Index: trunk/src/geometry_calib.m =================================================================== --- trunk/src/geometry_calib.m (revision 1111) +++ trunk/src/geometry_calib.m (revision 1112) @@ -256,12 +256,14 @@ [num2str(numel(ind_removed)) ' points removed']}); % SliceCoord_ref=[0 0 0]; %default reference plane +checkslice=0; if strcmp(answer,'Yes') %store the calibration data Z=Coord(:,3); if strcmp(calib_cell{val}(1:2),'3D') && isequal(max(Z),min(Z))%set the plane position for 3D (projection) calibration %set the Z position of the reference plane used for calibration - answer=msgbox_uvmat('INPUT_Y-N',{['Assume that the illuminated plane is at z=' num2str(Z(1)) ] ; 'can be later modified by MenuSetSlice in the upper bar menu of uvmat'}); + answer=msgbox_uvmat('INPUT_Y-N',{['Do you assume that the illuminated plane is at z=' num2str(Z(1)) '?' ] ; 'can be later modified by MenuSetSlice in the upper bar menu of uvmat'}); if strcmp(answer,'Yes') - GeometryCalib.NbSlice=1; - GeometryCalib.SliceCoord=[0 0 Z(1)]; + Slice.NbSlice=1; + Slice.SliceCoord=[0 0 Z(1)]; + checkslice=1;% will document the item in ImaDoc end end @@ -319,13 +321,17 @@ end errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file + dispmessage=''; + if checkslice + errormsg=update_imadoc(Slice,XmlName,'Slice');% introduce the slice position in the xml file + dispmessage=' and slice position'; + end if ~strcmp(errormsg,'') msgbox_uvmat('ERROR',errormsg); else if check_update - display([XmlName ' updated with calibration parameters']) + display([XmlName ' updated with calibration parameters' dispmessage]) else - display([XmlName ' created with calibration parameters']) + display([XmlName ' created with calibration parameters' dispmessage]) end - %nbcalib=nbcalib+1; end end @@ -333,6 +339,6 @@ msgbox_uvmat('CONFIMATION',['calibration replicated for ' num2str(NbExp) ' experiments']); else - %% copy the xml file from the old location if appropriate, then update with the calibration parameters - if ~exist(outputfile,'file') && ~isempty(SubDirBase) + %% update the calibration parameters in the currently opened uvmat GUI + if ~exist(outputfile,'file') && ~isempty(SubDirBase) %copy the xml file from the old location if appropriate oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml']; if exist(oldxml,'file') @@ -341,9 +347,12 @@ end errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file + if checkslice + errormsg=update_imadoc(Slice,outputfile,'Slice');% introduce the slice position in the xml file + end if ~strcmp(errormsg,'') msgbox_uvmat('ERROR',errormsg); end - %% display image with new calibration in the currently opened uvmat interface + %% display image with new calibration in the currently opened uvmat GUI FieldList=get(hhuvmat.FieldName,'String'); val=get(hhuvmat.FieldName,'Value'); @@ -413,5 +422,5 @@ x_ima=Coord(:,4); y_ima=Coord(:,5); -[Xpoints,Ypoints]=px_XYZ(GeometryCalib,Coord(:,1),Coord(:,2),Coord(:,3));% convention of downward z coordinate (facing the camera) +[Xpoints,Ypoints]=px_XYZ(GeometryCalib,[],Coord(:,1),Coord(:,2),Coord(:,3));% convention of downward z coordinate (facing the camera) GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); @@ -436,5 +445,5 @@ x_ima=Coord(:,4); y_ima=Coord(:,5); - [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z); + [Xpoints,Ypoints]=px_XYZ(GeometryCalib,[],X,Y,Z); GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); @@ -805,5 +814,5 @@ x_ima=Coord(:,4); y_ima=Coord(:,5); -[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z); +[Xpoints,Ypoints]=px_XYZ(Calib,[],X,Y,Z); ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); Index: trunk/src/mouse_motion.m =================================================================== --- trunk/src/mouse_motion.m (revision 1111) +++ trunk/src/mouse_motion.m (revision 1112) @@ -497,5 +497,5 @@ %% draw ruler if test_ruler && isfield(AxeData,'Drawing') && isequal(AxeData.Drawing,'ruler') - if isfield(AxeData,'RulerHandle') + if isfield(AxeData,'RulerHandle') && ~isempty(findobj(AxeData.RulerHandle)) && size(xy,2)>=2 pointershape='crosshair'; %give the mouse pointer a cross shape RulerCoord=[AxeData.RulerCoord ;xy(1,1:2)]; %coordinates defining the ruler segment Index: trunk/src/mouse_up.m =================================================================== --- trunk/src/mouse_up.m (revision 1111) +++ trunk/src/mouse_up.m (revision 1112) @@ -363,10 +363,12 @@ RulerCoord=[AxeData.RulerCoord ;xy(1,1:2)];% append the recorded ruler origin to the current mouse coordinates RulerCoord=diff(RulerCoord,1);% coordiante difference between segment end and beginning - RulerCoord=RulerCoord(1)+i*RulerCoord(2); + RulerCoord=RulerCoord(1)+1i*RulerCoord(2); distance=abs(RulerCoord); azimuth=(180/pi)*angle(RulerCoord); msgbox_uvmat('RULER','',['length: ' num2str(distance,3) ', angle(degrees): ' num2str(azimuth,3)]) + if isfield(AxeData,'RulerHanle')&&~isempty(findobj(AxeData.RulerHandle)) delete(AxeData.RulerHandle)%delete the ruler graphic object AxeData=rmfield(AxeData,'RulerHandle');%remove the ruler handle in AxeData + end AxeData.Drawing='off';%exit the ruler drawing mode end Index: trunk/src/phys_XYZ.m =================================================================== --- trunk/src/phys_XYZ.m (revision 1111) +++ trunk/src/phys_XYZ.m (revision 1112) @@ -33,20 +33,23 @@ %======================================================================= -function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Zindex) +function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,Slice,X,Y,Zindex) %------------------------------------------------------------------------ testangle=0;% =1 if the illumination plane is tilted with respect to the horizontal plane Xphys Yphys test_refraction=0;% =1 if the considered points are viewed through an horizontal interface (located at z=Calib.InterfaceCoord(3)') Zphys=0; %default output -if exist('Zindex','var')&& isequal(Zindex,round(Zindex))&& Zindex>0 && isfield(Calib,'SliceCoord')&&size(Calib.SliceCoord,1)>=Zindex - if isfield(Calib, 'SliceAngle') && size(Calib.SliceAngle,1)>=Zindex && ~isequal(Calib.SliceAngle(Zindex,:),[0 0 0]) +if isempty(Slice) + Slice=Calib;%old convention < 2022 +end +if exist('Zindex','var')&& isequal(Zindex,round(Zindex))&& Zindex>0 && isfield(Slice,'SliceCoord')&&size(Slice.SliceCoord,1)>=Zindex + if isfield(Slice, 'SliceAngle') && size(Slice.SliceAngle,1)>=Zindex && ~isequal(Slice.SliceAngle(Zindex,:),[0 0 0]) testangle=1; - norm_plane=angle2normal(Calib.SliceAngle(Zindex,:));% coordinates UVMAT-httpsof the unit vector normal to the current illumination plane + norm_plane=angle2normal(Slice.SliceAngle(Zindex,:));% coordinates UVMAT-httpsof the unit vector normal to the current illumination plane end - Z0=Calib.SliceCoord(Zindex,3);%horizontal plane z=cte + Z0=Slice.SliceCoord(Zindex,3);%horizontal plane z=cte Z0virt=Z0; - if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') - H=Calib.InterfaceCoord(3);% z position of the water surface + if isfield(Slice,'InterfaceCoord') && isfield(Slice,'RefractionIndex') + H=Slice.InterfaceCoord(3);% z position of the water surface if H>Z0 - Z0virt=H-(H-Z0)/Calib.RefractionIndex; %corrected z (virtual object) + Z0virt=H-(H-Z0)/Slice.RefractionIndex; %corrected z (virtual object) test_refraction=1; end @@ -86,13 +89,13 @@ b=-norm_plane(2)/norm_plane(3); if test_refraction - avirt=a/Calib.RefractionIndex; - bvirt=b/Calib.RefractionIndex; + avirt=a/Slice.RefractionIndex; + bvirt=b/Slice.RefractionIndex; else avirt=a; bvirt=b; end - cvirt=Z0virt-avirt*Calib.SliceCoord(Zindex,1)-bvirt*Calib.SliceCoord(Zindex,2);% Z0 = (virtual) z coordinate on the rotation axis (assumed horizontal) + cvirt=Z0virt-avirt*Slice.SliceCoord(Zindex,1)-bvirt*Slice.SliceCoord(Zindex,2);% Z0 = (virtual) z coordinate on the rotation axis (assumed horizontal) % c=z coordinate at (x,y)=(0,0) - c=Z0-a*Calib.SliceCoord(Zindex,1)-b*Calib.SliceCoord(Zindex,2); + c=Z0-a*Slice.SliceCoord(Zindex,1)-b*Slice.SliceCoord(Zindex,2); R(1)=R(1)+avirt*R(3); R(2)=R(2)+bvirt*R(3); Index: trunk/src/phys_ima.m =================================================================== --- trunk/src/phys_ima.m (revision 1111) +++ trunk/src/phys_ima.m (revision 1112) @@ -27,5 +27,9 @@ npx=[npx siz(2)]; npy=[npy siz(1)]; - Calib=XmlData{icell}.GeometryCalib; + Calib{icell}=XmlData{icell}.GeometryCalib; + Slice{icell}=Calib{icell}; + if isfield(XmlData{icell},'Slice') + Slice{icell}=XmlData{icell}.Slice; + end coord_x=[0.5 siz(2)-0.5]; coord_y=[0.5 siz(1)-0.5]; @@ -34,5 +38,5 @@ y_edge=[coord_y(1)*ones(1,npx(icell)) linspace(coord_y(1),coord_y(end),npy(icell))... coord_y(end)*ones(1,npx(icell)) linspace(coord_y(end),coord_y(1),npy(icell))];%y coordinates of the image edge(four sides) - [xcorner_new,ycorner_new]=phys_XYZ(Calib,x_edge,y_edge,ZIndex);%corresponding physical coordinates + [xcorner_new,ycorner_new]=phys_XYZ(Calib{icell},Slice{icell},x_edge,y_edge,ZIndex);%corresponding physical coordinates dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1); dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1); @@ -54,21 +58,20 @@ A_out=cell(1,numel(A)); -for icell=1:length(A) - Calib=XmlData{icell}.GeometryCalib; +for icell=1:numel(A) % rescaling of the image coordinates without change of the image array - if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib) + if strcmp(Calib{icell}.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib) A_out{icell}=A{icell};%no transform Rangx=[0.5 npx-0.5];%image coordiantes of corners Rangy=[npy-0.5 0.5]; - [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation - [~,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); + [Rangx]=phys_XYZ(Calib{icell},[],Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation + [~,Rangy]=phys_XYZ(Calib{icell},[],[0.5 0.5],Rangy,ZIndex); else % the image needs to be interpolated to the new coordinates Z=0; %default - if isfield(Calib,'SliceCoord')&& size(Calib.SliceCoord,1)>=ZIndex %.Z= index of plane - SliceCoord=Calib.SliceCoord(ZIndex,:); + if isfield(Slice{icell},'SliceCoord')&& size(Slice{icell}.SliceCoord,1)>=ZIndex %.Z= index of plane + SliceCoord=Slice{icell}.SliceCoord(ZIndex,:); Z=SliceCoord(3); - if isfield(Calib, 'SliceAngle') && size(Calib.SliceAngle,1)>=ZIndex && ~isequal(Calib.SliceAngle(ZIndex,:),[0 0 0]) - norm_plane=angle2normal(Calib.SliceAngle(ZIndex,:)); + if isfield(Slice{icell}, 'SliceAngle') && size(Slice{icell}.SliceAngle,1)>=ZIndex && ~isequal(Slice{icell}.SliceAngle(ZIndex,:),[0 0 0]) + norm_plane=angle2normal(Slice{icell}.SliceAngle(ZIndex,:)); Z=Z-(norm_plane(1)*(X-SliceCoord(1))+norm_plane(2)*(Y-SliceCoord(2)))/norm_plane(3); end @@ -77,5 +80,5 @@ yima=npy(icell)-0.5:-1:0.5; [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates - [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,Z);% image coordinates for each point in the real + [XIMA,YIMA]=px_XYZ(Calib{icell},Slice{icell},X,Y,Z);% image coordinates for each point in the real testuint8=isa(A{icell},'uint8'); testuint16=isa(A{icell},'uint16'); Index: trunk/src/px_XYZ.m =================================================================== --- trunk/src/px_XYZ.m (revision 1111) +++ trunk/src/px_XYZ.m (revision 1112) @@ -28,5 +28,5 @@ %======================================================================= -function [X,Y]=px_XYZ(Calib,Xphys,Yphys,Zphys) +function [X,Y]=px_XYZ(Calib,Slice,Xphys,Yphys,Zphys) if ~exist('Zphys','var') Zphys=0; @@ -40,12 +40,15 @@ %%%%%%%%%%%%% +if isempty(Slice) + Slice=Calib; +end % general case if isfield(Calib,'R') R=(Calib.R)'; %correct z for refraction if needed - if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') - H=Calib.InterfaceCoord(3); + if isfield(Slice,'InterfaceCoord') && isfield(Slice,'RefractionIndex') + H=Slice.InterfaceCoord(3); if H>Zphys - Zphys=H-(H-Zphys)/Calib.RefractionIndex; %corrected z (virtual object)Calib + Zphys=H-(H-Zphys)/Slice.RefractionIndex; %corrected z (virtual object)Calib % test_refraction=1; Index: trunk/src/series/extract_rdvision.m =================================================================== --- trunk/src/series/extract_rdvision.m (revision 1111) +++ trunk/src/series/extract_rdvision.m (revision 1112) @@ -1,3 +1,3 @@ -%'extract_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program +%'extunningact_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program %------------------------------------------------------------------------ % function ParamOut=extract_rdvision(Param) Index: trunk/src/set_grid.m =================================================================== --- trunk/src/set_grid.m (revision 1111) +++ trunk/src/set_grid.m (revision 1112) @@ -258,4 +258,5 @@ end tsaiA=[];%default + SliceA=[]; if exist(fileAxml,'file') [XmlDataA,errormsg]=imadoc2struct(fileAxml); @@ -266,4 +267,8 @@ if isfield(XmlDataA,'GeometryCalib') tsaiA=XmlDataA.GeometryCalib; + SliceA=tsaiA;%default + end + if isfield(XmlDataA,'Slice') + SliceA=XmlDataA.Slice; end end @@ -271,5 +276,5 @@ msgbox_uvmat('WARNING','no geometric calibration available for image A, phys =pixel') else - [grid_x_imaA,grid_y_imaA]=px_XYZ(tsaiA,grid_x,grid_y,GUI.Z); + [grid_x_imaA,grid_y_imaA]=px_XYZ(tsaiA,SliceA,grid_x,grid_y,GUI.Z); end end @@ -293,4 +298,5 @@ end tsaiB=[];%default + SliceB=[]; if exist(fileBxml,'file') [XmlDataB,errormsg]=imadoc2struct(fileBxml); @@ -301,4 +307,8 @@ if isfield(XmlDataB,'GeometryCalib') tsaiB=XmlDataB.GeometryCalib; + SliceB=tsaiB;%default + end + if isfield(XmlDataB,'Slice') + SliceB=XmlDataB.Slice; end end @@ -308,5 +318,5 @@ grid_y_imaB=grid_y; else - [grid_x_imaB,grid_y_imaB]=px_XYZ(tsaiB,grid_x,grid_y,GUI.Z); + [grid_x_imaB,grid_y_imaB]=px_XYZ(tsaiB,SliceB,grid_x,grid_y,GUI.Z); end B=imread(GUI.ImageB); Index: trunk/src/transform_field/phys.m =================================================================== --- trunk/src/transform_field/phys.m (revision 1111) +++ trunk/src/transform_field/phys.m (revision 1112) @@ -55,15 +55,23 @@ DataOut=DataIn;%default first output field if nargin>=2 % nargin =nbre of input variables + Calib{1}=[]; if isfield(XmlData,'GeometryCalib') Calib{1}=XmlData.GeometryCalib; - else - Calib{1}=[]; + end + Slice{1}=Calib{1}; + if isfield(XmlData,'Slice') + Slice{1}=XmlData.Slice; end if nargin>=3 %two input fields DataOut_1=DataIn_1;%default second output field - if nargin>=4 && isfield(XmlData_1,'GeometryCalib') - Calib{2}=XmlData_1.GeometryCalib; - else - Calib{2}=Calib{1}; + Calib{2}=Calib{1}; + if nargin>=4 + if isfield(XmlData_1,'GeometryCalib') + Calib{2}=XmlData_1.GeometryCalib; + end + Slice{2}=Calib{2}; + if isfield(XmlData_1,'Slice') + Slice{2}=XmlData_1.Slice; + end end end @@ -71,8 +79,7 @@ %% get the z index defining the section plane +ZIndex=1; if isfield(DataIn,'ZIndex')&&~isempty(DataIn.ZIndex)&&~isnan(DataIn.ZIndex) ZIndex=DataIn.ZIndex; -else - ZIndex=1; end @@ -82,5 +89,5 @@ if ~isempty(Calib{1}) if isfield(Calib{1},'CalibrationType')&& isfield(Calib{1},'CoordUnit') && isfield(DataIn,'CoordUnit')&& strcmp(DataIn.CoordUnit,'pixel') - DataOut=phys_1(DataIn,Calib{1},ZIndex);% transform coordinates and velocity components + DataOut=phys_1(DataIn,Calib{1},Slice{1},ZIndex);% transform coordinates and velocity components %case of images or scalar: in case of two input fields, we need to project the transform on the same regular grid if isfield(DataIn,'A') && isfield(DataIn,'Coord_x') && ~isempty(DataIn.Coord_x) && isfield(DataIn,'Coord_y')&&... @@ -94,11 +101,11 @@ %% document the selected plane position and angle if relevant -if checktransform && isfield(Calib{1},'SliceCoord')&&size(Calib{1}.SliceCoord,1)>=ZIndex - DataOut.PlaneCoord=Calib{1}.SliceCoord(ZIndex,:);% transfer the slice position corresponding to index ZIndex - if isfield(Calib{1},'SliceAngle') % transfer the slice rotation angles - if isequal(size(Calib{1}.SliceAngle,1),1)% case of a unique angle - DataOut.PlaneAngle=Calib{1}.SliceAngle; +if checktransform && isfield(Slice{1},'SliceCoord')&&size(Slice{1}.SliceCoord,1)>=ZIndex + DataOut.PlaneCoord=Slice{1}.SliceCoord(ZIndex,:);% transfer the slice position corresponding to index ZIndex + if isfield(Slice{1},'SliceAngle') % transfer the slice rotation angles + if isequal(size(Slice{1}.SliceAngle,1),1)% case of a unique angle + DataOut.PlaneAngle=Slice{1}.SliceAngle; else % case of multiple planes with different angles: select the plane with index ZIndex - DataOut.PlaneAngle=Calib{1}.SliceAngle(ZIndex,:); + DataOut.PlaneAngle=Slice{1}.SliceAngle(ZIndex,:); end end @@ -113,13 +120,13 @@ end if isfield(Calib{2},'CalibrationType')&&isfield(Calib{2},'CoordUnit') && isfield(DataIn_1,'CoordUnit')&& strcmp(DataIn_1.CoordUnit,'pixel') - DataOut_1=phys_1(DataOut_1,Calib{2},ZIndex); - if isfield(Calib{1},'SliceCoord') - if ~(isfield(Calib{2},'SliceCoord') && isequal(Calib{2}.SliceCoord,Calib{1}.SliceCoord)) + DataOut_1=phys_1(DataOut_1,Calib{2},Slice{2},ZIndex); + if isfield(Slice{2},'SliceCoord') + if ~(isfield(Slice{2},'SliceCoord') && isequal(Slice{2}.SliceCoord,Slice{1}.SliceCoord)) DataOut_1.Txt='different plane