source: trunk/src/geometry_calib.m @ 847

Last change on this file since 847 was 847, checked in by sommeria, 6 years ago

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1%'geometry_calib': associated to the GUI geometry_calib to perform geometric calibration from a set of reference points
2%------------------------------------------------------------------------
3% function hgeometry_calib = geometry_calib(inputfile,pos)
4%
5%OUTPUT:
6% hgeometry_calib=current handles of the GUI geometry_calib.fig
7%
8%INPUT:
9% inputfile: (optional) name of an xml file containing coordinates of reference points
10% pos: (optional) 4 element vector setting the 'Position' of the GUI
11
12%=======================================================================
13% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
14%   http://www.legi.grenoble-inp.fr
15%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
16%
17%     This file is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published
21%     by the Free Software Foundation; either version 2 of the license,
22%     or (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (see LICENSE.txt) for more details.
28%=======================================================================
29
30function varargout = geometry_calib(varargin)
31% GEOMETRY_CALIB M-file for geometry_calib.fig
32%      GEOMETRY_CALIB, by itself, creates a MenuCoord GEOMETRY_CALIB or raises the existing
33%      singleton*.
34%
35%      H = GEOMETRY_CALIB returns the handle to a MenuCoord GEOMETRY_CALIB or the handle to
36%      the existing singleton*.
37%
38%      GEOMETRY_CALIB('CALLBACK',hObject,eventData,handles,...) calls the local
39%      function named CALLBACK in GEOMETRY_CALIB.M with the given input arguments.
40%
41%      GEOMETRY_CALIB('Property','Value',...) creates a MenuCoord GEOMETRY_CALIB or raises the
42%      existing singleton*.  Starting from the left, property value pairs are
43%      applied to the GUI before geometry_calib_OpeningFunction gets called.  An
44%      unrecognized property name or invalid value makes property application
45%      stop.  All inputs are passed to geometry_calib_OpeningFcn via varargin.
46%
47%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
48%      instance to run (singleton)".
49%
50% See also: GUIDE, GUIDATA, GUIHANDLES
51
52% Edit the above text to modify the response to help geometry_calib
53
54% Last Modified by GUIDE v2.5 07-Dec-2014 15:50:44
55
56% Begin initialization code - DO NOT edit
57gui_Singleton = 1;
58gui_State = struct('gui_Name',       mfilename, ...
59                   'gui_Singleton',  gui_Singleton, ...
60                   'gui_OpeningFcn', @geometry_calib_OpeningFcn, ...
61                   'gui_OutputFcn',  @geometry_calib_OutputFcn, ...
62                   'gui_LayoutFcn',  [] , ...
63                   'gui_Callback',   []);
64if nargin
65   [pp,ff]=fileparts(which(varargin{1})); % name of the input file
66   if strcmp(ff,mfilename)% if we are activating a sub-function of geometry_calib
67   % ~isempty(regexp(varargin{1},'_Callback','once'))
68    gui_State.gui_Callback = str2func(varargin{1});
69   end
70end
71
72if nargout
73    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
74else
75    gui_mainfcn(gui_State, varargin{:});
76end
77% End initialization code - DO NOT edit
78
79
80% --- Executes just before geometry_calib is made visible.
81%INPUT:
82%handles: handles of the geometry_calib interface elements
83% PlotHandles: set of handles of the elements contolling the plotting
84% parameters on the uvmat interface (obtained by 'get_plot_handle.m')
85%------------------------------------------------------------------------
86function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile)
87%------------------------------------------------------------------------
88% Choose default command line output for geometry_calib
89
90handles.output = hObject;
91
92% Update handles structure
93guidata(hObject, handles);
94set(hObject,'DeleteFcn',{@closefcn})%
95%set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
96
97%% position
98set(0,'Unit','pixels')
99ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
100Left=ScreenSize(3)- 460; %right edge close to the right, with margin=40 (GUI width=420 px)
101if ScreenSize(4)>920
102    Height=840;%default height of the GUI
103    Bottom=ScreenSize(4)-Height-40; %put fig at top right
104else
105    Height=ScreenSize(4)-80;
106    Bottom=40; % GUI lies o the screen bottom (with margin =40)
107end
108set(handles.calib_type,'Position',[1 Height-40 194 30])%  rank 1
109set(handles.APPLY,'Position',[197 Height-40 110 30])%  rank 1
110set(handles.REPLICATE,'Position',[309 Height-40 110 30])%  rank 1
111set(handles.Intrinsic,'Position',[1 Height-40-2-92 418 92])%  rank 2
112set(handles.Extrinsic,'Position',[1 Height-40-4-92-75 418 75])%  rank 3
113set(handles.PointLists,'Position',[1 Height-40-6-92-75-117 418 117]) %  rank 4
114set(handles.CheckEnableMouse,'Position',[3 Height-362 208 30])%  rank 5
115set(handles.PLOT,'Position',[3 Height-394 120 30])%  rank 6
116set(handles.Copy,'Position',[151 Height-394 120 30])%  rank 6
117set(handles.ClearAll,'Position',[297 Height-394 120 30])%  rank 6
118set(handles.ClearPoint,'Position',[297 Height-362 120 30])%  rank 6
119set(handles.CoordLine,'Position',[211 Height-362 86 30])%  rank 6
120set(handles.phys_title,'Position',[38 Height-426 125 20])%  rank 7
121set(handles.CoordUnit,'Position',[151 Height-426 120 30])%  rank 7
122set(handles.px_title,'Position',[272 Height-426 125 20])%  rank 7
123set(handles.ListCoord,'Position',[1 20 418 Height-446])% rank 8
124set(handles.geometry_calib,'Position',[Left Bottom 420 Height])
125
126%set menu of calibration options
127set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
128if exist('inputfile','var')&& ~isempty(inputfile)
129    [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(inputfile);
130    struct.XmlInputFile=find_imadoc(RootPath,SubDir,RootFile,FileExt);
131    set(handles.ListCoord,'Data',[])
132    if exist(struct.XmlInputFile,'file')
133        Heading=loadfile(handles,struct.XmlInputFile);% load data from the xml file and fill the GUI
134        if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
135            struct.Campaign=Heading.Campaign;
136        end
137    end   
138    set(hObject,'UserData',struct)
139end
140
141%------------------------------------------------------------------------
142% --- Outputs from this function are returned to the command line.
