Ignore:
Timestamp:
Nov 29, 2018, 5:44:44 PM (2 years ago)
Author:
sommeria
Message:

various bugs repaired

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/geometry_calib.m

    r1027 r1059  
    5252% Edit the above text to modify the response to help geometry_calib
    5353
    54 % Last Modified by GUIDE v2.5 16-Apr-2015 17:29:02
     54% Last Modified by GUIDE v2.5 20-Sep-2018 19:04:30
    5555
    5656% Begin initialization code - DO NOT edit
     
    108108set(handles.calib_type,'Position',[1 Height-40 194 30])%  rank 1
    109109set(handles.APPLY,'Position',[197 Height-40 110 30])%  rank 1
    110 set(handles.REPLICATE,'Position',[309 Height-40 110 30])%  rank 1
     110set(handles.Replicate,'Position',[309 Height-40 110 30])%  rank 1
    111111set(handles.Intrinsic,'Position',[1 Height-40-2-92 418 92])%  rank 2
    112112set(handles.Extrinsic,'Position',[1 Height-40-4-92-75 418 75])%  rank 3
     
    167167%------------------------------------------------------------------------
    168168% --- Executes on button press APPLY (used to launch the calibration).
    169 function APPLY_Callback(hObject, eventdata, handles)
     169    function APPLY_Callback(hObject, eventdata, handles)
     170        set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
     171       
     172        %------------------------------------------------------------------------
     173        %% look for the GUI uvmat and check for an image as input
     174        set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation
     175        huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat
     176        hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
     177        if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
     178            msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
     179            return
     180        end
     181       
     182        RootPath='';
     183        if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
     184            RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image
     185            SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
     186            outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
     187        else
     188            question={'save the calibration data and point coordinates in'};
     189            def={fullfile(RootPath,'ObjectCalib.xml')};
     190            options.Resize='on';
     191            answer=inputdlg(question,'',1,def,options);
     192            outputfile=answer{1};
     193        end
     194       
     195        %% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image
     196        Coord=get(handles.ListCoord,'Data');
     197       
     198       
     199        %% read the type of calibration
     200        calib_cell=get(handles.calib_type,'String');
     201        val=get(handles.calib_type,'Value');
     202        CalibFcn=['calib_' calib_cell{val}];
     203       
     204        %% read the intrinsic parameters
     205        Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String'));
     206        Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String'));
     207        Intrinsic.coord_files=get(handles.ListCoordFiles,'String');
     208        Intrinsic.fx=str2num(get(handles.fx,'String'));
     209        Intrinsic.fy=str2num(get(handles.fy,'String'));
     210        Intrinsic.kc=str2num(get(handles.kc,'String'));
     211        Intrinsic.Cx=str2num(get(handles.Cx,'String'));
     212        Intrinsic.Cy=str2num(get(handles.Cy,'String'));
     213        if isempty(Intrinsic.kc)
     214            Intrinsic.kc=0;
     215        end
     216        if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy)
     217            Intrinsic.Cx=Intrinsic.Npx/2;
     218            Intrinsic.Cy=Intrinsic.Npy/2;
     219        end
     220       
     221        %% apply to cropped images if requested
     222        if get(handles.Replicate,'Value')
     223            answer=msgbox_uvmat('INPUT_Y-N','apply to full images (not cropped)?');
     224            if strcmp(answer,'No')
     225                prompt = {'npy_lower'};
     226                dlg_title = 'remove image the npy_lower image lines (removal of the upper line does not change calibration)';
     227                num_lines= 1;
     228                def     = {'0'};
     229                answer = inputdlg(prompt,dlg_title,num_lines,def);
     230                npy_crop=str2num(answer{1});
     231                Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window
     232                Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band
     233            end
     234        end
     235       
     236        %% Apply calibration
     237        [GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration
     238       
     239        %% record the coordinate unit
     240        unitlist=get(handles.CoordUnit,'String');
     241        unit=unitlist{get(handles.CoordUnit,'value')};
     242        GeometryCalib.CoordUnit=unit;
     243       
     244        %% record the coordinates of the calibration points
     245        GeometryCalib.SourceCalib.PointCoord=Coord;
     246       
     247        %% display calibration results on the GUI geometry_calib
     248        display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
     249        display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters
     250        %     (rotation and translation of camera with  respect to the phys coordinates)
     251       
     252        %% set the defqult plane and display the calibration data errors for validation
     253        answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
     254            ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
     255            ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels'];
     256            [num2str(numel(ind_removed)) ' points removed']});
     257        if strcmp(answer,'Yes') %store the calibration data
     258            if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
     259                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'});
     260                SliceCoord_ref=Z_plane'*[0 0 1];
     261            end
     262        else
     263            GeometryCalib=[];
     264            index=1;
     265        end
     266       
     267        if ~isempty(GeometryCalib) % if calibration is not cancelled
     268            if get(handles.Replicate,'Value')
     269                %% open the GUI browse_data
     270                hbrowse=findobj(allchild(0),'Tag','browse_data');
     271                if ~isempty(hbrowse)
     272                    BrowseHandles=guidata(hbrowse);
     273                    SourceDir=get(BrowseHandles.SourceDir,'String');
     274                    ListExperiments=get(BrowseHandles.ListExperiments,'String');
     275                    ListValues=get(BrowseHandles.ListExperiments,'Value');
     276                    ListExperiments=ListExperiments(ListValues);
     277                    ListDevices=get(BrowseHandles.ListDevices,'String');
     278                    Val=get(BrowseHandles.ListDevices,'Value');
     279                    DataFolder=ListDevices{Val};
     280                    nbcalib=0;
     281                    for ilist=1:numel(ListExperiments)
     282                        SubDirBase=regexprep(DataFolder,'+/','');
     283                        ListExperiments{ilist}=regexprep(ListExperiments{ilist},'+/','');
     284                        XmlName=fullfile(SourceDir,ListExperiments{ilist},[SubDirBase '.xml']);
     285                        % copy the xml file from the old location if appropriate, then update with the calibration parameters
     286                        %                 if ~exist(XmlName,'file') && ~isempty(SubDirBase)
     287                        %                     oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
     288                        GeometryCalib.SliceCoord=SliceCoord_ref;%default input
     289                        if exist(XmlName,'file')
     290                            %[success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
     291                            dispmesGeometryCalib=UvData.XmlData{1}.GeometryCalib;
     292                        else
     293                            msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices')
     294                            return
     295                        end
     296                        SliceCoord=GeometryCalib.SliceCoord;
     297                        InterfaceCoord=min(SliceCoord(:,3));
     298                        if isfield(GeometryCalib,'InterfaceCoord')
     299                            InterfaceCoord=GeometryCalib.InterfaceCoord(1,3);
     300                        end
     301                        NbSlice=size(SliceCoord,1);
     302                        CheckVolumeScan=0;
     303                        if isfield(GeometryCalib,'CheckVolumeScan')
     304                            CheckVolumeScan=GeometryCalib.CheckVolumeScan;
     305                        end
     306                        RefractionIndex=1.33;
     307                        CheckRefraction=0;% default value of the check box refraction
     308                        if isfield(GeometryCalib,'RefractionIndex')
     309                            RefractionIndex=GeometryCalib.RefractionIndex;
     310                            CheckRefraction=1;
     311                        end
     312                        SliceAngle=[0 0 0];
     313                        if isfield(GeometryCalib,'SliceAngle')
     314                            SliceAngle=GeometryCalib.SliceAngle;
     315                        end
     316                        dispmessage=' updated with calibration parameters';
     317                        %                         if ~strcmp(answer,'yes')
     318                        [XmlDataOld,warntext]=imadoc2struct(XmlName);
     319                        if isfield(XmlDataOld,'GeometryCalib')
     320                            if isfield(XmlDataOld.GeometryCalib,'SliceAngle')
     321                                GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.SliceAngle;
     322                            end