positions for the two input fields'; return end DataOut_1.PlaneCoord=DataOut.PlaneCoord;% same plane position for the two input fields - if isfield(Calib{1},'SliceAngle') - if ~(isfield(Calib{2},'SliceAngle') && isequal(Calib{2}.SliceAngle,Calib{1}.SliceAngle)) + if isfield(Slice{1},'SliceAngle') + if ~(isfield(Slice{2},'SliceAngle') && isequal(Slice{2}.SliceAngle,Slice{1}.SliceAngle)) DataOut_1.Txt='different plane angles for the two input fields'; return @@ -131,5 +138,5 @@ ~isempty(DataIn_1.Coord_y)&&length(DataIn_1.A)>1 iscalar=iscalar+1; - Calib{iscalar}=Calib{2}; +% Calib{iscalar}=Calib{2}; A{iscalar}=DataIn_1.A; end @@ -163,5 +170,5 @@ %------------------------------------------------ %--- transform a single field -function DataOut=phys_1(Data,Calib,ZIndex) +function DataOut=phys_1(Data,Calib,Slice,ZIndex) %------------------------------------------------ %% set default output @@ -171,5 +178,5 @@ %% transform X,Y coordinates for velocity fields (transform of an image or scalar done in phys_ima) if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y) - [DataOut.X,DataOut.Y]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex); + [DataOut.X,DataOut.Y]=phys_XYZ(Calib,Slice,Data.X,Data.Y,ZIndex); Dt=1; %default if isfield(Data,'dt')&&~isempty(Data.dt) @@ -180,6 +187,6 @@ end if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V) - [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); - [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); + [XOut_1,YOut_1]=phys_XYZ(Calib,Slice,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); + [XOut_2,YOut_2]=phys_XYZ(Calib,Slice,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); DataOut.U=(XOut_2-XOut_1)/Dt; DataOut.V=(YOut_2-YOut_1)/Dt; @@ -213,8 +220,8 @@ % estimate the Jacobian matrix DXpx/DXphys for ip=1:length(Data.X) - [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),ZIndex); - [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),ZIndex); - [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,ZIndex); - [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,ZIndex); + [Xp1,Yp1]=phys_XYZ(Calib,Slice,Data.X(ip)+0.5,Data.Y(ip),ZIndex); + [Xm1,Ym1]=phys_XYZ(Calib,Slice,Data.X(ip)-0.5,Data.Y(ip),ZIndex); + [Xp2,Yp2]=phys_XYZ(Calib,Slice,Data.X(ip),Data.Y(ip)+0.5,ZIndex); + [Xm2,Ym2]=phys_XYZ(Calib,Slice,Data.X(ip),Data.Y(ip)-0.5,ZIndex); %Jacobian matrix DXpphys/DXpx DjXi(1,1)=(Xp1-Xm1); Index: trunk/src/transform_field/phys_polar.m =================================================================== --- trunk/src/transform_field/phys_polar.m (revision 1111) +++ trunk/src/transform_field/phys_polar.m (revision 1112) @@ -78,5 +78,5 @@ Data=DataIn; %default output if isfield(Data,'CoordUnit') -Data=rmfield(Data,'CoordUnit'); + Data=rmfield(Data,'CoordUnit'); end Data.ListVarName = {}; @@ -85,7 +85,8 @@ DataCell{1}=DataIn; Calib{1}=[]; +Slice{1}=[]; DataCell{2}=[];%default checkpixel(1)=0; -if isfield(DataCell{1},'CoordUnit')&& strcmp(DataCell{1}.CoordUnit,'pixel') +if isfield(DataCell{1},'CoordUnit')&& strcmp(DataCell{1}.CoordUnit,'pixel') checkpixel(1)=1; end @@ -94,5 +95,10 @@ Calib{1}=XmlData.GeometryCalib; end + Slice{1}=Calib{1}; + if isfield(XmlData,'Slice') + Slice{1}=XmlData.Slice; + end Calib{2}=Calib{1}; + Slice{2}=Slice{1}; else Data.Txt='wrong input: need two or four structures'; @@ -101,10 +107,13 @@ if nargin==4% case of two input fields checkpixel(2)=0; -if isfield(DataCell{2},'CoordUnit')&& strcmp(DataCell{2}.CoordUnit,'pixel') - checkpixel(2)=1; -end + if isfield(DataCell{2},'CoordUnit')&& strcmp(DataCell{2}.CoordUnit,'pixel') + checkpixel(2)=1; + end DataCell{2}=DataIn_1;%default if isfield(XmlData_1,'GeometryCalib')&& ~isempty(XmlData_1.GeometryCalib) && checkpixel(2) Calib{2}=XmlData_1.GeometryCalib; + end + if isfield(XmlData_1,'Slice') + Slice{2}=XmlData_1.Slice; end nbinput=2; @@ -218,5 +227,5 @@ if ~isempty(Calib{ifield}) [X,Y,Z,DataCell{ifield}.(UName),DataCell{ifield}.