143function varargout = geometry_calib_OutputFcn(~, eventdata, handles)
144%------------------------------------------------------------------------
145% Get default command line output from handles structure
146varargout{1} = handles.output;
147varargout{2}=handles;
148%
149%------------------------------------------------------------------------
150% executed when closing: set the parent interface button to value 0
151function closefcn(gcbo,eventdata)
152%------------------------------------------------------------------------
153huvmat=findobj(allchild(0),'Name','uvmat');
154if ~isempty(huvmat)
155    handles=guidata(huvmat);
156    set(handles.MenuCalib,'Checked','off')
157    hobject=findobj(handles.PlotAxes,'tag','calib_points');
158    if ~isempty(hobject)
159        delete(hobject)
160    end
161    hobject=findobj(handles.PlotAxes,'tag','calib_marker');
162    if ~isempty(hobject)
163        delete(hobject)
164    end   
165end
166
167%------------------------------------------------------------------------
168% --- Executes on button press APPLY (used to launch the calibration).
169function APPLY_Callback(hObject, eventdata, handles)
170%------------------------------------------------------------------------
171%% look for the GUI uvmat and check for an image as input
172set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation
173huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat
174hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
175
176RootPath='';
177if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
178    RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image
179    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
180    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
181else
182    question={'save the calibration data and point coordinates in'};
183    def={fullfile(RootPath,'ObjectCalib.xml')};
184    options.Resize='on';
185    answer=inputdlg(question,'',1,def,options);
186    outputfile=answer{1};
187end
188[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration
189
190if isempty(GeometryCalib) % if calibration cancelled
191    set(handles.APPLY,'BackgroundColor',[1 0 1])
192else   % if calibration confirmed
193   
194    %% copy the xml file from the old location if appropriate, then update with the calibration parameters
195    if ~exist(outputfile,'file') && ~isempty(SubDirBase)
196        oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
197        if exist(oldxml,'file')
198            [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
199        end
200    end
201    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file
202    if ~strcmp(errormsg,'')
203        msgbox_uvmat('ERROR',errormsg);
204    end
205   
206    %% display image with new calibration in the currently opened uvmat interface
207    FieldList=get(hhuvmat.FieldName,'String');
208    val=get(hhuvmat.FieldName,'Value');
209    if strcmp(FieldList{val},'image')
210        set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image
211        UserData=get(handles.geometry_calib,'UserData');
212        UserData.XmlInputFile=outputfile;%save the current xml file name
213        set(handles.geometry_calib,'UserData',UserData)
214        uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
215        PLOT_Callback(hObject, eventdata, handles)
216        set(handles.CoordLine,'string',num2str(index))
217        Coord=get(handles.ListCoord,'Data');
218        update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration
219        figure(handles.geometry_calib)% put the GUI geometry_calib in front
220        set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color
221    else
222        msgbox_uvmat('WARNING','open the image to see the effect of the new calibration')
223    end
224end
225
226%------------------------------------------------------------------------
227% --- Executes on button press in REPLICATE
228function REPLICATE_Callback(hObject, eventdata, handles)
229%------------------------------------------------------------------------
230
231%% look for the GUI uvmat and check for an image as input
232huvmat=findobj(allchild(0),'Name','uvmat');
233hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
234GeometryCalib=calibrate(handles,hhuvmat);% apply calibration
235
236%% open the GUI browse_data
237CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
238if isfield(CalibData,'XmlInputFile')
239    InputDir=fileparts(fileparts(CalibData.XmlInputFile));
240end
241SubProject=uigetfile_uvmat('open folder of subproject to calibrate',InputDir,'uigetdir');
242% answer=msgbox_uvmat('INPUT_TXT','Campaign to calibrate?',InputDir);
243% if strcmp(answer,'Cancel')
244%     return
245% end
246OutPut=browse_data(SubProject);
247nbcalib=0;
248for ilist=1:numel(OutPut.Experiment)
249    SubDirBase=regexprep(OutPut.DataSeries{1},'\..+$','');
250    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
251    % copy the xml file from the old location if appropriate, then update with the calibration parameters
252    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
253        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
254        if exist(oldxml,'file')
255            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
256        end
257    end
258    errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
259    if ~strcmp(errormsg,'')
260        msgbox_uvmat('ERROR',errormsg);
261    else
262        display([XmlName ' updated with calibration parameters'])
263        nbcalib=nbcalib+1;
264    end
265end
266msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
267
268%------------------------------------------------------------------------
269% --- activate calibration and store parameters in ouputfile .
270function [GeometryCalib,index]=calibrate(handles,hhuvmat)
271%------------------------------------------------------------------------
272set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
273%% read the current calibration points
274index=[];
275Coord=get(handles.ListCoord,'Data');
276Coord(:,6)=[];
277% apply the calibration, whose type is selected in  handles.calib_type
278GeometryCalib=[];
279if ~isempty(Coord)
280    calib_cell=get(handles.calib_type,'String');
281    val=get(handles.calib_type,'Value');
282    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
283else
284    msgbox_uvmat('ERROR','No calibration points, abort')
285end
286if isempty(GeometryCalib)
287    return
288end
289Z_plane=[];
290if ~isempty(Coord)
291    %check error
292    X=Coord(:,1);
293    Y=Coord(:,2);
294    Z=Coord(:,3);
295    x_ima=Coord(:,4);
296    y_ima=Coord(:,5);
297    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
298    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
299    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
300    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
301    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
302    [tild,ind_dim]=max(GeometryCalib.ErrorMax);
303    index=index(ind_dim);
304    %set the Z position of the reference plane used for calibration
305    if isequal(max(Z),min(Z))%Z constant
306        Z_plane=Z(1);
307        GeometryCalib.NbSlice=1;
308        GeometryCalib.SliceCoord=[0 0 Z_plane];
309    end
310end
311%set the coordinate unit
312unitlist=get(handles.CoordUnit,'String');
313unit=unitlist{get(handles.CoordUnit,'value')};
314GeometryCalib.CoordUnit=unit;
315%record the points
316GeometryCalib.SourceCalib.PointCoord=Coord;
317display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
318
319% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
320set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
321set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
322set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
323set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
324set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
325set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
326
327%% store the calibration data, by default in the xml file of the currently displayed image
328answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
329    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
330    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
331if strcmp(answer,'Yes') %store the calibration data
332    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
333        msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'})
334        GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
335    end
336else
337    GeometryCalib=[];
338    index=1;
339end
340
341%------------------------------------------------------------------------
