Ignore:
Timestamp:
Feb 19, 2013, 7:19:07 PM (8 years ago)
Author:
sommeria
Message:

many corrections; introduction of browse_data to scan the whole set of data, used also to replicate data in calibration mode

File:
1 edited

Legend:

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Added
Removed
  • trunk/src/geometry_calib.m

    r565 r569  
    150150
    151151%------------------------------------------------------------------------
    152 % --- Executes on button press in calibrate_lin.
     152% --- Executes on button press APPLY (used to launch the calibration).
    153153function APPLY_Callback(hObject, eventdata, handles)
    154154%------------------------------------------------------------------------
     
    156156huvmat=findobj(allchild(0),'Name','uvmat');
    157157hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
    158 FileExt=get(hhuvmat.FileExt,'String');
    159 % check_input=0;
    160 % if ~isempty(FileExt)
    161 %     if ~isempty(imformats(FileExt(2:end))) ||strcmpi(FileExt,'.avi')
    162 %         check_input=1;
    163 %     end
    164 % end
    165 % % if ~check_input
    166 %     msgbox_uvmat('ERROR','open an image with uvmat to perform calibration')
    167 %     return
    168 % end
    169 
     158
     159RootPath='';
     160if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
     161    RootPath=get(hhuvmat.RootPath,'String');
     162    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
     163    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
     164else
     165    question={'save the calibration data and point coordinates in'};
     166    def={fullfile(RootPath,'ObjectCalib.xml')};
     167    options.Resize='on';
     168    answer=inputdlg(question,'',1,def,options);
     169    outputfile=answer{1};
     170end
     171[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration
     172
     173%% copy the xml file from the old location if appropriate, then update with the calibration parameters
     174if ~exist(outputfile,'file') && ~isempty(SubDirBase)
     175    oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
     176    if exist(oldxml,'file')
     177        [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
     178    end
     179end
     180errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
     181if ~strcmp(errormsg,'')
     182    msgbox_uvmat('ERROR',errormsg);
     183end
     184
     185%% display image with new calibration in the currently opened uvmat interface
     186hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers
     187if ~isempty(hhh)
     188    delete(hhh);
     189end
     190hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points');
     191if ~isempty(hhh)
     192    delete(hhh);
     193end
     194set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
     195set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
     196UserData=get(handles.geometry_calib,'UserData');
     197UserData.XmlInputFile=outputfile;%save the current xml file name
     198set(handles.geometry_calib,'UserData',UserData)
     199uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
     200MenuPlot_Callback(hObject, eventdata, handles)
     201set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
     202ListCoord_Callback(hObject, eventdata, handles)
     203figure(handles.geometry_calib)
     204
     205%------------------------------------------------------------------------
     206% --- Executes on button press in REPLICATE
     207function REPLICATE_Callback(hObject, eventdata, handles)
     208%------------------------------------------------------------------------
     209
     210%% look for the GUI uvmat and check for an image as input
     211huvmat=findobj(allchild(0),'Name','uvmat');
     212hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
     213GeometryCalib=calibrate(handles,hhuvmat);% apply calibration
     214
     215%% open the GUI browse_data
     216CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
     217if isfield(CalibData,'XmlInputFile')
     218    InputDir=fileparts(fileparts(CalibData.XmlInputFile));
     219end
     220answer=msgbox_uvmat('INPUT_TXT','Campaign to calibrate?',InputDir);
     221if strcmp(answer,'Cancel')
     222    return
     223end
     224OutPut=browse_data(answer);
     225nbcalib=0;
     226for ilist=1:numel(OutPut.Experiment)
     227    SubDirBase=regexprep(OutPut.Device{1},'\..+$','');
     228    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
     229    % copy the xml file from the old location if appropriate, then update with the calibration parameters
     230    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
     231        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
     232        if exist(oldxml,'file')
     233            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
     234        end
     235    end
     236    errormsg=update_imadoc(GeometryCalib,XmlName);% introduce the calibration data in the xml file
     237    if ~strcmp(errormsg,'')
     238        msgbox_uvmat('ERROR',errormsg);
     239    else
     240        display([XmlName ' updated with calibration parameters'])
     241        nbcalib=nbcalib+1;
     242    end
     243end
     244msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
     245
     246%------------------------------------------------------------------------
     247% --- activate calibration and store parameters in ouputfile .
     248function [GeometryCalib,index]=calibrate(handles,hhuvmat)
     249%------------------------------------------------------------------------
    170250%% read the current calibration points
    171251Coord_cell=get(handles.ListCoord,'String');
     
