Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 237) +++ /trunk/src/civ.m (revision 238) @@ -66,5 +66,5 @@ filebase=''; % root file name ('filebase'.civ) ext=[]; -testall=0; +set(handles.CivAll,'String',{'CivX';'CivAll';'CivUvmat'}) %default input parameters: num_i1=1; % set of field i numbers @@ -106,5 +106,4 @@ end set(handles.RootName,'String',filebase); -set(handles.ImaDoc,'UserData',testall); set(handles.ImaDoc,'String',ext) @@ -113,8 +112,5 @@ path_UVMAT=fileparts(path_uvmat); %path to UVMAT errormsg=[];%default error message -% xmlfile=fullfile(path_UVMAT,'PARAM.xml'); -% if ~exist(xmlfile,'file') xmlfile='PARAM.xml'; -% end if exist(xmlfile,'file') try @@ -269,12 +265,7 @@ oldfile=filebase; end -% testall=get(handles.ImaDoc,'UserData'); ind_opening=1;%default browse.incr_pair=[0 0]; %default -% if testall -% menu={'*.*', 'All Files (*.*)'; '*.xml; *.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... -% '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc','.nc files'}; -% else % menu selecting only .civ or .avi files - menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; +menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; '*.xml', '.xml files '; ... '*.civ', '.civ files '; ... @@ -285,8 +276,4 @@ '*.nc','.netcdf files'; ... '*.*', 'All Files (*.*)'}; - % menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... - % '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';... - % '*.*', 'All Files (*.*)'}; -% end [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); fileinput=[PathName FileName];%complete file name @@ -442,6 +429,4 @@ end set(handles.browse_root,'UserData',browse);% store information from browser -% testall=isequal(menu(filtindex,1),{'*.*'}); -% set(handles.ImaDoc,'UserData',testall); RootName_Callback(hObject, eventdata, handles); @@ -1583,6 +1568,13 @@ end end -civAll=isequal(get(handles.CivAll,'Value'),2); % Boolean for new civ programs -if civAll && isfield(sparam,'CivBin') + +%% choose the civ program +ProgList=get(handles.CivAll,'String'); +index=get(handles.CivAll,'Value'); +CivX=isequal(ProgList{index},'CivX'); +CivAll=isequal(ProgList{index},'CivAll'); +CivUvmat=isequal(ProgList{index},'CivUvmat'); +%CivAll=isequal(get(handles.CivAll,'Value'),2); % Boolean for new civ programs +if CivAll && isfield(sparam,'CivBin') CivBin=sparam.CivBin; if ~exist(CivBin,'file') || ~isempty(which(CivBin))% if path defined as relative to uvmat @@ -1739,8 +1731,8 @@ cmd=[cmd 'umask 002 \n'];%allow writting access to created files for user group end - if civAll - civAllxml=xmltree;% xml contents, all parameters - civAllCmd=''; - civAllxml=set(civAllxml,1,'name','CivDoc'); + if CivAll + CivAllxml=xmltree;% xml contents, all parameters + CivAllCmd=''; + CivAllxml=set(CivAllxml,1,'name','CivDoc'); end [Rootbat,Filebat]=fileparts(filecell.nc.civ1{ifile,j});%output netcdf file (without extention) @@ -1808,5 +1800,5 @@ % i_cmd=i_cmd+1; - if isequal(civAll,0) + if isequal(CivAll,0) civ1_exe=CIV1_CMD(fullfile(Rootbat,Filebat),'',par_civ1,handles,sparam);%create the parameter file .civ1.cmx and set the execution string civ1_exe % if(isunix) @@ -1818,13 +1810,13 @@ cmd=[cmd civ1_exe '\n']; else - civAllCmd=[civAllCmd ' civ1 ']; + CivAllCmd=[CivAllCmd ' civ1 ']; str=CIV1_CMD_Unified(fullfile(Rootbat,Filebat),'',par_civ1); fieldnames=fields(str); - [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1'); + [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1'); for ilist=1:length(fieldnames) val=eval(['str.' fieldnames{ilist}]); if ischar(val) - [civAllxml,uid_t]=add(civAllxml,uid_civ1,'element',fieldnames{ilist}); - [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist}); + [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end @@ -1844,5 +1836,5 @@ maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); end - if isequal(civAll,0) + if CivX if isunix %unix system cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(flagindex1(1)) ... @@ -1856,5 +1848,5 @@ end cmd=[cmd cmd_FIX '\n']; - else + elseif CivAll fix1.inputFileName=filecell.nc.civ1{ifile,j} ; fix1.fi1=num2str(flagindex1(1)); @@ -1864,13 +1856,13 @@ fix1.threshV=num2str(thresh_vel1); fieldnames=fields(fix1); - [civAllxml,uid_fix1]=add(civAllxml,1,'element','fix1'); + [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1'); for ilist=1:length(fieldnames) val=eval(['fix1.' fieldnames{ilist}]); if ischar(val) - [civAllxml,uid_t]=add(civAllxml,uid_fix1,'element',fieldnames{ilist}); - [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist}); + [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end - civAllCmd=[civAllCmd ' fix1 ']; + CivAllCmd=[CivAllCmd ' fix1 ']; end end @@ -1878,5 +1870,5 @@ %PATCH1 if box_test(3)==1 - if isequal(civAll,0) + if isequal(CivAll,0) cmd_PATCH=PATCH_CMD(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp,sparam.PatchBin); cmd=[cmd cmd_PATCH '\n']; @@ -1912,13 +1904,13 @@ patch1.convectFlow='n'; fieldnames=fields(patch1); - [civAllxml,uid_patch1]=add(civAllxml,1,'element','patch1'); + [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1'); for ilist=1:length(fieldnames) val=eval(['patch1.' fieldnames{ilist}]); if ischar(val) - [civAllxml,uid_t]=add(civAllxml,uid_patch1,'element',fieldnames{ilist}); - [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist}); + [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end - civAllCmd=[civAllCmd ' patch1 ']; + CivAllCmd=[CivAllCmd ' patch1 ']; end end @@ -1987,5 +1979,5 @@ flname=fullfile(Rootbat,Filebat); - if isequal(civAll,0) + if isequal(CivAll,0) cmd_CIV2=CIV2_CMD(flname,[],par_civ2,sparam);%creates the cmx file [fullfile(Rootbat,Filebat) '.civ2.cmx] % if(isunix) @@ -1996,13 +1988,13 @@ % end else - civAllCmd=[civAllCmd ' civ2 ']; + CivAllCmd=[CivAllCmd ' civ2 ']; str=CIV2_CMD_Unified(flname,'',par_civ2); fieldnames=fields(str); - [civAllxml,uid_civ2]=add(civAllxml,1,'element','civ2'); + [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2'); for ilist=1:length(fieldnames) val=eval(['str.' fieldnames{ilist}]); if ischar(val) - [civAllxml,uid_t]=add(civAllxml,uid_civ2,'element',fieldnames{ilist}); - [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist}); + [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end @@ -2022,5 +2014,5 @@ maskname =name_generator(maskbase,num1_mask,1,'.png','_i'); end - if isequal(civAll,0) + if isequal(CivAll,0) if isunix cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ... @@ -2042,13 +2034,13 @@ fix2.threshV=num2str(thresh_vel2); fieldnames=fields(fix2); - [civAllxml,uid_fix2]=add(civAllxml,1,'element','fix2'); + [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2'); for ilist=1:length(fieldnames) val=eval(['fix2.' fieldnames{ilist}]); if ischar(val) - [civAllxml,uid_t]=add(civAllxml,uid_fix2,'element',fieldnames{ilist}); - [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist}); + [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end - civAllCmd=[civAllCmd ' fix2 ']; + CivAllCmd=[CivAllCmd ' fix2 ']; end end @@ -2056,5 +2048,5 @@ %PATCH2 if box_test(6)==1 - if isequal(civAll,0) + if isequal(CivAll,0) cmd_PATCH=PATCH_CMD(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,test_interp,sparam.PatchBin); cmd=[cmd cmd_PATCH '\n']; @@ -2090,18 +2082,18 @@ patch2.convectFlow='n'; fieldnames=fields(patch2); - [civAllxml,uid_patch2]=add(civAllxml,1,'element','patch2'); + [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2'); for ilist=1:length(fieldnames) val=eval(['patch2.' fieldnames{ilist}]); if ischar(val) - [civAllxml,uid_t]=add(civAllxml,uid_patch2,'element',fieldnames{ilist}); - [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist}); + [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); end end - civAllCmd=[civAllCmd ' patch2 ']; - end - end - if isequal(civAll,1) - save(civAllxml,[flname '.xml']); - cmd=[cmd sparam.CivBin ' -f ' flname '.xml ' civAllCmd ' >' flname '.log' '\n']; + CivAllCmd=[CivAllCmd ' patch2 ']; + end + end + if CivAll + save(CivAllxml,[flname '.xml']); + cmd=[cmd sparam.CivBin ' -f ' flname '.xml ' CivAllCmd ' >' flname '.log' '\n']; end % create the .bat file: @@ -2120,5 +2112,5 @@ eval( ['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]); end - elseif ~isequal(get(handles.CivAll,'Value'),3) + elseif ~CivUvmat %% to lauch the jobs locally : if(isunix) @@ -2130,44 +2122,29 @@ disp(cmd_str); else %run PIVlab if selected - Data=civ_uvmat(par_civ1); -% image1=imread(par_civ1.filename_ima_a); -% image2=imread(par_civ1.filename_ima_b); -% stepx=str2num(par_civ1.dx); -% stepy=str2num(par_civ1.dy); -% ibx2=ceil(str2num(par_civ1.ibx)/2); -% iby2=ceil(str2num(par_civ1.iby)/2); -% isx2=ceil(str2num(par_civ1.isx)/2); -% isy2=ceil(str2num(par_civ1.isy)/2); -% shiftx=str2num(par_civ1.shiftx); -% shifty=str2num(par_civ1.shifty); -% % ibx=2*ibx2-1;%ibx and iby odd, reduced by 1 if even -% % iby=2*iby2-1; -% miniy=max(1+isy2-shifty,1+iby2); -% minix=max(1+isx2-shiftx,1+ibx2); -% maxiy=min(size(image1,1)-isy2-shifty,size(image1,1)-iby2); -% maxix=min(size(image1,2)-isx2-shiftx,size(image1,2)-ibx2); -% [GridX,GridY]=meshgrid(minix:stepx:maxix,miniy:stepy:maxiy); -% PointCoord(:,1)=reshape(GridX,[],1); -% PointCoord(:,2)=reshape(GridY,[],1); -% % caluclate velocity data (y and v in indices, reverse to y component) -% [xtable ytable utable vtable ctable typevector] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,shifty,PointCoord, 1, []); -% Data.ListGlobalAttribute={'title','Time','Dt'}; -% Data.title='PIVlab'; -% Data.Time=str2double(par_civ1.T0); -% Data.Dt=str2double(par_civ1.Dt); -% Data.ListVarName={'X','Y','U','V','C','FF'};% cell array containing the names of the fields to record -% Data.VarDimName={'nbvec','nbvec','nbvec','nbvec','nbvec','nbvec'}; -% Data.VarAttribute{1}.Role='coord_x'; -% Data.VarAttribute{2}.Role='coord_y'; -% Data.VarAttribute{3}.Role='vector_x'; -% Data.VarAttribute{4}.Role='vector_y'; -% Data.VarAttribute{5}.Role='errorflag'; -% Data.X=reshape(xtable,[],1); -% Data.Y=reshape(size(image1,1)-ytable+1,[],1); -% Data.U=reshape(utable,[],1); -% Data.V=reshape(-vtable,[],1); -% Data.C=reshape(ctable,[],1); -% Data.FF=reshape(~typevector,[],1); - errormsg=struct2nc(filecell.nc.civ1{ifile,j},Data); + if box_test(1)==1 + Param.Civ1=par_civ1; + end + if box_test(2)==1 + fix1.WarnFlags=[]; + if get(handles.vec_Fmin2,'Value') + fix1.WarnFlags=[fix1.WarnFlags -2]; + end + if get(handles.vec_F3,'Value') + fix1.WarnFlags=[fix1.WarnFlags 3]; + end + fix1.LowerBoundCorr=thresh_vecC1; + if get(handles.inf_sup1,'Value') + fix1.UppperBoundVel=thresh_vel1; + else + fix1.LowerBoundVel=thresh_vel1; + end + Param.Fix1=fix1; + end + if box_test(3)==1 + Param.Patch1.Rho=rho_patch1; + Param.Patch1.Threshold=thresh_patch1; + Param.Patch1.SubDomain=subdomain_patch1; + end + [Data,erromsg]=civ_uvmat(Param,filecell.nc.civ1{ifile,j}); if isempty(errormsg) display([filecell.nc.civ1{ifile,j} ' written']) @@ -2179,5 +2156,5 @@ end -if ~batch && ~isequal(get(handles.CivAll,'Value'),3) +if ~batch && ~CivUvmat [Rootbat,Filebat,extbat]=fileparts(filename_bat); filename_superbat=fullfile(Rootbat,'job_list.bat'); @@ -4006,4 +3983,8 @@ end par.rho=get(handles.rho,'String'); +if isequal(get(handles.rho,'Style'),'popupmenu') + index=get(handles.rho,'Value'); + par.rho=par.rho{index}; +end par.dx=get(handles.dx_civ1,'String'); par.dy=get(handles.dy_civ1,'String'); @@ -4301,50 +4282,50 @@ end -%------------------------------------------------------------------------ -% --- civ using pivlab -function Data=civ_uvmat(par_civ1) -%------------------------------------------------------------------------ -image1=imread(par_civ1.filename_ima_a); -image2=imread(par_civ1.filename_ima_b); -stepx=str2num(par_civ1.dx); -stepy=str2num(par_civ1.dy); -ibx2=ceil(str2num(par_civ1.ibx)/2); -iby2=ceil(str2num(par_civ1.iby)/2); -isx2=ceil(str2num(par_civ1.isx)/2); -isy2=ceil(str2num(par_civ1.isy)/2); -shiftx=str2num(par_civ1.shiftx); -shifty=str2num(par_civ1.shifty); -miniy=max(1+isy2-shifty,1+iby2); -minix=max(1+isx2-shiftx,1+ibx2); -maxiy=min(size(image1,1)-isy2-shifty,size(image1,1)-iby2); -maxix=min(size(image1,2)-isx2-shiftx,size(image1,2)-ibx2); -[GridX,GridY]=meshgrid(minix:stepx:maxix,miniy:stepy:maxiy); -PointCoord(:,1)=reshape(GridX,[],1); -PointCoord(:,2)=reshape(GridY,[],1); -% caluclate velocity data (y and v in indices, reverse to y component) -[xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,shifty,PointCoord, 1, []); -Data.ListGlobalAttribute=[{'Conventions','Program','CivStage'} {'Time','Dt'}]; -Data.Conventions='uvmat/civdata'; -Data.Program='civ_uvmat'; -Data.CivStage=1; -% list_param=fieldnames(Param.Civ1); -% for ilist=1:length(list_param) -% eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';']) -% end -Data.Time=str2double(par_civ1.T0); -Data.Dt=str2double(par_civ1.Dt); -Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};% cell array containing the names of the fields to record -Data.VarDimName={'nbvec','nbvec','nbvec','nbvec','nbvec','nbvec'}; -Data.VarAttribute{1}.Role='coord_x'; -Data.VarAttribute{2}.Role='coord_y'; -Data.VarAttribute{3}.Role='vector_x'; -Data.VarAttribute{4}.Role='vector_y'; -Data.VarAttribute{5}.Role='warnflag'; -Data.Civ1_X=reshape(xtable,[],1); -Data.Civ1_Y=reshape(size(image1,1)-ytable+1,[],1); -Data.Civ1_U=reshape(utable,[],1); -Data.Civ1_V=reshape(-vtable,[],1); -Data.Civ1_C=reshape(ctable,[],1); -Data.Civ1_F=reshape(F,[],1); +% %------------------------------------------------------------------------ +% % --- civ using pivlab +% function Data=civ_uvmat(par_civ1) +% %------------------------------------------------------------------------ +% image1=imread(par_civ1.filename_ima_a); +% image2=imread(par_civ1.filename_ima_b); +% stepx=str2num(par_civ1.dx); +% stepy=str2num(par_civ1.dy); +% ibx2=ceil(str2num(par_civ1.ibx)/2); +% iby2=ceil(str2num(par_civ1.iby)/2); +% isx2=ceil(str2num(par_civ1.isx)/2); +% isy2=ceil(str2num(par_civ1.isy)/2); +% shiftx=str2num(par_civ1.shiftx); +% shifty=str2num(par_civ1.shifty); +% miniy=max(1+isy2-shifty,1+iby2); +% minix=max(1+isx2-shiftx,1+ibx2); +% maxiy=min(size(image1,1)-isy2-shifty,size(image1,1)-iby2); +% maxix=min(size(image1,2)-isx2-shiftx,size(image1,2)-ibx2); +% [GridX,GridY]=meshgrid(minix:stepx:maxix,miniy:stepy:maxiy); +% PointCoord(:,1)=reshape(GridX,[],1); +% PointCoord(:,2)=reshape(GridY,[],1); +% % caluclate velocity data (y and v in indices, reverse to y component) +% [xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,shifty,PointCoord, 1, []); +% Data.ListGlobalAttribute=[{'Conventions','Program','CivStage'} {'Time','Dt'}]; +% Data.Conventions='uvmat/civdata'; +% Data.Program='civ_uvmat'; +% Data.CivStage=1; +% % list_param=fieldnames(Param.Civ1); +% % for ilist=1:length(list_param) +% % eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';']) +% % end +% Data.Time=str2double(par_civ1.T0); +% Data.Dt=str2double(par_civ1.Dt); +% Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};% cell array containing the names of the fields to record +% Data.VarDimName={'nbvec','nbvec','nbvec','nbvec','nbvec','nbvec'}; +% Data.VarAttribute{1}.Role='coord_x'; +% Data.VarAttribute{2}.Role='coord_y'; +% Data.VarAttribute{3}.Role='vector_x'; +% Data.VarAttribute{4}.Role='vector_y'; +% Data.VarAttribute{5}.Role='warnflag'; +% Data.Civ1_X=reshape(xtable,[],1); +% Data.Civ1_Y=reshape(size(image1,1)-ytable+1,[],1); +% Data.Civ1_U=reshape(utable,[],1); +% Data.Civ1_V=reshape(-vtable,[],1); +% Data.Civ1_C=reshape(ctable,[],1); +% Data.Civ1_F=reshape(F,[],1); %------------------------------------------------------------------------ @@ -4918,12 +4899,28 @@ % --- Executes on button press in CivAll. function CivAll_Callback(hObject, eventdata, handles) -if get(handles.CivAll,'Value')==2 - if get(handles.PATCH1,'Value') - set(handles.thresh_patch1,'Visible','on') - set(handles.thresh_text1,'Visible','on') - end -else - set(handles.thresh_patch1,'Visible','off') - set(handles.thresh_text1,'Visible','off') -end - +Listprog=get(handles.CivAll,'String'); +index=get(handles.CivAll,'Value'); +prog=Listprog{index}; +switch prog + case 'CivX' + set(handles.thresh_patch1,'Visible','off') + set(handles.thresh_text1,'Visible','off') + set(handles.rho,'Style','edit') + set(handles.rho,'String','1') + case 'CivAll' + if get(handles.PATCH1,'Value') + set(handles.thresh_patch1,'Visible','on') + set(handles.thresh_text1,'Visible','on') + end + set(handles.rho,'Style','edit') + set(handles.rho,'String','1') + case 'CivUvmat' + if get(handles.PATCH1,'Value') + set(handles.thresh_patch1,'Visible','on') + set(handles.thresh_text1,'Visible','on') + end + set(handles.rho,'Style','popupmenu') + set(handles.rho,'Value',1) + set(handles.rho,'String',{'1';'2'}) +end + Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 237) +++ /trunk/src/geometry_calib.m (revision 238) @@ -458,14 +458,20 @@ norm=abs(det(R)); GeometryCalib.CalibrationType='linear'; +if (a_X1(2)/a_Y1(3))>0 + epsilon=1; GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm); +else + GeometryCalib.fx_fy(1)=-sqrt((-a_X1(2)/a_Y1(3))*norm); + epsilon=-1; +end GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1); GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function %GeometryCalib.Tx_Ty_Tz=[a_X1(1) a_Y1(1) 1]; GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1]; -R(1,:)=R(1,:)/GeometryCalib.fx_fy(1); +R(1,:)=epsilon*R(1,:)/GeometryCalib.fx_fy(1); R(2,:)=R(2,:)/GeometryCalib.fx_fy(2); R=[R;[0 0]]; -GeometryCalib.R=[R [0;0;1]]; -GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0]; +GeometryCalib.R=[R [0;0;-1]]; +GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0] %------------------------------------------------------------------------ % determine the tsai parameters for a view normal to the grid plane Index: /trunk/src/mouse_down.m =================================================================== --- /trunk/src/mouse_down.m (revision 237) +++ /trunk/src/mouse_down.m (revision 238) @@ -109,4 +109,8 @@ haxes=[];%mouse out of axes end + break + elseif isequal(htype,'uicontrol') && isequal(get(hchild(ichild),'Visible'),'on') + msgbox(get(hchild(ichild),'String'),get(hchild(ichild),'Tag')) + break end end Index: /trunk/src/pivlab.m =================================================================== --- /trunk/src/pivlab.m (revision 237) +++ /trunk/src/pivlab.m (revision 238) @@ -90,17 +90,17 @@ result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 %Find the correlation max, at 255 - [y,x] = find(result_conv==255); - if ~isnan(y) & ~isnan(x) + [y,x] = find(result_conv==255,1); + if ~isnan(y) && ~isnan(x) try if subpixfinder==1 - [vector] = SUBPIXGAUSS (result_conv,x,y); + [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); elseif subpixfinder==2 - [vector] = SUBPIX2DGAUSS (result_conv,x,y); + [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); end sum_square=sum(sum(image1_crop.*image1_crop)); ctable(ivec)=corrmax/sum_square;% correlation value - if vector(1)>shiftx+isx2-ibx2+subpixfinder || vector(2)>shifty+isy2-iby2+subpixfinder - F(ivec)=-2;%vector reaches the border of the search zone - end +% if vector(1)>shiftx+isx2-ibx2+subpixfinder || vector(2)>shifty+isy2-iby2+subpixfinder +% F(ivec)=-2;%vector reaches the border of the search zone +% end catch ME vector=[0 0]; %if something goes wrong with cross correlation..... @@ -125,37 +125,43 @@ -function [vector] = SUBPIXGAUSS (result_conv,x,y) +function [vector,F] = SUBPIXGAUSS (result_conv,x,y) +vector=[0 0]; %default +F=0; +[npy,npx]=size(result_conv); -if size(x,1)>1 %if there are more than 1 peaks just take the first - x=x(1:1); -end -if size(y,1)>1 %if there are more than 1 peaks just take the first - y=y(1:1); -end -if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) +% if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion – Israel Institute of Technology %http://urapiv.wordpress.com - f0 = log(result_conv(y,x)); - f1 = log(result_conv(y-1,x)); - f2 = log(result_conv(y+1,x)); - peaky = y+ (f1-f2)/(2*f1-4*f0+2*f2); - f0 = log(result_conv(y,x)); - f1 = log(result_conv(y,x-1)); - f2 = log(result_conv(y,x+1)); - peakx = x+ (f1-f2)/(2*f1-4*f0+2*f2); - [npy,npx]=size(result_conv); + peaky = y; + if y <= npy-1 && y >= 1 + f0 = log(result_conv(y,x)); + f1 = log(result_conv(y-1,x)); + f2 = log(result_conv(y+1,x)); + peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); + else + F=-2; % warning flag for vector truncated by the limited search box + end + peakx=x; + if x <= npx-1 && x >= 1 + f0 = log(result_conv(y,x)); + f1 = log(result_conv(y,x-1)); + f2 = log(result_conv(y,x+1)); + peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); + else + F=-2; % warning flag for vector truncated by the limited search box + end vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; -else - vector=[NaN NaN]; -end +% else +% vector=[NaN NaN]; +% end -function [vector] = SUBPIX2DGAUSS (result_conv,x,y) -if size(x,1)>1 %if there are more than 1 peaks just take the first - x=x(1:1); -end -if size(y,1)>1 %if there are more than 1 peaks just take the first - y=y(1:1); -end -if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) +function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) +vector=[0 0]; %default +F=-2; +peaky=y; +peakx=x; +[npy,npx]=size(result_conv); +if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) + F=0; for i=-1:1 for j=-1:1 @@ -181,13 +187,10 @@ deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); - peakx=x+deltax; - peaky=y+deltay; - - [npy,npx]=size(result_conv); - vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; -% SubpixelX=peakx-(ibx/2)-SubPixOffset; -% SubpixelY=peaky-(iby/2)-SubPixOffset; -% vector=[SubpixelX, SubpixelY]; -else - vector=[NaN NaN]; + if abs(deltax)<1 + peakx=x+deltax; + end + if abs(deltay)<1 + peaky=y+deltay; + end end +vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 237) +++ /trunk/src/plot_field.m (revision 238) @@ -900,8 +900,6 @@ if MinA