Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 115) +++ /trunk/src/civ.m (revision 116) @@ -770,7 +770,6 @@ set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0]) -if isequal(get(handles.BATCH, 'Enable'),'On') + set(handles.BATCH,'Enable','On') set(handles.BATCH,'BackgroundColor',[1 0 0]) -end %%%%% store the root input filename for future opening @@ -2107,5 +2106,6 @@ s=convert(t); end -if batch + test_interp=0; + if batch if isfield(s,'BatchParam') sparam=s.BatchParam; @@ -2140,5 +2140,5 @@ end %test_interp=get(handles.test_interp,'Value'); - test_interp=0; + if isfield(sparam,'PatchBin') if ~exist(sparam.PatchBin,'file') Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 115) +++ /trunk/src/geometry_calib.m (revision 116) @@ -71,5 +71,5 @@ % parameters on the uvmat interface (obtained by 'get_plot_handle.m') %------------------------------------------------------------------------ -function geometry_calib_OpeningFcn(hObject, eventdata, handles, handles_uvmat,pos,inputfile) +function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile,pos) %------------------------------------------------------------------------ % Choose default command line output for geometry_calib @@ -81,5 +81,5 @@ %set the position of the interface -if exist('pos','var')& length(pos)>2 +if exist('pos','var')&& length(pos)>2 pos_gui=get(hObject,'Position'); pos_gui(1)=pos(1); @@ -92,13 +92,15 @@ set(handles.calib_type,'String',{'rescale';'linear';'quadr';'3D_linear';'3D_quadr';'3D_extrinsic'}) inputxml=''; -if exist('inputfile','var')& ~isempty(inputfile) +if exist('inputfile','var')&& ~isempty(inputfile) struct.XmlInputFile=inputfile; set(hObject,'UserData',struct) [Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(inputfile); - inputxml=[fullfile(Pathsub,RootFile) '.xml']; + if ~strcmp(ext,'.xml') + inputfile=[fullfile(Pathsub,RootFile) '.xml']%xml file corresponding to the input file + end end set(handles.ListCoord,'String',{'......'}) -if exist(inputxml,'file') - loadfile(handles,inputxml)% load the point coordiantes existing in the xml file +if exist(inputfile,'file') + loadfile(handles,inputfile)% load the point coordiantes existing in the xml file end set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function @@ -232,4 +234,7 @@ set(hhuvmat.FixedLimits,'Value',0)% put FixedLimits option to 'off' set(hhuvmat.FixedLimits,'BackgroundColor',[0.7 0.7 0.7]) + UserData=get(handles.geometry_calib,'UserData'); + UserData.XmlInputFile=outputfile;%save the current xml file name + set(handles.geometry_calib,'UserData',UserData) uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates MenuPlot_Callback(hObject, eventdata, handles) @@ -294,8 +299,8 @@ %record the points GeometryCalib.SourceCalib.PointCoord=Coord; - errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - end +% errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file +% if ~strcmp(errormsg,'') +% msgbox_uvmat('ERROR',errormsg); +% end end display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters @@ -412,12 +417,13 @@ % y1=XY_mat*a_Y1; % err_Y1=max(abs(y1-y_ima));%error +R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,0]; +norm=abs(det(R)); GeometryCalib.CalibrationType='linear'; -GeometryCalib.focal=1; +GeometryCalib.fx_fy=[norm norm]; GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,0]; -norm=det(R); -GeometryCalib.Tx_Ty_Tz=[a_X1(1) a_Y1(1) norm]; +GeometryCalib.Tx_Ty_Tz=[a_X1(1) a_Y1(1) 