Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 1061) +++ /trunk/src/geometry_calib.m (revision 1062) @@ -3,10 +3,10 @@ % function hgeometry_calib = geometry_calib(inputfile,pos) % -%OUTPUT: +%OUTPUT: % hgeometry_calib=current handles of the GUI geometry_calib.fig % %INPUT: % inputfile: (optional) name of an xml file containing coordinates of reference points -% pos: (optional) 4 element vector setting the 'Position' of the GUI +% pos: (optional) 4 element vector setting the 'Position' of the GUI %======================================================================= @@ -57,15 +57,15 @@ gui_Singleton = 1; gui_State = struct('gui_Name', mfilename, ... - 'gui_Singleton', gui_Singleton, ... - 'gui_OpeningFcn', @geometry_calib_OpeningFcn, ... - 'gui_OutputFcn', @geometry_calib_OutputFcn, ... - 'gui_LayoutFcn', [] , ... - 'gui_Callback', []); + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @geometry_calib_OpeningFcn, ... + 'gui_OutputFcn', @geometry_calib_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); if nargin - [pp,ff]=fileparts(which(varargin{1})); % name of the input file - if strcmp(ff,mfilename)% if we are activating a sub-function of geometry_calib - % ~isempty(regexp(varargin{1},'_Callback','once')) - gui_State.gui_Callback = str2func(varargin{1}); - end + [pp,ff]=fileparts(which(varargin{1})); % name of the input file + if strcmp(ff,mfilename)% if we are activating a sub-function of geometry_calib + % ~isempty(regexp(varargin{1},'_Callback','once')) + gui_State.gui_Callback = str2func(varargin{1}); + end end @@ -79,5 +79,5 @@ % --- Executes just before geometry_calib is made visible. -%INPUT: +%INPUT: %handles: handles of the geometry_calib interface elements % PlotHandles: set of handles of the elements contolling the plotting @@ -86,12 +86,9 @@ function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile) %------------------------------------------------------------------------ -% Choose default command line output for geometry_calib handles.output = hObject; - % Update handles structure guidata(hObject, handles); set(hObject,'DeleteFcn',{@closefcn})% -%set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display) %% position @@ -124,5 +121,5 @@ set(handles.geometry_calib,'Position',[Left Bottom 420 Height]) -%set menu of calibration options +%% set menu of calibration options set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'}) if exist('inputfile','var')&& ~isempty(inputfile) @@ -135,5 +132,5 @@ struct.Campaign=Heading.Campaign; end - end + end set(hObject,'UserData',struct) end @@ -146,5 +143,5 @@ varargout{1} = handles.output; varargout{2}=handles; -% + %------------------------------------------------------------------------ % executed when closing: set the parent interface button to value 0 @@ -162,225 +159,227 @@ if ~isempty(hobject) delete(hobject) - end -end - + end +end + %------------------------------------------------------------------------ % --- Executes on button press APPLY (used to launch the calibration). - function APPLY_Callback(hObject, eventdata, handles) - set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) - - %------------------------------------------------------------------------ - %% look for the GUI uvmat and check for an image as input - set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation - huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat - hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat - if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') - msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') - return - end - - RootPath=''; - if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile) - RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image - SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$',''); - outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image - else - question={'save the calibration data and point coordinates in'}; - def={fullfile(RootPath,'ObjectCalib.xml')}; - options.Resize='on'; - answer=inputdlg(question,'',1,def,options); - outputfile=answer{1}; - end - - %% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image - Coord=get(handles.ListCoord,'Data'); - - - %% read the type of calibration - calib_cell=get(handles.calib_type,'String'); - val=get(handles.calib_type,'Value'); - CalibFcn=['calib_' calib_cell{val}]; - - %% read the intrinsic parameters - Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); - Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); - Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); - Intrinsic.fx=str2num(get(handles.fx,'String')); - Intrinsic.fy=str2num(get(handles.fy,'String')); - Intrinsic.kc=str2num(get(handles.kc,'String')); - Intrinsic.Cx=str2num(get(handles.Cx,'String')); - Intrinsic.Cy=str2num(get(handles.Cy,'String')); - if isempty(Intrinsic.kc) - Intrinsic.kc=0; - end - if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) - Intrinsic.Cx=Intrinsic.Npx/2; - Intrinsic.Cy=Intrinsic.Npy/2; - end - - %% apply to cropped images if requested - if get(handles.Replicate,'Value') - answer=msgbox_uvmat('INPUT_Y-N','apply to full images (not cropped)?'); - if strcmp(answer,'No') - prompt = {'npy_lower'}; - dlg_title = 'remove image the npy_lower image lines (removal of the upper line does not change calibration)'; - num_lines= 1; - def = {'0'}; - answer = inputdlg(prompt,dlg_title,num_lines,def); - npy_crop=str2num(answer{1}); - Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window - Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band - end - end - - %% Apply calibration - [GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration - - %% record the coordinate unit - unitlist=get(handles.CoordUnit,'String'); - unit=unitlist{get(handles.CoordUnit,'value')}; - GeometryCalib.CoordUnit=unit; - - %% record the coordinates of the calibration points - 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 defqult 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']}); - if strcmp(answer,'Yes') %store the calibration data - if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration - answer=msgbox_uvmat('INPUT_Y-N',{['Assume that the current image is in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be later modified by MenuSetSlice in the upper bar menu of uvmat'}); - SliceCoord_ref=Z_plane'*[0 0 1]; - end - else - GeometryCalib=[]; - index=1; - end - - if ~isempty(GeometryCalib) % if calibration is not cancelled - if get(handles.Replicate,'Value') - %% open the GUI browse_data - hbrowse=findobj(allchild(0),'Tag','browse_data'); - if ~isempty(hbrowse) - BrowseHandles=guidata(hbrowse); - SourceDir=get(BrowseHandles.SourceDir,'String'); - ListExperiments=get(BrowseHandles.ListExperiments,'String'); - ListValues=get(BrowseHandles.ListExperiments,'Value'); - ListExperiments=ListExperiments(ListValues); - ListDevices=get(BrowseHandles.ListDevices,'String'); - Val=get(BrowseHandles.ListDevices,'Value'); - DataFolder=ListDevices{Val}; - nbcalib=0; - for ilist=1:numel(ListExperiments) - SubDirBase=regexprep(DataFolder,'+/',''); - ListExperiments{ilist}=regexprep(ListExperiments{ilist},'+/',''); - XmlName=fullfile(SourceDir,ListExperiments{ilist},[SubDirBase '.xml']); - % copy the xml file from the old location if appropriate, then update with the calibration parameters - % if ~exist(XmlName,'file') && ~isempty(SubDirBase) - % oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']); - GeometryCalib.SliceCoord=SliceCoord_ref;%default input - if exist(XmlName,'file') - %[success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention - dispmesGeometryCalib=UvData.XmlData{1}.GeometryCalib; - else - msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices') - return - end - SliceCoord=GeometryCalib.SliceCoord; - InterfaceCoord=min(SliceCoord(:,3)); - if isfield(GeometryCalib,'InterfaceCoord') - InterfaceCoord=GeometryCalib.InterfaceCoord(1,3); - end - NbSlice=size(SliceCoord,1); - CheckVolumeScan=0; - if isfield(GeometryCalib,'CheckVolumeScan') - CheckVolumeScan=GeometryCalib.CheckVolumeScan; - end - RefractionIndex=1.33; - CheckRefraction=0;% default value of the check box refraction - if isfield(GeometryCalib,'RefractionIndex') - RefractionIndex=GeometryCalib.RefractionIndex; - CheckRefraction=1; - end - SliceAngle=[0 0 0]; - if isfield(GeometryCalib,'SliceAngle') - SliceAngle=GeometryCalib.SliceAngle; - end - dispmessage=' updated with calibration parameters'; - % if ~strcmp(answer,'yes') - [XmlDataOld,warntext]=imadoc2struct(XmlName); - if isfield(XmlDataOld,'GeometryCalib') - if isfield(XmlDataOld.GeometryCalib,'SliceAngle') - GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.SliceAngle; - end - if isfield(XmlDataOld.GeometryCalib,'CheckRefraction') - GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.CheckRefraction; - end - if isfield(XmlDataOld.GeometryCalib,'RefractionIndex') - GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.RefractionIndex; - end - if isfield(XmlDataOld.GeometryCalib,'InterfaceCoord') - GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.InterfaceCoord; - end - end - - end - - else - dispmessage=' created with calibration parameters'; +function