Index: trunk/src/angle2normal.m =================================================================== --- trunk/src/angle2normal.m (revision 1178) +++ trunk/src/angle2normal.m (revision 1179) @@ -1,5 +1,9 @@ -%calculate the components of the unit vector norm_plane normal to the plane -%defined by the rotation vector PlaneAngle (in degree) +%angle2normal: calculate the components of the unit vector defined by a rotation vector % this gives the equation of the plane as norm_plane(1)x + norm_plane(2)y +norm_plane(3)z = cte + +% OUTPUT: +%norm_plane: three components of the normal unit vector +% INPUT: +%PlaneAngle: rotation vector, with three components in degree) function norm_plane=rotate(PlaneAngle) Index: trunk/src/binread_rdv.m =================================================================== --- trunk/src/binread_rdv.m (revision 1178) +++ (revision ) @@ -1,94 +1,0 @@ -%======================================================================= -% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France -% http://www.legi.grenoble-inp.fr -% Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr -% -% This file is part of the toolbox UVMAT. -% -% UVMAT is free software; you can redistribute it and/or modify -% it under the terms of the GNU General Public License as published -% by the Free Software Foundation; either version 2 of the license, -% or (at your option) any later version. -% -% UVMAT is distributed in the hope that it will be useful, -% but WITHOUT ANY WARRANTY; without even the implied warranty of -% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -% GNU General Public License (see LICENSE.txt) for more details. -%======================================================================= - -function [imgs,timestamps,nb_frames]=binread_rdv(filename,frame_idx) -% BINREAD_RDV Permet de lire les fichiers bin générés par Hiris à partir du -% fichier seq associé. -% [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit -% l'image d'indice FRAME_IDX de la séquence FILENAME. -% -% Entrées -% ------- -% FILENAME : Nom du fichier séquence (.seq). -% FRAME_IDX : Indice de l'image à lire. Si FRAME_IDX vaut -1 alors la -% séquence est entièrement lue. Si FRAME_IDX est un tableau d'indices -% alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX -% est un tableau vide alors aucune image n'est lue mais le nombre -% d'images et tous les timestamps sont renvoyés. Les indices commencent à -% 1 et se termines à NB_FRAMES. -% -% Sorties -% ------- -% IMGS : Images de sortie. -% TIMESTAMPS : Timestaps des images lues. -% NB_FRAMES : Nombres d'images dans la séquence. - - - -if nargin<2 - frame_idx=-1; -end - -s=ini2struct(filename); - -w=str2double(s.sequenceSettings.width); -h=str2double(s.sequenceSettings.height); -bpp=str2double(s.sequenceSettings.bytesperpixel); -bin_file=s.sequenceSettings.binfile; -nb_frames=str2double(s.sequenceSettings.numberoffiles); - -[p,f]=fileparts(filename); - -%bin_dir=s.sequenceSettings.bindirectory; -%if isempty(bin_dir) - bin_dir=p; -%end - -sqb_file=fullfile(p,[f '.sqb']); -m = memmapfile(sqb_file,'Format', { 'uint32' [1 1] 'offset'; ... - 'uint32' [1 1] 'garbage1';... - 'double' [1 1] 'timestamp';... - 'uint32' [1 1] 'file_idx';... - 'uint32' [1 1] 'garbage2' },'Repeat',nb_frames); - -data=m.Data; -off=[data.offset]; -timestamps=[data.timestamp]; -file_idx=[data.file_idx]; - -if frame_idx==-1 - frame_idx=1:nb_frames; -end - -classname=sprintf('uint%d',bpp*8); -imgs=zeros([h,w,length(frame_idx)],classname); - -classname=['*' classname]; - -for i=1:length(frame_idx) - ii=frame_idx(i); - f=fullfile(bin_dir,sprintf('%s%.5d.bin',bin_file,file_idx(ii))); - fid=fopen(f,'rb'); - fseek(fid,off(ii),-1); - imgs(:,:,i)=reshape(fread(fid,w*h,classname),w,h)'; - fclose(fid); -end - -if ~isempty(frame_idx) - timestamps=timestamps(frame_idx); -end Index: trunk/src/browse_data.m =================================================================== --- trunk/src/browse_data.m (revision 1178) +++ trunk/src/browse_data.m (revision 1179) @@ -242,5 +242,5 @@ ListExperiments_Callback([],[], handles) else - msgbox_uvmat('ERROR',['The input ' Campaign ' is not a directory']) + msgbox_uvmat('ERROR',['The input ' SourceDir ' is not a folder']) end Index: trunk/src/check_files.m =================================================================== --- trunk/src/check_files.m (revision 1178) +++ trunk/src/check_files.m (revision 1179) @@ -28,5 +28,5 @@ %======================================================================= -function [checkmsg,date_str,svn_info]=check_files +function [checkmsg,date_str,svn_info,list_fct]=check_files checkmsg={};%default svn_info.rep_rev=[]; @@ -35,4 +35,5 @@ list_fct={... 'activate';...% emulate the mouse selection of a GUI element, for demo + 'angle2normal';...%rotation vector PlaneAngle (in degree) 'browse_data';...% function for scanning directories in a project/campaign 'browse_data.fig';...% GUI corresponding to dataview @@ -41,4 +42,8 @@ 'cell2tab';... %transform a Matlab cell in a character array suitable for display in a table 'check_files';... + 'civ';... % key function for image correlations (called by series/cvi_series.m) + 'cluster_command';...% creates the command string for launching jobs in the cluster system 'oar'. + 'command_launch_matlab';% creates the command strings for opening a new Matlab session + 'command_load_python';% creates the command strings for loading Python 'compile';...% compile a Matlab function, create a binary in a subdirectory /bin 'copyfields';...% copy fields between two matlab structures Index: trunk/src/civ.m =================================================================== --- trunk/src/civ.m (revision 1178) +++ trunk/src/civ.m (revision 1179) @@ -1,4 +1,4 @@ %-------------------------------------------------------------------------- -% 'civ': function adapted from PIVlab http://pivlab.blogspot.com/ +% 'civ': key function for image correlations (called by series/cvi_series.m) % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) % Index: trunk/src/close_fig.m =================================================================== --- trunk/src/close_fig.m (revision 1178) +++ (revision ) @@ -1,30 +1,0 @@ -%'close_fig': function activated when a figure is closed -%---------------------------------------------------------------- -% function close_fig(ggg,eventdata,hparent,type) -% activated by the command: -%set(hObject,'DeleteFcn',{@close_fig,hparent,type}) -% where hObject is the handle of the figure -% - -%======================================================================= -% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France -% http://www.legi.grenoble-inp.fr -% Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr -% -% This file is part of the toolbox UVMAT. -% -% UVMAT is free software; you can redistribute it and/or modify -% it under the terms of the GNU General Public License as published -% by the Free Software Foundation; either version 2 of the license, -% or (at your option) any later version. -% -% UVMAT is distributed in the hope that it will be useful, -% but WITHOUT ANY WARRANTY; without even the implied warranty of -% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -% GNU General Public License (see LICENSE.txt) for more details. -%======================================================================= - -function close_fig(ggg,eventdata,hparent,type) -if isequal(type,'zoom') - delete(hparent) % delete the rectangle showing the zoom graph in the parent fig -end Index: trunk/src/cluster_command.m =================================================================== --- trunk/src/cluster_command.m (revision 1178) +++ trunk/src/cluster_command.m (revision 1179) @@ -1,4 +1,6 @@ -%'cluster_command': creates the command string for launching jobs in the cluster -%------------------------------------------------------------------------ +%'cluster_command': creates the command string for launching jobs in the cluster system 'oar' +% other cluster options 'pbs' and 'psmn' are available in cluster_command_pbs and +% cluster_command_psmn. The choice is made in the xml file for parameters: series.xml +%-- ---------------------------------------------------------------------- % function cmd=cluster_command(ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess) % @@ -19,27 +21,26 @@ filename_log=fullfile(DirLog,'job_list.stdout'); % file for output messages of the master oar process filename_errors=fullfile(DirLog,'job_list.stderr'); % file for error messages of the master oar process - if NbProcess>=6 - bigiojob_string=['+{type = ' char(39) 'bigiojob' char(39) '}/licence=1'];% char(39) is quote - bigiojob limit UVmat parallel launch on cluster to avoid saturation of disk access to data - else - bigiojob_string=''; - end +if NbProcess>=6 + bigiojob_string=['+{type = ' char(39) 'bigiojob' char(39) '}/licence=1'];% char(39) is quote - bigiojob limit UVmat parallel launch on cluster to avoid saturation of disk access to data +else + bigiojob_string=''; +end WallTimeMax=23;% absolute limit on computation time (in hours) -WallTimeTotal=min(WallTimeMax,4*CPUTimeProcess/60);% chosen limit on computation time (in hours),possibly smaller than the absolute limit to favor job priority in the system. -WallTimeOneProcess=min(4*CPUTimeProcess+10,WallTimeTotal*60/2); % estimated max time of an individual process, used for checkpoint: - %if less than this time remains before walltime, the job is stopped and a new one can be launched ( by the option 'idempotent') +WallTimeTotal=min(WallTimeMax,4*CPUTimeProcess/60);% chosen limit on computation time (in hours),possibly smaller than the absolute limit to favor job priority in the system. +WallTimeOneProcess=min(4*CPUTimeProcess+10,WallTimeTotal*60/2); % estimated max time of an individual process, used for checkpoint: +%if less than this time remains before walltime, the job is stopped and a new one can be launched ( by the option 'idempotent') - if NbCore==1 - corestring='cpu=1/core=4'; %increases the allowed memory in case of single core job - else - % corestring=['/core=' num2str(NbCore)]; - corestring=['{cluster=''calcul8''}/core=' num2str(NbCore)]; - end - cmd=['oarsub -n UVmat_' ActionFullName ' '... - '-t idempotent --checkpoint ' num2str(WallTimeOneProcess*60) ' '... - '-l "' corestring bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster - ',walltime=' datestr(WallTimeTotal/24,13) '" '... - '-E ' filename_errors ' '... - '-O ' filename_log ' '... - '"oar-parexec -s -f ' ListProcessFile ' '... - '-l ' ListProcessFile '.log"']; +% if NbCore==1 +% corestring='cpu=1/core=4'; %increases the allowed memory in case of single core job +% else + corestring=['{cluster=''calcul8''}/core=' num2str(max(NbCore,4))]; +% end +cmd=['oarsub -n UVmat_' ActionFullName ' '... + '-t idempotent --checkpoint ' num2str(WallTimeOneProcess*60) ' '... + '-l "' corestring bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster + ',walltime=' datestr(WallTimeTotal/24,13) '" '... + '-E ' filename_errors ' '... + '-O ' filename_log ' '... + '"oar-parexec -s -f ' ListProcessFile ' '... + '-l ' ListProcessFile '.log"']; Index: trunk/src/command_launch_matlab.m =================================================================== --- trunk/src/command_launch_matlab.m (revision 1178) +++ trunk/src/command_launch_matlab.m (revision 1179) @@ -1,4 +1,4 @@ -%'command_launch_matlab': creates the command strings for opening a new Matlab -%session and running a programme in a Linux system('GLNX86','GLNXA64','MACI64') +%'command_launch_matlab': creates the command strings for opening a new Matlab session +% and running a programme in a Linux system('GLNX86','GLNXA64','MACI64') %------------------------------------------------------------------------ % function cmd=command_launch_matlab(filelog,path_uvmat,ActionPath,ActionName,inputxml,option) @@ -47,19 +47,4 @@ end -%% case cluster: -% matlab_ver = ver('MATLAB'); -% matlab_version = matlab_ver.Version; -% cmd=[... -% '#!/bin/bash\n'... -% 'source /etc/profile\n'... -% 'module purge\n'... -% 'module load matlab/' matlab_version '\n'...% CHOICE OF CURRENT MATLAB VERSION -% 'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <