 'mask'];
1200    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1201        filebase_a=get(handles.RootFile_1,'String');
1202        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1203        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1204            mask_displ='no mask';
1205        end
1206    end
1207    if isequal(mask_displ,'no mask')
1208        [FileName, PathName, filterindex] = uigetfile( ...
1209            {'*.png', ' (*.png)';
1210            '*.png',  '.png files '; ...
1211            '*.*', 'All Files (*.*)'}, ...
1212            'Pick a mask file *.png',filebase);
1213        mask_displ=fullfile(PathName,FileName);
1214        if ~exist(mask_displ,'file')
1215            mask_displ='no mask';
1216        end
1217    end
1218    if isequal(mask_displ,'no mask')
1219        set(handles.CheckMask,'Value',0)
1220        set(handles.CheckMask,'Value',0)
1221    else
1222        set(handles.CheckMask,'Value',1)
1223    end
1224    set(handles.Mask,'String',mask_displ)
1225end
1226
1227% %------------------------------------------------------------------------
1228% % --- Executes on button press in CheckMask.
1229% function get_mask_fix2_Callback(hObject, eventdata, handles)
1230% %------------------------------------------------------------------------
1231% maskval=get(handles.CheckMask,'Value');
1232% if isequal(maskval,0)
1233%     set(handles.Mask,'String','')
1234% else
1235%     mask_displ='no mask'; %default
1236%     filebase=get(handles.RootPath,'String');
1237%     [nbslice, flag_mask]=get_mask(filebase,handles);
1238%     if isequal(flag_mask,1)
1239%         mask_displ=[num2str(nbslice) 'mask'];
1240%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
1241%         filebase_a=get(handles.RootFile_1,'String');
1242%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
1243%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
1244%             mask_displ='no mask';
1245%         end
1246%     end
1247%     if isequal(mask_displ,'no mask')
1248%         [FileName, PathName, filterindex] = uigetfile( ...
1249%             {'*.png', ' (*.png)';
1250%             '*.png',  '.png files '; ...
1251%             '*.*', 'All Files (*.*)'}, ...
1252%             'Pick a mask file *.png',filebase);
1253%         mask_displ=fullfile(PathName,FileName);
1254%         if ~exist(mask_displ,'file')
1255%             mask_displ='no mask';
1256%         end
1257%     end
1258%     if isequal(mask_displ,'no mask')
1259%         set(handles.CheckMask,'Value',0)
1260%     end
1261%     set(handles.Mask,'String',mask_displ)
1262% end
1263
1264%------------------------------------------------------------------------
1265% --- function called to look for mask files
1266function [nbslice, flag_mask]=get_mask(filebase,handles)
1267%------------------------------------------------------------------------
1268%detect mask files, images with appropriate file base
1269%[filebase '_' xx 'mask'], xx=nbslice
1270%flag_mask=1 indicates detection
1271
1272flag_mask=0;%default
1273nbslice=1;
1274
1275% subdir=get(handles.Civ1_ImageB,'String');
1276[Path,Name]=fileparts(filebase);
1277if ~isdir(Path)
1278    msgbox_uvmat('ERROR','no path for input files')
1279    return
1280end
1281% currentdir=pwd;
1282% cd(Path);%move in the dir of the root name filebase
1283maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
1284% cd(currentdir);%come back to the current working directory
1285if ~isempty(maskfiles)
1286    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
1287    % else
1288    flag_mask=1;
1289    maskname=maskfiles(1).name;% take the first mask file in the list
1290    [Path2,Name,ext]=fileparts(maskname);
1291    Namedouble=double(Name);
1292    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1293    ind_mask=findstr('mask',Name);
1294    i=ind_mask-1;
1295    while val(i)==0 && i>0
1296        i=i-1;
1297    end
1298    nbslice=str2double(Name(i+1:ind_mask-1));
1299    if ~isnan(nbslice) && Name(i)=='_'
1300        flag_mask=1;
1301    else
1302        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
1303        return
1304        nbslice=1;
1305    end
1306end
1307
1308%------------------------------------------------------------------------
1309% --- function called to look for grid files
1310function [nbslice, flag_grid]=get_grid(filebase,handles)
1311%------------------------------------------------------------------------
1312flag_grid=0;%default
1313nbslice=1;
1314[Path,Name]=fileparts(filebase);
1315currentdir=pwd;
1316cd(Path);%move in the dir of the root name filebase
1317gridfiles=dir([Name '_*grid_*.grid']);%look for grid files
1318cd(currentdir);%come back to the current working directory
1319if ~isempty(gridfiles)
1320    flag_grid=1;
1321    gridname=gridfiles(1).name;% take the first grid file in the list
1322    [Path2,Name,ext]=fileparts(gridname);
1323    Namedouble=double(Name);
1324    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1325    ind_grid=findstr('grid',Name);
1326    i=ind_grid-1;
1327    while val(i)==0 && i>0
1328        i=i-1;
1329    end
1330    nbslice=str2double(Name(i+1:ind_grid-1));
1331    if ~isnan(nbslice) && Name(i)=='_'
1332        flag_grid=1;
1333    else
1334        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
1335        return
1336        nbslice=1;
1337    end
1338end
1339
1340%------------------------------------------------------------------------
1341% --- transform numbers to letters
1342function str=num2stra(num,nom_type)
1343%------------------------------------------------------------------------
1344if isempty(nom_type)
1345    str='';
1346elseif strcmp(nom_type(end),'a')
1347    str=char(96+num);
1348elseif strcmp(nom_type(end),'A')
1349    str=char(96+num);
1350elseif isempty(nom_type(2:end))%a single index
1351    str='';
1352else
1353    str=num2str(num);
1354end
1355
1356% %------------------------------------------------------------------------
1357% % --- Executes on button press in ListSubdirCiv1.