APPLY_Callback(hObject, eventdata, handles) +set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) + +%------------------------------------------------------------------------ +%% look for the GUI uvmat and check for an image as input +set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation +huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat +hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat +if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') + msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') + return +end + +RootPath=''; +if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile) + RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image + SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$',''); + outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image +else + question={'save the calibration data and point coordinates in'}; + def={fullfile(RootPath,'ObjectCalib.xml')}; + options.Resize='on'; + answer=inputdlg(question,'',1,def,options); + outputfile=answer{1}; +end + +%% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image +Coord=get(handles.ListCoord,'Data'); + + +%% read the type of calibration +calib_cell=get(handles.calib_type,'String'); +val=get(handles.calib_type,'Value'); +CalibFcn=['calib_' calib_cell{val}]; + +%% read the intrinsic parameters +Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); +Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); +Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); +Intrinsic.fx=str2num(get(handles.fx,'String')); +Intrinsic.fy=str2num(get(handles.fy,'String')); +Intrinsic.kc=str2num(get(handles.kc,'String')); +Intrinsic.Cx=str2num(get(handles.Cx,'String')); +Intrinsic.Cy=str2num(get(handles.Cy,'String')); +if isempty(Intrinsic.kc) + Intrinsic.kc=0; +end +if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) + Intrinsic.Cx=Intrinsic.Npx/2; + Intrinsic.Cy=Intrinsic.Npy/2; +end + +%% apply to cropped images if requested +if get(handles.Replicate,'Value') + answer=msgbox_uvmat('INPUT_Y-N','apply to full images (not cropped)?'); + if strcmp(answer,'No') + prompt = {'npy_lower'}; + dlg_title = 'remove image the npy_lower image lines (removal of the upper line does not change calibration)'; + num_lines= 1; + def = {'0'}; + answer = inputdlg(prompt,dlg_title,num_lines,def); + npy_crop=str2num(answer{1}); + Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window + Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band + end +end + +%% Apply calibration +[GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration +if isempty(GeometryCalib) + return +end + +%% record the coordinate unit +unitlist=get(handles.CoordUnit,'String'); +unit=unitlist{get(handles.CoordUnit,'value')}; +GeometryCalib.CoordUnit=unit; + +%% record the coordinates of the calibration points +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']}); +if strcmp(answer,'Yes') %store the calibration data + if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration + answer=msgbox_uvmat('INPUT_Y-N',{['Assume that the current image is in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be later modified by MenuSetSlice in the upper bar menu of uvmat'}); + SliceCoord_ref=Z_plane'*[0 0 1]; + end +else + GeometryCalib=[]; + index=1; +end + +if ~isempty(GeometryCalib) % if calibration is not cancelled + %%%%% use of the option 'replicate' + if get(handles.Replicate,'Value')% if the option replicate is activated + %% open the GUI browse_data + hbrowse=findobj(allchild(0),'Tag','browse_data'); + if ~isempty(hbrowse)% look for the GUI 'replicate' + BrowseHandles=guidata(hbrowse); + SourceDir=get(BrowseHandles.SourceDir,'String'); + ListExperiments=get(BrowseHandles.ListExperiments,'String'); + ListValues=get(BrowseHandles.ListExperiments,'Value'); + ListExperiments=ListExperiments(ListValues); + ListDevices=get(BrowseHandles.ListDevices,'String'); + Val=get(BrowseHandles.ListDevices,'Value'); + DataFolder=ListDevices{Val}; + nbcalib=0; + for ilist=1:numel(ListExperiments) + SubDirBase=regexprep(DataFolder,'+/',''); + ListExperiments{ilist}=regexprep(ListExperiments{ilist},'+/',''); + XmlName=fullfile(SourceDir,ListExperiments{ilist},[SubDirBase '.xml']); + % copy the xml file from the old location if appropriate, then update with the calibration parameters + % if ~exist(XmlName,'file') && ~isempty(SubDirBase) + % oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']); + GeometryCalib.SliceCoord=SliceCoord_ref;%default input + if exist(XmlName,'file') + %[success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention + dispmesGeometryCalib=UvData.XmlData{1}.GeometryCalib; + else + msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices') + return + end + SliceCoord=GeometryCalib.SliceCoord; + InterfaceCoord=min(SliceCoord(:,3)); + if isfield(GeometryCalib,'InterfaceCoord') + InterfaceCoord=GeometryCalib.InterfaceCoord(1,3); + end + NbSlice=size(SliceCoord,1); + CheckVolumeScan=0; + if isfield(GeometryCalib,'CheckVolumeScan') + CheckVolumeScan=GeometryCalib.CheckVolumeScan; + end + RefractionIndex=1.33; + CheckRefraction=0;% default value of the check box refraction + if isfield(GeometryCalib,'RefractionIndex') + RefractionIndex=GeometryCalib.RefractionIndex; + CheckRefraction=1; + end + SliceAngle=[0 0 0]; + if isfield(GeometryCalib,'SliceAngle') + SliceAngle=GeometryCalib.SliceAngle; + end + dispmessage=' updated with calibration parameters'; + % if ~strcmp(answer,'yes') + [XmlDataOld,warntext]=imadoc2struct(XmlName); + if isfield(XmlDataOld,'GeometryCalib') + if isfield(XmlDataOld.GeometryCalib,'SliceAngle') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.SliceAngle; end - errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - else - display([XmlName dispmessage]) - nbcalib=nbcalib+1; + if isfield(XmlDataOld.GeometryCalib,'CheckRefraction') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.CheckRefraction; + end + if isfield(XmlDataOld.GeometryCalib,'RefractionIndex') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.RefractionIndex; + end + if isfield(XmlDataOld.GeometryCalib,'InterfaceCoord') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.InterfaceCoord; end end - end - msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']); + + else % in case the GUI 'replicate'is not found + dispmessage=' created with calibration parameters'; + end + errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file + if ~strcmp(errormsg,'') + msgbox_uvmat('ERROR',errormsg); else - - %% copy the xml file from the old location if appropriate, then update with the calibration parameters - if ~exist(outputfile,'file') && ~isempty(SubDirBase) - oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml']; - if exist(oldxml,'file') - [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention - end - end - errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - end - - %% display image with new calibration in the currently opened uvmat interface - FieldList=get(hhuvmat.FieldName,'String'); - val=get(hhuvmat.FieldName,'Value'); - if strcmp(FieldList{val},'image') - set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image - UserData=get(handles.geometry_calib,'UserData'); - UserData.XmlInputFile=outputfile;%save the current xml file name - set(handles.geometry_calib,'UserData',UserData) - uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates - PLOT_Callback(hObject, eventdata, handles) - set(handles.CoordLine,'string',num2str(index)) - Coord=get(handles.ListCoord,'Data'); - update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration - figure(handles.geometry_calib)% put the GUI geometry_calib in front - else - msgbox_uvmat('WARNING','open the image to see the effect of the new calibration') - end + display([XmlName dispmessage]) + nbcalib=nbcalib+1; end end - set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color - + % Use of the option replicate +end +msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']); + + +%% copy the xml file from the old location if appropriate, then update with the calibration parameters +if ~exist(outputfile,'file') && ~isempty(SubDirBase) + oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml']; + if exist(oldxml,'file') + [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention + end +end +errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file +if ~strcmp(errormsg,'') + msgbox_uvmat('ERROR',errormsg); +end + +%% display image with new calibration in the currently opened uvmat interface +FieldList=get(hhuvmat.FieldName,'String'); +val=get(hhuvmat.FieldName,'Value'); +if strcmp(FieldList{val},'image') + set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image + UserData=get(handles.geometry_calib,'UserData'); + UserData.XmlInputFile=outputfile;%save the current xml file name + set(handles.geometry_calib,'UserData',UserData) + uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates + PLOT_Callback(hObject, eventdata, handles) + set(handles.CoordLine,'string',num2str(index)) + Coord=get(handles.ListCoord,'Data'); + update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration + figure(handles.geometry_calib)% put the GUI geometry_calib in front +else + msgbox_uvmat('WARNING','open the image to see the effect of the new calibration') +end + +set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color + %------------------------------------------------------------------------ % --- Executes on button press in Replicate @@ -409,4 +408,5 @@ index=[]; GeometryCalib=[]; +ind_max=[];ind_removed=[];Z_plane=[]; % apply the calibration, whose type is selected in handles.calib_type if ~isempty(Coord) @@ -414,5 +414,5 @@ else msgbox_uvmat('ERROR','No calibration points, abort') -end +end if isempty(GeometryCalib) return @@ -441,5 +441,5 @@ ind_removed=find(check_x | check_y) % repeat calibration without the excluded points: -if ~isempty(ind_removed) +if ~isempty(ind_removed) Coord(ind_removed,:)=[]; GeometryCalib=feval(CalibFcn,Coord,Intrinsic); @@ -482,5 +482,5 @@ %------------------------------------------------------------------------ % --- determine the parameters for a calibration by a linear transform matrix (rescale and rotation) -function GeometryCalib=calib_linear(Coord,Intrinsic) +function GeometryCalib=calib_linear(Coord,Intrinsic) %------------------------------------------------------------------------ X=Coord(:,1); @@ -534,5 +534,5 @@ Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2; Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2; -end +end %tsai parameters Calib.dpx=0.012;%arbitrary @@ -570,5 +570,5 @@ GeometryCalib.kappa1=calib_param(1); GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function -GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)]; +GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)]; alpha=calib_param(5); GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1]; @@ -592,22 +592,22 @@ X_1=Coord(:,1:3)';%phys coordinates of the ref points n_ima=numel(coord_files)+1; -if ~isempty(coord_files) +if ~isempty(coord_files) msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used']) for ifile=1:numel(coord_files) - t=xmltree(coord_files{ifile}); - s=convert(t);%convert to matlab structure + t=xmltree(coord_files{ifile}); + s=convert(t);%convert to matlab structure if isfield(s,'GeometryCalib') if isfield(s.GeometryCalib,'SourceCalib') if isfield(s.GeometryCalib.SourceCalib,'PointCoord') - PointCoord=s.GeometryCalib.SourceCalib.PointCoord; - Coord_file=zeros(length(PointCoord),5);%default - for i=1:length(PointCoord) - line=str2num(PointCoord{i}); - Coord_file(i,4:5)=line(4:5);%px x - Coord_file(i,1:3)=line(1:3);%phys x - end - eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']); - eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]); - eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']); + PointCoord=s.GeometryCalib.SourceCalib.PointCoord; + Coord_file=zeros(length(PointCoord),5);%default + for i=1:length(PointCoord) + line=str2num(PointCoord{i}); + Coord_file(i,4:5)=line(4:5);%px x + Coord_file(i,1:3)=line(1:3);%phys x + end + eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']); + eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]); + eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']); end end @@ -652,5 +652,5 @@ if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') - return + return end % check_cond=0; @@ -672,22 +672,22 @@ X_1=Coord(:,1:3)';%phys coordinates of the ref points n_ima=numel(coord_files)+1; -if ~isempty(coord_files) +if ~isempty(coord_files) msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used']) for ifile=1:numel(coord_files) - t=xmltree(coord_files{ifile}); - s=convert(t);%convert to matlab structure + t=xmltree(coord_files{ifile}); + s=convert(t);%convert to matlab structure if isfield(s,'GeometryCalib') if isfield(s.GeometryCalib,'SourceCalib') if isfield(s.GeometryCalib.SourceCalib,'PointCoord') - PointCoord=s.GeometryCalib.SourceCalib.PointCoord; - Coord_file=zeros(length(PointCoord),5);%default - for i=1:length(PointCoord) - line=str2num(PointCoord{i}); - Coord_file(i,4:5)=line(4:5);%px x - Coord_file(i,1:3)=line(1:3);%phys x - end - eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']); - eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]); - eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']); + PointCoord=s.GeometryCalib.SourceCalib.PointCoord; + Coord_file=zeros(length(PointCoord),5);%default + for i=1:length(PointCoord) + line=str2num(PointCoord{i}); + Coord_file(i,4:5)=line(4:5);%px x + Coord_file(i,1:3)=line(1:3);%phys x + end + eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']); + eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]); + eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']); end end @@ -731,5 +731,5 @@ if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') - return + return end ny=str2double(get(hhuvmat.num_Npy,'String')); @@ -766,9 +766,9 @@ GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate) [omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,... - (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]); + (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]); rmpath(fct_path); GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function GeometryCalib.Tx_Ty_Tz=Tc1'; -%inversion of z axis +%inversion of z axis GeometryCalib.R=Rc1; GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate @@ -817,5 +817,5 @@ Z=Coord(:,3); x_ima=Coord(:,4); -y_ima=Coord(:,5); +y_ima=Coord(:,5); [Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z); ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); @@ -839,5 +839,5 @@ % RootFile=''; if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile) -% testhandle=1; + % testhandle=1; RootPath=get(hhuvmat.RootPath,'String'); RootFile=get(hhuvmat.RootFile,'String'); @@ -897,9 +897,10 @@ % -------------------------------------------------------------------- -function MenuHelp_Callback(hObject, eventdata, handles) -web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#GeometryCalib') - -% -------------------------------------------------------------------- -function MenuSetScale_Callback(hObject, eventdata, handles) + +% function MenuHelp_Callback(hObject, eventdata, handles) +% web('http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp#GeometryCalib') + +% +function MenuSetScale_Callback(hObject,eventdata,handles) answer=msgbox_uvmat('INPUT_TXT','scale pixel/cm?',''); @@ -942,5 +943,5 @@ % ----------------------------------------------------------------------- -% --- automatic grid dectection from local maxima of the images +% --- automatic grid dectection from local maxima of the images function MenuDetectGrid_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ @@ -953,5 +954,5 @@ end % corners_X=(Coord(end:-1:end-3,4)); %pixel absissa of the four corners -% corners_Y=(Coord(end:-1:end-3,5)); +% corners_Y=(Coord(end:-1:end-3,5)); corners_X=(Coord(:,4)); %pixel absissa of the four corners corners_Y=(Coord(:,5)); @@ -964,10 +965,10 @@ angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1))); if abs(angles(4)-angles(2))>abs(angles(3)-angles(2)) - X_end=corners_X(4); - Y_end=corners_Y(4); - corners_X(4)=corners_X(3); - corners_Y(4)=corners_Y(3); - corners_X(3)=X_end; - corners_Y(3)=Y_end; + X_end=corners_X(4); + Y_end=corners_Y(4); + corners_X(4)=corners_X(3); + corners_Y(4)=corners_Y(3); + corners_X(3)=X_end; + corners_Y(3)=Y_end; end @@ -992,5 +993,5 @@ % reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren B = [ X Y ones(size(X)) zeros(4,3) -X.*corners_X -Y.*corners_X ... - zeros(4,3) X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ]; + zeros(4,3) X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ]; B = reshape (B', 8 , 8 )'; D = [ corners_X , corners_Y ]; @@ -1000,5 +1001,5 @@ C = [l(7:8)' 1]; -%% transform grid image into 'phys' coordinates +%% transform grid image into 'phys' coordinates GeometryCalib.CalibrationType='3D_linear'; GeometryCalib.fx_fy=[1 1]; @@ -1022,6 +1023,6 @@ rmpath(fullfile(path_UVMAT,'transform_field')) Amod=DataOut.A;% current image expressed in 'phys' coord -Rangx=DataOut.Coord_x;% x coordinates of first and last pixel centres in phys -Rangy=DataOut.Coord_y;% y coordinates of first and last pixel centres in phys +Rangx=DataOut.Coord_x;% x coordinates of first and last pixel centres in phys +Rangy=DataOut.Coord_y;% y coordinates of first and last pixel centres in phys if CalibData.grid.CheckWhite Amod=double(Amod);%case of white grid markers: will look for image maxima @@ -1072,5 +1073,5 @@ x_profile=sum(Asub,1);%profile of subimage summed over y y_profile=sum(Asub,2);%profile of subimage summed over x - + [tild,ind_x_max]=max(x_profile);% index of max for the x profile [tild,ind_y_max]=max(y_profile);% index of max for the y profile @@ -1086,14 +1087,14 @@ y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop); end - %%%% -% if ipoint==9 -% figure(11) -% imagesc(Asub) -% figure(12) -% plot(x_profile,'r') -% hold on -% plot(y_profile,'b') -% grid on -% end + %%%% + % if ipoint==9 + % figure(11) + % imagesc(Asub) + % figure(12) + % plot(x_profile,'r') + % hold on + % plot(y_profile,'b') + % grid on + % end %%%% TIndex(ipoint,1)=(i0min+ind_x_max-1+x_shift);% x position of the maximum (in index of Amod) @@ -1102,5 +1103,5 @@ Tmod(:,1)=(TIndex(:,1)-1)*Dx+Rangx(1); Tmod(:,2)=(TIndex(:,2)-1)*Dy+Rangy(1); -%Tmod=T(:,(1:2))+Delta;% 