342% --- determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
343function GeometryCalib=calib_rescale(Coord,handles)
344%------------------------------------------------------------------------
345X=Coord(:,1);
346Y=Coord(:,2);% Z not used
347x_ima=Coord(:,4);
348y_ima=Coord(:,5);
349[px]=polyfit(X,x_ima,1);
350[py]=polyfit(Y,y_ima,1);
351% T_x=px(2);
352% T_y=py(2);
353GeometryCalib.CalibrationType='rescale';
354GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
355GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
356GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
357GeometryCalib.omc=[0 0 0];
358
359%------------------------------------------------------------------------
360% --- determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
361function GeometryCalib=calib_linear(Coord,handles)
362%------------------------------------------------------------------------
363X=Coord(:,1);
364Y=Coord(:,2);% Z not used
365x_ima=Coord(:,4);
366y_ima=Coord(:,5);
367XY_mat=[ones(size(X)) X Y];
368a_X1=XY_mat\x_ima; %transformation matrix for X
369a_Y1=XY_mat\y_ima;%transformation matrix for X
370R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
371epsilon=sign(det(R));
372norm=abs(det(R));
373GeometryCalib.CalibrationType='linear';
374if (a_X1(2)/a_Y1(3))>0
375    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
376else
377    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
378end
379GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
380GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
381GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
382R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
383R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
384R=[R;[0 0]];
385GeometryCalib.R=[R [0;0;-epsilon]];
386GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
387
388%------------------------------------------------------------------------
389% --- determine the tsai parameters for a view normal to the grid plane
390% NOT USED
391function GeometryCalib=calib_normal(Coord,handles)
392%------------------------------------------------------------------------
393Calib.f1=str2num(get(handles.fx,'String'));
394Calib.f2=str2num(get(handles.fy,'String'));
395Calib.k=str2num(get(handles.kc,'String'));
396Calib.Cx=str2num(get(handles.Cx,'String'));
397Calib.Cy=str2num(get(handles.Cy,'String'));
398%default
399if isempty(Calib.f1)
400    Calib.f1=25/0.012;
401end
402if isempty(Calib.f2)
403    Calib.f2=25/0.012;
404end
405if isempty(Calib.k)
406    Calib.k=0;
407end
408if isempty(Calib.Cx)||isempty(Calib.Cy)
409    huvmat=findobj(allchild(0),'Tag','uvmat');
410    hhuvmat=guidata(huvmat);
411    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
412    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
413end   
414%tsai parameters
415Calib.dpx=0.012;%arbitrary
416Calib.dpy=0.012;
417Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
418Calib.f=Calib.f2*Calib.dpy;
419Calib.kappa1=Calib.k/(Calib.f*Calib.f);
420
421%initial guess
422X=Coord(:,1);
423Y=Coord(:,2);
424Zmean=mean(Coord(:,3));
425x_ima=Coord(:,4)-Calib.Cx;
426y_ima=Coord(:,5)-Calib.Cy;
427XY_mat=[ones(size(X)) X Y];
428a_X1=XY_mat\x_ima; %transformation matrix for X
429a_Y1=XY_mat\y_ima;%transformation matrix for Y
430R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
431norm=sqrt(det(-R));
432calib_param(1)=0;% quadratic distortion
433calib_param(2)=a_X1(1);
434calib_param(3)=a_Y1(1);
435calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
436calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
437display(['initial guess=' num2str(calib_param)])
438
439%optimise the parameters: minimisation of error
440calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
441
442GeometryCalib.CalibrationType='tsai_normal';
443GeometryCalib.focal=Calib.f;
444GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
445GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
446GeometryCalib.sx=Calib.sx;
447GeometryCalib.kappa1=calib_param(1);
448GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
449GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
450alpha=calib_param(5);
451GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
452
453%------------------------------------------------------------------------
454function GeometryCalib=calib_3D_linear(Coord,handles)
455%------------------------------------------------------------------------
456path_uvmat=which('uvmat');% check the path detected for source file uvmat
457path_UVMAT=fileparts(path_uvmat); %path to UVMAT
458huvmat=findobj(allchild(0),'Tag','uvmat');
459hhuvmat=guidata(huvmat);
460coord_files=get(handles.ListCoordFiles,'String');
461if ischar(coord_files)
462    coord_files={coord_files};
463end
464if isempty(coord_files{1}) || isequal(coord_files,{''})
465    coord_files={};
466end
467%retrieve the calibration points stored in the files listed in the popup list ListCoordFiles
468x_1=Coord(:,4:5)';%px coordinates of the ref points
469if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
470    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
471  return
472end
473nx=str2num(get(hhuvmat.num_Npx,'String'));
474ny=str2num(get(hhuvmat.num_Npy,'String'));
475x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
476X_1=Coord(:,1:3)';%phys coordinates of the ref points
477n_ima=numel(coord_files)+1;
478if ~isempty(coord_files)
479    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
480    for ifile=1:numel(coord_files)
481    t=xmltree(coord_files{ifile});
482    s=convert(t);%convert to matlab structure
483        if isfield(s,'GeometryCalib')
484            if isfield(s.GeometryCalib,'SourceCalib')
485                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
486                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
487                Coord_file=zeros(length(PointCoord),5);%default
488                for i=1:length(PointCoord)
489                    line=str2num(PointCoord{i});
490                    Coord_file(i,4:5)=line(4:5);%px x
491                    Coord_file(i,1:3)=line(1:3);%phys x
492                end
493                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
494                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
495                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
496                end
497            end
498        end
499    end
500end
501n_ima=numel(coord_files)+1;
502est_dist=[0;0;0;0;0];
503est_aspect_ratio=0;
504est_fc=[1;1];
505center_optim=0;
506run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim'
507if exist('Rc_1','var')
508    GeometryCalib.CalibrationType='3D_linear';
509    GeometryCalib.fx_fy=fc';
510    GeometryCalib.Cx_Cy=cc';
511    GeometryCalib.kc=kc(1);
512    GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
513    GeometryCalib.Tx_Ty_Tz=Tc_1';
514    GeometryCalib.R=Rc_1;
515    GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
516    GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
517    GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
518    GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
519    GeometryCalib.ErrorRMS=[];
520    GeometryCalib.ErrorMax=[];
521else
522    msgbox_uvmat('ERROR',['calibration function ' fullfile('toolbox_calib','go_calib_optim') ' did not converge: use multiple views or option 3D_extrinsic'])
523    GeometryCalib=[];
524end
525
526%------------------------------------------------------------------------
527function GeometryCalib=calib_3D_quadr(Coord,handles)
528%------------------------------------------------------------------
529
530path_uvmat=which('uvmat');% check the path detected for source file uvmat
531path_UVMAT=fileparts(path_uvmat); %path to UVMAT
532huvmat=findobj(allchild(0),'Tag','uvmat');
533hhuvmat=guidata(huvmat);
534if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
535    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
536  return
537end
538% check_cond=0;
539coord_files=get(handles.ListCoordFiles,'String');
540if ischar(coord_files)
541    coord_files={coord_files};
542end
543if isempty(coord_files{1}) || isequal(coord_files,{''})
544    coord_files={};
545end
546
547%retrieve the calibration points stored in the files listed in the popup list ListCoordFiles
548x_1=Coord(:,4:5)';%px coordinates of the ref points
549nx=str2num(get(hhuvmat.num_Npx,'String'));
550ny=str2num(get(hhuvmat.num_Npy,'String'));
551x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
552X_1=Coord(:,1:3)';%phys coordinates of the ref points
553n_ima=numel(coord_files)+1;
554if ~isempty(coord_files)
555    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
