source: trunk/src/geometry_calib.m @ 940

Last change on this file since 940 was 926, checked in by sommeria, 5 years ago

geometry cqlib updated

File size: 59.3 KB
Line 
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 2008-2016, LEGI UMR 5519 / CNRS UGA 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 16-Apr-2015 17:29:02
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
241DataSeries=uigetfile_uvmat('open a folder of images to calibrate',InputDir,'uigetdir');
242%SubProject=uigetfile_uvmat('open folder of subproject to calibrate',InputDir,'uigetdir');
243OutPut=browse_data(DataSeries);
244nbcalib=0;
245for ilist=1:numel(OutPut.Experiment)
246    SubDirBase=regexprep(OutPut.DataSeries{1},'\..+$','');
247    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
248    % copy the xml file from the old location if appropriate, then update with the calibration parameters
249    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
250        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
251        if exist(oldxml,'file')
252            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
253        end
254    end
255    errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
256    if ~strcmp(errormsg,'')
257        msgbox_uvmat('ERROR',errormsg);
258    else
259        display([XmlName ' updated with calibration parameters'])
260        nbcalib=nbcalib+1;
261    end
262end
263msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
264
265%------------------------------------------------------------------------
266% --- activate calibration and store parameters in ouputfile .
267function [GeometryCalib,index]=calibrate(handles,hhuvmat)
268%------------------------------------------------------------------------
269set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
270%% read the current calibration points
271index=[];
272Coord=get(handles.ListCoord,'Data');
273Coord(:,6)=[];
274% apply the calibration, whose type is selected in  handles.calib_type
275GeometryCalib=[];
276if ~isempty(Coord)
277    calib_cell=get(handles.calib_type,'String');
278    val=get(handles.calib_type,'Value');
279    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
280else
281    msgbox_uvmat('ERROR','No calibration points, abort')
282end
283if isempty(GeometryCalib)
284    return
285end
286Z_plane=[];
287if ~isempty(Coord)
288    %check error
289    X=Coord(:,1);
290    Y=Coord(:,2);
291    Z=Coord(:,3);
292    x_ima=Coord(:,4);
293    y_ima=Coord(:,5);
294    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
295    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
296    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
297    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
298    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
299    [tild,ind_dim]=max(GeometryCalib.ErrorMax);
300    index=index(ind_dim);
301    %set the Z position of the reference plane used for calibration
302    if isequal(max(Z),min(Z))%Z constant
303        Z_plane=Z(1);
304        GeometryCalib.NbSlice=1;
305        GeometryCalib.SliceCoord=[0 0 Z_plane];
306    end
307end
308%set the coordinate unit
309unitlist=get(handles.CoordUnit,'String');
310unit=unitlist{get(handles.CoordUnit,'value')};
311GeometryCalib.CoordUnit=unit;
312%record the points
313GeometryCalib.SourceCalib.PointCoord=Coord;
314display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
315
316% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
317set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
318set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
319set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
320set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
321set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
322set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
323
324%% store the calibration data, by default in the xml file of the currently displayed image
325answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
326    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
327    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
328if strcmp(answer,'Yes') %store the calibration data
329    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
330        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'})
331        GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
332    end
333else
334    GeometryCalib=[];
335    index=1;
336end
337
338%------------------------------------------------------------------------
339% --- determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
340function GeometryCalib=calib_rescale(Coord,handles)
341%------------------------------------------------------------------------
342X=Coord(:,1);
343Y=Coord(:,2);% Z not used
344x_ima=Coord(:,4);
345y_ima=Coord(:,5);
346[px]=polyfit(X,x_ima,1);
347[py]=polyfit(Y,y_ima,1);
348% T_x=px(2);
349% T_y=py(2);
350GeometryCalib.CalibrationType='rescale';
351GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
352GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
353GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
354GeometryCalib.omc=[0 0 0];
355
356%------------------------------------------------------------------------
357% --- determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
358function GeometryCalib=calib_linear(Coord,handles)
359%------------------------------------------------------------------------
360X=Coord(:,1);
361Y=Coord(:,2);% Z not used
362x_ima=Coord(:,4);
363y_ima=Coord(:,5);
364XY_mat=[ones(size(X)) X Y];
365a_X1=XY_mat\x_ima; %transformation matrix for X
366a_Y1=XY_mat\y_ima;%transformation matrix for X
367R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
368epsilon=sign(det(R));
369norm=abs(det(R));
370GeometryCalib.CalibrationType='linear';
371if (a_X1(2)/a_Y1(3))>0
372    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
373else
374    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
375end
376GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
377GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
378GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
379R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
380R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
381R=[R;[0 0]];
382GeometryCalib.R=[R [0;0;-epsilon]];
383GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
384
385%------------------------------------------------------------------------
