Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 983) +++ /trunk/src/series.m (revision 984) @@ -155,13 +155,15 @@ set(handles.CPUTime_txt,'Visible','on'); % make visible button for access to Monika end -[s,w]=system('qstat --version');% look for cluster system 'sge' +[s,w]=system('qstat -help');% look for cluster system 'sge' if isequal(s,0) if regexp(w,'^pbs') RunModeList=[RunModeList;{'cluster_pbs'}]; + elseif regexp(w,'^SGE') + RunModeList=[RunModeList;{'cluster_sge'}]; else - RunModeList=[RunModeList;{'cluster_sge'}]; - end -end -set(handles.RunMode,'String',RunModeList) + RunModeList=[RunModeList;{'cluster_qstat_unknown'}]; + end +end +set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager %% list of builtin transform functions in the menu TransformName @@ -1502,5 +1504,5 @@ if exist(xmlfile,'file') s=xml2struct(xmlfile); - if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam') + if (strcmp(RunMode,'cluster_oar') || strcmp(RunMode, 'cluster_pbs') || strcmp(RunMode, 'cluster_sge')) && isfield(s,'BatchParam') if isfield(s.BatchParam,'NbCore') NbCore=s.BatchParam.NbCore; @@ -1591,5 +1593,5 @@ extra_oar=answer{2}; % end - case 'cluster_pbs' + case {'cluster_pbs', 'cluster_sge', 'cluster_qstat_unknown'} if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) NbCore=1;% one core used only (limitation of Matlab licences) @@ -1601,6 +1603,7 @@ extra_oar=''; else - answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); + answer=inputdlg({'Number of jobs (max 1000)','Queue'},'qsub parameters',1,{'100','piv_debian'}); NbCore=str2double(answer{1}); + qstat_Queue=answer{2}; %extra_oar=answer{2};%TODO : fix this for LMFA cluster. Maybe %extrs_oar and extra_pbs are not the best names @@ -1729,5 +1732,5 @@ NbProcess=1; switch RunMode - case {'cluster_oar','cluster_pbs'} + case {'cluster_oar','cluster_pbs','cluster_sge','cluster_qstat_unknown'} if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined BlockLength= ceil(20/(CPUTime*nbfield_j));% short iterations are grouped such that the minimum time of a process is 20 min. @@ -2059,5 +2062,5 @@ fclose(fid); system(['chmod +x ' filename_joblist]);% set the file to executable - pbs_command=['qstat -n CIVX '... + pbs_command=['qsub -n CIVX '... '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... '-l /core=' num2str(NbCore) ','... @@ -2065,5 +2068,5 @@ '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '... - extra_oar ' '... + extra_qstat ' '... '"oar-parexec -s -f ' filename_joblist ' '... '-l ' filename_joblist '.log"']; @@ -2075,4 +2078,63 @@ %system(pbs_command); msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster']) + + case 'cluster_sge' % for PSMN + % Au PSMN, on ne crée pas 1 job avec plusieurs cœurs, mais N jobs de 1 cœurs + % où N < 1000. + %create subdirectory for pbs command and log files + + DirSGE=fullfile(OutputDir,'0_SGE'); + if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input + curdir=pwd; + cd(DirSGE) + delete('*') + cd(curdir) + else + [tild,msg1]=mkdir(DirSGE); + if ~strcmp(msg1,'') + errormsg=['cannot create ' DirSGE ': ' msg1];%error message for directory creation + return + end + end + maxImgsPerJob = ceil(length(batch_file_list)/NbCore); + disp(['Max number of jobs: ' num2str(NbCore)]) + disp(['Images per job: ' num2str(maxImgsPerJob)]) + + iprocess = 1; + imgsInJob = []; + currJobIndex = 1; + done = 0; + while(~done) + if(iprocess <= length(batch_file_list)) + imgsInJob = [imgsInJob, iprocess]; + end + if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list))) + cmd=['#!/bin/sh \n'... + '#$ -cwd \n'... + 'hostname && date\n'] + for ii=1:numel(imgsInJob) + cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n']; + end + [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w'); + fprintf(fid, cmd); + fclose(fid); + system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh']) + sge_command=['qsub -N civ_' num2str(currJobIndex) ' '... + '-q ' qstat_Queue ' '... + '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... + '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... + fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])]; + fprintf(sge_command);% display in command line + [status, result] = system(sge_command); + fprintf(result); + currJobIndex = currJobIndex + 1; + imgsInJob = []; + end + if(iprocess == length(batch_file_list)) + done = 1; + end + iprocess = iprocess + 1; + end + msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.']) case 'python' command = [ @@ -2356,4 +2418,6 @@ end end + else + set(handles.FieldName,'Visible','off') end @@ -2382,5 +2446,5 @@ end if warn_coord - msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file') + msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file') end Index: /trunk/src/series/aver_stat.m =================================================================== --- /trunk/src/series/aver_stat.m (revision 983) +++ /trunk/src/series/aver_stat.m (revision 984) @@ -167,5 +167,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/beam_forming.m =================================================================== --- /trunk/src/series/beam_forming.m (revision 983) +++ /trunk/src/series/beam_forming.m (revision 984) @@ -93,5 +93,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/check_data_files.m =================================================================== --- /trunk/src/series/check_data_files.m (revision 983) +++ /trunk/src/series/check_data_files.m (revision 984) @@ -108,5 +108,5 @@ %determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:nbview Index: /trunk/src/series/check_peaklock.m =================================================================== --- /trunk/src/series/check_peaklock.m (revision 983) +++ /trunk/src/series/check_peaklock.m (revision 984) @@ -125,5 +125,5 @@ %determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:nbview @@ -528,5 +528,5 @@ Integ(izero)=min(Integ(inonzero)); aa=log(Integ);%initial guess for a coeff -spli=spline4(aa,mini,nbb); %appel à la fonction spline4 +spli=spline4(aa,mini,nbb); %appel ï¿œ la fonction spline4 histsmooth=exp(spli); @@ -581,5 +581,5 @@ %data -% n=10;% résolution de la pdf: nbre de points par unite de u +% n=10;% rï¿œsolution de la pdf: nbre de points par unite de u % mini=-10.0;%general mini=uint16(min(values)-1 CHOOSE maxi-mini+1 EVEN % maxi=9.0; % general maxi=uint16(max(values))+1 @@ -588,5 +588,5 @@ nint=siz(2); maxi=mini+nint-1; -npdf=nint*n;% nbre total d'intervals à introduire dans la pdf: hist(u,npdf) +npdf=nint*n;% nbre total d'intervals ï¿œ introduire dans la pdf: hist(u,npdf) %simulation de pdf xfin=[mini-0.5+1/(2*n):(1/n):maxi+0.5-(1/(2*n))];% valeurs d'interpolation: we take n values in each integer interval Index: /trunk/src/series/civ2vel_3C.m =================================================================== --- /trunk/src/series/civ2vel_3C.m (revision 983) +++ /trunk/src/series/civ2vel_3C.m (revision 984) @@ -335,5 +335,5 @@ for iview=1:2 %% reading PIV input file(s) - [Data{iview},tild,errormsg]=read_civdata(filecell{iview,field_index},{'vec(U,V)'},'*'); + [Data{iview},tild,errormsg]=read_civdata(filecell{iview,field_index},{'vec(U,V)'},Param.InputFields.VelType); if ~isempty(errormsg) disp_uvmat('ERROR',['ERROR in civ2vel_3C/read_field/' errormsg],checkrun) Index: /trunk/src/series/float_tracking.m =================================================================== --- /trunk/src/series/float_tracking.m (revision 983) +++ /trunk/src/series/float_tracking.m (revision 984) @@ -20,5 +20,5 @@ % global hfig1 hfig2 scalar % global Abackg nbpart lum diam -%%%%%%%%%%%%%%ù +%%%%%%%%%%%%%%ï¿œ % %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -147,5 +147,5 @@ [FileInfo,VideoObject]=get_file_info(filecell{1,1}); FileType=FileInfo.FileType; -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; if isempty(find(strcmp(FileType,ImageTypeOptions))) disp('input file not images') Index: /trunk/src/series/ima_threshold.m =================================================================== --- /trunk/src/series/ima_threshold.m (revision 983) +++ /trunk/src/series/ima_threshold.m (revision 984) @@ -154,5 +154,5 @@ [FileInfo,VideoObject]=get_file_info(filecell{1,1}); FileType=FileInfo.FileType; -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; if isempty(find(strcmp(FileType,ImageTypeOptions))) disp('input file not images') Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 983) +++ /trunk/src/series/merge_proj.m (revision 984) @@ -134,5 +134,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/merge_proj_polar.m =================================================================== --- /trunk/src/series/merge_proj_polar.m (revision 983) +++ /trunk/src/series/merge_proj_polar.m (revision 984) @@ -162,5 +162,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/merge_proj_polar_multifile.m =================================================================== --- /trunk/src/series/merge_proj_polar_multifile.m (revision 983) +++ /trunk/src/series/merge_proj_polar_multifile.m (revision 984) @@ -165,5 +165,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/merge_proj_polar_singlefile.m =================================================================== --- /trunk/src/series/merge_proj_polar_singlefile.m (revision 983) +++ /trunk/src/series/merge_proj_polar_singlefile.m (revision 984) @@ -212,5 +212,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/particle_tracking.m =================================================================== --- /trunk/src/series/particle_tracking.m (revision 983) +++ /trunk/src/series/particle_tracking.m (revision 984) @@ -20,5 +20,5 @@ % global hfig1 hfig2 scalar % global Abackg nbpart lum diam -%%%%%%%%%%%%%%ù +%%%%%%%%%%%%%%ï¿œ % %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -147,5 +147,5 @@ [FileInfo,VideoObject]=get_file_info(filecell{1,1}); FileType=FileInfo.FileType; -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; if isempty(find(strcmp(FileType,ImageTypeOptions))) disp('input file not images') Index: /trunk/src/series/stereo_civ.m =================================================================== --- /trunk/src/series/stereo_civ.m (revision 983) +++ /trunk/src/series/stereo_civ.m (revision 984) @@ -244,5 +244,5 @@ %% get timing from input video -if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input +if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input time=zeros(FileInfo_A.NumberOfFrames+1,2); time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; Index: /trunk/src/series/stereo_input.m =================================================================== --- /trunk/src/series/stereo_input.m (revision 983) +++ /trunk/src/series/stereo_input.m (revision 984) @@ -111,5 +111,5 @@ iview_image=1;%line # for the input images switch FileType - case {'image','multimage','video','mmreader','netcdf'} + case {'image','multimage','video','mmreader','cine_phantom','netcdf'} % NomTypeImaA=NomTypeInput; % iview_image=1;%line # for the input images Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 983) +++ /trunk/src/series/sub_background.m (revision 984) @@ -107,5 +107,5 @@ %% check the validity of input file types - ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) + ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'};%allowed input file types(images) FileInfo=get_file_info(FirstFileName); FileType=FileInfo.FileType; Index: /trunk/src/series/time_series.m =================================================================== --- /trunk/src/series/time_series.m (revision 983) +++ /trunk/src/series/time_series.m (revision 984) @@ -170,5 +170,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; FileType=cell(1,NbView); Index: /trunk/src/series/turb_correlation.m =================================================================== --- /trunk/src/series/turb_correlation.m (revision 983) +++ /trunk/src/series/turb_correlation.m (revision 984) @@ -114,5 +114,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/turb_stat.m =================================================================== --- /trunk/src/series/turb_stat.m (revision 983) +++ /trunk/src/series/turb_stat.m (revision 984) @@ -114,5 +114,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/series/usr_fct/merge_proj_images.m =================================================================== --- /trunk/src/series/usr_fct/merge_proj_images.m (revision 983) +++ /trunk/src/series/usr_fct/merge_proj_images.m (revision 984) @@ -60,5 +60,5 @@ %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; if isstruct(Param) && isequal(Param.Action.RUN,0) ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) @@ -141,5 +141,5 @@ %% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video'}; +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:NbView Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 983) +++ /trunk/src/uvmat.m (revision 984) @@ -3520,22 +3520,22 @@ end %put W as background image by default if NbDim=2: -if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3); - set(handles.SubField,'Value',1); - set(handles.RootPath_1,'String','"') - set(handles.RootFile_1,'String','"') - set(handles.SubDir_1,'String','"'); - indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2); - set(handles.FileIndex_1,'String',indices) - set(handles.FileExt_1,'String','"'); - set(handles.FieldName_1,'Visible','on'); - set(handles.FieldName_1,'Visible','on'); - set(handles.RootPath_1,'Visible','on') - set(handles.RootFile_1,'Visible','on') - set(handles.SubDir_1,'Visible','on'); - set(handles.FileIndex_1,'Visible','on'); - set(handles.FileExt_1,'Visible','on'); - set(handles.FieldName_1,'Visible','on'); - Field{1}.AName='w'; -end +% if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3); +% set(handles.SubField,'Value',1); +% set(handles.RootPath_1,'String','"') +% set(handles.RootFile_1,'String','"') +% set(handles.SubDir_1,'String','"'); +% indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2); +% set(handles.FileIndex_1,'String',indices) +% set(handles.FileExt_1,'String','"'); +% set(handles.FieldName_1,'Visible','on'); +% set(handles.FieldName_1,'Visible','on'); +% set(handles.RootPath_1,'Visible','on') +% set(handles.RootFile_1,'Visible','on') +% set(handles.SubDir_1,'Visible','on'); +% set(handles.FileIndex_1,'Visible','on'); +% set(handles.FileExt_1,'Visible','on'); +% set(handles.FieldName_1,'Visible','on'); +% Field{1}.AName='w'; +% end %% display time value of the current file