Index: /trunk/src/find_imadoc.m =================================================================== --- /trunk/src/find_imadoc.m (revision 737) +++ /trunk/src/find_imadoc.m (revision 738) @@ -22,6 +22,4 @@ end end -% SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' -% XmlFileName=[fullfile(RootPath,SubDirBase) '.xml'];%new convention: xml at the level of the image folder if ~exist(XmlFileName,'file') XmlFileName=[fullfile(RootPath,SubDirBase,RootFile) '.xml']; % old convention: xml inside the image folder, case of images or new civ files Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 737) +++ /trunk/src/geometry_calib.m (revision 738) @@ -50,5 +50,5 @@ % Edit the above text to modify the response to help geometry_calib -% Last Modified by GUIDE v2.5 29-Oct-2013 06:46:10 +% Last Modified by GUIDE v2.5 11-Apr-2014 23:10:57 % Begin initialization code - DO NOT edit @@ -110,9 +110,10 @@ set(handles.Extrinsic,'Position',[1 Height-40-4-92-75 418 75])% rank 3 set(handles.PointLists,'Position',[1 Height-40-6-92-75-117 418 117]) % rank 4 -set(handles.CheckEnableMouse,'Position',[3 Height-40-8-92-75-117-30 203 30])% rank 5 +set(handles.CheckEnableMouse,'Position',[3 Height-40-8-92-75-117-30 180 30])% rank 5 set(handles.PLOT,'Position',[3 Height-394 120 30])% rank 6 set(handles.Copy,'Position',[151 Height-394 120 30])% rank 6 set(handles.CLEAR_PTS,'Position',[297 Height-394 120 30])% rank 6 set(handles.ClearLine,'Position',[297 Height-364 120 30])% rank 6 +set(handles.CoordLine,'Position',[177 Height-364 120 30])% rank 6 set(handles.phys_title,'Position',[38 Height-426 125 20])% rank 7 set(handles.CoordUnit,'Position',[151 Height-426 120 30])% rank 7 @@ -124,21 +125,22 @@ set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'}) if exist('inputfile','var')&& ~isempty(inputfile) - struct.XmlInputFile=inputfile; +% struct.XmlInputFile=inputfile; [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(inputfile); - if ~strcmp(FileExt,'.xml') - inputfile=fullfile(RootPath,[SubDir '.xml']);%xml file corresponding to the input file - if ~exist(inputfile,'file')% case of civ files , removes the extension for subdir - inputfile=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']); - if ~exist(inputfile,'file') - inputfile=[fullfile(RootPath,SubDir,RootFile) '.xml'];%old convention - if ~exist(inputfile,'file') - inputfile=''; - end - end - end - end + struct.XmlInputFile=find_imadoc(RootPath,SubDir,RootFile,FileExt); +% if ~strcmp(FileExt,'.xml') +% inputfile=fullfile(RootPath,[SubDir '.xml']);%xml file corresponding to the input file +% if ~exist(inputfile,'file')% case of civ files , removes the extension for subdir +% inputfile=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']); +% if ~exist(inputfile,'file') +% inputfile=[fullfile(RootPath,SubDir,RootFile) '.xml'];%old convention +% if ~exist(inputfile,'file') +% inputfile=''; +% end +% end +% end +% end set(handles.ListCoord,'Data',[]) - if exist(inputfile,'file') - Heading=loadfile(handles,inputfile);% load data from the xml file + if exist(struct.XmlInputFile,'file') + Heading=loadfile(handles,struct.XmlInputFile);% load data from the xml file if isfield(Heading,'Campaign')&& ischar(Heading.Campaign) struct.Campaign=Heading.Campaign; @@ -214,25 +216,15 @@ %% display image with new calibration in the currently opened uvmat interface - hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers - if ~isempty(hhh) - delete(hhh); - end - hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points'); - if ~isempty(hhh) - delete(hhh); - end - set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' - set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7]) + 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('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates + uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates PLOT_Callback(hObject, eventdata, handles) - Data=get(handles.ListCoord,'Data'); - Data(:,6)=zeros(size(Data,1),1); - Data(index,6)=-1;% indicate in the list the point with max deviation (possible mistake) - set(handles.ListCoord,'Data',Data)% indicate in the list the point with max deviation (possible mistake) - figure(handles.geometry_calib) - set(handles.APPLY,'BackgroundColor',[1 0 0]) + 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 + set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color