556    for ifile=1:numel(coord_files)
557    t=xmltree(coord_files{ifile});
558    s=convert(t);%convert to matlab structure
559        if isfield(s,'GeometryCalib')
560            if isfield(s.GeometryCalib,'SourceCalib')
561                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
562                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
563                Coord_file=zeros(length(PointCoord),5);%default
564                for i=1:length(PointCoord)
565                    line=str2num(PointCoord{i});
566                    Coord_file(i,4:5)=line(4:5);%px x
567                    Coord_file(i,1:3)=line(1:3);%phys x
568                end
569                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
570                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
571                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
572                end
573            end
574        end
575    end
576end
577n_ima=numel(coord_files)+1;
578est_dist=[1;0;0;0;0];
579est_aspect_ratio=1;
580center_optim=0;
581run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim'
582
583if exist('Rc_1','var')
584    GeometryCalib.CalibrationType='3D_quadr';
585    GeometryCalib.fx_fy=fc';
586    GeometryCalib.Cx_Cy=cc';
587    GeometryCalib.kc=kc(1);
588    GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
589    GeometryCalib.Tx_Ty_Tz=Tc_1';
590    GeometryCalib.R=Rc_1;
591    GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
592    GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
593    GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
594    GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
595    GeometryCalib.ErrorRMS=[];
596    GeometryCalib.ErrorMax=[];
597else
598    msgbox_uvmat('ERROR',['calibration function ' fullfile('toolbox_calib','go_calib_optim') ' did not converge: use multiple views or option 3D_extrinsic'])
599    GeometryCalib=[];
600end
601
602%------------------------------------------------------------------------
603function GeometryCalib=calib_3D_extrinsic(Coord,handles)
604%------------------------------------------------------------------
605path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
606path_UVMAT=fileparts(path_uvmat); %path to UVMAT
607x_1=double(Coord(:,4:5)');%image coordinates
608X_1=double(Coord(:,1:3)');% phys coordinates
609huvmat=findobj(allchild(0),'Tag','uvmat');
610hhuvmat=guidata(huvmat);
611if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
612    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
613  return
614end
615ny=str2double(get(hhuvmat.num_Npy,'String'));
616x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
617n_ima=1;
618GeometryCalib.CalibrationType='3D_extrinsic';
619fx=str2num(get(handles.fx,'String'));
620fy=str2num(get(handles.fy,'String'));
621Cx=str2num(get(handles.Cx,'String'));
622Cy=str2num(get(handles.Cy,'String'));
623errormsg='';
624if isempty(fx)
625    errormsg='focal length fx needs to be introduced';
626elseif isempty(fy)
627    errormsg='focal length fy needs to be introduced';
628elseif isempty(Cx)
629    errormsg='shift Cx to image centre needs to be introduced';
630elseif isempty(Cy)
631    errormsg='shift Cy to image centre needs to be introduced';
632end
633if ~isempty(errormsg)
634    GeometryCalib=[];
635    msgbox_uvmat('ERROR',errormsg)
636    return
637end
638GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
639GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
640GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
641GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
642GeometryCalib.kc=str2num(get(handles.kc,'String'));
643fct_path=fullfile(path_UVMAT,'toolbox_calib');
644addpath(fct_path)
645GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
646[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
647   (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
648rmpath(fct_path);
649GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
650GeometryCalib.Tx_Ty_Tz=Tc1';
651%inversion of z axis
652GeometryCalib.R=Rc1;
653GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
654GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
655GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
656GeometryCalib.omc=(180/pi)*omc';
657
658%------------------------------------------------------------------------
659%function GeometryCalib=calib_tsai_heikkila(Coord)
660% TEST: NOT IMPLEMENTED
661%------------------------------------------------------------------
662% path_uvmat=which('uvmat');% check the path detected for source file uvmat
663% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
664% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
665% addpath(path_calib)
666% npoints=size(Coord,1);
667% Coord(:,1:3)=10*Coord(:,1:3);
668% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
669% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
670% GeometryCalib.CalibrationType='tsai';
671% GeometryCalib.focal=par(2);
672
673
674%------------------------------------------------------------------------
675% --- determine the rms of calibration error
676function ErrorRms=error_calib(calib_param,Calib,Coord)
677%------------------------------------------------------------------------
678%calib_param: vector of free calibration parameters (to optimise)
679%Calib: structure of the given calibration parameters
680%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
681Calib.f=25;
682Calib.dpx=0.012;
683Calib.dpy=0.012;
684Calib.sx=1;
685Calib.Cx=512;
686Calib.Cy=512;
687Calib.kappa1=calib_param(1);
688Calib.Tx=calib_param(2);
689Calib.Ty=calib_param(3);
690Calib.Tz=calib_param(4);
691alpha=calib_param(5);
692Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
693
694X=Coord(:,1);
695Y=Coord(:,2);
696Z=Coord(:,3);
697x_ima=Coord(:,4);
698y_ima=Coord(:,5);
699[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
700ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
701ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
702ErrorRms=mean(ErrorRms);
703
704
705%------------------------------------------------------------------------
706% --- Executes on button press in STORE.
707function STORE_Callback(hObject, eventdata, handles)
708%------------------------------------------------------------------------
709Coord=get(handles.ListCoord,'Data');
710%Object=read_geometry_calib(Coord_cell);
711unitlist=get(handles.CoordUnit,'String');
712unit=unitlist{get(handles.CoordUnit,'value')};
713GeometryCalib.CoordUnit=unit;
714GeometryCalib.SourceCalib.PointCoord=Coord(:,1:5);
715huvmat=findobj(allchild(0),'Name','uvmat');
716hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
717% RootPath='';
718% RootFile='';
719if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
720%     testhandle=1;
721    RootPath=get(hhuvmat.RootPath,'String');
722    RootFile=get(hhuvmat.RootFile,'String');
723    filebase=[fullfile(RootPath,RootFile) '~'];
724    while exist([filebase '.xml'],'file')
725        filebase=[filebase '~'];
726    end
727    outputfile=[filebase '.xml'];
728    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');
729    if ~strcmp(errormsg,'')
730        msgbox_uvmat('ERROR',errormsg);
731    end
732    listfile=get(handles.ListCoordFiles,'string');
733    if isequal(listfile,{''})
734        listfile={outputfile};
735    else
736        listfile=[listfile;{outputfile}];%update the list of coord files
737    end
738    set(handles.ListCoordFiles,'string',listfile);
739end
740ClearAll_Callback(hObject, eventdata, handles)% clear the current list and point plots
741
742% --------------------------------------------------------------------
743% --- Executes on button press in ClearAll: clear the list of calibration points
744function ClearAll_Callback(hObject, eventdata, handles)
745% --------------------------------------------------------------------
746set(handles.ListCoord,'Data',[])
747PLOT_Callback(hObject, eventdata, handles)
748update_calib_marker([]);%remove circle marker
749set(handles.APPLY,'backgroundColor',[1 0 0])% set APPLY button to red color: no calibration wanted without points
750set(handles.CheckEnableMouse,'value',1); %activate mouse to pick new points
751
752%------------------------------------------------------------------------
753% --- Executes on button press in CLEAR LIST
754function CLEAR_Callback(hObject, eventdata, handles)
755%------------------------------------------------------------------------
756set(handles.ListCoordFiles,'Value',1)
757set(handles.ListCoordFiles,'String',{''})
758
759%------------------------------------------------------------------------
760% --- Executes on selection change in CheckEnableMouse.