     323                            if isfield(XmlDataOld.GeometryCalib,'CheckRefraction')
     324                                GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.CheckRefraction;
     325                            end
     326                            if isfield(XmlDataOld.GeometryCalib,'RefractionIndex')
     327                                GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.RefractionIndex;
     328                            end
     329                            if isfield(XmlDataOld.GeometryCalib,'InterfaceCoord')
     330                                GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.InterfaceCoord;
     331                            end
     332                        end
     333                       
     334                        end
     335                       
     336                        else
     337                            dispmessage=' created with calibration parameters';
     338                    end
     339                    errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
     340                    if ~strcmp(errormsg,'')
     341                        msgbox_uvmat('ERROR',errormsg);
     342                    else
     343                        display([XmlName dispmessage])
     344                        nbcalib=nbcalib+1;
     345                    end
     346                end
     347               
     348            end
     349            msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
     350        else
     351           
     352            %% copy the xml file from the old location if appropriate, then update with the calibration parameters
     353            if ~exist(outputfile,'file') && ~isempty(SubDirBase)
     354                oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
     355                if exist(oldxml,'file')
     356                    [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
     357                end
     358            end
     359            errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file
     360            if ~strcmp(errormsg,'')
     361                msgbox_uvmat('ERROR',errormsg);
     362            end
     363           
     364            %% display image with new calibration in the currently opened uvmat interface
     365            FieldList=get(hhuvmat.FieldName,'String');
     366            val=get(hhuvmat.FieldName,'Value');
     367            if strcmp(FieldList{val},'image')
     368                set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image
     369                UserData=get(handles.geometry_calib,'UserData');
     370                UserData.XmlInputFile=outputfile;%save the current xml file name
     371                set(handles.geometry_calib,'UserData',UserData)
     372                uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
     373                PLOT_Callback(hObject, eventdata, handles)
     374                set(handles.CoordLine,'string',num2str(index))
     375                Coord=get(handles.ListCoord,'Data');
     376                update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration
     377                figure(handles.geometry_calib)% put the GUI geometry_calib in front
     378            else
     379                msgbox_uvmat('WARNING','open the image to see the effect of the new calibration')
     380            end
     381        end
     382    end
     383    set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color
     384
     385%------------------------------------------------------------------------
     386% --- Executes on button press in Replicate
     387function Replicate_Callback(hObject, eventdata, handles)
     388% %------------------------------------------------------------------------
    170389set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
    171390
    172 %------------------------------------------------------------------------
    173 %% look for the GUI uvmat and check for an image as input
    174 set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation
    175 huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat
    176 hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
    177 if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on')
    178     msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration')
    179   return
    180 end
    181 
    182 RootPath='';
    183 if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
    184     RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image
    185     SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
    186     outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
     391if get(handles.Replicate,'Value') %open the GUI browse_data
     392    % look for the GUI uvmat and check for an image as input
     393    huvmat=findobj(allchild(0),'Name','uvmat');
     394    hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
     395    RootPath=get(hhuvmat.RootPath,'String');
     396    SubDir=get(hhuvmat.SubDir,'String');
     397    browse_data(fullfile(RootPath,SubDir))
    187398else