end @@ -338,16 +330,16 @@ %% store the calibration data, by default in the xml file of the currently displayed image UvData=get(hhuvmat.uvmat,'UserData'); -NbSlice_j=1;%default -ZStart=Z_plane; -ZEnd=Z_plane; -volume_scan='n'; -if isfield(UvData,'XmlData') - if isfield(UvData.XmlData,'TranslationMotor') - NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice; - ZStart=UvData.XmlData.TranslationMotor.ZStart/10; - ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10; - volume_scan='y'; - end -end +% NbSlice_j=1;%default +% ZStart=Z_plane; +% ZEnd=Z_plane; +% volume_scan='n'; +% if isfield(UvData,'XmlData') +% if isfield(UvData.XmlData,'TranslationMotor') +% NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice; +% ZStart=UvData.XmlData.TranslationMotor.ZStart/10; +% ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10; +% volume_scan='y'; +% end +% end answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... @@ -362,26 +354,25 @@ end if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration - 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'}; - input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}]; - answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on'); - GeometryCalib.NbSlice=str2double(answer{5}); - GeometryCalib.VolumeScan=answer{6}; - if isempty(answer) - Z_plane=0; %default - else - Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice); - end - GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; - GeometryCalib.SliceAngle(:,3)=0; - GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise) - GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise) - GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})]; - GeometryCalib.RefractionIndex=str2double(answer{4}); -end - - - -%------------------------------------------------------------------------ -% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation) + 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'}) +% 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'}; +% input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}]; +% answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on'); +% GeometryCalib.NbSlice=str2double(answer{5}); +% GeometryCalib.VolumeScan=answer{6}; +% if isempty(answer) +% Z_plane=0; %default +% else +% Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice); +% end + GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; +% GeometryCalib.SliceAngle(:,3)=0; +% GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise) +% GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise) +% GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})]; +% GeometryCalib.RefractionIndex=str2double(answer{4}); +end + +%------------------------------------------------------------------------ +% --- determine the parameters for a calibration by an affine function (rescaling and offset, no rotation) function GeometryCalib=calib_rescale(Coord,handles) %------------------------------------------------------------------------ @@ -401,7 +392,5 @@ %------------------------------------------------------------------------ -% determine the parameters for a calibration by a linear transform matrix (rescale and rotation) - - +% --- determine the parameters for a calibration by a linear transform matrix (rescale and rotation) function GeometryCalib=calib_linear(Coord,handles) %------------------------------------------------------------------------ @@ -432,5 +421,5 @@ %------------------------------------------------------------------------ -% determine the tsai parameters for a view normal to the grid plane +% --- determine the tsai parameters for a view normal to the grid plane % NOT USED function GeometryCalib=calib_normal(Coord,handles) @@ -498,5 +487,5 @@ %------------------------------------------------------------------------ function GeometryCalib=calib_3D_linear(Coord,handles) -%------------------------------------------------------------------ +%------------------------------------------------------------------------ path_uvmat=which('uvmat');% check the path detected for source file uvmat path_UVMAT=fileparts(path_uvmat); %path to UVMAT @@ -708,4 +697,5 @@ % --- determine the rms of calibration error function ErrorRms=error_calib(calib_param,Calib,Coord) +%------------------------------------------------------------------------ %calib_param: vector of free calibration parameters (to optimise) %Calib: structure of the given calibration parameters @@ -734,17 +724,9 @@ ErrorRms=mean(ErrorRms); -% %------------------------------------------------------------------------ -% function XImage_Callback(hObject, eventdata, handles) -% %------------------------------------------------------------------------ -% update_list(hObject, eventdata,handles) -% -% %------------------------------------------------------------------------ -% function YImage_Callback(hObject, eventdata, handles) -% %------------------------------------------------------------------------ -% update_list(hObject, eventdata,handles) %------------------------------------------------------------------------ % --- Executes on button press in STORE. function STORE_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------------ Coord=get(handles.ListCoord,'Data'); %Object=read_geometry_calib(Coord_cell); @@ -761,5 +743,5 @@ RootPath=get(hhuvmat.RootPath,'String'); RootFile=get(hhuvmat.RootFile,'String'); - filebase=fullfile(RootPath,RootFile); + filebase=[fullfile(RootPath,RootFile) '~']; while exist([filebase '.xml'],'file') filebase=[filebase '~']; @@ -778,5 +760,5 @@ set(handles.ListCoordFiles,'string',listfile); end -set(handles.ListCoord,'Data',[]) +CLEAR_PTS_Callback(hObject, eventdata, handles)% clear the current list and point plots % -------------------------------------------------------------------- @@ -786,7 +768,10 @@ set(handles.ListCoord,'Data',[]) PLOT_Callback(hObject, eventdata, handles) - -%------------------------------------------------------------------------ -% --- Executes on button press in CLEAR. +update_calib_marker([]);%remove circle marker +set(handles.APPLY,'backgroundColor',[1 0 0])% set APPLY button to red color: no calibration wanted without points +set(handles.CheckEnableMouse,'value',1); %activate mouse to pick new points + +%------------------------------------------------------------------------ +% --- Executes on button press in CLEAR LIST function CLEAR_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ @@ -800,15 +785,14 @@ choice=get(handles.CheckEnableMouse,'Value'); if choice - set(handles.CheckEnableMouse,'BackgroundColor',[1 1 0]) huvmat=findobj(allchild(0),'tag','uvmat'); if ishandle(huvmat) hhuvmat=guidata(huvmat); + set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler if get(hhuvmat.CheckEditObject,'Value') - set(hhuvmat.CheckEditObject,'Value',0) - uvmat('CheckEditObject_Callback',hhuvmat.CheckEditObject,[],hhuvmat) + set(hhuvmat.CheckEditObject,'Value',0) + uvmat('CheckEditObject_Callback',hhuvmat.CheckEditObject,[],hhuvmat) end - end -else - set(handles.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7]) + set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler + end end @@ -841,4 +825,5 @@ set(handles.ListCoord,'Data',Coord) set(handles.APPLY,'BackgroundColor',[1 0 1]) +set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points %------------------------------------------------------------------------ @@ -858,4 +843,5 @@ set(handles.ListCoord,'Data',Coord) set(handles.APPLY,'BackgroundColor',[1 0 1]) +set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points % ----------------------------------------------------------------------- @@ -1002,10 +988,5 @@ PLOT_Callback(hObject, eventdata, handles) set(handles.APPLY,'BackgroundColor',[1 0 1]) - -% figure(10) -% hold off -% imagesc(Amod) -% hold on -% plot(Tmod(:,1),Tmod(:,2),'+') +set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points @@ -1085,4 +1066,5 @@ PLOT_Callback(handles.geometry_calib, [], handles) set(handles.APPLY,'BackgroundColor',[1 0 1]) +set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default % ----------------------------------------------------------------------- @@ -1104,4 +1086,5 @@ loadfile(handles,fileinput) end +set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default % ----------------------------------------------------------------------- @@ -1116,5 +1099,5 @@ listfile=[listfile;{inputfile}];%update the list of coord files end -set(handles.ListCoordFiles,'string',listfile); +set(handles.ListCoordFiles,'String',listfile); @@ -1243,8 +1226,7 @@ menu=get(h_menu_coord,'String'); choice=get(h_menu_coord,'Value'); +option=''; if iscell(menu) option=menu{choice}; -else - option='px'; %default end Coord=get(handles.ListCoord,'Data'); @@ -1252,8 +1234,8 @@ if isequal(option,'phys') Coord_plot=Coord(:,1:3); - elseif isequal(option,'px')||isequal(option,'') + elseif isempty(option);%optionoption,'px')||isequal(option,'') Coord_plot=Coord(:,4:5); else - msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank, px or phys ') + msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ') end end @@ -1290,9 +1272,7 @@ if ~isempty(eventdata.Indices) iline=eventdata.Indices(1);% selected line number - Data=get(handles.ListCoord,'Data'); - Data(:,6)=zeros(size(Data,1),1); - Data(iline,6)=-1;% mark the selected line - set(handles.ListCoord,'Data',Data) - update_calib_marker(Data(iline,:)) + set(handles.CoordLine,'String',num2str(iline)) + Data=get(handles.ListCoord,'Data'); + update_calib_marker(Data(iline,:)) end @@ -1316,23 +1296,20 @@ %------------------------------------------------------------------------ function ListCoord_KeyPressFcn(hObject, eventdata, handles) +iline=str2num(get(handles.CoordLine,'String')); xx=double(get(handles.geometry_calib,'CurrentCharacter'));%get the keyboard character -if ismember(xx,[30 31 127])% arrow upward, downward, or delete +if ismember(xx,[28 29 30 31])% directional arrow Coord=get(handles.ListCoord,'Data'); - ind=find(Coord(:,6));%find the marker '+' for line selection - Coord(:,6)=zeros(size(Coord,1),1);% desactivate the current line mark switch xx case 30 % arrow upward - Coord(ind-1,6)=1; + iline=iline-1; case 31% arrow downward - Coord(ind+1,6)=1; - case 127% remove line - Coord(ind,:)=[]; - PLOT_Callback(hObject,eventdata,handles) - set(handles.APPLY,'BackgroundColor',[1 0 1]) - otherwise - end - set(handles.ListCoord,'Data',Coord); + iline=iline+1; + end + if iline>=1 && iline<=size(Coord,1) + set(handles.CoordLine,'String',num2str(iline)) + update_calib_marker(Coord(iline,1:5))% show the point corresponding to the selected line + end else - set(handles.APPLY,'BackgroundColor',[1 0 1]) + set(handles.APPLY,'BackgroundColor',[1 0 1])% paint APPLY in magenta to indicate that the table content has be modified end @@ -1341,42 +1318,74 @@ % --- 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) -%% update the plot on uvmat + +%% read config on uvmat huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle -hplot=findobj(huvmat,'Tag','PlotAxes');%main plotting axis of uvmat -hhh=findobj(hplot,'Tag','calib_marker'); - -h_menu_coord=findobj(huvmat,'Tag','TransformName'); -menu=get(h_menu_coord,'String'); -choice=get(h_menu_coord,'Value'); +hhuvmat=guidata(huvmat); +hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker'); +if numel(Coord)<5 + if ~isempty(hhh) + delete(hhh)%delete the circle marker in case of no valid input + end + return +end +menu=get(hhuvmat.TransformName,'String'); +choice=get(hhuvmat.TransformName,'Value'); +option=''; if iscell(menu) option=menu{choice}; -else - option='px'; %default -end -if isequal(option,'phys') +end + +%% read appropriate coordinates (px or phys) in the table ListCoord +if isequal(option,'phys') % use phys coord XCoord=Coord(1); YCoord=Coord(2); -elseif isequal(option,'px')|| isequal(option,'') +elseif isempty(option)% use coord in pixels XCoord=Coord(4); YCoord=Coord(5); else - msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank, px or phys ') -end -if isempty(XCoord)||isempty(YCoord) - if ~isempty(hhh) - delete(hhh)%delete the circle marker - end + msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ') return end -xlim=get(hplot,'XLim'); -ylim=get(hplot,'YLim'); -ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker + +%% adjust the plot limits if needed +xlim=get(hhuvmat.PlotAxes,'XLim'); +ylim=get(hhuvmat.PlotAxes,'YLim'); +ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/25;%defines the size of the circle marker +check_xlim=0; +if XCoord>xlim(2) + xlim=xlim+XCoord-xlim(2)+ind_range;% translate plot limit + check_xlim=1; +elseif XCoordylim(2) + ylim=ylim+YCoord-ylim(2)+ind_range;% translate plot limit + check_ylim=1; +elseif YCoordxy(1,1)-ind_range) & ...%flagx=1 for the vectors with x position selected by the mouse - (YCoordxy(1,2)-ind_range),1);%find the first calibration point in the neighborhood of the mouse + ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/25;%defines the size of the circle marker +% ind_range_y=abs((ylim(2)-ylim(1))/50); +% ind_range=sqrt(ind_range_x*ind_range_y); + index_point=find((XCoordxy(1,1)-ind_range/2) & ...