(VName)]=... - phys_XYUV(DataCell{ifield},Calib{ifield},ZIndex); + phys_XYUV(DataCell{ifield},Calib{ifield},Slice{ifield},ZIndex); end end @@ -304,4 +313,5 @@ ZInd(nbgrid)=ZIndex; Calib_new{nbgrid}=Calib{ifield}; + Slice_new{nbgrid}=Slice{ifield}; end if isfield(CellInfo{icell},'VarIndex_vector_x')&& isfield(CellInfo{icell},'VarIndex_vector_y') @@ -325,4 +335,6 @@ Calib_new{nbgrid+1}=Calib{ifield}; Calib_new{nbgrid+2}=Calib{ifield}; + Slice_new{nbgrid+1}=Calib{ifield}; + Slice_new{nbgrid+2}=Calib{ifield}; nbgrid=nbgrid+2; nbvar=nbvar+2; @@ -335,5 +347,5 @@ %% tranform cartesian to polar coordinates for gridded data if nbgrid~=0 - [A,Data.radius,Data.theta]=phys_Ima_polar(A,coord_x,coord_y,Calib_new,ZInd,origin_xy,radius_offset,angle_offset,angle_scale); + [A,Data.radius,Data.theta]=phys_Ima_polar(A,coord_x,coord_y,Calib_new,Slice_new,ZInd,origin_xy,radius_offset,angle_offset,angle_scale); for icell=1:numel(A) if icell<=numel(A)-1 && check_vector(icell)==1 && check_vector(icell+1)==1 %transform u,v into polar coordinates @@ -373,5 +385,5 @@ %------------------------------------------------ %--- transform a single field into phys coordiantes -function [X,Y,Z,U,V]=phys_XYUV(Data,Calib,ZIndex) +function [X,Y,Z,U,V]=phys_XYUV(Data,Calib,Slice,ZIndex) %------------------------------------------------ %% set default output @@ -385,5 +397,5 @@ %% transform X,Y coordinates for velocity fields (transform of an image or scalar done in phys_ima) if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y) - [X,Y,Z]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex); + [X,Y,Z]=phys_XYZ(Calib,Slice,Data.X,Data.Y,ZIndex); Dt=1; %default if isfield(Data,'dt')&&~isempty(Data.dt) @@ -394,6 +406,6 @@ end if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V) - [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); - [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); + [XOut_1,YOut_1]=phys_XYZ(Calib,Slice,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); + [XOut_2,YOut_2]=phys_XYZ(Calib,Slice,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); U=(XOut_2-XOut_1)/Dt; V=(YOut_2-YOut_1)/Dt; @@ -404,5 +416,5 @@ % tranform gridded field into polar coordiantes on a regular polar grid, % transform to phys coordiantes if requested by calibration input -function [A_out,radius,theta]=phys_Ima_polar(A,coord_x,coord_y,CalibIn,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale) +function [A_out,radius,theta]=phys_Ima_polar(A,coord_x,coord_y,CalibIn,SliceIn,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale) rcorner=[]; thetacorner=[]; @@ -420,5 +432,5 @@ % transform edges into phys coordinates if requested if ~isempty(CalibIn{icell}) - [x_edge,y_edge]=phys_XYZ(CalibIn{icell},x_edge,y_edge,ZIndex(icell));% physical coordinates of the image edge + [x_edge,y_edge]=phys_XYZ(CalibIn{icell},SliceIn{icell},x_edge,y_edge,ZIndex(icell));% physical coordinates of the image edge end Index: trunk/src/uvmat.m =================================================================== --- trunk/src/uvmat.m (revision 1111) +++ trunk/src/uvmat.m (revision 1112) @@ -1208,30 +1208,34 @@ 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; -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); +Slice=[]; +if isfield(UvData,'XmlData') + if isfield(UvData.XmlData{1},'GeometryCalib')&& isfield(UvData.XmlData{1}.GeometryCalib,'SliceCoord') + Slice=UvData.XmlData{1}.GeometryCalib;%old convention < 2022 + elseif isfield(UvData.XmlData{1},'Slice') + Slice=UvData.XmlData{1}.Slice;% new convention ( 2022) + end +end +% default input +if ~(isfield(Slice,'SliceCoord') && size(Slice.SliceCoord,2)==3) + Slice.SliceCoord=[0 0 0]; +end +InterfaceCoord=min(Slice.SliceCoord(:,3)); +if isfield(Slice,'InterfaceCoord') + InterfaceCoord=Slice.InterfaceCoord(1,3); +end +NbSlice=size(Slice.SliceCoord,1); CheckVolumeScan=0; -if isfield(GeometryCalib,'CheckVolumeScan') - CheckVolumeScan=GeometryCalib.CheckVolumeScan; +if isfield(Slice,'CheckVolumeScan') + CheckVolumeScan=Slice.CheckVolumeScan; end RefractionIndex=1.33; CheckRefraction=0;% default value of the check box refraction -if isfield(GeometryCalib,'RefractionIndex') - RefractionIndex=GeometryCalib.RefractionIndex; +if isfield(Slice,'RefractionIndex') + RefractionIndex=Slice.RefractionIndex; CheckRefraction=1; end SliceAngle=[0 0 0]; -if isfield(GeometryCalib,'SliceAngle') - SliceAngle=GeometryCalib.SliceAngle; +if isfield(Slice,'SliceAngle') + SliceAngle=Slice.SliceAngle; end @@ -1244,6 +1248,6 @@ Bottom=ScreenSize(4)-Height-40; %put fig at top right