    188     question={'save the calibration data and point coordinates in'};
    189     def={fullfile(RootPath,'ObjectCalib.xml')};
    190     options.Resize='on';
    191     answer=inputdlg(question,'',1,def,options);
    192     outputfile=answer{1};
    193 end
    194 
    195 %% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image
    196 Coord=get(handles.ListCoord,'Data');
    197 
    198  
    199 %% read the type of calibration
    200 calib_cell=get(handles.calib_type,'String');
    201 val=get(handles.calib_type,'Value');
    202 CalibFcn=['calib_' calib_cell{val}];
    203 
    204 %% read the intrinsic parameters
    205 Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String'));
    206 Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String'));
    207 Intrinsic.coord_files=get(handles.ListCoordFiles,'String');
    208 Intrinsic.fx=str2num(get(handles.fx,'String'));
    209 Intrinsic.fy=str2num(get(handles.fy,'String'));
    210 Intrinsic.kc=str2num(get(handles.kc,'String'));
    211 Intrinsic.Cx=str2num(get(handles.Cx,'String'));
    212 Intrinsic.Cy=str2num(get(handles.Cy,'String'));
    213 if isempty(Intrinsic.kc)
    214     Intrinsic.kc=0;
    215 end
    216 if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy)
    217     Intrinsic.Cx=Intrinsic.Npx/2;
    218     Intrinsic.Cy=Intrinsic.Npy/2;
    219 end 
    220 
    221 %% Apply calibration
    222 [GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration
    223 
    224 %% record the coordinate unit
    225 unitlist=get(handles.CoordUnit,'String');
    226 unit=unitlist{get(handles.CoordUnit,'value')};
    227 GeometryCalib.CoordUnit=unit;
    228 
    229 %% record the coordinates of the calibration points
    230 GeometryCalib.SourceCalib.PointCoord=Coord;
    231 
    232 %% display calibration results on the GUI geometry_calib
    233 display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
    234 display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters
    235 %     (rotation and translation of camera with  respect to the phys coordinates)
    236 
    237 %% store the calibration data, by default in the xml file of the currently displayed image
    238 answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
    239     ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
    240     ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels'];
    241     [num2str(numel(ind_removed)) ' points removed']});
    242 if strcmp(answer,'Yes') %store the calibration data
    243     if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
    244         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'})
    245         GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
    246     end   
    247 else
    248     GeometryCalib=[];
    249     index=1;
    250 end
    251 
    252 if isempty(GeometryCalib) % if calibration cancelled
    253     set(handles.APPLY,'BackgroundColor',[1 0 1])
    254 else   % if calibration confirmed
    255    
    256     %% copy the xml file from the old location if appropriate, then update with the calibration parameters
    257     if ~exist(outputfile,'file') && ~isempty(SubDirBase)
    258         oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
    259         if exist(oldxml,'file')
    260             [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
    261         end
    262     end
    263     errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file
    264     if ~strcmp(errormsg,'')
    265         msgbox_uvmat('ERROR',errormsg);
    266     end
    267    
    268     %% display image with new calibration in the currently opened uvmat interface
    269     FieldList=get(hhuvmat.FieldName,'String');
    270     val=get(hhuvmat.FieldName,'Value');
    271     if strcmp(FieldList{val},'image')
    272         set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image
    273         UserData=get(handles.geometry_calib,'UserData');
    274         UserData.XmlInputFile=outputfile;%save the current xml file name
    275         set(handles.geometry_calib,'UserData',UserData)
    276         uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
    277         PLOT_Callback(hObject, eventdata, handles)
    278         set(handles.CoordLine,'string',num2str(index))
    279         Coord=get(handles.ListCoord,'Data');
    280         update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration
    281         figure(handles.geometry_calib)% put the GUI geometry_calib in front
    282         set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color
    283     else
    284         msgbox_uvmat('WARNING','open the image to see the effect of the new calibration')
    285     end
    286 end
    287 
    288 %------------------------------------------------------------------------
    289 % --- Executes on button press in REPLICATE
    290 function REPLICATE_Callback(hObject, eventdata, handles)
    291 %------------------------------------------------------------------------
    292 set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
    293 
    294 %% look for the GUI uvmat and check for an image as input
    295 huvmat=findobj(allchild(0),'Name','uvmat');
    296 hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
    297 
    298 %% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image
    299 Coord=get(handles.ListCoord,'Data');
    300  
    301 %% read the type of calibration
    302 calib_cell=get(handles.calib_type,'String');
    303 val=get(handles.calib_type,'Value');
    304 CalibFcn=['calib_' calib_cell{val}];
    305 
    306 %% read the intrinsic parameters
    307 Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String'));
    308 Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String'));
    309 Intrinsic.coord_files=get(handles.ListCoordFiles,'String');
    310 Intrinsic.fx=str2num(get(handles.fx,'String'));
    311 Intrinsic.fy=str2num(get(handles.fy,'String'));
    312 Intrinsic.kc=str2num(get(handles.kc,'String'));
    313 Intrinsic.Cx=str2num(get(handles.Cx,'String'));
    314 Intrinsic.Cy=str2num(get(handles.Cy,'String'));
    315 if isempty(Intrinsic.kc)
    316     Intrinsic.kc=0;
    317 end
    318 if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy)
    319     Intrinsic.Cx=Intrinsic.Npx/2;
    320     Intrinsic.Cy=Intrinsic.Npy/2;
    321 end
    322 
    323 %% apply to cropped images if requested
    324 answer=msgbox_uvmat('INPUT_Y-N','apply to cropped images?');
    325 if strcmp(answer,'Yes')
    326     prompt = {'npy_lower'};
    327     dlg_title = 'remove image the npy_lower image lines (removal of the upper linedoes not change calibration)';
    328     num_lines= 1;
    329     def     = {'0'};
    330     answer = inputdlg(prompt,dlg_title,num_lines,def);
    331     npy_crop=str2num(answer{1});
    332     Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window
    333     Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band
    334 end
    335 
    336 %% Apply calibration
    337 [GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration
    338 
    339 
    340 %% record the coordinate unit
    341 unitlist=get(handles.CoordUnit,'String');
    342 unit=unitlist{get(handles.CoordUnit,'value')};
    343 GeometryCalib.CoordUnit=unit;
    344 
    345 %% record the coordinates of the calibration points
    346 GeometryCalib.SourceCalib.PointCoord=Coord;
    347 
    348 %% display calibration results on the GUI geometry_calib
    349 display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
    350 display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters
    351 %     (rotation and translation of camera with  respect to the phys coordinates)
    352 
    353 %% store the calibration data, by default in the xml file of the currently displayed image
    354 answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
    355     ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
    356     ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels'];...
    357     [num2str(numel(ind_removed)) ' points removed']});
    358 if strcmp(answer,'Yes') %store the calibration data
    359     if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
    360         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'})
    361         GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
    362     end   
    363 else
    364     GeometryCalib=[];
    365     index=1;
    366 end
    367 
    368 %% open the GUI browse_data
    369 CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
    370 if isfield(CalibData,'XmlInputFile')
    371     InputDir=fileparts(fileparts(CalibData.XmlInputFile));
    372 end
    373 DataSeries=uigetfile_uvmat('open a folder of images to calibrate',InputDir,'uigetdir');
    374 %SubProject=uigetfile_uvmat('open folder of subproject to calibrate',InputDir,'uigetdir');
    375 OutPut=browse_data(DataSeries);
    376 nbcalib=0;
    377 for ilist=1:numel(OutPut.Experiment)
    378     SubDirBase=regexprep(OutPut.DataSeries{1},'\..+$','');
    379     XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
    380     dispmessage=' created with calibration parameters';
    381     % copy the xml file from the old location if appropriate, then update with the calibration parameters
    382     if ~exist(XmlName,'file') && ~isempty(SubDirBase)
    383         oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
    384         if exist(oldxml,'file')
    385             [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
    386             dispmessage=' updated with calibration parameters';
    387         end
    388     end
    389     errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
    390     if ~strcmp(errormsg,'')
    391         msgbox_uvmat('ERROR',errormsg);
    392     else
    393         display([XmlName dispmessage])
    394         nbcalib=nbcalib+1;
    395     end
    396 end
    397 msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
    398 
     399    hbrowse=findobj(allchild(0),'Tag','browse_data');
     400    if ~isempty(hbrowse)
     401        delete(hbrowse)
     402    end
     403end
    399404%------------------------------------------------------------------------
    400405% --- activate calibration and store parameters in ouputfile .
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