761function CheckEnableMouse_Callback(hObject, eventdata, handles)
762%------------------------------------------------------------------------
763choice=get(handles.CheckEnableMouse,'Value');
764if choice
765    huvmat=findobj(allchild(0),'tag','uvmat');
766    if ishandle(huvmat)
767        hhuvmat=guidata(huvmat);
768        set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler
769        if get(hhuvmat.CheckEditObject,'Value')
770            set(hhuvmat.CheckEditObject,'Value',0)
771            uvmat('CheckEditObject_Callback',hhuvmat.CheckEditObject,[],hhuvmat)
772        end
773        set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler
774    end
775end
776
777% --------------------------------------------------------------------
778function MenuHelp_Callback(hObject, eventdata, handles)
779web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#GeometryCalib')
780
781% --------------------------------------------------------------------
782function MenuSetScale_Callback(hObject, eventdata, handles)
783
784answer=msgbox_uvmat('INPUT_TXT','scale pixel/cm?','');
785%create test points
786huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
787hhuvmat=guidata(huvmat);
788if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
789    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
790    return
791end
792set(handles.calib_type,'Value',1)% set calib option to 'rescale'
793npx=str2num(get(hhuvmat.num_Npx,'String'))/2;
794npy=str2num(get(hhuvmat.num_Npy,'String'))/2;
795Xima=[0.25*npx 0.75*npx 0.75*npx 0.25*npx]';
796Yima=[0.25*npy 0.25*npy 0.75*npy 0.75*npy]';
797x=Xima/str2num(answer);
798y=Yima/str2num(answer);
799Coord=[x y zeros(4,1) Xima Yima zeros(4,1)];
800set(handles.ListCoord,'Data',Coord)
801set(handles.APPLY,'BackgroundColor',[1 0 1])
802set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
803
804%------------------------------------------------------------------------
805function MenuCreateGrid_Callback(hObject, eventdata, handles)
806%------------------------------------------------------------------------
807CalibData=get(handles.geometry_calib,'UserData');
808Tinput=[];%default
809if isfield(CalibData,'grid')
810    Tinput=CalibData.grid;
811end
812[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
813set(handles.geometry_calib,'UserData',CalibData)
814
815%grid in phys space
816Coord=get(handles.ListCoord,'Data');
817Coord(1:size(T,1),1:3)=T;%update the existing list of phys coordinates from the GUI create_grid
818set(handles.ListCoord,'Data',Coord)
819set(handles.APPLY,'BackgroundColor',[1 0 1])
820set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
821
822% -----------------------------------------------------------------------
823% --- automatic grid dectection from local maxima of the images
824function MenuDetectGrid_Callback(hObject, eventdata, handles)
825%------------------------------------------------------------------------
826%% read the four last point coordinates in pixels
827Coord=get(handles.ListCoord,'Data');%read list of coordinates on geometry_calib
828nbpoints=size(Coord,1); %nbre of calibration points
829if nbpoints~=4
830    msgbox_uvmat('ERROR','four points must have be selected by the mouse to delimitate the phys grid area; the Ox axis will be defined by the two first points')
831    return
832end
833% corners_X=(Coord(end:-1:end-3,4)); %pixel absissa of the four corners
834% corners_Y=(Coord(end:-1:end-3,5));
835corners_X=(Coord(:,4)); %pixel absissa of the four corners
836corners_Y=(Coord(:,5));
837
838%%%%%%
839%   corners_X=1000*[1.5415  1.7557 1.7539 1.5415]';
840%   corners_Y=1000*[1.1515 1.1509 1.3645  1.3639]';
841
842%reorder the last two points (the two first in the list) if needed
843angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
844if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
845      X_end=corners_X(4);
846      Y_end=corners_Y(4);
847      corners_X(4)=corners_X(3);
848      corners_Y(4)=corners_Y(3);
849      corners_X(3)=X_end;
850      corners_Y(3)=Y_end;
851end
852
853%% initiate the grid in phys coordinates
854CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
855grid_input=[];%default
856if isfield(CalibData,'grid')
857    grid_input=CalibData.grid;%retrieve the previously used grid
858end
859[T,CalibData.grid,CalibData.grid.CheckWhite]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
860set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
861X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
862Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
863
864%% read the current image, displayed in the GUI uvmat
865huvmat=findobj(allchild(0),'Name','uvmat');
866UvData=get(huvmat,'UserData');
867A=UvData.Field.A;%currently displayed image
868npxy=size(A);
869
870%% calculate transform matrices for plane projection: rectangle assumed to be viewed in perspective
871% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
872B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
873      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
874B = reshape (B', 8 , 8 )';
875D = [ corners_X , corners_Y ];
876D = reshape (D', 8 , 1 );
877l = (B' * B)\B' * D;
878Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
879C = [l(7:8)' 1];
880
881%% transform grid image into 'phys' coordinates
882GeometryCalib.CalibrationType='3D_linear';
883GeometryCalib.fx_fy=[1 1];
884GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
885GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
886GeometryCalib.CoordUnit='cm';
887path_uvmat=which('uvmat');% check the path detected for source file uvmat
888path_UVMAT=fileparts(path_uvmat); %path to UVMAT
889addpath(fullfile(path_UVMAT,'transform_field'))
890Data.ListVarName={'Coord_y','Coord_x','A'};
891Data.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}};
892if ndims(A)==3
893    A=mean(A,3);
894end
895Data.A=A-min(min(A));
896Data.Coord_y=[npxy(1)-0.5 0.5];
897Data.Coord_x=[0.5 npxy(2)];
898Data.CoordUnit='pixel';
899Calib.GeometryCalib=GeometryCalib;
900DataOut=phys(Data,Calib);
901rmpath(fullfile(path_UVMAT,'transform_field'))
902Amod=DataOut.A;% current image expressed in 'phys' coord
903Rangx=DataOut.Coord_x;% x coordinates of first and last pixel centres in phys
904Rangy=DataOut.Coord_y;% y coordinates of first and last pixel centres in phys
905if CalibData.grid.CheckWhite
906    Amod=double(Amod);%case of white grid markers: will look for image maxima
907else
908    Amod=-double(Amod);%case of black grid markers: will look for image minima
909end
910
911%% detection of local image extrema in each direction
912Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
913Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
914ind_range_x=ceil(abs(GeometryCalib.R(1,1)*CalibData.grid.Dx/3));% range of search of image ma around each point obtained by linear interpolation from the marked points
915ind_range_y=ceil(abs(GeometryCalib.R(2,2)*CalibData.grid.Dy/3));% range of search of image ma around each point obtained by linear interpolation from the marked points
916nbpoints=size(T,1);
917TIndex=ones(size(T));% image indices corresponding to point coordinates
918%look for image maxima around each expected grid point
919for ipoint=1:nbpoints
920    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);% x index of the expected point in the phys image Amod