1358% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
1359% %------------------------------------------------------------------------
1360% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
1361% val=get(handles.ListSubdirCiv1,'Value');
1362% SubDir=list_subdir_civ1{val};
1363% if strcmp(SubDir,'new...')
1364%     if get(handles.CheckCiv1,'Value')
1365%         SubDir='CIV_INPUT'; %default subdirectory
1366%     else
1367%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new civ_input operation')
1368%         return
1369%     end   
1370% end
1371% set(handles.Civ1_ImageB,'String',SubDir);
1372% errormsg=find_netcpair_civ(handles,1);
1373% if ~isempty(errormsg)
1374%     msgbox_uvmat('ERROR',errormsg)
1375% end
1376%     
1377%------------------------------------------------------------------------
1378% % --- Executes on button press in ListSubdirCiv2.
1379% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
1380% %------------------------------------------------------------------------
1381% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
1382% val=get(handles.ListSubdirCiv2,'Value');
1383% SubDir=list_subdir_civ2{val};
1384% if strcmp(SubDir,'new...')
1385%     if get(handles.CheckCiv2,'Value')
1386%         SubDir='CIV_INPUT'; %default subdirectory
1387%     else
1388%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new civ_input operation')
1389%         return
1390%     end
1391% end
1392% set(handles.Civ2_ImageA,'String',SubDir);
1393
1394%------------------------------------------------------------------------
1395% --- Executes on button press in CheckGrid.
1396function CheckGrid_Callback(hObject, eventdata, handles)
1397%------------------------------------------------------------------------
1398value=get(hObject,'Value');
1399hparent=get(hObject,'parent');%handles of the parent panel
1400hchildren=get(hparent,'children');
1401handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel
1402handle_dx=findobj(hchildren,'tag','num_Dx');
1403handle_dy=findobj(hchildren,'tag','num_Dy');
1404handle_title_dx=findobj(hchildren,'tag','title_Dx');
1405handle_title_dy=findobj(hchildren,'tag','title_Dy');
1406testgrid=0;
1407filegrid='';
1408if value
1409        hseries=findobj(allchild(0),'Tag','series');
1410    hhseries=guidata(hseries);
1411    InputTable=get(hhseries.InputTable,'Data');
1412     ind_A=1;% line index of the (first) image series
1413    if strcmp(InputTable{1,5},'.nc');
1414        ind_A=2;
1415    end
1416    filebase=InputTable{ind_A,1};
1417    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
1418    if isequal(flag_grid,1)
1419        filegrid=[num2str(nbslice) 'grid'];
1420        testgrid=1;
1421    else % browse for a grid
1422        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
1423        if exist(filegrid,'file')
1424            filebase=filegrid;
1425        end
1426       filegrid = uigetfile_uvmat('pick a grid file .grid:',filebase,'.grid');
1427        set(hObject,'UserData',filegrid);%store for future use
1428        if ~isempty(filegrid)
1429            testgrid=1;
1430        end
1431        set(hObject,'UserData',filegrid);%store for future use
1432    end
1433end
1434if testgrid
1435    set(handle_dx,'Visible','off');
1436    set(handle_dy,'Visible','off');
1437    set(handle_title_dy,'Visible','off');
1438    set(handle_title_dx,'Visible','off');
1439    set(handle_txtbox,'Visible','on')
1440    set(handle_txtbox,'String',filegrid)
1441else
1442    set(hObject,'Value',0);
1443    set(handle_dx,'Visible','on');
1444    set(handle_dy,'Visible','on');
1445    set(handle_title_dy,'Visible','on');
1446    set(handle_title_dx,'Visible','on');
1447    set(handle_txtbox,'Visible','off')
1448end
1449
1450%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
1451PanelName=get(hparent,'tag');
1452if strcmp(PanelName,'Civ1')
1453    hchildren=get(handles.Civ2,'children');
1454    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
1455    handle_txtbox=findobj(hchildren,'tag','Grid');
1456    handle_dx=findobj(hchildren,'tag','num_Dx');
1457    handle_dy=findobj(hchildren,'tag','num_Dy');
1458    handle_title_dx=findobj(hchildren,'tag','title_Dx');
1459    handle_title_dy=findobj(hchildren,'tag','title_Dy');
1460    set(handle_checkbox,'UserData',filegrid);%store for future use
1461    if testgrid
1462        set(handle_checkbox,'Value',1);
1463        set(handle_dx,'Visible','off');
1464        set(handle_dy,'Visible','off');
1465        set(handle_title_dx,'Visible','off');
1466        set(handle_title_dy,'Visible','off');
1467        set(handle_txtbox,'Visible','on')
1468        set(handle_txtbox,'String',filegrid)
1469    end
1470end
1471set(hObject,'BackgroundColor',[1 0 1])
1472set(handles.configSource,'String','NEW')
1473set(handles.OK,'BackgroundColor',[1 0 1])
1474%------------------------------------------------------------------------
1475% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
1476function CheckMask_Callback(hObject, eventdata, handles)
1477%------------------------------------------------------------------------
1478value=get(hObject,'Value');
1479hparent=get(hObject,'parent');
1480parent_tag=get(hparent,'Tag');
1481hchildren=get(hparent,'children');
1482handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
1483
1484testmask=0;
1485if value
1486    hseries=findobj(allchild(0),'Tag','series');
1487    hhseries=guidata(hseries);
1488    InputTable=get(hhseries.InputTable,'Data');
1489    ind_A=1;% line index of the (first) image series
1490    if strcmp(InputTable{1,5},'.nc');
1491        ind_A=2;
1492    end
1493    [nbslice, flag_mask]=get_mask(InputTable{ind_A,1},handles);% look for a mask with appropriate name
1494    if isequal(flag_mask,1)
1495        filemask=[num2str(nbslice) 'mask'];
1496        testmask=1;
1497    else % browse for a mask
1498%         filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
1499%         if exist(filemask,'file')
1500%             filebase=filemask;
1501%         end
1502        filemask= uigetfile_uvmat('pick a mask image file:',InputTable{ind_A,1},'image');
1503        set(hObject,'UserData',filemask);%store for future use
1504        if ~isempty(filemask)
1505            testmask=1;
1506        end
1507    end
1508end
1509if testmask
1510    set(handles.Mask,'Visible','on')
1511    set(handles.Mask,'String',filemask)
1512    set(handles.CheckMask,'Value',1)
1513else
1514    set(hObject,'Value',0);
1515    set(handle_txtbox,'Visible','off')
1516end
1517set(handles.configSource,'String','NEW')
1518set(handles.configSource,'BackgroundColor',[1 0 1])
1519
1520% %------------------------------------------------------------------------
1521% % --- Executes on button press in get_gridpatch1.
