Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 1112) +++ /trunk/src/geometry_calib.m (revision 1113) @@ -52,5 +52,5 @@ % Edit the above text to modify the response to help geometry_calib -% Last Modified by GUIDE v2.5 20-Sep-2018 19:04:30 +% Last Modified by GUIDE v2.5 05-Feb-2022 22:24:55 % Begin initialization code - DO NOT edit @@ -232,5 +232,5 @@ %% Apply calibration -[GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration +[GeometryCalib,index,ind_removed]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration if isempty(GeometryCalib) return @@ -245,17 +245,13 @@ GeometryCalib.SourceCalib.PointCoord=Coord; -%% display calibration results on the GUI geometry_calib -display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters -display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters -% (rotation and translation of camera with respect to the phys coordinates) - %% set the default plane and display the calibration data errors for validation answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']; - [num2str(numel(ind_removed)) ' points removed']}); -% SliceCoord_ref=[0 0 0]; %default reference plane + [num2str(numel(ind_removed)) ' points removed with ErrorMax > 3 rms']}); checkslice=0; if strcmp(answer,'Yes') %store the calibration data + display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters on the GUI geometry_calib + display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters on the GUI geometry_calib Z=Coord(:,3); if strcmp(calib_cell{val}(1:2),'3D') && isequal(max(Z),min(Z))%set the plane position for 3D (projection) calibration @@ -348,10 +344,10 @@ errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file if checkslice - errormsg=update_imadoc(Slice,outputfile,'Slice');% introduce the slice position in the xml file + errormsg=update_imadoc(Slice,outputfile,'Slice');% introduce the slice position in the xml file end if ~strcmp(errormsg,'') msgbox_uvmat('ERROR',errormsg); end - + %% display image with new calibration in the currently opened uvmat GUI FieldList=get(hhuvmat.FieldName,'String'); @@ -397,13 +393,13 @@ %------------------------------------------------------------------------ % --- activate calibration and store parameters in ouputfile . -function [GeometryCalib,ind_max,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic) +function [GeometryCalib,ind_max,ind_removed]=calibrate(Coord,CalibFcn,Intrinsic) %------------------------------------------------------------------------ index=[]; GeometryCalib=[]; -ind_max=[];ind_removed=[];Z_plane=[]; +ind_max=[];ind_removed=[]; % apply the calibration, whose type is selected in handles.calib_type CoordFlip=Coord; -CoordFlip(:,3)=-Coord(:,3); +CoordFlip(:,3)=Coord(:,3);% the calibration function assume a z ccordinate along the camera view, opposite to ours if ~isempty(Coord) GeometryCalib=feval(CalibFcn,CoordFlip,Intrinsic); @@ -414,13 +410,9 @@ return end -Z_plane=[]; % estimate calibration error rms and max -% X=Coord(:,1); -% Y=Coord(:,2); -Z=Coord(:,3); x_ima=Coord(:,4); y_ima=Coord(:,5); -[Xpoints,Ypoints]=px_XYZ(GeometryCalib,[],Coord(:,1),Coord(:,2),Coord(:,3));% convention of downward z coordinate (facing the camera) +[Xpoints,Ypoints]=px_XYZ(GeometryCalib,[],Coord(:,1),Coord(:,2),Coord(:,3)); GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); @@ -430,14 +422,16 @@ ind_max=index(ind_dim); % mark the index with maximum deviation -% detect bad calibration points, marked by indices ind_bad, if the +% detect bad calibration points, marked by indices ind_removed, if the % difference of actual image coordinates and those given by calibration is -% greater than 2 pixels and greater than 4 rms. +% greater than 2 pixels and greater than 3 rms. check_x=abs(Xpoints-x_ima)>max(2,3*GeometryCalib.ErrorRms(1)); check_y=abs(Ypoints-y_ima)>max(2,3*GeometryCalib.ErrorRms(2)); -ind_removed=find(check_x | check_y) +ind_removed=find(check_x | check_y); % repeat calibration without the excluded points: if ~isempty(ind_removed) Coord(ind_removed,:)=[]; - GeometryCalib=feval(CalibFcn,Coord,Intrinsic); + CoordFlip=Coord; + CoordFlip(:,3)=Coord(:,3);% the calibration function assume a z ccordinate along the camera view, opposite to ours + GeometryCalib=feval(CalibFcn,CoordFlip,Intrinsic); X=Coord(:,1); Y=Coord(:,2); @@ -450,10 +444,4 @@ end GeometryCalib.ErrorMax=ErrorMax; -% %set the Z position of the reference plane used for calibration -% if isequal(max(Z),min(Z))%Z constant -% Z_plane=Z(1); -% GeometryCalib.NbSlice=1; -% GeometryCalib.SliceCoord=[0 0 Z_plane]; -% end @@ -468,6 +456,4 @@ [px]=polyfit(X,x_ima,1); [py]=polyfit(Y,y_ima,1); -% T_x=px(2); -% T_y=py(2); GeometryCalib.CalibrationType='rescale'; GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y @@ -620,5 +606,5 @@ run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim' if exist('Rc_1','var') - GeometryCalib.CalibrationType='3D_linear'; + GeometryCalib.CalibrationType='3D_extrinsic'; GeometryCalib.fx_fy=fc'; GeometryCalib.Cx_Cy=cc'; @@ -698,5 +684,5 @@ if exist('Rc_1','var') - GeometryCalib.CalibrationType='3D_quadr'; + GeometryCalib.CalibrationType='3D_extrinsic'; GeometryCalib.fx_fy=fc'; GeometryCalib.Cx_Cy=cc'; @@ -1163,13 +1149,15 @@ % -------------------------------------------------------------------- -function MenuFlip_x_Callback(hObject, eventdata, handles) +function MenuFlip_xy_Callback(hObject, eventdata, handles) Coord=get(handles.ListCoord,'Data'); Coord(:,1)=-Coord(:,1); +Coord(:,2)=-Coord(:,2); set(handles.ListCoord,'Data',Coord) % -------------------------------------------------------------------- -function MenuFlip_y_Callback(hObject, eventdata, handles) +function MenuFlip_xz_Callback(hObject, eventdata, handles) Coord=get(handles.ListCoord,'Data'); -Coord(:,2)=-Coord(:,2); +Coord(:,1)=-Coord(:,1); +Coord(:,3)=-Coord(:,3); set(handles.ListCoord,'Data',Coord) Index: /trunk/src/phys_XYZ.m =================================================================== --- /trunk/src/phys_XYZ.m (revision 1112) +++ /trunk/src/phys_XYZ.m (revision 1113) @@ -79,7 +79,7 @@ if isfield(Calib,'R') R=(Calib.R)'; - R(3)=-R(3); - R(6)=-R(6); - R(9)=-R(9); +% R(3)=-R(3); +% R(6)=-R(6); +% R(9)=-R(9); c=Z0virt; cvirt=Z0virt; Index: /trunk/src/px_XYZ.m =================================================================== --- /trunk/src/px_XYZ.m (revision 1112) +++ /trunk/src/px_XYZ.m (revision 1113) @@ -57,5 +57,5 @@ %camera coordinates - Zphys=-Zphys;%flip z coordinates + Zphys=Zphys;%flip z coordinates xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx_Ty_Tz(1); yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Tx_Ty_Tz(2); Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1112) +++ /trunk/src/series.m (revision 1113) @@ -3143,9 +3143,9 @@ if get(handles.CheckObject,'Value') SeriesData=get(handles.series,'UserData'); - if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject) + if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)% a projection object is already loaded in the GUI series set(handles.ViewObject,'Value',1) ViewObject_Callback(hObject, eventdata, handles) else - if ishandle(hset_object) + if ishandle(hset_object)% a projection object is already displayed in a GUI set_object uistack(hset_object,'top')% show the GUI set_object if opened else @@ -3215,7 +3215,11 @@ set(handles.ViewObject,'Value',0) UserData=get(handles.series,'UserData'); + if isfield(UserData,'ProjObject') hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','edit_object_series') set(get(hset_object,'Children'),'Enable','on') + else + msgbox_uvmat('ERROR','no projection object available'); + end else hset_object=findobj(allchild(0),'Tag','set_object'); Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 1112) +++ /trunk/src/series/extract_rdvision.m (revision 1113) @@ -206,9 +206,18 @@ logdir=[Param.OutputSubDir Param.OutputDirExt]; [success,errormsg] = copyfile(filename_seq,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.seq']); %copy the seq file in the upper folder + if ~success + disp(errormsg) + end [success,errormsg] = copyfile(filename_sqb,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.sqb']); %copy the sqb file in the upper folder + if ~success + disp(errormsg) + end if check_xml [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder + if ~success + disp(errormsg) + end else - errormsg=[filexml ' missing']; + disp(['error:' filexml ' missing']); return end Index: /trunk/src/transform_field/FFT2_detrend.m =================================================================== --- /trunk/src/transform_field/FFT2_detrend.m (revision 1112) +++ /trunk/src/transform_field/FFT2_detrend.m (revision 1113) @@ -85,4 +85,7 @@ DataOut.ListVarName=[CoordName {VarName}];%list of variables DataOut.VarDimName=[CoordName {CoordName}];%list of dimensions for variables + DataOut.VarAttribute{1}.Role='coord_y'; + DataOut.VarAttribute{2}.Role='coord_x'; + DataOut.VarAttribute{3}.Role='scalar'; break end Index: /trunk/src/xml2struct.m =================================================================== --- /trunk/src/xml2struct.m (revision 1112) +++ /trunk/src/xml2struct.m (revision 1113) @@ -84,7 +84,7 @@ case 'char' % try to convert to number if the char does not correspond to a function (otherwise str2num calls this function as it uses 'eval') - if exist(ss,'builtin')||exist(ss,'file')% ss corresponds to the name of a builtin Matlab function or a file - out=ss; %reproduce the input string - else +% if exist(ss,'builtin')||exist(ss,'file')% ss corresponds to the name of a builtin Matlab function or a file +% out=ss; %reproduce the input string +% else out=str2num(ss);% convert to number or vector (str2num applied to a fct name executes this fct by 'eval', thus this possibility had to be ruled out above if isempty(out) @@ -100,5 +100,5 @@ end end - end +% end case 'cell' out={};%default