921    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);% y index of the expected point in the phys image Amod
922    j0min=max(j0-ind_range_y,1);% min y index selected for the subimage (cut at the edge to avoid index <1)
923    j0max=min(j0+ind_range_y,size(Amod,1));% max y index selected for the subimage (cut at the edge to avoid index > size)
924    i0min=max(i0-ind_range_x,1);% min x index selected for the subimage (cut at the edge to avoid index <1)
925    i0max=min(i0+ind_range_x,size(Amod,2));% max x index selected for the subimage (cut at the edge to avoid index > size)
926    Asub=Amod(j0min:j0max,i0min:i0max); %subimage used to find brigthness extremum
927    x_profile=sum(Asub,1);%profile of subimage summed over y
928    y_profile=sum(Asub,2);%profile of subimage summed over x
929
930    [tild,ind_x_max]=max(x_profile);% index of max for the x profile
931    [tild,ind_y_max]=max(y_profile);% index of max for the y profile
932    %sub-pixel improvement using moments
933    x_shift=0;
934    y_shift=0;
935    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
936        Atop=x_profile(ind_x_max-2:ind_x_max+2);% extract x profile around the max
937        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
938    end
939    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
940        Atop=y_profile(ind_y_max-2:ind_y_max+2);% extract y profile around the max
941        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
942    end
943        %%%%
944%     if ipoint==9
945%                 figure(11)
946%   imagesc(Asub)
947%     figure(12)
948%     plot(x_profile,'r')
949%     hold on
950%     plot(y_profile,'b')
951%     grid on
952%     end
953    %%%%
954    TIndex(ipoint,1)=(i0min+ind_x_max-1+x_shift);% x position of the maximum (in index of Amod)
955    TIndex(ipoint,2)=(j0min+ind_y_max-1+y_shift);% y position of the maximum (in index of Amod)
956end
957Tmod(:,1)=(TIndex(:,1)-1)*Dx+Rangx(1);
958Tmod(:,2)=(TIndex(:,2)-1)*Dy+Rangy(1);
959%Tmod=T(:,(1:2))+Delta;% 'phys' coordinates of the detected points
960[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));% image coordinates of the detected points
961Coord=[T Xpx Ypx zeros(size(T,1),1)];
962set(handles.ListCoord,'Data',Coord)
963PLOT_Callback(hObject, eventdata, handles)
964set(handles.APPLY,'BackgroundColor',[1 0 1])
965set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
966
967
968%-----------------------------------------------------------------------
969function MenuTranslatePoints_Callback(hObject, eventdata, handles)
970%-----------------------------------------------------------------------
971%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
972CalibData=get(handles.geometry_calib,'UserData');
973Tinput=[];%default
974if isfield(CalibData,'translate')
975    Tinput=CalibData.translate;
976end
977T=translate_points(Tinput);%display translate_points GUI and get shift parameters
978CalibData.translate=T;
979set(handles.geometry_calib,'UserData',CalibData)
980%translation
981Coord=get(handles.ListCoord,'Data');
982Coord(:,1)=T(1)+Coord(:,1);
983Coord(:,2)=T(2)+Coord(:,2);
984Coord(:,3)=T(3)+Coord(:,3);
985set(handles.ListCoord,'Data',Coord);
986set(handles.APPLY,'BackgroundColor',[1 0 1])
987
988% --------------------------------------------------------------------
989function MenuRotatePoints_Callback(hObject, eventdata, handles)
990%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
991CalibData=get(handles.geometry_calib,'UserData');
992Tinput=[];%default
993if isfield(CalibData,'rotate')
994    Tinput=CalibData.rotate;
995end
996T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
997CalibData.rotate=T;
998set(handles.geometry_calib,'UserData',CalibData)
999%-----------------------------------------------------
1000%rotation
1001Phi=T(1);
1002O_x=0;%default
1003O_y=0;%default
1004if numel(T)>=2
1005    O_x=T(2);%default
1006end
1007if numel(T)>=3
1008    O_y=T(3);%default
1009end
1010Coord=get(handles.ListCoord,'Data');
1011r1=cos(pi*Phi/180);
1012r2=-sin(pi*Phi/180);
1013r3=sin(pi*Phi/180);
1014r4=cos(pi*Phi/180);
1015x=Coord(:,1)-O_x;
1016y=Coord(:,2)-O_y;
1017Coord(:,1)=r1*x+r2*y;
1018Coord(:,2)=r3*x+r4*y;
1019set(handles.ListCoord,'Data',Coord)
1020set(handles.APPLY,'BackgroundColor',[1 0 1])
1021
1022% --------------------------------------------------------------------
1023function MenuImportPoints_Callback(hObject, eventdata, handles)
1024fileinput=browse_xml(hObject, eventdata, handles);
1025if isempty(fileinput)
1026    return
1027end
1028[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1029if ~isfield(s,'GeometryCalib')
1030    msgbox_uvmat('ERROR','invalid input file: no geometry_calib data')
1031    return
1032end
1033GeometryCalib=s.GeometryCalib;
1034if ~(isfield(GeometryCalib,'SourceCalib')&&isfield(GeometryCalib.SourceCalib,'PointCoord'))
1035        msgbox_uvmat('ERROR','invalid input file: no calibration points')
1036    return
1037end
1038Coord=GeometryCalib.SourceCalib.PointCoord;
1039Coord=[Coord zeros(size(Coord,1),1)];
1040set(handles.ListCoord,'Data',Coord)
1041PLOT_Callback(handles.geometry_calib, [], handles)
1042set(handles.APPLY,'BackgroundColor',[1 0 1])
1043set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default
1044
1045% -----------------------------------------------------------------------
1046function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1047%------------------------------------------------------------------------
1048fileinput=browse_xml(hObject, eventdata, handles);
1049if isempty(fileinput)
1050    return
1051end
1052[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1053GeometryCalib=s.GeometryCalib;
1054display_intrinsic(GeometryCalib,handles)
1055
1056% -----------------------------------------------------------------------
1057function MenuImportAll_Callback(hObject, eventdata, handles)
1058%------------------------------------------------------------------------
1059fileinput=browse_xml(hObject, eventdata, handles);
1060if ~isempty(fileinput)
1061    loadfile(handles,fileinput)
1062end
1063set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default
1064
1065% -----------------------------------------------------------------------
1066% --- Executes on menubar option Import/Grid file: introduce previous grid files
1067function MenuGridFile_Callback(hObject, eventdata, handles)
1068% -----------------------------------------------------------------------
1069inputfile=browse_xml(hObject, eventdata, handles);
1070listfile=get(handles.ListCoordFiles,'String');
1071if isequal(listfile,{''})
1072    listfile={inputfile};
1073else
1074    listfile=[listfile;{inputfile}];%update the list of coord files
1075end
1076set(handles.ListCoordFiles,'String',listfile);
1077
1078
1079%------------------------------------------------------------------------
1080function fileinput=browse_xml(hObject, eventdata, handles)
1081%------------------------------------------------------------------------
1082fileinput=[];%default
1083oldfile=''; %default
1084UserData=get(handles.geometry_calib,'UserData');
1085if isfield(UserData,'XmlInputFile')
1086    oldfile=UserData.XmlInputFile;
1087end
1088[FileName, PathName, filterindex] = uigetfile( ...
1089       {'*.xml;*.mat', ' (*.xml,*.mat)';
1090       '*.xml',  '.xml files '; ...
1091        '*.mat',  '.mat matlab files '}, ...
1092        'Pick a file',oldfile);
1093fileinput=[PathName FileName];%complete file name
1094testblank=findstr(fileinput,' ');%look for blanks
1095if ~isempty(testblank)
1096    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1097    return
1098end
1099sizf=size(fileinput);
1100if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1101UserData.XmlInputFile=fileinput;
1102set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1103
1104% -----------------------------------------------------------------------
1105function Heading=loadfile(handles,fileinput)
1106%------------------------------------------------------------------------
1107Heading=[];%default
1108[s,errormsg]=imadoc2struct(fileinput,'Heading','GeometryCalib');
1109if ~isempty(errormsg)
1110    msgbox_uvmat('ERROR',errormsg)
1111    return
1112end
1113if ~isempty(s.Heading)
1114    Heading=s.Heading;
1115end
1116
1117GeometryCalib=s.GeometryCalib;
1118fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1119CoordCell={};
1120Tabchar={};%default
1121val_cal=1;%default
1122if ~isempty(GeometryCalib)
1123    % choose the calibration option
1124    if isfield(GeometryCalib,'CalibrationType')
1125        calib_list=get(handles.calib_type,'String');
1126        for ilist=1:numel(calib_list)
1127            if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1128                val_cal=ilist;
1129                break
1130            end
1131        end
1132    end
1133    display_intrinsic(GeometryCalib,handles)%intrinsic param
1134    %extrinsic param
1135    if isfield(GeometryCalib,'Tx_Ty_Tz')
1136        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1137        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1138        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1139        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1140    end
1141    if isfield(GeometryCalib,'omc')
1142        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1143        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1144        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1145    end
1146    if isfield(GeometryCalib,'SourceCalib')&& isfield(GeometryCalib.SourceCalib,'PointCoord')
1147        calib=GeometryCalib.SourceCalib.PointCoord;
1148        Coord=[calib zeros(size(calib,1),1)];
1149        set(handles.ListCoord,'Data',Coord)
1150    end
1151    PLOT_Callback(handles.geometry_calib, [], handles)
1152    set(handles.APPLY,'BackgroundColor',[1 0 1])
1153end
1154set(handles.calib_type,'Value',val_cal)
1155
1156if isempty(CoordCell)% allow mouse action by default in the absence of input points
1157    set(handles.CheckEnableMouse,'Value',1)
1158    set(handles.CheckEnableMouse,'BackgroundColor',[1 1 0])
1159else % does not allow mouse action by default in the presence of input points
1160    set(handles.CheckEnableMouse,'Value',0)
1161    set(handles.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7])
1162end
1163
1164%------------------------------------------------------------------------
1165%---display calibration intrinsic parameters
1166function display_intrinsic(GeometryCalib,handles)
1167%------------------------------------------------------------------------
1168fx=[];
1169fy=[];
1170if isfield(GeometryCalib,'fx_fy')
1171    fx=GeometryCalib.fx_fy(1);
1172    fy=GeometryCalib.fx_fy(2);
1173end
1174Cx_Cy=[0 0];%default
1175if isfield(GeometryCalib,'Cx_Cy')
1176    Cx_Cy=GeometryCalib.Cx_Cy;
1177end
1178kc=0;
1179if isfield(GeometryCalib,'kc')
1180    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1181end
1182set(handles.fx,'String',num2str(fx,5))
1183set(handles.fy,'String',num2str(fy,5))
1184set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1185set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1186set(handles.kc,'String',num2str(kc,'%1.4f'))
1187
1188
1189% --- Executes when user attempts to close geometry_calib.
1190function geometry_calib_CloseRequestFcn(hObject, eventdata, handles)
1191
1192delete(hObject); % closes the figure
1193
1194%------------------------------------------------------------------------
1195% --- Executes on button press in PLOT.
1196%------------------------------------------------------------------------
1197function PLOT_Callback(hObject, eventdata, handles)
1198huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1199hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
1200h_menu_coord=findobj(huvmat,'Tag','TransformName');
1201menu=get(h_menu_coord,'String');
1202choice=get(h_menu_coord,'Value');
1203option='';
1204if iscell(menu)
1205    option=menu{choice};
1206end
1207Coord=get(handles.ListCoord,'Data');
1208if ~isempty(Coord)
1209    if isequal(option,'phys')
1210        Coord_plot=Coord(:,1:3);
1211    elseif isempty(option);%optionoption,'px')||isequal(option,'')
1212        Coord_plot=Coord(:,4:5);
1213    else
1214        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ')
1215    end
1216end
1217
1218set(0,'CurrentFigure',huvmat)
1219set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
1220hh=findobj('Tag','calib_points');
1221if  ~isempty(Coord) && isempty(hh)
1222    hh=line(Coord_plot(:,1),Coord_plot(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+','MarkerSize',10);
1223elseif isempty(Coord)%empty list of points, suppress the plot
1224    delete(hh)
1225else
1226    set(hh,'XData',Coord_plot(:,1))
1227    set(hh,'YData',Coord_plot(:,2))
1228end
1229pause(.1)
1230figure(handles.geometry_calib)
1231
1232%------------------------------------------------------------------------
1233% --- Executes on button press in Copy: display Coord on the Matlab work space
1234%------------------------------------------------------------------------
1235function Copy_Callback(hObject, eventdata, handles)
1236global Coord
1237evalin('base','global Coord')%make CurData global in the workspace
1238Coord=get(handles.ListCoord,'Data');
1239display('coordinates of calibration points (phys,px,marker) :')
1240evalin('base','Coord') %display CurData in the workspace
1241commandwindow; %brings the Matlab command window to the front
1242
1243%------------------------------------------------------------------------
1244% --- Executes when selected cell(s) is changed in ListCoord.