386% --- determine the tsai parameters for a view normal to the grid plane
387% NOT USED
388function GeometryCalib=calib_normal(Coord,handles)
389%------------------------------------------------------------------------
390Calib.f1=str2num(get(handles.fx,'String'));
391Calib.f2=str2num(get(handles.fy,'String'));
392Calib.k=str2num(get(handles.kc,'String'));
393Calib.Cx=str2num(get(handles.Cx,'String'));
394Calib.Cy=str2num(get(handles.Cy,'String'));
395%default
396if isempty(Calib.f1)
397    Calib.f1=25/0.012;
398end
399if isempty(Calib.f2)
400    Calib.f2=25/0.012;
401end
402if isempty(Calib.k)
403    Calib.k=0;
404end
405if isempty(Calib.Cx)||isempty(Calib.Cy)
406    huvmat=findobj(allchild(0),'Tag','uvmat');
407    hhuvmat=guidata(huvmat);
408    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
409    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
410end   
411%tsai parameters
412Calib.dpx=0.012;%arbitrary
413Calib.dpy=0.012;
414Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
415Calib.f=Calib.f2*Calib.dpy;
416Calib.kappa1=Calib.k/(Calib.f*Calib.f);
417
418%initial guess
419X=Coord(:,1);
420Y=Coord(:,2);
421Zmean=mean(Coord(:,3));
422x_ima=Coord(:,4)-Calib.Cx;
423y_ima=Coord(:,5)-Calib.Cy;
424XY_mat=[ones(size(X)) X Y];
425a_X1=XY_mat\x_ima; %transformation matrix for X
426a_Y1=XY_mat\y_ima;%transformation matrix for Y
427R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
428norm=sqrt(det(-R));
429calib_param(1)=0;% quadratic distortion
430calib_param(2)=a_X1(1);
431calib_param(3)=a_Y1(1);
432calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
433calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
434display(['initial guess=' num2str(calib_param)])
435
436%optimise the parameters: minimisation of error
437calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
438
439GeometryCalib.CalibrationType='tsai_normal';
440GeometryCalib.focal=Calib.f;
441GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
442GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
443GeometryCalib.sx=Calib.sx;
444GeometryCalib.kappa1=calib_param(1);
445GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
446GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
447alpha=calib_param(5);
448GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
449
450%------------------------------------------------------------------------
451function GeometryCalib=calib_3D_linear(Coord,handles)
452%------------------------------------------------------------------------
453path_uvmat=which('uvmat');% check the path detected for source file uvmat
454path_UVMAT=fileparts(path_uvmat); %path to UVMAT
455huvmat=findobj(allchild(0),'Tag','uvmat');
456hhuvmat=guidata(huvmat);
457coord_files=get(handles.ListCoordFiles,'String');
458if ischar(coord_files)
459    coord_files={coord_files};
460end
461if isempty(coord_files{1}) || isequal(coord_files,{''})
462    coord_files={};
463end
464%retrieve the calibration points stored in the files listed in the popup list ListCoordFiles
465x_1=Coord(:,4:5)';%px coordinates of the ref points
466if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
467    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
468  return
469end
470nx=str2num(get(hhuvmat.num_Npx,'String'));
471ny=str2num(get(hhuvmat.num_Npy,'String'));
472x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
473X_1=Coord(:,1:3)';%phys coordinates of the ref points
474n_ima=numel(coord_files)+1;
475if ~isempty(coord_files)
476    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
477    for ifile=1:numel(coord_files)
478    t=xmltree(coord_files{ifile});
479    s=convert(t);%convert to matlab structure
480        if isfield(s,'GeometryCalib')
481            if isfield(s.GeometryCalib,'SourceCalib')
482                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
483                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
484                Coord_file=zeros(length(PointCoord),5);%default
485                for i=1:length(PointCoord)
486                    line=str2num(PointCoord{i});
487                    Coord_file(i,4:5)=line(4:5);%px x
488                    Coord_file(i,1:3)=line(1:3);%phys x
489                end
490                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
491                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
492                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
493                end
494            end
495        end
496    end
497end
498n_ima=numel(coord_files)+1;
499est_dist=[0;0;0;0;0];
500est_aspect_ratio=0;
501est_fc=[1;1];
502center_optim=0;
503run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim'
504if exist('Rc_1','var')
505    GeometryCalib.CalibrationType='3D_linear';
506    GeometryCalib.fx_fy=fc';
507    GeometryCalib.Cx_Cy=cc';
508    GeometryCalib.kc=kc(1);
509    GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
510    GeometryCalib.Tx_Ty_Tz=Tc_1';
511    GeometryCalib.R=Rc_1;
512    GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
513    GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
514    GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
515    GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
516    GeometryCalib.ErrorRMS=[];
517    GeometryCalib.ErrorMax=[];
518else
519    msgbox_uvmat('ERROR',['calibration function ' fullfile('toolbox_calib','go_calib_optim') ' did not converge: use multiple views or option 3D_extrinsic'])
520    GeometryCalib=[];
521end
522
523%------------------------------------------------------------------------
524function GeometryCalib=calib_3D_quadr(Coord,handles)
525%------------------------------------------------------------------
526
527path_uvmat=which('uvmat');% check the path detected for source file uvmat
528path_UVMAT=fileparts(path_uvmat); %path to UVMAT
529huvmat=findobj(allchild(0),'Tag','uvmat');
530hhuvmat=guidata(huvmat);
531if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
532    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
533  return
534end
535% check_cond=0;
536coord_files=get(handles.ListCoordFiles,'String');
537if ischar(coord_files)
538    coord_files={coord_files};
539end
540if isempty(coord_files{1}) || isequal(coord_files,{''})
541    coord_files={};
542end
543
544%retrieve the calibration points stored in the files listed in the popup list ListCoordFiles
545x_1=Coord(:,4:5)';%px coordinates of the ref points
546nx=str2num(get(hhuvmat.num_Npx,'String'));
547ny=str2num(get(hhuvmat.num_Npy,'String'));
548x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
549X_1=Coord(:,1:3)';%phys coordinates of the ref points
550n_ima=numel(coord_files)+1;
551if ~isempty(coord_files)
552    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
553    for ifile=1:numel(coord_files)
554    t=xmltree(coord_files{ifile});
555    s=convert(t);%convert to matlab structure
556        if isfield(s,'GeometryCalib')
557            if isfield(s.GeometryCalib,'SourceCalib')
558                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
559                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
560                Coord_file=zeros(length(PointCoord),5);%default
561                for i=1:length(PointCoord)
562                    line=str2num(PointCoord{i});
563                    Coord_file(i,4:5)=line(4:5);%px x
564                    Coord_file(i,1:3)=line(1:3);%phys x
565                end
566                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
567                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
568                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
569                end
570            end
571        end
572    end
573end
574n_ima=numel(coord_files)+1;
575est_dist=[1;0;0;0;0];
576est_aspect_ratio=1;
577center_optim=0;
578run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim'
579
580if exist('Rc_1','var')
581    GeometryCalib.CalibrationType='3D_quadr';
582    GeometryCalib.fx_fy=fc';
583    GeometryCalib.Cx_Cy=cc';
584    GeometryCalib.kc=kc(1);
585    GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
586    GeometryCalib.Tx_Ty_Tz=Tc_1';
587    GeometryCalib.R=Rc_1;
588    GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
589    GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
590    GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
591    GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
592    GeometryCalib.ErrorRMS=[];
593    GeometryCalib.ErrorMax=[];
594else
595    msgbox_uvmat('ERROR',['calibration function ' fullfile('toolbox_calib','go_calib_optim') ' did not converge: use multiple views or option 3D_extrinsic'])
596    GeometryCalib=[];
597end
598
599%------------------------------------------------------------------------
600function GeometryCalib=calib_3D_extrinsic(Coord,handles)
601%------------------------------------------------------------------
602path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
603path_UVMAT=fileparts(path_uvmat); %path to UVMAT
604x_1=double(Coord(:,4:5)');%image coordinates
605X_1=double(Coord(:,1:3)');% phys coordinates
606huvmat=findobj(allchild(0),'Tag','uvmat');
607hhuvmat=guidata(huvmat);
608if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
609    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
610  return
611end
612ny=str2double(get(hhuvmat.num_Npy,'String'));
613x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
614n_ima=1;
615GeometryCalib.CalibrationType='3D_extrinsic';
616fx=str2num(get(handles.fx,'String'));
617fy=str2num(get(handles.fy,'String'));
618Cx=str2num(get(handles.Cx,'String'));
619Cy=str2num(get(handles.Cy,'String'));
620errormsg='';
621if isempty(fx)
622    errormsg='focal length fx needs to be introduced';
623elseif isempty(fy)
624    errormsg='focal length fy needs to be introduced';
625elseif isempty(Cx)
626    errormsg='shift Cx to image centre needs to be introduced';
627elseif isempty(Cy)
628    errormsg='shift Cy to image centre needs to be introduced';
629end
630if ~isempty(errormsg)
631    GeometryCalib=[];
632    msgbox_uvmat('ERROR',errormsg)
633    return
634end
635GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
636GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
637GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
638GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
639GeometryCalib.kc=str2num(get(handles.kc,'String'));
640fct_path=fullfile(path_UVMAT,'toolbox_calib');
641addpath(fct_path)
642GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
643[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
644   (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
645rmpath(fct_path);
646GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
647GeometryCalib.Tx_Ty_Tz=Tc1';
648%inversion of z axis
649GeometryCalib.R=Rc1;
650GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
651GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
652GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
653GeometryCalib.omc=(180/pi)*omc';
654
655%------------------------------------------------------------------------
656%function GeometryCalib=calib_tsai_heikkila(Coord)
657% TEST: NOT IMPLEMENTED
658%------------------------------------------------------------------
659% path_uvmat=which('uvmat');% check the path detected for source file uvmat
660% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
661% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
662% addpath(path_calib)
663% npoints=size(Coord,1);
664% Coord(:,1:3)=10*Coord(:,1:3);
665% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
666% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
667% GeometryCalib.CalibrationType='tsai';
668% GeometryCalib.focal=par(2);
669
670
671%------------------------------------------------------------------------
672% --- determine the rms of calibration error
673function ErrorRms=error_calib(calib_param,Calib,Coord)
674%------------------------------------------------------------------------
675%calib_param: vector of free calibration parameters (to optimise)
676%Calib: structure of the given calibration parameters
677%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
678Calib.f=25;
679Calib.dpx=0.012;
680Calib.dpy=0.012;
681Calib.sx=1;
682Calib.Cx=512;
683Calib.Cy=512;
684Calib.kappa1=calib_param(1);
685Calib.Tx=calib_param(2);
686Calib.Ty=calib_param(3);
687Calib.Tz=calib_param(4);
688alpha=calib_param(5);
689Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
690
691X=Coord(:,1);
692Y=Coord(:,2);
693Z=Coord(:,3);
694x_ima=Coord(:,4);
695y_ima=Coord(:,5);
696[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
697ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
698ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
699ErrorRms=mean(ErrorRms);
700
701
702%------------------------------------------------------------------------
703% --- Executes on button press in STORE.