1522% function get_gridpatch1_Callback(hObject, eventdata, handles)
1523% %------------------------------------------------------------------------
1524% filebase=get(handles.RootPath,'String');
1525% [FileName, PathName, filterindex] = uigetfile( ...
1526%     {'*.grid', ' (*.grid)';
1527%     '*.grid',  '.grid files '; ...
1528%     '*.*', 'All Files (*.*)'}, ...
1529%     'Pick a file',filebase);
1530% filegrid=fullfile(PathName,FileName);
1531% set(handles.grid_patch1,'string',filegrid);
1532% set(hObject,'BackgroundColor',[1 0 1])
1533
1534%------------------------------------------------------------------------
1535% --- STEREO Interp
1536function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
1537%------------------------------------------------------------------------
1538namelog=[filename_nc(1:end-3) '_stinterp.log'];
1539cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
1540    ' -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
1541
1542% %------------------------------------------------------------------------
1543% %--read images and convert them to the uint16 format used for PIV
1544% function A=read_image(filename,type_ima,num,movieobject)
1545% %------------------------------------------------------------------------
1546% %num is the view number needed for an avi movie
1547% switch type_ima
1548%     case 'movie'
1549%         A=read(movieobject,num);
1550%     case 'avi'
1551%         mov=aviread(filename,num);
1552%         A=frame2im(mov(1));
1553%     case 'multimage'
1554%         A=imread(filename,num);
1555%     case 'image'
1556%         A=imread(filename);
1557% end
1558% siz=size(A);
1559% if length(siz)==3;%color images
1560%     A=sum(double(A),3);
1561%     A=uint16(A);
1562% end
1563
1564
1565%------------------------------------------------------------------------
1566% --- Executes on button press in get_ref_fix1.
1567function get_ref_fix1_Callback(hObject, eventdata, handles)
1568%------------------------------------------------------------------------
1569filebase=get(handles.RootPath,'String');
1570[FileName, PathName, filterindex] = uigetfile( ...
1571    {'*.nc', ' (*.nc)';
1572    '*.nc',  'netcdf files '; ...
1573    '*.*', 'All Files (*.*)'}, ...
1574    'Pick a file',filebase);
1575
1576fileinput=[PathName FileName];
1577sizf=size(fileinput);
1578if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1579%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1580[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1581ref.filebase=fullfile(Path,File);
1582% ref.num_a=stra2num(str_a);
1583% ref.num_b=stra2num(str_b);
1584% ref.num1=str2double(field_count);
1585% ref.num2=str2double(str2);
1586browse=[];%initialisation
1587if ~isequal(ref.ext,'.nc')
1588    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1589    return
1590end
1591set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
1592set(handles.ref_fix1,'UserData',ref)
1593menu_field{1}='civ1';
1594Data=nc2struct(fileinput,[]);
1595if isfield(Data,'patch') && isequal(Data.patch,1)
1596    menu_field{2}='filter1';
1597end
1598if isfield(Data,'civ2') && isequal(Data.civ2,1)
1599    menu_field{3}='civ2';
1600end
1601if isfield(Data,'patch2') && isequal(Data.patch2,1)
1602    menu_field{4}='filter2';
1603end
1604set(handles.field_ref1,'String',menu_field);
1605set(handles.field_ref1,'Value',length(menu_field));
1606set(handles.num_MinVel,'Value',2);
1607set(handles.num_MinVel,'String','1');%default threshold
1608set(handles.ref_fix1,'Enable','on')
1609
1610%------------------------------------------------------------------------
1611% --- Executes on button press in get_ref_fix2.
1612function get_ref_fix2_Callback(hObject, eventdata, handles)
1613%------------------------------------------------------------------------
1614if isequal(get(handles.get_ref_fix2,'Value'),1)
1615    filebase=get(handles.RootPath,'String');
1616    [FileName, PathName, filterindex] = uigetfile( ...
1617        {'*.nc', ' (*.nc)';
1618        '*.nc',  'netcdf files '; ...
1619        '*.*', 'All Files (*.*)'}, ...