1]; GeometryCalib.R=R/norm; - +GeometryCalib.omc=(180/pi)*[acos(R(1,1)) 0 0]; %------------------------------------------------------------------------ % determine the tsai parameters for a view normal to the grid plane @@ -600,9 +606,9 @@ path_uvmat=which('geometry_calib');% check the path detected for source file uvmat path_UVMAT=fileparts(path_uvmat); %path to UVMAT -x_1=Coord(:,4:5)'; -X_1=Coord(:,1:3)'; +x_1=double(Coord(:,4:5)');%image coordiantes +X_1=double(Coord(:,1:3)');% phys coordinates huvmat=findobj(allchild(0),'Tag','uvmat'); hhuvmat=guidata(huvmat); -ny=str2num(get(hhuvmat.npy,'String')); +ny=str2double(get(hhuvmat.npy,'String')); x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates n_ima=1; @@ -615,5 +621,5 @@ fct_path=fullfile(path_UVMAT,'toolbox_calib'); addpath(fct_path) -Cx_Cy=ny-(GeometryCalib.Cx_Cy)';%reverse Cx_Cy(2) for calibration (inversion of px ordinate) +GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate) % [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,... % [Calib.f Calib.f*Calib.sx]',... @@ -621,10 +627,6 @@ % [-Calib.kappa1*Calib.f^2 0 0 0 0]); [omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,... - (GeometryCalib.fx_fy)',... - Cx_Cy,[GeometryCalib.kc 0 0 0 0]); -%get the euler angles ??? + (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]); rmpath(fct_path); - -std(ex') GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function GeometryCalib.Tx_Ty_Tz=Tc1'; @@ -633,7 +635,8 @@ GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate -%GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate +GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate GeometryCalib.omc=(180/pi)*omc'; %GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward + @@ -993,7 +996,7 @@ % -------------------------------------------------------------------- function MenuHelp_Callback(hObject, eventdata, handles) -path_to_uvmat=which ('uvmat');% check the path of uvmat +path_to_uvmat=which('uvmat');% check the path of uvmat pathelp=fileparts(path_to_uvmat); - helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html'); +helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html'); if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package') else @@ -1409,5 +1412,5 @@ GeometryCalib=s.GeometryCalib; %GeometryCalib=load_calib(hObject, eventdata, handles) -calib=reshape(GeometryCalib.PointCoord',[],1); +calib=reshape(GeometryCalib.PointCoord,[],1); for ilist=1:numel(calib) CoordCell{ilist}=num2str(calib(ilist)); @@ -1474,5 +1477,5 @@ fileinput=[];%default oldfile=''; %default -UserData=get(handles.geometry_calib,'UserData') +UserData=get(handles.geometry_calib,'UserData'); if isfield(UserData,'XmlInputFile') oldfile=UserData.XmlInputFile; @@ -1497,6 +1500,7 @@ function loadfile(handles,fileinput) %------------------------------------------------------------------------ -[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib'); -GeometryCalib=s.GeometryCalib +fileinput +[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib') +GeometryCalib=s.GeometryCalib; fx=1;fy=1;Cx=0;Cy=0;kc=0; %default % Tabchar={}; @@ -1534,5 +1538,5 @@ set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4)) end - calib=reshape(GeometryCalib.PointCoord',[],1); + calib=reshape(GeometryCalib.PointCoord,[],1); for ilist=1:numel(calib) CoordCell{ilist}=num2str(calib(ilist)); Index: /trunk/src/griddata_uvmat.m =================================================================== --- /trunk/src/griddata_uvmat.m (revision 115) +++ /trunk/src/griddata_uvmat.m (revision 116) @@ -2,8 +2,7 @@ %adapt the input of the matlab function griddata to the appropriate version of Matlab function ZI = griddata_uvmat(X,Y,Z,XI,YI) -whos X Y Z XI YI txt=ver; Release=txt(1).Release; -relnumb=str2num(Release(3:4)) +relnumb=str2num(Release(3:4)); if relnumb >= 20 ZI=griddata(double(X),double(Y),double(Z),double(XI),double(YI),'linear',{'QJ'}); Index: /trunk/src/imadoc2struct.m =================================================================== --- /trunk/src/imadoc2struct.m (revision 115) +++ /trunk/src/imadoc2struct.m (revision 116) @@ -217,4 +217,5 @@ if strcmp(option,'GeometryCalib') tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);%time in TimeUnit + size(tsai.PointCoord) end s.GeometryCalib=tsai; @@ -228,9 +229,9 @@ val=default; uid=find(t,label);%find the element iud(s) -if ~isempty(uid) - uid_child=children(t,uid); +if ~isempty(uid) %if the element named label exists + uid_child=children(t,uid);%find the children if ~isempty(uid_child) - data=get(t,uid_child,'type'); - if iscell(data) + data=get(t,uid_child,'type');%get the type of child + if iscell(data)% case of multiple element for icell=1:numel(data) val_read=str2num(get(t,uid_child(icell),'value')); @@ -239,6 +240,6 @@ end end - val=val'; - else +% val=val'; + else % case of unique element value val_read=str2num(get(t,uid_child,'value')); if ~isempty(val_read) Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 115) +++ /trunk/src/series/merge_proj.m (revision 116) @@ -23,4 +23,6 @@ WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame %------------------------------------------------- + + %projection object @@ -229,7 +231,12 @@ if ~exist(res_subdir,'dir') dircur=pwd; - cd(fulldir) - error=mkdir(subdir); - cd(dircur) + cd(fulldir); + succeed=mkdir(subdir); + if succeed + cd(dircur); + else + msgbox_uvmat('ERROR',['Cannot create directory ' fulldir]) + return + end end filebasesub=fullfile(res_subdir,Series.RootFile{1}); @@ -286,9 +293,13 @@ % coord transform % z index + if ~isempty(NbSlice_calib) - Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; - end + Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1 + end +% Field{iview}.ZIndex=1; if ~isempty(transform_fct) - Field{iview}=transform_fct(Field{iview},XmlData{iview});%transform to phys if requested + XmlData{iview}.GeometryCalib + Field{iview}=transform_fct(Field{iview},XmlData{iview}); + %transform to phys if requested end if testcivx @@ -301,5 +312,4 @@ end end - %----------END LOOP ON VIEWS---------------------- @@ -376,5 +386,5 @@ %MergeData.dt=1; MergeData.Time=time_i; - error=struct2nc(mergename,MergeData); %save result file + error=struct2nc(mergename,MergeData);%save result file if isempty(error) display(['output file ' mergename ' written']) Index: /trunk/src/transform_field/phys.m =================================================================== --- /trunk/src/transform_field/phys.m (revision 115) +++ /trunk/src/transform_field/phys.m (revision 116) @@ -58,8 +58,8 @@ end %transform of X,Y coordinates for vector fields -if isfield(Data,'ZIndex')&&~isempty(Data.ZIndex) +if isfield(Data,'ZIndex')&&~isempty(Data.ZIndex)&&~isnan(Data.ZIndex) ZIndex=Data.ZIndex; else - ZIndex=0; + ZIndex=1; end if test_1 @@ -111,6 +111,6 @@ DataOut.TimeUnit='s'; %transform of X,Y coordinates for vector fields - if isfield(Data,'ZIndex') && ~isempty(Data.ZIndex) - Z=Data.ZIndex; + if isfield(Data,'ZIndex') && ~isempty(Data.ZIndex)&&~isnan(Data.ZIndex) + Z=Data.ZIndex else Z=0; @@ -153,11 +153,18 @@ end - %%%%%%%%%%%%%%%%%%%% function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex) + +if ndims(A)==3 + A=mean(A,3); +end + + xcorner=[]; ycorner=[]; npx=[]; npy=[]; +dx=ones(1,length(A)); +dy=ones(1,length(A)); for icell=1:length(A) siz=size(A{icell}); @@ -165,5 +172,5 @@ npy=[npy siz(1)]; Calib=CalibIn{icell}; - xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordiantes of corners + xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5]; [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates @@ -177,5 +184,5 @@ Rangy(2)=min(ycorner); Rangy(1)=max(ycorner); -test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy)); +test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images) npY=1+round((Rangy(1)-Rangy(2))/min(dy)); @@ -187,6 +194,5 @@ for icell=1:length(A) Calib=CalibIn{icell}; - if (isfield(Calib,'R') && ~isequal(Calib.R(2,1),0) && ~isequal(Calib.R(1,2),0)) ||... - ((isfield(Calib,'kappa1')&& ~isequal(Calib.kappa1,0))) || test_multi || ~isequal(Calib,CalibIn{1}) + if isfield(Calib,'R') || isfield(Calib,'kc')|| test_multi ||~isequal(Calib,CalibIn{1})% the image needs to be interpolated to the new coordinates zphys=0; %default if isfield(Calib,'SliceCoord') %.Z= index of plane @@ -227,14 +233,14 @@ A_out{icell}=uint16(A_out{icell}); end - else% - + else% A_out{icell}=A{icell};%no transform Rangx=[0.5 npx-0.5];%image coordiantes of corners Rangy=[npy-0.5 0.5]; - [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],[ZIndex ZIndex]);%case of translations without rotation and quadratic deformation - [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,[ZIndex ZIndex]); - end -end - + [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation + [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); + end +end + +%------------------------------------------------------------------------ %'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters % function [Xphys,Yphys]=phys_XYZ(Calib,X,Y,Z) @@ -245,13 +251,10 @@ %Z: index of plane function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z) -if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z +%------------------------------------------------------------------------ +if exist('Z','var')&& isequal(Z,round(Z))&& Z>0 && isfield(Calib,'SliceCoord')&&length(Calib.SliceCoord)>=Z Zindex=Z; Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE else -% if exist('Z','var') -% Zphys=Z; -% else - Zphys=0; -% end + Zphys=0; end if ~exist('X','var')||~exist('Y','var') @@ -260,12 +263,27 @@ return end -Xphys=X;%default -Yphys=Y; -%image transform +%coordinate transform +if ~isfield(Calib,'fx_fy') + Calib.fx_fy=[1 1]; +end +if ~isfield(Calib,'Tx_Ty_Tz') + Calib.Tx_Ty_Tz=[0 0 1]; +end +if ~isfield(Calib,'Cx_Cy') + Calib.Cx_Cy=[0 0]; +end +if ~isfield(Calib,'kc') + Calib.kc=0; +end if isfield(Calib,'R') R=(Calib.R)'; + Tx=Calib.Tx_Ty_Tz(1); + Ty=Calib.Tx_Ty_Tz(2); + Tz=Calib.Tx_Ty_Tz(3); + f=Calib.fx_fy(1);%dpy=1; sx=1 + dpx=Calib.fx_fy(2)/Calib.fx_fy(1); Dx=R(5)*R(7)-R(4)*R(8); Dy=R(1)*R(8)-R(2)*R(7); - D0=Calib.f*(R(2)*R(4)-R(1)*R(5)); + D0=f*(R(2)*R(4)-R(1)*R(5)); Z11=R(6)*R(8)-R(5)*R(9); Z12=R(2)*R(9)-R(3)*R(8); @@ -274,20 +292,37 @@ Zx0=R(3)*R(5)-R(2)*R(6); Zy0=R(1)*R(6)-R(3)*R(4); - A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys; - A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys; - A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys; - A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys; - X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys); - Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys); + A11=R(8)*Ty-R(5)*Tz+Z11*Zphys; + A12=R(2)*Tz-R(8)*Tx+Z12*Zphys; + A21=-R(7)*Ty+R(4)*Tz+Z21*Zphys; + A22=-R(1)*Tz+R(7)*Tx+Z22*Zphys; + X0=f*(R(5)*Tx-R(2)*Ty+Zx0*Zphys); + Y0=f*(-R(4)*Tx+R(1)*Ty+Zy0*Zphys); %px to camera: - Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates - Yd=Calib.dpy*(Y-Calib.Cy); - dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor - Xu=dist_fact.*Xd;%undistorted sensor coordinates - Yu=dist_fact.*Yd; + Xd=dpx*(X-Calib.Cx_Cy(1)); % sensor coordinates + Yd=(Y-Calib.Cx_Cy(2)); + dist_fact=1+Calib.kc*(Xd.*Xd+Yd.*Yd)/(f*f); %distortion factor + Xu=Xd./dist_fact;%undistorted sensor coordinates + Yu=Yd./dist_fact; denom=Dx*Xu+Dy*Yu+D0; % denom2=denom.*denom; Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates Yphys=(A21.*Xu+A22.*Yu+Y0)./denom; +% Xd=(X-Calib.Cx_Cy(1))/Calib.fx_fy(1); % sensor coordinates +% Yd=(Y-Calib.Cx_Cy(2))/Calib.fx_fy(2); +% dist_fact=1+Calib.kc*(Xd.*Xd+Yd.*Yd); %distortion factor +% Xu=Xd./dist_fact;%undistorted sensor coordinates +% Yu=Yd./dist_fact; +% A11=R(7)*Xu-R(1); +% A12=R(8)*Xu-R(2); +% A21=R(7)*Yu-R(4); +% A22=R(8)*Yu-R(5); +% B1=(R(3)-R(9)*Xu)*Zphys-Tz*Xu+Tx; +% B2=(R(6)-R(9)*Yu)*Zphys-Tz*Yu+Ty; +% deter=A12.*A21-A11.*A22; +% Xphys=(A21.*B1-A11.*B2)./deter; +% Yphys=(-A22.*B1+A12.*B2)./deter; +else + Xphys=-Calib.Tx_Ty_Tz(1)+X/Calib.fx_fy(1); + Yphys=-Calib.Tx_Ty_Tz(2)+Y/Calib.fx_fy(2); end Index: /trunk/src/transform_field/px.m =================================================================== --- /trunk/src/transform_field/px.m (revision 115) +++ /trunk/src/transform_field/px.m (revision 116) @@ -18,5 +18,5 @@ % DataIn.A, AX, AY : image or scalar input -> EMPTY CORRESPONDING OUTPUT (A REVOIR) % Other fields in DataIn: copied to DataOut without modification -% Calib: structure containing the calibration parameters (Tsai) or containing a subtree Calib.GeometryCalib with these parameters +% Calib: structure containing the substructure Calib.GeometryCalib with the calibration parameters % % call the function px_XYZ (case of images) for pointwise coordinate transforms @@ -36,5 +36,8 @@ DataOut=px_1(Data,CalibData.GeometryCalib); end -if exist('Data_1','var') +if isfield(DataOut,'Z') + DataOut=rmfield(DataOut,'Z'); +end +if exist('Data_1','var')% if there is a second input field, it is also transformed if ~(exist('CalibData_1','var') && isfield(CalibData_1,'GeometryCalib')) DataOut_1=Data_1; @@ -42,5 +45,8 @@ DataOut_1=px_1(Data_1,CalibData_1.GeometryCalib); end -else + if isfield(DataOut_1,'Z') + DataOut_1=rmfield(DataOut_1,'Z'); + end +else % no second input field then empty second output field DataOut_1=[]; end @@ -52,9 +58,9 @@ %Act only if .CoordType=phys, and Calib defined -if isfield(Data,'CoordType')& isequal(Data.CoordType,'phys')& ~isempty(Calib) +if isfield(Data,'CoordType')&& isequal(Data.CoordType,'phys')&& ~isempty(Calib) DataOut.CoordType='px'; %put flag for pixel coordinates DataOut.CoordUnit='px'; %transform of X,Y coordinates - if isfield(Data,'Z')&~isempty(Data.Z) + if isfield(Data,'Z')&&~isempty(Data.Z) Z=Data.Z; else @@ -97,41 +103,41 @@ % [Zphys]: corresponding array of z physical coordinates (0 by