%flagx=1 for the vectors with x position selected by the mouse + (YCoordxy(1,2)-ind_range/2),1);%find the first calibration point in the neighborhood of the mouse if ~isempty(index_point) - pointershape='arrow';% default pointer is an arrow + pointershape='arrow';% default pointer is an arrow end hh=findobj('Tag','calib_points');%look for handle of calibration points - if ~isempty(hh) && ~isempty(get(hh,'UserData')) %&& get(hh_geometry_calib.CheckEnableMouse,'Value') - %set(hh,'UserData',index_point) + if ~isempty(hh) && ~isempty(get(hh,'UserData')) %&& get(hh_geometry_calib.CheckEnableMouse,'Value') + %set(hh,'UserData',index_point) index_point=get(hh,'UserData'); XCoord(index_point)=xy(1,1); @@ -429,17 +430,18 @@ set(hh,'XData',XCoord) set(hh,'YData',YCoord) - end + end if ~isempty(index_point) - Data=get(h_ListCoord,'Data'); - Data(:,6)=zeros(size(Data,1),1); - Data(index_point,6)=-1;%mrk the point on the GUI geometry_calib - set(h_ListCoord,'Data',Data); + set(hh_geometry_calib.CoordLine,'String',num2str(index_point)) + % Data=get(h_ListCoord,'Data'); +% Data(:,6)=zeros(size(Data,1),1); +% Data(index_point,6)=-1;%mrk the point on the GUI geometry_calib +% set(h_ListCoord,'Data',Data); hhh=findobj('Tag','calib_marker');%look for handle of point marker (circle) if ~isempty(hhh) set(hhh,'Position',[XCoord(index_point)-ind_range/2 YCoord(index_point)-ind_range/2 ind_range ind_range]) else - rectangle('Curvature',[1 1],... - 'Position',[xy(1,1)-ind_range/2 xy(1,2)-ind_range/2 ind_range ind_range],'EdgeColor','m',... - 'LineStyle','-','Tag','calib_marker'); + rectangle('Curvature',[1 1],... + 'Position',[XCoord(index_point)-ind_range/2 YCoord(index_point)-ind_range/2 ind_range ind_range],'EdgeColor','m',... + 'LineStyle','-','Tag','calib_marker'); end end Index: /trunk/src/mouse_up.m =================================================================== --- /trunk/src/mouse_up.m (revision 737) +++ /trunk/src/mouse_up.m (revision 738) @@ -349,5 +349,5 @@ %% finalising ruler if test_ruler && ~isempty(xy) - set(hhuvmat.MenuRuler,'checked','off')%desable the ruler option in uvmat + %set(hhuvmat.MenuRuler,'checked','off')%desable the ruler option in uvmat xy=get(hcurrentaxes,'CurrentPoint');% get the current mouse coordinates RulerCoord=[AxeData.RulerCoord ;xy(1,1:2)];% append the recorded ruler origin to the current mouse coordinates Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 737) +++ /trunk/src/proj_field.m (revision 738) @@ -920,19 +920,19 @@ %% extrema along each axis -testXMin=0; -testXMax=0; -testYMin=0; -testYMax=0; -if isfield(ObjectData,'RangeX') +testXMin=0;% test if min of X coordinates defined on the projection object, =0 by default +testXMax=0;% test if max of X coordinates defined on the projection object, =0 by default +testYMin=0;% test if min of Y coordinates defined on the projection object, =0 by default +testYMax=0;% test if max of Y coordinates defined on the projection object, =0 by default +if isfield(ObjectData,'RangeX') % rangeX defined by the projection object XMin=min(ObjectData.RangeX); XMax=max(ObjectData.RangeX); - testXMin=XMax>XMin;%=1 if XMin defined (i.e. RangeY has tow distinct elements) - testXMax=1;% range restriction along X -end -if isfield(ObjectData,'RangeY') + testXMin=XMax>XMin;%=1 if XMin defined (i.e. RangeY has two distinct elements) + testXMax=1;% max of X coordinates defined on the projection object +end +if isfield(ObjectData,'RangeY') % rangeY defined by the projection object YMin=min(ObjectData.RangeY); YMax=max(ObjectData.RangeY); testYMin=YMax>YMin;%=1 if YMin defined (i.e. RangeY has tow distinct elements) - testYMax=1; + testYMax=1;% max of Y coordinates defined on the projection object end width=0;%default width of the projection band @@ -1371,5 +1371,5 @@ end end - else % case with interpolation + else % case with interpolation on a grid if NbDim==2 %2D case if isequal(ProjMode{icell},'interp_tps') @@ -1383,22 +1383,24 @@ Coord{1}=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(1)}); Coord{2}=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(2)}); - xcorner=[min(Coord{NbDim}) max(Coord{NbDim}) max(Coord{NbDim}) min(Coord{NbDim})]-ObjectData.Coord(1,1);% corner absissa