704function STORE_Callback(hObject, eventdata, handles)
705%------------------------------------------------------------------------
706Coord=get(handles.ListCoord,'Data');
707%Object=read_geometry_calib(Coord_cell);
708unitlist=get(handles.CoordUnit,'String');
709unit=unitlist{get(handles.CoordUnit,'value')};
710GeometryCalib.CoordUnit=unit;
711GeometryCalib.SourceCalib.PointCoord=Coord(:,1:5);
712huvmat=findobj(allchild(0),'Name','uvmat');
713hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
714% RootPath='';
715% RootFile='';
716if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
717%     testhandle=1;
718    RootPath=get(hhuvmat.RootPath,'String');
719    RootFile=get(hhuvmat.RootFile,'String');
720    filebase=[fullfile(RootPath,RootFile) '~'];
721    while exist([filebase '.xml'],'file')
722        filebase=[filebase '~'];
723    end
724    outputfile=[filebase '.xml'];
725    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');
726    if ~strcmp(errormsg,'')
727        msgbox_uvmat('ERROR',errormsg);
728    end
729    listfile=get(handles.ListCoordFiles,'string');
730    if isequal(listfile,{''})
731        listfile={outputfile};
732    else
733        listfile=[listfile;{outputfile}];%update the list of coord files
734    end
735    set(handles.ListCoordFiles,'string',listfile);
736end
737ClearAll_Callback(hObject, eventdata, handles)% clear the current list and point plots
738
739% --------------------------------------------------------------------
740% --- Executes on button press in ClearAll: clear the list of calibration points
741function ClearAll_Callback(hObject, eventdata, handles)
742% --------------------------------------------------------------------
743set(handles.ListCoord,'Data',[])
744PLOT_Callback(hObject, eventdata, handles)
745update_calib_marker([]);%remove circle marker
746set(handles.APPLY,'backgroundColor',[1 0 0])% set APPLY button to red color: no calibration wanted without points
747set(handles.CheckEnableMouse,'value',1); %activate mouse to pick new points
748
749%------------------------------------------------------------------------
750% --- Executes on button press in CLEAR LIST
751function CLEAR_Callback(hObject, eventdata, handles)
752%------------------------------------------------------------------------
753set(handles.ListCoordFiles,'Value',1)
754set(handles.ListCoordFiles,'String',{''})
755
756%------------------------------------------------------------------------
757% --- Executes on selection change in CheckEnableMouse.
758function CheckEnableMouse_Callback(hObject, eventdata, handles)
759%------------------------------------------------------------------------
760choice=get(handles.CheckEnableMouse,'Value');
761if choice
762    huvmat=findobj(allchild(0),'tag','uvmat');
763    if ishandle(huvmat)
764        hhuvmat=guidata(huvmat);
765        set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler
766        if get(hhuvmat.CheckEditObject,'Value')
767            set(hhuvmat.CheckEditObject,'Value',0)
768            uvmat('CheckEditObject_Callback',hhuvmat.CheckEditObject,[],hhuvmat)
769        end
770        set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler
771    end
772end
773
774% --------------------------------------------------------------------
775function MenuHelp_Callback(hObject, eventdata, handles)
776web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#GeometryCalib')
777
778% --------------------------------------------------------------------
779function MenuSetScale_Callback(hObject, eventdata, handles)
780
781answer=msgbox_uvmat('INPUT_TXT','scale pixel/cm?','');
782%create test points
783huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
784hhuvmat=guidata(huvmat);
785if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
786    msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
787    return
788end
789set(handles.calib_type,'Value',1)% set calib option to 'rescale'
790npx=str2num(get(hhuvmat.num_Npx,'String'))/2;
791npy=str2num(get(hhuvmat.num_Npy,'String'))/2;
792Xima=[0.25*npx 0.75*npx 0.75*npx 0.25*npx]';
793Yima=[0.25*npy 0.25*npy 0.75*npy 0.75*npy]';
794x=Xima/str2num(answer);
795y=Yima/str2num(answer);
796Coord=[x y zeros(4,1) Xima Yima zeros(4,1)];
797set(handles.ListCoord,'Data',Coord)
798set(handles.APPLY,'BackgroundColor',[1 0 1])
799set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
800
801%------------------------------------------------------------------------
802function MenuCreateGrid_Callback(hObject, eventdata, handles)
803%------------------------------------------------------------------------
804CalibData=get(handles.geometry_calib,'UserData');
805Tinput=[];%default
806if isfield(CalibData,'grid')
807    Tinput=CalibData.grid;
808end
809[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
810set(handles.geometry_calib,'UserData',CalibData)
811
812%grid in phys space
813Coord=get(handles.ListCoord,'Data');
814Coord(1:size(T,1),1:3)=T;%update the existing list of phys coordinates from the GUI create_grid
815set(handles.ListCoord,'Data',Coord)
816set(handles.APPLY,'BackgroundColor',[1 0 1])
817set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
818
819% -----------------------------------------------------------------------
820% --- automatic grid dectection from local maxima of the images
821function MenuDetectGrid_Callback(hObject, eventdata, handles)
822%------------------------------------------------------------------------
823%% read the four last point coordinates in pixels
824Coord=get(handles.ListCoord,'Data');%read list of coordinates on geometry_calib
825nbpoints=size(Coord,1); %nbre of calibration points
826if nbpoints~=4
827    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')
828    return
829end
830% corners_X=(Coord(end:-1:end-3,4)); %pixel absissa of the four corners