'phys' coordinates of the detected points +%Tmod=T(:,(1:2))+Delta;% 'phys' coordinates of the detected points [Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));% image coordinates of the detected points Coord=[T Xpx Ypx zeros(size(T,1),1)]; @@ -1120,5 +1121,5 @@ Tinput=CalibData.translate; end -T=translate_points(Tinput);%display translate_points GUI and get shift parameters +T=translate_points(Tinput);%display translate_points GUI and get shift parameters CalibData.translate=T; set(handles.geometry_calib,'UserData',CalibData) @@ -1139,5 +1140,5 @@ Tinput=CalibData.rotate; end -T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters +T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters CalibData.rotate=T; set(handles.geometry_calib,'UserData',CalibData) @@ -1190,5 +1191,5 @@ GeometryCalib=s.GeometryCalib; if ~(isfield(GeometryCalib,'SourceCalib')&&isfield(GeometryCalib.SourceCalib,'PointCoord')) - msgbox_uvmat('ERROR','invalid input file: no calibration points') + msgbox_uvmat('ERROR','invalid input file: no calibration points') return end @@ -1244,9 +1245,9 @@ end [FileName, PathName, filterindex] = uigetfile( ... - {'*.xml;*.mat', ' (*.xml,*.mat)'; - '*.xml', '.xml files '; ... - '*.mat', '.mat matlab files '}, ... - 'Pick a file',oldfile); -fileinput=[PathName FileName];%complete file name + {'*.xml;*.mat', ' (*.xml,*.mat)'; + '*.xml', '.xml files '; ... + '*.mat', '.mat matlab files '}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name testblank=findstr(fileinput,' ');%look for blanks if ~isempty(testblank) @@ -1398,5 +1399,5 @@ figure(handles.geometry_calib) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ % --- Executes on button press in Copy: display Coord on the Matlab work space %------------------------------------------------------------------------ @@ -1409,18 +1410,18 @@ commandwindow; %brings the Matlab command window to the front -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ % --- Executes when selected cell(s) is changed in ListCoord. -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ function ListCoord_CellSelectionCallback(hObject, eventdata, handles) if ~isempty(eventdata.Indices) iline=eventdata.Indices(1);% selected line number set(handles.CoordLine,'String',num2str(iline)) - Data=get(handles.ListCoord,'Data'); - update_calib_marker(Data(iline,:)) -end - -%------------------------------------------------------------------------ + Data=get(handles.ListCoord,'Data'); + update_calib_marker(Data(iline,:)) +end + +%------------------------------------------------------------------------ % --- Executes when entered data in editable cell(s) in ListCoord. -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ function ListCoord_CellEditCallback(hObject, eventdata, handles) @@ -1471,5 +1472,5 @@ %------------------------------------------------------------------------ % --- update the plot of calibration points -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ % draw a circle around the point defined by the input coordinates Coord as given by line in the table Listcoord function update_calib_marker(Coord) @@ -1493,5 +1494,5 @@ %% read appropriate coordinates (px or phys) in the table ListCoord -if isequal(option,'phys') % use phys coord +if isequal(option,'phys') % use phys coord XCoord=Coord(1); YCoord=Coord(2); Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 1061) +++ /trunk/src/proj_field.m (revision 1062) @@ -574,8 +574,8 @@ NbSegment=0; case 'rectangle' - LineCoord([1 4],1)=ObjectData.Coord(1,1)-ObjectData.RangeX; - LineCoord([1 2],2)=ObjectData.Coord(1,2)-ObjectData.RangeY; - LineCoord([2 3],1)=ObjectData.Coord(1,1)+ObjectData.RangeX; - LineCoord([4 1],2)=ObjectData.Coord(1,2)+ObjectData.RangeY; + LineCoord([1 4],1)=ObjectData.Coord(1,1)-ObjectData.num_RangeX_2; + LineCoord([1 2],2)=ObjectData.Coord(1,2)-ObjectData.num_RangeX_2; + LineCoord([2 3],1)=ObjectData.Coord(1,1)+ObjectData_RangeX_2; + LineCoord([4 1],2)=ObjectData.Coord(1,2)+ObjectData.RangeY-Y2; case 'polygon' LineCoord(NbPoints+1)=LineCoord(1); @@ -1610,6 +1610,6 @@ ProjData.