default) - -function [X,Y]=px_XYZ(Calib,Xphys,Yphys,Zphys) -X=[];%default -Y=[]; -% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'PlanePos')&length(Calib.PlanePos)>=Z -% Zindex=Z; -% planepos=Calib.PlanePos{Zindex}; -% zphys=planepos(3);%A GENERALISER CAS AVEC ANGLE -% else -% zphys=0; +% +% function [X,Y]=px_XYZ(Calib,Xphys,Yphys,Zphys) +% X=[];%default +% Y=[]; +% % if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'PlanePos')&length(Calib.PlanePos)>=Z +% % Zindex=Z; +% % planepos=Calib.PlanePos{Zindex}; +% % zphys=planepos(3);%A GENERALISER CAS AVEC ANGLE +% % else +% % zphys=0; +% % end +% if ~exist('Zphys','var') +% Zphys=0; % end -if ~exist('Zphys','var') - Zphys=0; -end - -%%%%%%%%%%%%% -if isfield(Calib,'R') - R=(Calib.R)'; - xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx; - yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Ty; - zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tz; -%undistorted image coordinates - Xu=Calib.f*xc./zc; - Yu=Calib.f*yc./zc; -%distorted image coordinates - distortion=(Calib.kappa1)*(Xu.*Xu+Yu.*Yu)+1; %A REVOIR -% distortion=1; - Xd=Xu./distortion; - Yd=Yu./distortion; -%pixel coordinates - X=Xd*Calib.sx/Calib.dpx+Calib.Cx; - Y=Yd/Calib.dpy+Calib.Cy; - -elseif isfield(Calib,'Pxcmx')&isfield(Calib,'Pxcmy')%old calib - X=Xphys*Calib.Pxcmx; - Y=Yphys*Calib.Pxcmy; -end +% +% %%%%%%%%%%%%% +% if isfield(Calib,'R') +% R=(Calib.R)'; +% xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx; +% yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Ty; +% zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tz; +% %undistorted image coordinates +% Xu=Calib.f*xc./zc; +% Yu=Calib.f*yc./zc; +% %distorted image coordinates +% distortion=(Calib.kappa1)*(Xu.*Xu+Yu.*Yu)+1; %A REVOIR +% % distortion=1; +% Xd=Xu./distortion; +% Yd=Yu./distortion; +% %pixel coordinates +% X=Xd*Calib.sx/Calib.dpx+Calib.Cx; +% Y=Yd/Calib.dpy+Calib.Cy; +% +% elseif isfield(Calib,'Pxcmx')&isfield(Calib,'Pxcmy')%old calib +% X=Xphys*Calib.Pxcmx; +% Y=Yphys*Calib.Pxcmy; +% end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 115) +++ /trunk/src/uvmat.m (revision 116) @@ -744,4 +744,16 @@ set(handles.view_xml,'BackgroundColor',[1 1 1]) drawnow + if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib) + hgeometry_calib=findobj('tag','geometry_calib'); + if ~isempty(hgeometry_calib) + GUserData=get(hgeometry_calib,'UserData'); + if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml)) + answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?'); + if strcmp(answer,'Yes') + geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib + end + end + end + end elseif exist(fileciv,'file')% if .civ file found [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']); @@ -4565,5 +4577,5 @@ pos(2)=pos(2)-0.02; [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles); -[UvData.hset_object,UvData.sethandles]=geometry_calib(handles,pos,FileName);% call the set_object interface +[UvData.hset_object,UvData.sethandles]=geometry_calib(FileName,pos);% call the geometry_calib interface pos_uvmat=get(handles.uvmat,'Position'); Index: /trunk/src/view_field.m =================================================================== --- /trunk/src/view_field.m (revision 115) +++ /trunk/src/view_field.m (revision 116) @@ -605,4 +605,5 @@ %------------------------------------------------------- function decimate4_Callback(hObject, eventdata, handles) +'TEST' update_plot(handles)