    220300
    221301%% store the calibration data, by default in the xml file of the currently displayed image
    222 UvData=get(huvmat,'UserData');
     302UvData=get(hhuvmat.uvmat,'UserData');
    223303NbSlice_j=1;%default
    224304ZStart=Z_plane;
     
    233313    end
    234314end
    235 RootPath='';
    236 % RootFile='';
    237 if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
    238     RootPath=get(hhuvmat.RootPath,'String');
    239     SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
    240     outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
    241 else
    242     SubDirBase='';
    243     question={'save the calibration data and point coordinates in'};
    244     def={fullfile(RootPath,'ObjectCalib.xml')};
    245     options.Resize='on';
    246     answer=inputdlg(question,'save average in a new file',1,def,options);
    247     outputfile=answer{1};
    248 end
    249 answer=msgbox_uvmat('INPUT_Y-N',{[outputfile ' updated with calibration data'];...
     315
     316answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
    250317    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
    251318    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
    252319
    253 %% record the calibration parameters and display the current image of uvmat in the new phys coordinates
    254 if strcmp(answer,'Yes')
    255     if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
    256        input_key={'Z (first position)','Z (last position)','Z (water surface)', 'refractive index','NbSlice','volume scan (y/n)','tilt angle y axis','tilt angle x axis'};
    257        input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
    258         answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
    259         %answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
    260         GeometryCalib.NbSlice=str2double(answer{5});
    261         GeometryCalib.VolumeScan=answer{6};
    262         if isempty(answer)
    263             Z_plane=0; %default
    264         else
    265             Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
    266         end     
    267         GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
    268         GeometryCalib.SliceAngle(:,3)=0;
    269         GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
    270         GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
    271         GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
    272         GeometryCalib.RefractionIndex=str2double(answer{4});     
    273     end
    274     UserData=get(handles.geometry_calib,'UserData');
    275    
    276     % get the timing from the xml file using the old convention if appropriate
    277     if ~exist(outputfile,'file') && ~isempty(SubDirBase)     
    278         oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
    279         if exist(oldxml,'file')
    280         [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
    281         end
    282     end   
    283     errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
    284     if ~strcmp(errormsg,'')
    285         msgbox_uvmat('ERROR',errormsg);
    286     end
    287    
    288     %display image with new calibration in the currently opened uvmat interface
    289     hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers
    290     if ~isempty(hhh)
    291         delete(hhh);     
    292     end
    293     hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points');
    294     if ~isempty(hhh)
    295         delete(hhh);
    296     end
    297     set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
    298     set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
    299    
    300     UserData.XmlInputFile=outputfile;%save the current xml file name
    301     set(handles.geometry_calib,'UserData',UserData)
    302     uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
    303     MenuPlot_Callback(hObject, eventdata, handles)
    304     set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
    305     ListCoord_Callback(hObject, eventdata, handles)
    306     figure(handles.geometry_calib)
    307 end
    308 
    309 %------------------------------------------------------------------
    310 % --- Executes on button press in calibrate_lin.
    311 
    312 function REPLICATE_Callback(hObject, eventdata, handles)
    313 %------------------------------------------------------------------------
    314 
    315 %% Apply calibration
    316 calib_cell=get(handles.calib_type,'String'); %#ok<NASGU>
    317 val=get(handles.calib_type,'Value'); %#ok<NASGU>
    318 
    319 %read the current calibration points
    320 Coord_cell=get(handles.ListCoord,'String');
    321 Object=read_geometry_calib(Coord_cell);
    322 Coord=Object.Coord;
    323 
    324 % apply the calibration, whose type is selected in  handles.calib_type