1620        'Pick a file',filebase);
1621    fileinput=[PathName FileName];
1622    sizf=size(fileinput);
1623    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
1624    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
1625    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
1626    ref.filebase=fullfile(Path,File);
1627    %     ref.num_a=stra2num(str_a);
1628    %     ref.num_b=stra2num(str_b);
1629    %     ref.num1=str2num(field_count);
1630    %     ref.num2=str2num(str2);
1631    browse=[];%initialisation
1632    if ~isequal(ref.ext,'.nc')
1633        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
1634        return
1635    end
1636    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
1637    set(handles.ref_fix2,'UserData',ref)
1638    menu_field{1}='civ1';
1639    Data=nc2struct(fileinput,[]);
1640    if isfield(Data,'patch') && isequal(Data.patch,1)
1641        menu_field{2}='filter1';
1642    end
1643    if isfield(Data,'civ2') && isequal(Data.civ2,1)
1644        menu_field{3}='civ2';
1645    end
1646    if isfield(Data,'patch2') && isequal(Data.patch2,1)
1647        menu_field{4}='filter2';
1648    end
1649    set(handles.field_ref2,'String',menu_field);
1650    set(handles.field_ref2,'Value',length(menu_field));
1651    set(handles.num_MinVel,'Value',2);
1652    set(handles.num_MinVel,'String','1');%default threshold
1653    set(handles.ref_fix2,'Enable','on')
1654    set(handles.ref_fix2,'Visible','on')
1655    set(handles.field_ref2,'Visible','on')
1656else
1657    set(handles.ref_fix2,'Visible','off')
1658    set(handles.field_ref2,'Visible','off')
1659end
1660
1661%------------------------------------------------------------------------
1662function ref_fix1_Callback(hObject, eventdata, handles)
1663%------------------------------------------------------------------------
1664set(handles.num_MinVel,'Value',1);
1665set(handles.field_ref1,'Value',1)
1666set(handles.field_ref1,'String',{' '})
1667set(handles.ref_fix1,'UserData',[]);
1668set(handles.ref_fix1,'String','');
1669set(handles.thresh_vel1,'String','0');
1670
1671%------------------------------------------------------------------------
1672function ref_fix2_Callback(hObject, eventdata, handles)
1673%------------------------------------------------------------------------
1674set(handles.num_MinVel,'Value',1);
1675set(handles.field_ref2,'Value',1)
1676set(handles.field_ref2,'String',{' '})
1677set(handles.ref_fix2,'UserData',[]);
1678set(handles.ref_fix2,'String','');
1679set(handles.num_MinVel,'String','0');
1680
1681%------------------------------------------------------------------------
1682% --- TO ABANDON Executes on button press in test_stereo1.
1683function CheckStereo_Callback(hObject, eventdata, handles)
1684%------------------------------------------------------------------------
1685hparent=get(hObject,'parent');
1686parent_tag=get(hparent,'Tag');
1687hchildren=get(hparent,'children');
1688handle_txtbox=findobj(hchildren,'tag','txt_Mask');
1689if isequal(get(hObject,'Value'),0)
1690    set(handles.num_SubDomainSize,'Visible','on')
1691    set(handles.num_FieldSmooth,'Visible','on')
1692else
1693    set(handles.num_SubDomainSize,'Visible','off')
1694    set(handles.num_FieldSmooth,'Visible','off')
1695end
1696
1697% %------------------------------------------------------------------------
1698% % --- Executes on button press in CheckStereo.
1699% function StereoCheck_Callback(hObject, eventdata, handles)
1700% %------------------------------------------------------------------------
1701% if isequal(get(handles.CheckStereo,'Value'),0)
1702%     set(handles.num_subdomainsize,'Visible','on')
1703%     set(handles.num_FieldSmooth,'Visible','on')
1704% else
1705
1706%     set(handles.num_subdomainsize,'Visible','off')
1707%     set(handles.num_FieldSmooth,'Visible','off')
1708% end
1709
1710
1711
1712%------------------------------------------------------------------------
1713%----function introduced for the correlation window figure, activated by deleting this window
1714function closeview_field(gcbo,eventdata)
1715%------------------------------------------------------------------------
1716hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1717if ~isempty(hview_field)
1718    delete(hview_field)
1719end
1720
1721%------------------------------------------------------------------------
1722% --- Executes on button press in CheckThreshold.
1723function CheckThreshold_Callback(hObject, eventdata, handles)
1724%------------------------------------------------------------------------
1725huipanel=get(hObject,'parent');
1726obj(1)=findobj(huipanel,'Tag','num_MinIma');
1727obj(2)=findobj(huipanel,'Tag','num_MaxIma');
1728obj(3)=findobj(huipanel,'Tag','title_Threshold');
1729if get(hObject,'Value')
1730    set(obj,'Visible','on')
1731else
1732    set(obj,'Visible','off')
1733end
1734set(handles.configSource,'String','NEW')
1735set(handles.OK,'BackgroundColor',[1 0 1])
1736%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1737%%%%%%%%%%%%%%   TEST functions
1738%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1739%------------------------------------------------------------------------
1740% --- Executes on button press in TestCiv1: prepare the image correlation function
1741%     activated by mouse motion
1742function TestCiv1_Callback(hObject, eventdata, handles)
1743%------------------------------------------------------------------------
1744drawnow
1745if get(handles.TestCiv1,'Value')
1746    set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch 
1747    %Param.Action.RUN=1;
1748   
1749      hseries=findobj(allchild(0),'Tag','series');
1750     Param=read_GUI(hseries);
1751     Param.Action.RUN=1;
1752     Param.ActionInput=read_GUI(handles.civ_input);
1753     if isfield(Param,'OutputSubDir')
1754     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1755     end
1756     Param.ActionInput.Civ1.CorrSmooth=0;% launch Civ1 with no data point (to get the image names for A and B)
1757     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1758   
1759 %% create image data ImageData for display
1760     ImageData.ListVarName={'ny','nx','A'};
1761     ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
1762     ImageData.A=imread(Data.Civ1_ImageA); % read the first image
1763     if ndims(ImageData.A)==3 %case of color image
1764         ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
1765     end
1766     ImageData.ny=[size(ImageData.A,1) 1];
1767     ImageData.nx=[1 size(ImageData.A,2)];
1768     ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
1769
1770     %% create the figure view_field for image visualization
1771     hview_field=view_field(ImageData); %view the image in the GUI view_field
1772     set(0,'CurrentFigure',hview_field)
1773     hhview_field=guihandles(hview_field);
1774     set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
1775     ViewData=get(hview_field,'UserData');
1776     ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
1777     ViewData.PlotAxes.X=Data.Civ1_X';
1778     ViewData.PlotAxes.Y=Data.Civ1_Y';
1779     ViewData.PlotAxes.B=imread(Data.Civ1_ImageB);%store the second image in the UserData of the GUI view_field
1780     set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field
1781   
1782    %% look for a current figure for image correlation display
1783    corrfig=findobj(allchild(0),'tag','corrfig');
1784    if isempty(corrfig)
1785        corrfig=figure;
1786        set(corrfig,'tag','corrfig')
1787        set(corrfig,'name','image correlation')
1788        set(corrfig,'DeleteFcn',{@closeview_field})%
1789        set(handles.TestCiv1,'BackgroundColor',[1 0 0])
1790    else
1791        set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
1792        corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1793        if ~isempty(corrfig)
1794            delete(corrfig)
1795        end
1796        hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1797        if ~isempty(hview_field)
1798            delete(hview_field)
1799        end
1800    end
1801else
1802    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
1803    if ~isempty(hview_field)
1804        delete(hview_field)
1805    end     
1806end
1807
1808% --------------------------------------------------------------------
1809% --- Executes on button press in TestPatch1.