831% corners_Y=(Coord(end:-1:end-3,5));
832corners_X=(Coord(:,4)); %pixel absissa of the four corners
833corners_Y=(Coord(:,5));
834
835%%%%%%
836%   corners_X=1000*[1.5415  1.7557 1.7539 1.5415]';
837%   corners_Y=1000*[1.1515 1.1509 1.3645  1.3639]';
838
839%reorder the last two points (the two first in the list) if needed
840angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
841if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
842      X_end=corners_X(4);
843      Y_end=corners_Y(4);
844      corners_X(4)=corners_X(3);
845      corners_Y(4)=corners_Y(3);
846      corners_X(3)=X_end;
847      corners_Y(3)=Y_end;
848end
849
850%% initiate the grid in phys coordinates
851CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
852grid_input=[];%default
853if isfield(CalibData,'grid')
854    grid_input=CalibData.grid;%retrieve the previously used grid
855end
856[T,CalibData.grid,CalibData.grid.CheckWhite]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
857set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
858X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
859Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
860
861%% read the current image, displayed in the GUI uvmat
862huvmat=findobj(allchild(0),'Name','uvmat');
863UvData=get(huvmat,'UserData');
864A=UvData.Field.A;%currently displayed image
865npxy=size(A);
866
867%% calculate transform matrices for plane projection: rectangle assumed to be viewed in perspective
868% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
869B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
870      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
871B = reshape (B', 8 , 8 )';
872D = [ corners_X , corners_Y ];
873D = reshape (D', 8 , 1 );
874l = (B' * B)\B' * D;
875Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
876C = [l(7:8)' 1];
877
878%% transform grid image into 'phys' coordinates
879GeometryCalib.CalibrationType='3D_linear';
880GeometryCalib.fx_fy=[1 1];
881GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
882GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
883GeometryCalib.CoordUnit='cm';
884path_uvmat=which('uvmat');% check the path detected for source file uvmat
885path_UVMAT=fileparts(path_uvmat); %path to UVMAT
886addpath(fullfile(path_UVMAT,'transform_field'))
887Data.ListVarName={'Coord_y','Coord_x','A'};
888Data.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}};
889if ndims(A)==3
890    A=mean(A,3);
891end
892Data.A=A-min(min(A));
893Data.Coord_y=[npxy(1)-0.5 0.5];
894Data.Coord_x=[0.5 npxy(2)];
895Data.CoordUnit='pixel';
896Calib.GeometryCalib=GeometryCalib;
897DataOut=phys(Data,Calib);
898rmpath(fullfile(path_UVMAT,'transform_field'))
899Amod=DataOut.A;% current image expressed in 'phys' coord
900Rangx=DataOut.Coord_x;% x coordinates of first and last pixel centres in phys
901Rangy=DataOut.Coord_y;% y coordinates of first and last pixel centres in phys
902if CalibData.grid.CheckWhite
903    Amod=double(Amod);%case of white grid markers: will look for image maxima
904else
905    Amod=-double(Amod);%case of black grid markers: will look for image minima
906end
907
908%% detection of local image extrema in each direction
909Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
910Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
911ind_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
912ind_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
913nbpoints=size(T,1);
914TIndex=ones(size(T));% image indices corresponding to point coordinates
915%look for image maxima around each expected grid point
916for ipoint=1:nbpoints
917    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);% x index of the expected point in the phys image Amod
918    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);% y index of the expected point in the phys image Amod
919    j0min=max(j0-ind_range_y,1);% min y index selected for the subimage (cut at the edge to avoid index <1)
920    j0max=min(j0+ind_range_y,size(Amod,1));% max y index selected for the subimage (cut at the edge to avoid index > size)
921    i0min=max(i0-ind_range_x,1);% min x index selected for the subimage (cut at the edge to avoid index <1)
922    i0max=min(i0+ind_range_x,size(Amod,2));% max x index selected for the subimage (cut at the edge to avoid index > size)
923    Asub=Amod(j0min:j0max,i0min:i0max); %subimage used to find brigthness extremum
924    x_profile=sum(Asub,1);%profile of subimage summed over y
925    y_profile=sum(Asub,2);%profile of subimage summed over x
926
927    [tild,ind_x_max]=max(x_profile);% index of max for the x profile
928    [tild,ind_y_max]=max(y_profile);% index of max for the y profile
929    %sub-pixel improvement using moments
930    x_shift=0;
931    y_shift=0;
932    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
933        Atop=x_profile(ind_x_max-2:ind_x_max+2);% extract x profile around the max
934        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
935    end
936    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
937        Atop=y_profile(ind_y_max-2:ind_y_max+2);% extract y profile around the max
938        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
939    end
940        %%%%
941%     if ipoint==9
942%                 figure(11)
943%   imagesc(Asub)
944%     figure(12)
945%     plot(x_profile,'r')
946%     hold on
947%     plot(y_profile,'b')
948%     grid on
949%     end
950    %%%%
951    TIndex(ipoint,1)=(i0min+ind_x_max-1+x_shift);% x position of the maximum (in index of Amod)
952    TIndex(ipoint,2)=(j0min+ind_y_max-1+y_shift);% y position of the maximum (in index of Amod)
953end
954Tmod(:,1)=(TIndex(:,1)-1)*Dx+Rangx(1);
955Tmod(:,2)=(TIndex(:,2)-1)*Dy+Rangy(1);
956%Tmod=T(:,(1:2))+Delta;% 'phys' coordinates of the detected points