1245%------------------------------------------------------------------------
1246function ListCoord_CellSelectionCallback(hObject, eventdata, handles)
1247if ~isempty(eventdata.Indices)
1248    iline=eventdata.Indices(1);% selected line number
1249    set(handles.CoordLine,'String',num2str(iline))
1250     Data=get(handles.ListCoord,'Data');
1251     update_calib_marker(Data(iline,:))
1252end
1253
1254%------------------------------------------------------------------------
1255% --- Executes when entered data in editable cell(s) in ListCoord.
1256%------------------------------------------------------------------------
1257function ListCoord_CellEditCallback(hObject, eventdata, handles)
1258
1259Input=str2num(eventdata.EditData);%pasted input
1260Coord=get(handles.ListCoord,'Data');
1261iline=eventdata.Indices(1);% selected line number
1262if size(Coord,1)<iline+numel(Input)
1263    Coord=[Coord ; zeros(iline+numel(Input)-size(Coord,1),6)];% append zeros to fit the new column
1264end
1265Coord(iline:iline+numel(Input)-1,eventdata.Indices(2))=Input';
1266set(handles.ListCoord,'Data',Coord)
1267PLOT_Callback(hObject, eventdata, handles)
1268
1269%------------------------------------------------------------------------
1270% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1271%------------------------------------------------------------------------
1272function ListCoord_KeyPressFcn(hObject, eventdata, handles)
1273iline=str2num(get(handles.CoordLine,'String'));
1274xx=double(get(handles.geometry_calib,'CurrentCharacter'));%get the keyboard character
1275if ismember(xx,[28 29 30 31])% directional arrow
1276    Coord=get(handles.ListCoord,'Data');
1277    switch xx
1278        case 30 % arrow upward
1279            iline=iline-1;
1280        case 31% arrow downward
1281            iline=iline+1;
1282    end
1283    if iline>=1 && iline<=size(Coord,1)
1284        set(handles.CoordLine,'String',num2str(iline))
1285        update_calib_marker(Coord(iline,1:5))% show the point corresponding to the selected line
1286    end
1287else
1288    set(handles.APPLY,'BackgroundColor',[1 0 1])% paint APPLY in magenta to indicate that the table content has be modified
1289end
1290
1291
1292%------------------------------------------------------------------------
1293% --- update the plot of calibration points
1294%------------------------------------------------------------------------
1295% draw a circle around the point defined by the input coordinates Coord as given by line in the table Listcoord
1296function update_calib_marker(Coord)
1297
1298%% read config on uvmat
1299huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1300hhuvmat=guidata(huvmat);
1301hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');
1302if numel(Coord)<5
1303    if ~isempty(hhh)
1304        delete(hhh)%delete the circle marker in case of no valid input
1305    end
1306    return
1307end
1308menu=get(hhuvmat.TransformName,'String');
1309choice=get(hhuvmat.TransformName,'Value');
1310option='';
1311if iscell(menu)
1312    option=menu{choice};
1313end
1314
1315%% read appropriate coordinates (px or phys) in the table ListCoord
1316if isequal(option,'phys') % use phys coord
1317    XCoord=Coord(1);
1318    YCoord=Coord(2);
1319elseif isempty(option)% use coord in pixels
1320    XCoord=Coord(4);
1321    YCoord=Coord(5);
1322else
1323    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ')
1324    return
1325end
1326
1327%% adjust the plot limits if needed
1328xlim=get(hhuvmat.PlotAxes,'XLim');
1329ylim=get(hhuvmat.PlotAxes,'YLim');
1330ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/25;%defines the size of the circle marker
1331check_xlim=0;
1332if XCoord>xlim(2)
1333    xlim=xlim+XCoord-xlim(2)+ind_range;% translate plot limit
1334    check_xlim=1;
1335elseif XCoord<xlim(1)
1336    xlim=xlim-XCoord+xlim(1)-ind_range;% translate plot limit
1337    check_xlim=1;
1338end
1339if check_xlim
1340    set(hhuvmat.PlotAxes,'XLim',xlim);
1341    set(hhuvmat.num_MaxX,'String',num2str(xlim(2)));
1342    set(hhuvmat.num_MinX,'String',num2str(xlim(1)));
1343end
1344check_ylim=0;
1345if YCoord>ylim(2)
1346    ylim=ylim+YCoord-ylim(2)+ind_range;% translate plot limit
1347    check_ylim=1;
1348elseif YCoord<ylim(1)
1349    ylim=ylim-YCoord+ylim(1)-ind_range;% translate plot limit
1350    check_ylim=1;
1351end
1352if check_ylim
1353    set(hhuvmat.PlotAxes,'YLim',ylim);
1354    set(hhuvmat.num_MaxY,'String',num2str(ylim(2)));
1355    set(hhuvmat.num_MinY,'String',num2str(ylim(1)));
1356end
1357
1358%% plot a circle around the selected point
1359if isempty(hhh)
1360    set(0,'CurrentFig',huvmat)
1361    set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
1362    rectangle('Curvature',[1 1],...
1363        'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
1364        'LineStyle','-','Tag','calib_marker');
1365else
1366    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
1367end
1368
1369%------------------------------------------------------------------------
1370% --- Executes on button press in ClearPoint: remove the selected line in the table Coord
1371%------------------------------------------------------------------------
1372function ClearPoint_Callback(hObject, eventdata, handles)
1373
1374Coord=get(handles.ListCoord,'Data');
1375iline=str2num(get(handles.CoordLine,'String'));
1376if isempty(iline)
1377    msgbox_uvmat('WARNING','no line suppressed, select a line in the table')
1378else
1379    answer=msgbox_uvmat('INPUT_Y-N',['suppress line ' num2str(iline) '?']);
1380    if isequal(answer,'Yes')
1381        Coord(iline,:)=[];
1382        set(handles.APPLY,'BackgroundColor',[1 0 1])
1383        set(handles.ListCoord,'Data',Coord);
1384        set(handles.CoordLine,'String','')
1385        PLOT_Callback(hObject,eventdata,handles)
1386        update_calib_marker([]);%remove circle marker
1387    end
1388end
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