of the original grid with respect to the new origin - ycorner=[min(Coord{NbDim-1}) min(Coord{NbDim-1}) max(Coord{NbDim-1}) max(Coord{NbDim-1})]-ObjectData.Coord(1,2);% corner ordinates of the original grid - xcor_new=xcorner*cos(PlaneAngle(3))+ycorner*sin(PlaneAngle(3));%coordinates of the corners in new frame - ycor_new=-xcorner*sin(PlaneAngle(3))+ycorner*cos(PlaneAngle(3)); - if testXMin - xcor_new=max(xcor_new,XMin); - end - if testXMax - xcor_new=min(xcor_new,XMax); - end - if testYMin - ycor_new=max(ycor_new,YMin); - end - if testYMax - ycor_new=min(ycor_new,YMax); - end - coord_x_proj=min(xcor_new):DX:max(xcor_new); - coord_y_proj=min(ycor_new):DY:max(ycor_new); + if ~(testXMin && testYMin)% % if the range of the projected coordinates is not fully defined by the projection object, find the extrema of the projected field + xcorner=[min(Coord{NbDim}) max(Coord{NbDim}) max(Coord{NbDim}) min(Coord{NbDim})]-ObjectData.Coord(1,1);% corner absissa of the original grid with respect to the new origin + ycorner=[min(Coord{NbDim-1}) min(Coord{NbDim-1}) max(Coord{NbDim-1}) max(Coord{NbDim-1})]-ObjectData.Coord(1,2);% corner ordinates of the original grid + xcor_new=xcorner*cos(PlaneAngle(3))+ycorner*sin(PlaneAngle(3));%coordinates of the corners in new frame + ycor_new=-xcorner*sin(PlaneAngle(3))+ycorner*cos(PlaneAngle(3)); + if ~testXMin + XMin=min(xcor_new); + end + if ~testXMax + XMax=max(xcor_new); + end + if ~testYMin + YMin=min(ycor_new); + end + if ~testYMax + YMax=max(ycor_new); + end + end + coord_x_proj=XMin:DX:XMax; + coord_y_proj=YMin:DY:YMax; ProjData.(AYName)=[coord_y_proj(1) coord_y_proj(end)]; %record the new (projected ) y coordinates ProjData.(AXName)=[coord_x_proj(1) coord_x_proj(end)]; %record the new (projected ) x coordinates Index: /trunk/src/set_object.m =================================================================== --- /trunk/src/set_object.m (revision 737) +++ /trunk/src/set_object.m (revision 738) @@ -36,5 +36,5 @@ function varargout = set_object(varargin) -% Last Modified by GUIDE v2.5 11-Feb-2014 20:08:17 +% Last Modified by GUIDE v2.5 13-Apr-2014 19:31:58 % Begin initialization code - DO NOT REFRESH @@ -594,8 +594,13 @@ set(handles.num_RangeY_2,'BackgroundColor',[1 1 1]) -%------------------------------------------------------------------------ -% --- Executes on button press in MenuCoord. -function MenuCoord_Callback(hObject, eventdata, handles) -%------------------------------------------------------------------------ +% --- Executes on button press in ExportCoord. +function ExportCoord_Callback(hObject, eventdata, handles) +global Coord +Coord=get(handles.Coord,'Data'); +evalin('base','global Coord')%make Coord global in the workspace +display('object coordinates:') +evalin('base','Coord') %display Coord in the workspace +commandwindow; %brings the Matlab command window to the front + %---------------------------------------------------- function num_RangeY_1_Callback(hObject, eventdata, handles) @@ -785,2 +790,6 @@ set(handles.Coord,'Data',Coord); end + + + + Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 737) +++ /trunk/src/uvmat.m (revision 738) @@ -3811,7 +3811,6 @@ %% delete drawn objects if the output CooordUnit is different from the previous one -if ~strcmp(CoordUnit,CoordUnitPrev) +if ~strcmp(CoordUnit,CoordUnitPrev) set(handles.CheckFixLimits,'Value',0) -% set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7]) hother=findobj('Tag','proj_object');%find all the proj objects for iobj=1:length(hother) @@ -4544,8 +4543,7 @@ UvData.ProjObject(IndexObj)=[]; end - if ~isempty(list_str) - list_str(IndexObj)=[]; - end -% end +if numel(list_str)>=IndexObj + list_str(IndexObj)=[]; +end set(huvmat,'UserData',UvData); set(hlist_object,'String',list_str) @@ -4837,4 +4835,5 @@ %------------------------------------------------------------------------ %% desactivate concurrent tools +set(handles.MenuRuler,'checked','off')%desactivate ruler hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration if ishandle(hgeometry_calib) @@ -4945,12 +4944,18 @@ function MenuCalib_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ - +%% suppress the second field if exists +if get(handles.SubField,'Value') + set(handles.SubField,'Value',0) + SubField_Callback(hObject, eventdata, handles) +end UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface -%suppress competing options +%% suppress competing tools +set(handles.MenuRuler,'checked','off')%desactivate ruler set(handles.CheckZoom,'Value',0) set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) -set(handles.ListObject,'Value',1) -% initiate display of GUI geometry_calib +set(handles.ListObject,'Value',1) + +%% initiate display of the GUI geometry_calib data=[]; %default if isfield(UvData,'CoordType') @@ -4964,4 +4969,74 @@ set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action + +% -------------------------------------------------------------------- +% --- set the slice plane ro the set of slice planes when volume scan is used +function MenuSetSlice_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- +%% suppress the second input field if exists +if get(handles.SubField,'Value') + set(handles.SubField,'Value',0) + SubField_Callback(hObject, eventdata, handles) +end + +UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface +check=0; +if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'GeometryCalib')&& isfield(UvData.XmlData{1}.GeometryCalib,'SliceCoord') + GeometryCalib=UvData.XmlData{1}.GeometryCalib; + SliceCoord=GeometryCalib.SliceCoord; +else + msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices') + return +end +NbSlice_j=1;%default +Z=SliceCoord(:,3); +% index=index(ind_dim); +%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 +ZStart=SliceCoord(1,3);% first Z coordinate present in the calibration file +ZEnd=SliceCoord(end,3);% last Z coordinate present in the calibration file +volume_scan='n'; +if isfield(UvData,'XmlData') + if isfield(UvData.XmlData{1},'TranslationMotor') + NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice; + ZStart=UvData.XmlData.TranslationMotor.ZStart/10; + ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10; + volume_scan='y'; + end +end +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'}; +input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}]; +answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on'); +GeometryCalib.NbSlice=str2double(answer{5}); +GeometryCalib.VolumeScan=answer{6}; +if isempty(answer) + Z_plane=0; %default +else + Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice); +end +GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; +GeometryCalib.SliceAngle(:,3)=0; +GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise) +GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise) +GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})]; +GeometryCalib.RefractionIndex=str2double(answer{4}); + +%% store the result in the xml file used for calibration +[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); +FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%name of the xml file for calibration +[RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(FileName); +XmlFile=find_imadoc(RootPath,SubDir,RootFile,FileExt); +errormsg=update_imadoc(GeometryCalib,XmlFile,'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 +set(handles.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image +InputFileREFRESH_Callback(hObject,eventdata,handles); %file input with xml reading in uvmat, show the image in phys coordinates %----------------------------------------------------------------------- @@ -5234,10 +5309,14 @@ function MenuRuler_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ -set(handles.CheckZoom,'Value',0) -CheckZoom_Callback(handles.uvmat, [], handles) -set(handles.MenuRuler,'checked','on') -UvData=get(handles.uvmat,'UserData'); -UvData.MouseAction='ruler'; -set(handles.uvmat,'UserData',UvData); +if strcmp(get(handles.MenuRuler,'checked'),'on') + set(handles.MenuRuler,'checked','off')%desactivate if activated +else + set(handles.MenuRuler,'checked','on')%activate if selected + set(handles.CheckZoom,'Value',0) + CheckZoom_Callback(handles.uvmat, [], handles) + UvData=get(handles.uvmat,'UserData'); + UvData.MouseAction='ruler'; + set(handles.uvmat,'UserData',UvData); +end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -5453,6 +5532,7 @@ end - +% -------------------------------------------------------------------- % --- Executes on button press in CheckTable. +% -------------------------------------------------------------------- function CheckTable_Callback(hObject, eventdata, handles) if get(handles.CheckTable,'Value')