957[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));% image coordinates of the detected points
958Coord=[T Xpx Ypx zeros(size(T,1),1)];
959set(handles.ListCoord,'Data',Coord)
960PLOT_Callback(hObject, eventdata, handles)
961set(handles.APPLY,'BackgroundColor',[1 0 1])
962set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
963
964
965%-----------------------------------------------------------------------
966function MenuTranslatePoints_Callback(hObject, eventdata, handles)
967%-----------------------------------------------------------------------
968%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
969CalibData=get(handles.geometry_calib,'UserData');
970Tinput=[];%default
971if isfield(CalibData,'translate')
972    Tinput=CalibData.translate;
973end
974T=translate_points(Tinput);%display translate_points GUI and get shift parameters
975CalibData.translate=T;
976set(handles.geometry_calib,'UserData',CalibData)
977%translation
978Coord=get(handles.ListCoord,'Data');
979Coord(:,1)=T(1)+Coord(:,1);
980Coord(:,2)=T(2)+Coord(:,2);
981Coord(:,3)=T(3)+Coord(:,3);
982set(handles.ListCoord,'Data',Coord);
983set(handles.APPLY,'BackgroundColor',[1 0 1])
984
985% --------------------------------------------------------------------
986function MenuRotatePoints_Callback(hObject, eventdata, handles)
987%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
988CalibData=get(handles.geometry_calib,'UserData');
989Tinput=[];%default
990if isfield(CalibData,'rotate')
991    Tinput=CalibData.rotate;
992end
993T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
994CalibData.rotate=T;
995set(handles.geometry_calib,'UserData',CalibData)
996%-----------------------------------------------------
997%rotation
998Phi=T(1);
999O_x=0;%default
1000O_y=0;%default
1001if numel(T)>=2
1002    O_x=T(2);%default
1003end
1004if numel(T)>=3
1005    O_y=T(3);%default
1006end
1007Coord=get(handles.ListCoord,'Data');
1008r1=cos(pi*Phi/180);
1009r2=-sin(pi*Phi/180);
1010r3=sin(pi*Phi/180);
1011r4=cos(pi*Phi/180);
1012x=Coord(:,1)-O_x;
1013y=Coord(:,2)-O_y;
1014Coord(:,1)=r1*x+r2*y;
1015Coord(:,2)=r3*x+r4*y;
1016set(handles.ListCoord,'Data',Coord)
1017set(handles.APPLY,'BackgroundColor',[1 0 1])
1018
1019% --------------------------------------------------------------------
1020function MenuFlip_x_Callback(hObject, eventdata, handles)
1021Coord=get(handles.ListCoord,'Data');
1022Coord(:,1)=-Coord(:,1);
1023set(handles.ListCoord,'Data',Coord)
1024
1025% --------------------------------------------------------------------
1026function MenuFlip_y_Callback(hObject, eventdata, handles)
1027Coord=get(handles.ListCoord,'Data');
1028Coord(:,2)=-Coord(:,2);
1029set(handles.ListCoord,'Data',Coord)
1030
1031% --------------------------------------------------------------------
1032function MenuImportPoints_Callback(hObject, eventdata, handles)
1033fileinput=browse_xml(hObject, eventdata, handles);
1034if isempty(fileinput)
1035    return
1036end
1037[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1038if ~isfield(s,'GeometryCalib')
1039    msgbox_uvmat('ERROR','invalid input file: no geometry_calib data')
1040    return
1041end
1042GeometryCalib=s.GeometryCalib;
1043if ~(isfield(GeometryCalib,'SourceCalib')&&isfield(GeometryCalib.SourceCalib,'PointCoord'))
1044        msgbox_uvmat('ERROR','invalid input file: no calibration points')
1045    return
1046end
1047Coord=GeometryCalib.SourceCalib.PointCoord;
1048Coord=[Coord zeros(size(Coord,1),1)];
1049set(handles.ListCoord,'Data',Coord)
1050PLOT_Callback(handles.geometry_calib, [], handles)
1051set(handles.APPLY,'BackgroundColor',[1 0 1])
1052set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default
1053
1054% -----------------------------------------------------------------------
1055function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1056%------------------------------------------------------------------------
1057fileinput=browse_xml(hObject, eventdata, handles);
1058if isempty(fileinput)
1059    return
1060end
1061[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1062GeometryCalib=s.GeometryCalib;
1063display_intrinsic(GeometryCalib,handles)
1064
1065% -----------------------------------------------------------------------
1066function MenuImportAll_Callback(hObject, eventdata, handles)
1067%------------------------------------------------------------------------
1068fileinput=browse_xml(hObject, eventdata, handles);
1069if ~isempty(fileinput)
1070    loadfile(handles,fileinput)
1071end
1072set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default
1073
1074% -----------------------------------------------------------------------
1075% --- Executes on menubar option Import/Grid file: introduce previous grid files
1076function MenuGridFile_Callback(hObject, eventdata, handles)
1077% -----------------------------------------------------------------------
1078inputfile=browse_xml(hObject, eventdata, handles);
1079listfile=get(handles.ListCoordFiles,'String');
1080if isequal(listfile,{''})
1081    listfile={inputfile};
1082else
1083    listfile=[listfile;{inputfile}];%update the list of coord files
1084end
1085set(handles.ListCoordFiles,'String',listfile);
1086
1087
1088%------------------------------------------------------------------------
1089function fileinput=browse_xml(hObject, eventdata, handles)
1090%------------------------------------------------------------------------
1091fileinput=[];%default
1092oldfile=''; %default
1093UserData=get(handles.geometry_calib,'UserData');
1094if isfield(UserData,'XmlInputFile')
1095    oldfile=UserData.XmlInputFile;
1096end
1097[FileName, PathName, filterindex] = uigetfile( ...
1098       {'*.xml;*.mat', ' (*.xml,*.mat)';
1099       '*.xml',  '.xml files '; ...
1100        '*.mat',  '.mat matlab files '}, ...