    325 if ~isempty(Coord)
    326     calib_cell=get(handles.calib_type,'String');
    327     val=get(handles.calib_type,'Value');
    328     GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
    329 else
    330     msgbox_uvmat('ERROR','No calibration points, abort')
     320%% get plane position(s)
     321if ~strcmp(answer,'Yes')
    331322    return
    332 end
    333 
    334 if ~isempty(Coord)
    335     %check error
    336     X=Coord(:,1);
    337     Y=Coord(:,2);
    338     Z=Coord(:,3);
    339     x_ima=Coord(:,4);
    340     y_ima=Coord(:,5);
    341     [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
    342     GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
    343     [GeometryCalib.ErrorMax(1)]=max(abs(Xpoints-x_ima));
    344     GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
    345     [GeometryCalib.ErrorMax(2)]=max(abs(Ypoints-y_ima));
    346 %     [EM,ind_dim]=max(GeometryCalib.ErrorMax);
    347     %set the Z position of the reference plane used for calibration
    348     Z_plane=[];
    349     if isequal(max(Z),min(Z))
    350         Z_plane=Z(1);
    351     end
    352     answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
    353     Z_plane=str2double(answer_1);
    354     GeometryCalib.NbSlice=1;
    355     GeometryCalib.SliceCoord=[0 0 Z_plane];
    356     %set the coordinate unit
    357     unitlist=get(handles.CoordUnit,'String');
    358     unit=unitlist{get(handles.CoordUnit,'value')};
    359     GeometryCalib.CoordUnit=unit;
    360     %record the points
    361     GeometryCalib.SourceCalib.PointCoord=Coord;
    362 end
    363 
    364 %% display calibration paprameters
    365 display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
    366 
    367 % Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
    368 set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
    369 set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
    370 set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
    371 set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
    372 set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
    373 set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
    374 
    375 %% open the GUI dataview
    376 h_dataview=findobj(allchild(0),'name','dataview');
    377 if ~isempty(h_dataview)
    378     delete(h_dataview)
    379 end
    380 CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
    381 % InputFile='';
    382 if isfield(CalibData,'XmlInputFile')
    383     InputDir=fileparts(CalibData.XmlInputFile);
    384     [InputDir,DirName]=fileparts(InputDir);
    385 end
    386 SubCampaignTest='n'; %default
    387 testup=0;
    388 if isfield(CalibData,'SubCampaign')
    389     SubCampaignTest='y';
    390     dir_ref=CalibData.SubCampaign;
    391     testup=1;
    392 elseif isfield(CalibData,'Campaign')
    393     dir_ref=CalibData.Campaign;
    394     testup=1;
    395 end
    396 while testup
    397     [InputDir,DirName]=fileparts(InputDir);
    398     if strcmp(DirName,dir_ref)
    399         break
    400     end
    401 end
    402 InputDir=fullfile(InputDir,DirName);
    403 answer=msgbox_uvmat('INPUT_TXT','Campaign ?',InputDir);
    404 if strcmp(answer,'Cancel')
    405     return
    406 end
    407 
    408 dataview(answer,SubCampaignTest,GeometryCalib);
     323end
     324if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
     325    input_key={'Z (first position)','Z (last position)','Z (water surface)', 'refractive index','NbSlice','volume scan (y/n)','tilt angle y axis','tilt angle x axis'};
     326    input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
     327    answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
     328    GeometryCalib.NbSlice=str2double(answer{5});
     329    GeometryCalib.VolumeScan=answer{6};
     330    if isempty(answer)
     331        Z_plane=0; %default
     332    else
     333        Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
     334    end
     335    GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
     336    GeometryCalib.SliceAngle(:,3)=0;
     337    GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
     338    GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
     339    GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
     340    GeometryCalib.RefractionIndex=str2double(answer{4});
     341end
     342
     343
    409344
    410345%------------------------------------------------------------------------
     
    456391GeometryCalib.R=[R [0;0;-epsilon]];
    457392GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
     393
    458394%------------------------------------------------------------------------
    459395% determine the tsai parameters for a view normal to the grid plane
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