(AXName)=[coord_x_proj(1) coord_x_proj(end)]; %record the new (projected ) x coordinates [X,YI]=meshgrid(coord_x_proj,coord_y_proj);%grid in the new coordinates - XI=ObjectData.Coord(1,1)+(X)*cos(PlaneAngle(2))-YI*sin(PlaneAngle(1));%corresponding coordinates in the original system - YI=ObjectData.Coord(1,2)+(X)*sin(PlaneAngle(2))+YI*cos(PlaneAngle(1)); + XI=ObjectData.Coord(1,1)+(X)*cos(PlaneAngle(1))-YI*sin(PlaneAngle(1));%corresponding coordinates in the original system + YI=ObjectData.Coord(1,2)+(X)*sin(PlaneAngle(1))+YI*cos(PlaneAngle(1)); if numel(Coord{1})==2% x coordinate defined by its bounds, get the whole set Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1061) +++ /trunk/src/series/civ_series.m (revision 1062) @@ -455,12 +455,16 @@ par_civ1.Mask=mask; %use mask already opened else - try - par_civ1.Mask=imread(maskname);%update the mask, an store it for future use - catch ME - if ~isempty(ME.message) - errormsg=['error reading input image: ' ME.message]; - disp_uvmat('ERROR',errormsg,checkrun) - return + if exist(maskname,'file') + try + par_civ1.Mask=imread(maskname);%update the mask, an store it for future use + catch ME + if ~isempty(ME.message) + errormsg=['error reading input image: ' ME.message]; + disp_uvmat('ERROR',errormsg,checkrun) + return + end end + else + par_civ1.Mask=[]; end mask=par_civ1.Mask; @@ -711,4 +715,5 @@ par_civ2.Mask=mask; %use mask already opened else + if exist(maskname,'file') try par_civ2.Mask=imread(maskname);%update the mask, an store it for future use @@ -719,4 +724,7 @@ return end + end + else + par_civ2.Mask=[]; end mask=par_civ2.Mask; Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 1061) +++ /trunk/src/series/merge_proj.m (revision 1062) @@ -288,5 +288,7 @@ %% reading input file(s) [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index)); - if ~isempty(errormsg) + if isempty(errormsg) + disp([filecell{iview,index} ' read']) + else disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) return Index: /trunk/src/set_object.m =================================================================== --- /trunk/src/set_object.m (revision 1061) +++ /trunk/src/set_object.m (revision 1062) @@ -293,16 +293,10 @@ %set(handles.num_Angle_3,'Visible','off') set(handles.num_RangeX_1,'Visible','off') -set(handles.num_RangeX_2,'Visible','off') set(handles.num_RangeY_1,'Visible','off') -if isequal(ProjMode,'interp_lin')|| isequal(ProjMode,'interp_tps') - set(handles.num_RangeY_2,'Visible','off') -else - set(handles.num_RangeY_2,'Visible','on') -end -if strcmp(ObjectStyle,'rectangle')||strcmp(ObjectStyle,'ellipse') - set(handles.num_RangeX_2,'Visible','on') -else - set(handles.num_RangeX_2,'Visible','off') -end +% if isequal(ProjMode,'interp_lin')|| isequal(ProjMode,'interp_tps') +% set(handles.num_RangeY_2,'Visible','off') +% else +% set(handles.num_RangeY_2,'Visible','on') + set(handles.num_RangeZ_1,'Visible','off') set(handles.num_RangeZ_2,'Visible','off') @@ -310,14 +304,17 @@ set(handles.num_DY,'Visible','off') set(handles.num_DZ,'Visible','off') -set(handles.num_RangeInterp,'Visible','off') - +%default + set(handles.num_RangeX_2,'Visible','off') + set(handles.num_RangeY_2,'Visible','off') switch ObjectStyle case 'points' - set(handles.num_RangeY_2,'TooltipString','num_RangeY_2: range of projection around each point') + set(handles.num_RangeInterp,'TooltipString','num_RangeY_2: range of projection around each point') % set(handles.XObject,'TooltipString','XObject: set of x coordinates of the points') % set(handles.YObject,'TooltipString','YObject: set of y coordinates of the points') % set(handles.ZObject,'TooltipString','ZObject: set of z coordinates of the points') case {'line','polyline','polygon'} - set(handles.num_RangeY_2,'TooltipString','num_RangeY_2: range of projection around the line') + set(handles.num_RangeX_2,'Visible','off') + set(handles.num_RangeY_2,'Visible','off') + %set(handles.num_RangeY_2,'TooltipString','num_RangeY_2: range of projection around the line') set(handles.Coord,'TooltipString','Coord: table of x,y, z coordinates defining the line') % set(handles.YObject,'TooltipString','YObject: set of y coordinates defining the line') @@ -329,6 +326,13 @@ end case {'rectangle','ellipse'} + set(handles.num_RangeX_2,'Visible','on') + set(handles.num_RangeY_2,'Visible','on') set(handles.num_RangeX_2,'TooltipString',['num_RangeX_2: half length of the ' ObjectStyle]) set(handles.num_RangeY_2,'TooltipString',['num_RangeY_2: half width of the ' ObjectStyle]) + if isequal(ProjMode,'interp_lin')|| isequal(ProjMode,'interp_tps') + set(handles.num_DX,'Visible','on') + set(handles.num_DX,'TooltipString','num_DX: mesh for the interpolated field along the line') + set(handles.num_RangeInterp,'Visible','on') + end case {'plane','plane_z'} set(handles.num_Angle_1,'Visible','on') @@ -336,5 +340,5 @@ set(handles.num_RangeX_2,'Visible','on') set(handles.num_RangeY_1,'Visible','on') - set(handles.num_RangeY_2,'Visible','on') + %set(handles.num_RangeY_2,'Visible','on') set(handles.num_RangeZ_2,'TooltipString','num_ZMax: range of projection normal to the plane') if test3D