1101        'Pick a file',oldfile);
1102fileinput=[PathName FileName];%complete file name
1103testblank=findstr(fileinput,' ');%look for blanks
1104if ~isempty(testblank)
1105    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1106    return
1107end
1108sizf=size(fileinput);
1109if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1110UserData.XmlInputFile=fileinput;
1111set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1112
1113% -----------------------------------------------------------------------
1114function Heading=loadfile(handles,fileinput)
1115%------------------------------------------------------------------------
1116Heading=[];%default
1117[s,errormsg]=imadoc2struct(fileinput,'Heading','GeometryCalib');
1118if ~isempty(errormsg)
1119    msgbox_uvmat('ERROR',errormsg)
1120    return
1121end
1122if ~isempty(s.Heading)
1123    Heading=s.Heading;
1124end
1125
1126GeometryCalib=s.GeometryCalib;
1127fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1128CoordCell={};
1129Tabchar={};%default
1130val_cal=1;%default
1131if ~isempty(GeometryCalib)
1132    % choose the calibration option
1133    if isfield(GeometryCalib,'CalibrationType')
1134        calib_list=get(handles.calib_type,'String');
1135        for ilist=1:numel(calib_list)
1136            if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1137                val_cal=ilist;
1138                break
1139            end
1140        end
1141    end
1142    display_intrinsic(GeometryCalib,handles)%intrinsic param
1143    %extrinsic param
1144    if isfield(GeometryCalib,'Tx_Ty_Tz')
1145        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1146        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1147        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1148        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1149    end
1150    if isfield(GeometryCalib,'omc')
1151        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1152        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1153        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1154    end
1155    if isfield(GeometryCalib,'SourceCalib')&& isfield(GeometryCalib.SourceCalib,'PointCoord')
1156        calib=GeometryCalib.SourceCalib.PointCoord;
1157        Coord=[calib zeros(size(calib,1),1)];
1158        set(handles.ListCoord,'Data',Coord)
1159    end
1160    PLOT_Callback(handles.geometry_calib, [], handles)
1161    set(handles.APPLY,'BackgroundColor',[1 0 1])
1162end
1163set(handles.calib_type,'Value',val_cal)
1164
1165if isempty(CoordCell)% allow mouse action by default in the absence of input points
1166    set(handles.CheckEnableMouse,'Value',1)
1167    set(handles.CheckEnableMouse,'BackgroundColor',[1 1 0])
1168else % does not allow mouse action by default in the presence of input points
1169    set(handles.CheckEnableMouse,'Value',0)
1170    set(handles.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7])
1171end
1172
1173%------------------------------------------------------------------------
1174%---display calibration intrinsic parameters
1175function display_intrinsic(GeometryCalib,handles)
1176%------------------------------------------------------------------------
1177fx=[];
1178fy=[];
1179if isfield(GeometryCalib,'fx_fy')
1180    fx=GeometryCalib.fx_fy(1);
1181    fy=GeometryCalib.fx_fy(2);
1182end
1183Cx_Cy=[0 0];%default
1184if isfield(GeometryCalib,'Cx_Cy')
1185    Cx_Cy=GeometryCalib.Cx_Cy;
1186end
1187kc=0;
1188if isfield(GeometryCalib,'kc')
1189    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1190end
1191set(handles.fx,'String',num2str(fx,5))
1192set(handles.fy,'String',num2str(fy,5))
1193set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1194set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1195set(handles.kc,'String',num2str(kc,'%1.4f'))
1196
1197
1198% --- Executes when user attempts to close geometry_calib.
1199function geometry_calib_CloseRequestFcn(hObject, eventdata, handles)
1200
1201delete(hObject); % closes the figure
1202
1203%------------------------------------------------------------------------
1204% --- Executes on button press in PLOT.
1205%------------------------------------------------------------------------
1206function PLOT_Callback(hObject, eventdata, handles)
1207huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1208hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
1209h_menu_coord=findobj(huvmat,'Tag','TransformName');
1210menu=get(h_menu_coord,'String');
1211choice=get(h_menu_coord,'Value');
1212option='';
1213if iscell(menu)
1214    option=menu{choice};
1215end
1216Coord=get(handles.ListCoord,'Data');
1217if ~isempty(Coord)
1218    if isequal(option,'phys')
1219        Coord_plot=Coord(:,1:3);
1220    elseif isempty(option);%optionoption,'px')||isequal(option,'')
1221        Coord_plot=Coord(:,4:5);
1222    else
1223        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ')
1224    end
1225end
1226
1227set(0,'CurrentFigure',huvmat)
1228set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
1229hh=findobj('Tag','calib_points');
1230if  ~isempty(Coord) && isempty(hh)
1231    hh=line(Coord_plot(:,1),Coord_plot(:,2),'Color','m','Tag','calib_points','LineStyle','none','Marker','+','MarkerSize',10);
1232elseif isempty(Coord)%empty list of points, suppress the plot
1233    delete(hh)
1234else
1235    set(hh,'XData',Coord_plot(:,1))
1236    set(hh,'YData',Coord_plot(:,2))
1237end
1238pause(.1)
1239figure(handles.geometry_calib)
1240
1241%------------------------------------------------------------------------
1242% --- Executes on button press in Copy: display Coord on the Matlab work space
1243%------------------------------------------------------------------------
1244function Copy_Callback(hObject, eventdata, handles)
1245global Coord
1246evalin('base','global Coord')%make CurData global in the workspace
1247Coord=get(handles.ListCoord,'Data');
1248display('coordinates of calibration points (phys,px,marker) :')
1249evalin('base','Coord') %display CurData in the workspace
1250commandwindow; %brings the Matlab command window to the front
1251
1252%------------------------------------------------------------------------
1253% --- Executes when selected cell(s) is changed in ListCoord.
1254%------------------------------------------------------------------------
1255function ListCoord_CellSelectionCallback(hObject, eventdata, handles)
1256if ~isempty(eventdata.Indices)
1257    iline=eventdata.Indices(1);% selected line number
1258    set(handles.CoordLine,'String',num2str(iline))
1259     Data=get(handles.ListCoord,'Data');
1260     update_calib_marker(Data(iline,:))
1261end
1262
1263%------------------------------------------------------------------------
1264% --- Executes when entered data in editable cell(s) in ListCoord.