hfig=findobj(allchild(0),'Tag','set_slice'); -if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI -hfig=figure('name','set_slices','tag','set_slice','MenuBar','none','NumberTitle','off','Units','pixels','Position',[Left,Bottom,Width,Height],'UserData',GeometryCalib); +if ~isempty(hfig),delete(hfig), end %delete existing version of the GUI +hfig=figure('name','set_slices','tag','set_slice','MenuBar','none','NumberTitle','off','Units','pixels','Position',[Left,Bottom,Width,Height],'UserData',Slice); BackgroundColor=get(hfig,'Color'); hh=0.14; % box height (relative) @@ -1262,7 +1266,7 @@ 'String','Z','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title uicontrol('Style','edit','Units','normalized', 'Position', [2*ii+ww 0.95-2*ii-hh ww hh],'tag','num_Z_1','BackgroundColor',[1 1 1],... - 'String',num2str(SliceCoord(1,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_1'': z position of first slice');%edit box + 'String',num2str(Slice.SliceCoord(1,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_1'': z position of first slice');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-2*ii-hh ww hh],'tag','num_Z_2','BackgroundColor',[1 1 1],... - 'String',num2str(SliceCoord(end,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_2'': z position of last slice');%edit box + 'String',num2str(Slice.SliceCoord(end,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_2'': z position of last slice');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-2*ii-hh ww hh],'tag','num_H','BackgroundColor',[1 1 1],... 'String',num2str(InterfaceCoord),'Visible','off','FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_H'': z position of the water surface (=Z_1 in air)');%edit box @@ -1291,7 +1295,7 @@ uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceCoord_1','BackgroundColor',[1 1 1],... - 'String',num2str(SliceCoord(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceCoord_1'':x position of the tild origin');%edit box + 'String',num2str(Slice.SliceCoord(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceCoord_1'':x position of the tild origin');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceCoord_2','BackgroundColor',[1 1 1],... - 'String',num2str(SliceCoord(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceCoord_2'':y position of the tild origin');%edit box + 'String',num2str(Slice.SliceCoord(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceCoord_2'':y position of the tild origin');%edit box uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-5*ii-4*hh 1.3*ww hh/2],'BackgroundColor',BackgroundColor,'Tag','Angle_title_1',... @@ -1349,10 +1353,10 @@ [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(FileName); XmlFile=find_imadoc(RootPath,SubDir,RootFile,FileExt);%find name of the relevant xml file -[s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib');%read the xml file -if~isempty(errormsg) - msgbox_uvmat('ERROR',errormsg) - return -end -GeometryCalib=s.GeometryCalib;% get thegeometric calibration data +% [s,errormsg]=imadoc2struct(XmlFile,'Slice');%read the xml file +% if~isempty(errormsg) +% msgbox_uvmat('ERROR',errormsg) +% return +% end +% Slice=s.Slice;% get thegeometric calibration data %% read the content of the GUI set_slice @@ -1361,6 +1365,6 @@ Z_plane=str2num(get(hZ,'String'));% set of Z positions explicitly entered as a Matlab vector SliceData=read_GUI(hset_slice); -GeometryCalib.NbSlice=SliceData.NbSlice; -GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; +Slice.NbSlice=SliceData.NbSlice; +Slice.CheckVolumeScan=SliceData.CheckVolumeScan; if numel(Z_plane)<=2 Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); @@ -1368,19 +1372,19 @@ set(hZ,'String',num2str(Z_plane))% restitute the display qfter reqding by read_GUI end -GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; -GeometryCalib.SliceCoord(:,1)=SliceData.SliceCoord(1); -GeometryCalib.SliceCoord(:,2)=SliceData.SliceCoord(2); -GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); +Slice.SliceCoord=Z_plane'*[0 0 1]; +Slice.SliceCoord(:,1)=SliceData.SliceCoord(1); +Slice.SliceCoord(:,2)=SliceData.SliceCoord(2); +Slice.SliceAngle=zeros(Slice.NbSlice,3); Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); -GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation angle around x axis -GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation angle around y axis -GeometryCalib.SliceAngle(:,3)=0; +Slice.SliceAngle(:,1)=Angle_1';%rotation angle around x axis +Slice.SliceAngle(:,2)=Angle_2';%rotation angle around y axis +Slice.SliceAngle(:,3)=0; if SliceData.CheckRefraction - GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; - GeometryCalib.RefractionIndex=SliceData.RefractionIndex; -elseif isfield(GeometryCalib,'RefractionIndex') - GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); - GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); + Slice.InterfaceCoord=[0 0 SliceData.H]; + Slice.RefractionIndex=SliceData.RefractionIndex; +elseif isfield(Slice,'RefractionIndex') + Slice=rmfield(Slice,'RefractionIndex'); + Slice=rmfield(Slice,'InterfaceCoord'); end @@ -1430,5 +1434,5 @@ check_update=0; end - errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file + errormsg=update_imadoc(Slice,XmlName,'Slice');% introduce the calibration data in the xml file if ~strcmp(errormsg,'') msgbox_uvmat('ERROR',errormsg); @@ -1446,5 +1450,5 @@ %% store the result in the xml file used for calibration - errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file + errormsg=update_imadoc(Slice,XmlFile,'Slice');% introduce the calibration data in the xml file if strcmp(errormsg,'') msgbox_uvmat('CONFIRMATION',['slice positions saved in ' XmlFile]); @@ -1925,5 +1929,5 @@ pos(:,3)=pos(:,3)+Calib.SliceCoord(3); end - [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3)); + [X,Y]=px_XYZ(Calib,Slice,pos(:,1),pos(:,2),pos(:,3)); end flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside @@ -2479,20 +2483,24 @@ drawnow if isfield(XmlDataRead, 'GeometryCalib') && ~isempty(XmlDataRead.GeometryCalib) - XmlData.GeometryCalib=XmlDataRead.GeometryCalib; - if isfield(XmlData.GeometryCalib,'CheckVolumeScan') && isequal(XmlData.GeometryCalib.CheckVolumeScan,1) + XmlData.GeometryCalib=XmlDataRead.GeometryCalib; + end + XmlData.Slice=XmlData.GeometryCalib;%default + if isfield(XmlDataRead, 'Slice') && ~isempty(XmlDataRead.Slice) + XmlData.Slice=XmlDataRead.Slice; + % check whether the GUI geometry_calib is opened +% hgeometry_calib=findobj('tag','geometry_calib'); +% if ~isempty(hgeometry_calib) % check whether the display of the GUI geometry_calib is consistent with the current calib param +% GUserData=get(hgeometry_calib,'UserData'); +% if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName)) +% answer=msgbox_uvmat('INPUT_Y-N','refresh the display of the GUI geometry_calib with the new input data?'); +% if strcmp(answer,'Yes') +% geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib +% end +% end +% end + end + if isfield(XmlData.Slice,'CheckVolumeScan') && isequal(XmlData.Slice.CheckVolumeScan,1) set (handles.slices,'String','volume') end - % check whether the GUI geometry_calib is opened - hgeometry_calib=findobj('tag','geometry_calib'); - if ~isempty(hgeometry_calib) % check whether the display of the GUI geometry_calib is consistent with the current calib param - GUserData=get(hgeometry_calib,'UserData'); - if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName)) - answer=msgbox_uvmat('INPUT_Y-N','refresh the display of the GUI geometry_calib with the new input data?'); - if strcmp(answer,'Yes') - geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib - end - end - end - end if isfield(XmlDataRead, 'LIFCalib') XmlData.LIFCalib=XmlDataRead.LIFCalib; @@ -2571,6 +2579,6 @@ set(handles.TransformName,'Value',3); % phys transform by default if fixedLimits is off end - if isfield(GeometryCalib,'SliceCoord') - siz=size(GeometryCalib.SliceCoord); + if isfield(XmlData.Slice,'SliceCoord') + siz=size(XmlData.Slice.SliceCoord); if siz(1)>1 NbSlice=siz(1); @@ -2578,5 +2586,5 @@ set(handles.slices,'Value',1) end - if isfield(GeometryCalib,'CheckVolumeScan') && isequal(GeometryCalib.CheckVolumeScan,1) + if isfield(XmlData.Slice,'CheckVolumeScan') && isequal(XmlData.Slice.CheckVolumeScan,1) set(handles.num_NbSlice,'Visible','off') else @@ -5183,5 +5191,5 @@ Y=ObjectData.Coord(:,2); if testphys - [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases + [X,Y]=px_XYZ(Calib,[],X,Y,0);% to generalise with 3D cases end flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside