Index: /trunk/src/phys_ima.m =================================================================== --- /trunk/src/phys_ima.m (revision 921) +++ /trunk/src/phys_ima.m (revision 922) @@ -40,6 +40,11 @@ Rangy(1)=max(ycorner); test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths -npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images) -npY=1+round((Rangy(1)-Rangy(2))/min(dy)); +% npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images) +% npY=1+round((Rangy(1)-Rangy(2))/min(dy)); + +npX=1+round((Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images) +npY=1+round((Rangy(1)-Rangy(2))/max(dy)); + + x=linspace(Rangx(1),Rangx(2),npX); y=linspace(Rangy(1),Rangy(2),npY); @@ -69,6 +74,6 @@ % end end - xima=0.5:npx-0.5;%image coordinates of corners - yima=npy-0.5:-1:0.5; + xima=0.5:npx(icell)-0.5;%image coordinates of corners + 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,zphys);% image coordinates for each point in the real Index: /trunk/src/plot_object.m =================================================================== --- /trunk/src/plot_object.m (revision 921) +++ /trunk/src/plot_object.m (revision 922) @@ -386,5 +386,5 @@ if nbpoints>length(PlotData.DeformPoint) for ipt=length(PlotData.DeformPoint)+1:nbpoints - PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','.','Tag','DeformPoint',... + PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','-','Tag','DeformPoint',... 'SelectionHighlight','off','UserData',hplot); end Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 921) +++ /trunk/src/series.m (revision 922) @@ -1768,4 +1768,7 @@ extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process for iprocess=1:NbProcess + extxml{iprocess}='.xml'; +end +for iprocess=1:NbProcess if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action disp('program stopped by user') @@ -1828,7 +1831,7 @@ case {'PCWIN','PCWIN64'} %Windows system filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters - system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system + system([ActionFullName ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system case {'GLNX86','GLNXA64','MACI64'}%Linux system - system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]); + system([ActionFullName ' ' RunTime ' ' filexml]); end end @@ -1941,5 +1944,5 @@ 'hostname && date \n '... 'umask 002 \n'... - fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group + ActionFullName ' ' RunTime ' ' filexml];%allow writting access to created files for user group fprintf(fid,cmd);%fill the executable file with the char string cmd fclose(fid);% close the executable file @@ -1951,5 +1954,5 @@ end end - msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results']) + msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results']) end @@ -1967,5 +1970,5 @@ 'hostname && date \n '... 'umask 002 \n'... - fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group + ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group else cmd=[... @@ -2021,5 +2024,5 @@ WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes']) - oar_command=['oarsub -n UVmat_' ActionName ' '... + oar_command=['oarsub -n UVmat_' ActionFullName ' '... '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '... '-l /core=' num2str(NbCore) ','... @@ -2028,6 +2031,9 @@ '-O ' filename_log ' '... extra_oar ' '... - '"oar-parexec -s -f ' filename_joblist ' '... + '"oar-parexec -s -f ' filename_joblist ' '... '-l ' filename_joblist '.log"']; + + + fprintf(oar_command);% display system command on the Matlab command window [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window @@ -2037,5 +2043,5 @@ fprintf(fid,result);% store the result (job ID number) fclose(fid); - msgbox_uvmat('CONFIRMATION',[ActionName ' launched as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) + msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) case 'cluster_pbs' % for LMFA Kepler machine @@ -2078,5 +2084,5 @@ fprintf(pbs_command);% display in command line %system(pbs_command); - msgbox_uvmat('CONFIRMATION',[ActionName ' command ready to be launched in cluster']) + msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster']) case 'python' command = [ Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 921) +++ /trunk/src/series/extract_rdvision.m (revision 922) @@ -70,5 +70,6 @@ ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on', ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default) - ParamOut.OutputSubDirMode='custom'; %output folder given by the program, not by the GUI series + ParamOut.OutputDirExt='.extract';%set the output dir extension + ParamOut.OutputSubDirMode='one'; %output folder given by the program, not by the GUI series % detect the set of image folder RootPath=Param.InputTable{1,1}; @@ -143,5 +144,5 @@ msgbox_uvmat('ERROR',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once']) %rmfield(OutputDir) - return +% return end %% interactive input of specific parameters (for RDvision system) @@ -183,5 +184,10 @@ checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end for iview=1:size(Param.InputTable,1) - filexml=[fullfile(RootPath,Param.InputTable{iview,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder + for iview_xml=1:size(Param.InputTable,1)% loojk for the xml files in the different data directories + filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder + if exist(filexml,'file') + break + end + end if ~exist(filexml,'file') disp_uvmat('ERROR',[filexml ' missing'],checkrun) @@ -275,11 +281,11 @@ time_diff_min=min(diff_time'); if max(time_diff_max)>0.005 - disp_uvmat('WARNING',['timestamps exceeds xml time by' num2str(max(time_diff_max))],checkrun) + disp(['WARNING:timestamps exceeds xml time by' num2str(max(time_diff_max))]) checkpreserve=1; elseif min(time_diff_min)<-0.005 - disp_uvmat('WARNING',['timestamps is lower than xml time by' num2str(min(time_diff_min))],checkrun) + disp(['timestamps is lower than xml time by' num2str(min(time_diff_min))]) checkpreserve=1; else - disp_uvmat('CONFIRMATION','time from xml file correct within better than 5 ms',checkrun) + disp('CONFIRMATION:time from xml file correct within better than 5 ms') end if checkpreserve @@ -303,12 +309,13 @@ % check images - delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished - if ~checkpreserve - for ibin=1:numel(BinList) - delete(BinList{ibin}) - end - rmdir(fullfile(RootPath,Param.InputTable{iview,2})) - end -end +% delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished +% if ~checkpreserve +% for ibin=1:numel(BinList) +% delete(BinList{ibin}) +% end +% rmdir(fullfile(RootPath,Param.InputTable{iview,2})) +% end +end +delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Index: /trunk/src/set_object.m =================================================================== --- /trunk/src/set_object.m (revision 921) +++ /trunk/src/set_object.m (revision 922) @@ -391,5 +391,5 @@ end end - if isempty(str2num(get(handles.num_RangeInterp,'String'))) + if isempty(str2num(get(handles.num_RangeInterp,'String'))) && isfield(UvData,'Field') set(handles.num_RangeInterp,'String',num2str(3*UvData.Field.CoordMesh))% default interpolationlength= 3 meshes end