1810% --------------------------------------------------------------------
1811function TestPatch1_Callback(hObject, eventdata, handles)
1812
1813if get(handles.TestPatch1,'Value')% if TestPatch1 is activated
1814     set(handles.TestPatch1,'BackgroundColor',[1 1 0])%paint TestPatch1 button in yellow to indicate activation
1815     set(handles.Civ1,'BackgroundColor',[1 1 0])% indicate civ1 calculation is performed
1816     hseries=findobj(allchild(0),'Tag','series');
1817     Param=read_GUI(hseries);
1818     Param.Action.RUN=1;
1819     Param.ActionInput=read_GUI(handles.civ_input);
1820     if isfield(Param,'OutputSubDir')
1821     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1822     end
1823     ParamPatch1=Param.ActionInput.Patch1; %store the patch1 parameters
1824     Param.ActionInput=rmfield(Param.ActionInput,'Patch1');% does not execute Patch
1825     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1826     bckcolor=get(handles.civ_input,'Color');
1827     set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calculation is finished
1828     
1829     %% prepare Param for iterative Patch processing without input file reading
1830     Param.Civ1_X=Data.Civ1_X;
1831     Param.Civ1_Y=Data.Civ1_Y;
1832     Param.Civ1_U=Data.Civ1_U;
1833     Param.Civ1_V=Data.Civ1_V;
1834     Param.Civ1_FF=Data.Civ1_FF;
1835     Param=rmfield(Param,'InputTable');%desactivate input file reading
1836    if isfield(Param.ActionInput,'Civ1')
1837        Param.ActionInput=rmfield(Param.ActionInput,'Civ1');%desactivate civ1: remove civ1 input param if relevant
1838    end
1839    if isfield(Param.ActionInput,'Fix1')
1840        Param.ActionInput=rmfield(Param.ActionInput,'Fix1');%desactivate fix1:remove fix1 input param if relevant
1841    end
1842    SmoothingParam=(ParamPatch1.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
1843    NbGood=numel(find(Data.Civ1_FF==0));
1844    NbExclude=zeros(1,7);% initialize the set of smoothing parameters
1845    DiffVel=zeros(1,7);% initialize the rms difference between patch and civ
1846    Param.ActionInput.Patch1=ParamPatch1;% retrieve Patch1 parameters
1847    for irho=1:7
1848        Param.ActionInput.Patch1.FieldSmooth=SmoothingParam(irho);
1849        [Data,errormsg]= civ_series(Param);%apply the processing fct
1850        if ~isempty(errormsg)
1851            msgbox_uvmat('ERROR',errormsg)
1852            return
1853        end
1854        ind_good=find(Data.Civ1_FF==0);
1855        Civ1_U_Diff=Data.Civ1_U(ind_good)-Data.Civ1_U_smooth(ind_good);
1856        Civ1_V_Diff=Data.Civ1_V(ind_good)-Data.Civ1_V_smooth(ind_good);
1857        DiffVel(irho)=sqrt(mean(Civ1_U_Diff.*Civ1_U_Diff+Civ1_V_Diff.*Civ1_V_Diff));
1858        NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
1859    end
1860    figure(1)
1861    hold on
1862    semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r')
1863    grid on
1864    legend('rms velocity diff. Patch1-Civ1 (pixels)','proportion of excluded vectors (between 0 to 1)')
1865    xlabel('smoothing parameter')
1866    ylabel('smoothing effect')
1867    set(handles.TestPatch1,'BackgroundColor',[0 1 0])
1868else
1869    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1870    if ~isempty(corrfig)
1871        delete(corrfig)
1872    end
1873    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1874    if ~isempty(hview_field)
1875        delete(hview_field)
1876    end
1877end
1878
1879%------------------------------------------------------------------------
1880% --- Executes on button press in TestCiv2.
1881%------------------------------------------------------------------------
1882function TestCiv2_Callback(hObject, eventdata, handles)
1883drawnow
1884if get(handles.TestCiv2,'Value')
1885    set(handles.TestCiv2,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch
1886      hseries=findobj(allchild(0),'Tag','series');
1887     Param=read_GUI(hseries);
1888     Param.Action.RUN=1;
1889     Param.ActionInput=read_GUI(handles.civ_input);
1890     if isfield(Param,'OutputSubDir')
1891     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1892     end
1893     Param.ActionInput.Civ2.CorrSmooth=0;% launch Civ2 with no data point (to get the image names for A and B)
1894     set(handles.Civ1,'BackgroundColor',[1 1 0])
1895     set(handles.Fix1,'BackgroundColor',[1 1 0])
1896     set(handles.Patch1,'BackgroundColor',[1 1 0])
1897     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1898     
1899     %% create image data ImageData for display
1900     ImageData.ListVarName={'ny','nx','A'};
1901     ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
1902     ImageData.A=imread(Data.Civ2_ImageA); % read the first image
1903     if ndims(ImageData.A)==3 %case of color image
1904         ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
1905     end
1906     ImageData.ny=[size(ImageData.A,1) 1];
1907     ImageData.nx=[1 size(ImageData.A,2)];
1908     ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly
1909
1910     %% create the figure view_field for image visualization
1911    hview_field=view_field(ImageData); %view the image in the GUI view_field
1912    set(0,'CurrentFigure',hview_field)
1913    % plot the boundaries of the subdomains used for patch
1914    for isub=1:size(Data.Civ1_SubRange,3);
1915        pos_x=Data.Civ1_SubRange(1,1,isub);
1916        pos_y=Data.Civ1_SubRange(2,1,isub);
1917        width=Data.Civ1_SubRange(1,2,isub)-Data.Civ1_SubRange(1,1,isub);
1918        height=Data.Civ1_SubRange(2,2,isub)-Data.Civ1_SubRange(2,1,isub);
1919        rectangle('Position',[pos_x pos_y width height],'EdgeColor',[0 0 1])
1920    end
1921    hhview_field=guihandles(hview_field);%
1922    set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
1923    ViewData=get(hview_field,'UserData'); % get the currently plotted field (the image A)
1924    % store info in the UserData of view-field
1925    ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field
1926    ViewData.PlotAxes.B=imread(Data.Civ2_ImageB);%store the second image in the UserData of the GUI view_field
1927    ViewData.PlotAxes.X=Data.Civ2_X';
1928    ViewData.PlotAxes.Y=Data.Civ2_Y';
1929    ViewData.PlotAxes.ShiftX=Data.Civ2_U';% shift at each point (from patch1) estimated by running civ2
1930    ViewData.PlotAxes.ShiftY=Data.Civ2_V';
1931    ViewData.PlotAxes.Civ1_SubRange=Data.Civ1_SubRange;
1932    ViewData.PlotAxes.Civ1_NbCentres=Data.Civ1_NbCentres;
1933    ViewData.PlotAxes.Civ1_Coord_tps=Data.Civ1_Coord_tps;
1934    ViewData.PlotAxes.Civ1_U_tps=Data.Civ1_U_tps;
1935    ViewData.PlotAxes.Civ1_V_tps=Data.Civ1_V_tps;
1936    ViewData.PlotAxes.Civ1_Dt=Data.Civ1_Dt;
1937    ViewData.PlotAxes.Civ2_Dt=Data.Civ2_Dt;
1938    set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field
1939    bckcolor=get(handles.civ_input,'Color');
1940    set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calmculation is finished
1941    set(handles.Fix1,'BackgroundColor',bckcolor)
1942    set(handles.Patch1,'BackgroundColor',bckcolor)
1943    drawnow
1944   
1945    %% look for a current figure for image correlation display
1946    corrfig=findobj(allchild(0),'tag','corrfig');
1947    if isempty(corrfig)
1948        corrfig=figure;
1949        set(corrfig,'tag','corrfig')
1950        set(corrfig,'name','image correlation')
1951        set(corrfig,'DeleteFcn',{@closeview_field})%
1952        set(handles.TestCiv1,'BackgroundColor',[1 0 0])
1953    else
1954        set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
1955        corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
1956        if ~isempty(corrfig)
1957            delete(corrfig)
1958        end
1959        hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
1960        if ~isempty(hview_field)
1961            delete(hview_field)
1962        end
1963    end   
1964else
1965    hview_field=findobj(allchild(0),'Tag','view_field'); %view the image in the GUI view_field
1966    if ~isempty(hview_field)
1967        delete(hview_field)
1968    end     
1969end
1970
1971
1972% --- Executes on button press in TestPatch2.
1973function TestPatch2_Callback(hObject, eventdata, handles)
1974if get(handles.TestPatch2,'Value')% if TestPatch2 is activated
1975     set(handles.TestPatch2,'BackgroundColor',[1 1 0])%paint TestPatch2 button in yellow to indicate activation
1976     set(handles.Civ1,'BackgroundColor',[1 1 0])% indicate civ1 calculation is activated
1977     set(handles.Fix1,'BackgroundColor',[1 1 0])% indicate fix1 calculation is activated
1978     set(handles.Patch1,'BackgroundColor',[1 1 0])% indicate Patch1 calculation is activated
1979     set(handles.Civ2,'BackgroundColor',[1 1 0])% indicate civ2 calculation is activated
1980     set(handles.Fix2,'BackgroundColor',[1 1 0])% indicate fix2 calculation is activated
1981     hseries=findobj(allchild(0),'Tag','series');
1982     Param=read_GUI(hseries);
1983     Param.Action.RUN=1;
1984     Param.ActionInput=read_GUI(handles.civ_input);
1985     if isfield(Param,'OutputSubDir')
1986     Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series
1987     end
1988     ParamPatch2=Param.ActionInput.Patch2; %store the patch1 parameters
1989     Param.ActionInput=rmfield(Param.ActionInput,'Patch2');% does not execute Patch
1990     [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results
1991     bckcolor=get(handles.civ_input,'Color');
1992     set(handles.Civ1,'BackgroundColor',bckcolor)% indicate civ1 calculation is finished
1993     set(handles.Fix1,'BackgroundColor',bckcolor)% indicate fix1 calculation is finished
1994     set(handles.Patch1,'BackgroundColor',bckcolor)% indicate Patch1 calculation is finished
1995     set(handles.Civ2,'BackgroundColor',bckcolor)% indicate civ2 calculation is finished
1996     set(handles.Fix2,'BackgroundColor',bckcolor)% indicate fix2 calculation is finished
1997     
1998     %% prepare Param for iterative Patch processing without input file reading
1999     Param.Civ2_X=Data.Civ2_X;
2000     Param.Civ2_Y=Data.Civ2_Y;
2001     Param.Civ2_U=Data.Civ2_U;
2002     Param.Civ2_V=Data.Civ2_V;
2003     Param.Civ2_FF=Data.Civ2_FF;
2004     Param=rmfield(Param,'InputTable');%desactivate input file reading
2005    if isfield(Param.ActionInput,'Civ1')
2006        Param.ActionInput=rmfield(Param.ActionInput,'Civ1');%desactivate civ1: remove civ1 input param if relevant
2007    end
2008    if isfield(Param.ActionInput,'Fix1')
2009        Param.ActionInput=rmfield(Param.ActionInput,'Fix1');%desactivate fix1:remove fix1 input param if relevant
2010    end
2011    if isfield(Param.ActionInput,'Patch1')
2012        Param.ActionInput=rmfield(Param.ActionInput,'Patch1');%desactivate fix1:remove fix1 input param if relevant
2013    end
2014    if isfield(Param.ActionInput,'Civ2')
2015        Param.ActionInput=rmfield(Param.ActionInput,'Civ2');%desactivate civ2: remove civ2 input param if relevant
2016    end
2017    if isfield(Param.ActionInput,'Fix2')
2018        Param.ActionInput=rmfield(Param.ActionInput,'Fix2');%desactivate fix1:remove fix1 input param if relevant
2019    end
2020    SmoothingParam=(ParamPatch2.FieldSmooth/10)*2.^(1:7);%scan the smoothing param from 1/10 to 12.8 current value
2021    NbGood=numel(find(Data.Civ2_FF==0));
2022    NbExclude=zeros(1,7);% initialize the set of smoothing parameters
2023    DiffVel=zeros(1,7);% initialize the rms difference between patch and civ
2024    Param.ActionInput.Patch2=ParamPatch2;% retrieve Patch2 parameters
2025    for irho=1:7
2026        Param.ActionInput.Patch2.FieldSmooth=SmoothingParam(irho);
2027        [Data,errormsg]= civ_series(Param);%apply the processing fct
2028        if ~isempty(errormsg)
2029            msgbox_uvmat('ERROR',errormsg)
2030            return
2031        end
2032        ind_good=find(Data.Civ2_FF==0);
2033        Civ2_U_Diff=Data.Civ2_U(ind_good)-Data.Civ2_U_smooth(ind_good);
2034        Civ2_V_Diff=Data.Civ2_V(ind_good)-Data.Civ2_V_smooth(ind_good);
2035        DiffVel(irho)=sqrt(mean(Civ2_U_Diff.*Civ2_U_Diff+Civ2_V_Diff.*Civ2_V_Diff));
2036        NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
2037    end
2038    figure(1)
2039    hold on
2040    semilogx(SmoothingParam,DiffVel,'b',SmoothingParam,NbExclude,'r')
2041    grid on
2042    legend('rms velocity diff. Patch2-Civ2 (pixels)','proportion of excluded vectors (between 0 to 1)')
2043    xlabel('smoothing parameter')
2044    ylabel('smoothing effect')
2045    set(handles.TestPatch2,'BackgroundColor',[0 1 0])
2046else
2047    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
2048    if ~isempty(corrfig)
2049        delete(corrfig)
2050    end
2051    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
2052    if ~isempty(hview_field)
2053        delete(hview_field)
2054    end
2055end
2056   
2057
2058%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
2059%---------------------------------------------------------------------
2060function NomTypeNc=nomtype2pair(NomTypeIma,mode)
2061%---------------------------------------------------------------------           
2062% OUTPUT:
2063% NomTypeNc
2064%---------------------------------------------------------------------
2065% INPUT:
2066% 'NomTypeIma': string defining the kind of nomenclature used for images
2067
2068NomTypeNc=NomTypeIma;%default
2069switch mode
2070    case 'pair j1-j2'     
2071    if ~isempty(regexp(NomTypeIma,'a$'))
2072        NomTypeNc=[NomTypeIma 'b'];
2073    elseif ~isempty(regexp(NomTypeIma,'A$'))
2074        NomTypeNc=[NomTypeIma 'B'];
2075    else
2076        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2077        if ~isempty(r)
2078            NomTypeNc='_1_1-2';
2079        end
2080    end
2081    case 'series(Dj)' 
2082%         r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2083%         if ~isempty(r)
2084            NomTypeNc='_1_1-2';
2085%         end
2086   case 'series(Di)'
2087        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
2088        if ~isempty(r)
2089            NomTypeNc='_1-2_1';
2090        else
2091            NomTypeNc='_1-2';
2092        end
2093end
2094
2095
2096%------------------------------------------------------------------------
2097% --- determine the list of index pairs of processing file
2098function [ind1,ind2,mode]=...
2099    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
2100%------------------------------------------------------------------------
2101ind1='';
2102ind2='';
2103r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
2104if ~isempty(r)
2105    mode=['D' r.ind];
2106    ind1=stra2num(r.num1);
2107    ind2=stra2num(r.num2);
2108else
2109    mode='burst';
2110    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
2111    if ~isempty(r)
2112        NomTypeNc='_1ab';
2113    else
2114        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
2115        if ~isempty(r)
2116            NomTypeNc='_1AB';
2117        else
2118            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
2119            if ~isempty(r)
2120                NomTypeNc='_1_1-2';
2121            end           
2122        end
2123    end
2124    if isempty(r)
2125        display('wrong pair mode input option')
2126    else
2127    ind1=stra2num(r.num1);
2128    ind2=stra2num(r.num2);
2129    end
2130end
2131
2132%------------------------------------------------------------------------
2133% --- fill civ_input with the parameters retrieved from an input Civ file
2134%------------------------------------------------------------------------
2135function fill_civ_input(Data,handles)
2136
2137%% Civ param
2138% lists of parameters to enter
2139ListParamNum={'CorrBoxSize','SearchBoxSize','SearchBoxShift','Dx','Dy','Dz','MinIma','MaxIma'};% list of numerical values (to transform in strings)
2140ListParamValue={'CorrSmooth','CheckGrid','CheckMask','CheckThreshold'};
2141ListParamString={'Grid','Mask'};
2142% CorrSmooth ??
2143option={'Civ1','Civ2'};
2144for ichoice=1:2
2145    if isfield(Data,[option{ichoice} '_CorrBoxSize'])
2146        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2147    end
2148end
2149
2150%% Fix param
2151option={'Fix1','Fix2'};
2152for ichoice=1:2
2153    if isfield(Data,[option{ichoice} '_CheckFmin2'])
2154        ListParamNum={'MinVel','MaxVel','MinCorr'};% list of numerical values (to transform in strings)
2155        ListParamValue={'CheckFmin2','CheckF3','CheckF4'};
2156        ListParamString={'ref_fix_1'};
2157        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2158    end
2159end
2160
2161%% Patch param
2162option={'Patch1','Patch2'};
2163for ichoice=1:2
2164    if isfield(Data,[option{ichoice} '_FieldSmooth'])
2165        ListParamNum={'FieldSmooth','MaxDiff','SubDomainSize'};% list of numerical values (to transform in strings)
2166        ListParamValue={};
2167        ListParamString={};
2168        fill_panel(Data,handles,option{ichoice},ListParamNum,ListParamValue,ListParamString)
2169    end
2170end
2171%------------------------------------------------------------------------
2172% --- fill a panel of civ_input with the parameters retrieved from an input Civ file
2173%------------------------------------------------------------------------
2174function fill_panel(Data,handles,panel,ListParamNum,ListParamValue,ListParamString)
2175children=get(handles.(panel),'children');%handles of the children of the input GUI with handle 'GUI_handle'
2176handles_panel=[];
2177for ichild=1:numel(children)
2178    if ~isempty(get(children(ichild),'tag'))
2179        handles_panel.(get(children(ichild),'tag'))=children(ichild);
2180    end
2181end
2182for ilist=1:numel(ListParamNum)
2183    ParamName=ListParamNum{ilist};
2184    CivParamName=[panel '_' ParamName];
2185    if isfield(Data,CivParamName)
2186        for icoord=1:numel(Data.(CivParamName))
2187            if numel(Data.(CivParamName))>1
2188                Tag=['num_' ParamName '_' num2str(icoord)];
2189            else
2190                Tag=['num_' ParamName];
2191            end
2192            if isfield(handles_panel,Tag)
2193                set(handles_panel.(Tag),'String',num2str(Data.(CivParamName)(icoord)))
2194                set(handles_panel.(Tag),'Visible','on')
2195            end
2196        end
2197    end
2198end
2199for ilist=1:numel(ListParamValue)
2200    ParamName=ListParamValue{ilist};
2201    CivParamName=[panel '_' ParamName];
2202    if strcmp(ParamName,'CorrSmooth')
2203        ParamName=['num_' ParamName];
2204    end
2205    if isfield(Data,CivParamName)
2206        if isfield(handles_panel,ParamName)
2207            set(handles_panel.(ParamName),'Value',Data.(CivParamName))
2208        end
2209    end
2210end
2211for ilist=1:numel(ListParamString)
2212    ParamName=ListParamString{ilist};
2213    CivParamName=[panel '_' ParamName];
2214    if isfield(Data,CivParamName)
2215        if isfield(handles_panel,ParamName)
2216            set(handles_panel.(ParamName),'String',Data.(CivParamName))
2217        end
2218    end
2219end
2220
2221%------------------------------------------------------------------------
2222% --- Executes on button press in ImportParam.
2223%------------------------------------------------------------------------
2224function ImportParam_Callback(hObject, eventdata, handles)
2225hseries=findobj(allchild(0),'Tag','series');
2226hhseries=guidata(hseries);
2227InputTable=get(hhseries.InputTable,'Data');% read the input file(s) table in the GUI series
2228oldfile=InputTable{1,1};
2229if isempty(oldfile)
2230    % use a file name stored in prefdir
2231    dir_perso=prefdir;
2232    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2233    if exist(profil_perso,'file')
2234        h=load (profil_perso);
2235        if isfield(h,'RootPath') && ischar(h.RootPath)
2236            oldfile=h.RootPath;
2237        end
2238    end
2239end
2240filexml=uigetfile_uvmat('pick a xml parameter file for civ',oldfile,'.xml');% get the xml file containing processing parameters
2241%proceed only if a file has been introduced by the browser
2242if ~isempty(filexml)
2243    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2244
2245   % Param.Action.RUN=0; %desactivate the input RUN=1
2246    if ~isfield(Param,'InputTable')||~isfield(Param,'IndexRange')
2247        msgbox_uvmat('ERROR','invalid config file: open a file in a folder ''/0_XML''')
2248        return
2249    end
2250    check_input=0;
2251    if isfield(Param,'ActionInput')
2252        if isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'civ_series')
2253            fill_GUI(Param.ActionInput,handles.civ_input)% fill the elements of the GUI series with the input parameters
2254            set(handles.ConfigSource,'String',filexml)
2255            check_input=1;
2256            update_CivOptions(handles,0)             
2257        end
2258    end
2259    if ~check_input
2260        msgbox_uvmat('ERROR','invalid config file (not for civ_series')
2261        return
2262    end
2263end
2264
2265% --- Executes on selection change in CheckCiv3.
2266function CheckCiv3_Callback(hObject, eventdata, handles)
2267
2268
2269%------------------------------------------------------------------------
2270% --- Executes on key press with selection of a uicontrol
2271%------------------------------------------------------------------------
2272function keyboard_callback(hObject,eventdata,handles)
2273   
2274ListExclude={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2','ref_i'};
2275if isempty(find(strcmp(get(gco,'Tag'),ListExclude),1))% if the selected uicontrol is not in the Exclude list
2276    set(handles.ConfigSource,'String','NEW')% indicate that the configuration is new
2277    set(handles.OK,'BackgroundColor',[1 0 1])%
2278    drawnow
2279end
2280
2281
2282
2283
2284
2285
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