1265%------------------------------------------------------------------------
1266function ListCoord_CellEditCallback(hObject, eventdata, handles)
1267
1268Input=str2num(eventdata.EditData);%pasted input
1269Coord=get(handles.ListCoord,'Data');
1270iline=eventdata.Indices(1);% selected line number
1271if size(Coord,1)<iline+numel(Input)
1272    Coord=[Coord ; zeros(iline+numel(Input)-size(Coord,1),6)];% append zeros to fit the new column
1273end
1274Coord(iline:iline+numel(Input)-1,eventdata.Indices(2))=Input';
1275set(handles.ListCoord,'Data',Coord)
1276PLOT_Callback(hObject, eventdata, handles)
1277
1278%------------------------------------------------------------------------
1279% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1280%------------------------------------------------------------------------
1281function ListCoord_KeyPressFcn(hObject, eventdata, handles)
1282iline=str2num(get(handles.CoordLine,'String'));
1283xx=double(get(handles.geometry_calib,'CurrentCharacter'));%get the keyboard character
1284if ismember(xx,[28 29 30 31])% directional arrow
1285    Coord=get(handles.ListCoord,'Data');
1286    switch xx
1287        case 30 % arrow upward
1288            iline=iline-1;
1289        case 31% arrow downward
1290            iline=iline+1;
1291    end
1292    if iline>=1 && iline<=size(Coord,1)
1293        set(handles.CoordLine,'String',num2str(iline))
1294        update_calib_marker(Coord(iline,1:5))% show the point corresponding to the selected line
1295    end
1296else
1297    set(handles.APPLY,'BackgroundColor',[1 0 1])% paint APPLY in magenta to indicate that the table content has be modified
1298    if ismember(xx,[127 31])% delete, or downward
1299        Coord=get(handles.ListCoord,'Data');
1300        iline=str2double(get(handles.CoordLine,'String'));
1301        if isequal(xx, 31)
1302            if isequal(iline,size(Coord,1))% arrow downward
1303                Coord=[Coord;zeros(1,size(Coord,2))];
1304            end
1305        else
1306            Coord(iline,:)=[];% suppress the current line
1307        end
1308        set(handles.ListCoord,'Data',Coord);
1309    end
1310end
1311
1312%------------------------------------------------------------------------
1313% --- update the plot of calibration points
1314%------------------------------------------------------------------------
1315% draw a circle around the point defined by the input coordinates Coord as given by line in the table Listcoord
1316function update_calib_marker(Coord)
1317
1318%% read config on uvmat
1319huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1320hhuvmat=guidata(huvmat);
1321hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');
1322if numel(Coord)<5
1323    if ~isempty(hhh)
1324        delete(hhh)%delete the circle marker in case of no valid input
1325    end
1326    return
1327end
1328menu=get(hhuvmat.TransformName,'String');
1329choice=get(hhuvmat.TransformName,'Value');
1330option='';
1331if iscell(menu)
1332    option=menu{choice};
1333end
1334
1335%% read appropriate coordinates (px or phys) in the table ListCoord
1336if isequal(option,'phys') % use phys coord
1337    XCoord=Coord(1);
1338    YCoord=Coord(2);
1339elseif isempty(option)% use coord in pixels
1340    XCoord=Coord(4);
1341    YCoord=Coord(5);
1342else
1343    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ')
1344    return
1345end
1346
1347%% adjust the plot limits if needed
1348xlim=get(hhuvmat.PlotAxes,'XLim');
1349ylim=get(hhuvmat.PlotAxes,'YLim');
1350ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/25;%defines the size of the circle marker
1351check_xlim=0;
1352if XCoord>xlim(2)
1353    xlim=xlim+XCoord-xlim(2)+ind_range;% translate plot limit
1354    check_xlim=1;
1355elseif XCoord<xlim(1)
1356    xlim=xlim-XCoord+xlim(1)-ind_range;% translate plot limit
1357    check_xlim=1;
1358end
1359if check_xlim
1360    set(hhuvmat.PlotAxes,'XLim',xlim);
1361    set(hhuvmat.num_MaxX,'String',num2str(xlim(2)));
1362    set(hhuvmat.num_MinX,'String',num2str(xlim(1)));
1363end
1364check_ylim=0;
1365if YCoord>ylim(2)
1366    ylim=ylim+YCoord-ylim(2)+ind_range;% translate plot limit
1367    check_ylim=1;
1368elseif YCoord<ylim(1)
1369    ylim=ylim-YCoord+ylim(1)-ind_range;% translate plot limit
1370    check_ylim=1;
1371end
1372if check_ylim
1373    set(hhuvmat.PlotAxes,'YLim',ylim);
1374    set(hhuvmat.num_MaxY,'String',num2str(ylim(2)));
1375    set(hhuvmat.num_MinY,'String',num2str(ylim(1)));
1376end
1377
1378%% plot a circle around the selected point
1379if isempty(hhh)
1380    set(0,'CurrentFig',huvmat)
1381    set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
1382    rectangle('Curvature',[1 1],...
1383        'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
1384        'LineStyle','-','Tag','calib_marker');
1385else
1386    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
1387end
1388
1389%------------------------------------------------------------------------
1390% --- Executes on button press in ClearPoint: remove the selected line in the table Coord
1391%------------------------------------------------------------------------
1392function ClearPoint_Callback(hObject, eventdata, handles)
1393
1394Coord=get(handles.ListCoord,'Data');
1395iline=str2num(get(handles.CoordLine,'String'));
1396if isempty(iline)
1397    msgbox_uvmat('WARNING','no line suppressed, select a line in the table')
1398else
1399    answer=msgbox_uvmat('INPUT_Y-N',['suppress line ' num2str(iline) '?']);
1400    if isequal(answer,'Yes')
1401        Coord(iline,:)=[];
1402        set(handles.APPLY,'BackgroundColor',[1 0 1])
1403        set(handles.ListCoord,'Data',Coord);
1404        set(handles.CoordLine,'String','')
1405        PLOT_Callback(hObject,eventdata,handles)
1406        update_calib_marker([]);%remove circle marker
1407    end
1408end
1409
1410
1411
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