Description of eidors

0001 function eidors_startup( path_array )
0002 % Script to start EIDORS
0003 % Set path and variables correctly
0004 % USAGE:
0005 %   startup - setup basic eidors usage functions
0006 %   startup( { dev directory paths })
0007 
0008 % NOTE: this is a function, so that we don't put variables into the
0009 % workspace
0010 
0011 % (C) 2005 Andy Adler. License: GPL version 2 or version 3
0012 % $Id: eidors_startup.m 6512 2022-12-30 19:09:30Z aadler $
0013 
0014 if nargin == 0
0015     path_array = {};
0016 end
0017 
0018 eidors_msg('=== SETTING UP EIDORS version %s ===',  ...
0019      eidors_obj('eidors_version'), 0);
0020 
0021 HOMEDIR=strrep(pwd,'\','/');
0022 ver = version_check;
0023 archdir = set_paths(HOMEDIR, ver, path_array);
0024 eidors_cache('init');
0025 % make EIDORS less verbose by default
0026 eidors_msg('log_level', 2); 
0027 set_defaults(HOMEDIR);
0028 print_welcome(HOMEDIR,archdir, ver);
0029 
0030 function set_defaults(HOMEDIR)
0031     % default functions
0032     eidors_default('set','fwd_solve','fwd_solve_1st_order');
0033     eidors_default('set','calc_system_mat','system_mat_1st_order');
0034     eidors_default('set','calc_jacobian','jacobian_adjoint');
0035     eidors_default('set','inv_solve','inv_solve_diff_GN_one_step');
0036     eidors_default('set','calc_RtR_prior','prior_laplace');
0037     eidors_default('set','calc_R_prior','prior_laplace');
0038     eidors_default('set','fwd_solve','fwd_solve_1st_order');
0039     eidors_default('set','GREIT_desired_img','GREIT_desired_img_sigmoid');
0040     eidors_default('set','mk_coarse_fine_mapping','mk_analytic_c2f');
0041     %models are NOT normalized by default
0042     eidors_default('set','mdl_normalize',@(x) 0); 
0043     %netgen finelevel is coarse
0044     eidors_default('set','call_netgen_finelevel','');
0045 
0046     calc_colours('defaults'); % default calc_colours
0047 
0048     %  Set max cache size. Not completely sure about this
0049     %  but 1GB should be available in most modern machines
0050     eidors_cache('cache_size', 1024^3 );
0051     eidors_cache('boost_priority', 0 ); % set default priority
0052 
0053     % Set default model cache location
0054     mk_library_model('LIBRARY_PATH',[HOMEDIR, '/models/cache']);
0055     eidors_cache('cache_path',[HOMEDIR, '/models/cache']);
0056 
0057     eidors_cache('eidors_path',HOMEDIR);
0058 
0059 
0060 function ver = version_check
0061     ver= eidors_obj('interpreter_version');
0062 
0063     if ver.isoctave
0064         if ver.ver < 3.008
0065             warning(['EIDORS REQUIRES AT LEAST OCTAVE V3.8.0\n' ...
0066                 'Several functions may not work with your version']);
0067         end
0068         % EIDORS does this a lot, so we remove the warning
0069         warning('off','Octave:load-file-in-path') 
0070     else
0071         if ver.ver < 7.006
0072             warning(['EIDORS REQUIRES AT LEAST MATLAB V7.6.\n' ...
0073                 'Several functions may not work with your version']);
0074         end
0075     end
0076 
0077 function archdir = set_paths(HOMEDIR, ver,path_array)
0078     % we will be overloading built-in functions. Disable the warning.
0079     warning off MATLAB:dispatcher:nameConflict
0080     addpath( HOMEDIR );
0081     addpath([HOMEDIR, '/solvers']);
0082     addpath([HOMEDIR, '/solvers/inverse']);
0083     addpath([HOMEDIR, '/solvers/forward']);
0084     addpath([HOMEDIR, '/solvers/forward/tools-beta']); % Tools for MC's solvers which are not yet general
0085     addpath([HOMEDIR, '/algorithms']);
0086     addpath([HOMEDIR, '/interface']);
0087     addpath([HOMEDIR, '/models']);
0088     addpath([HOMEDIR, '/meshing']);
0089     addpath([HOMEDIR, '/meshing/netgen']);
0090     addpath([HOMEDIR, '/meshing/distmesh']);
0091     addpath([HOMEDIR, '/meshing/gmsh']);
0092     addpath([HOMEDIR, '/meshing/stl']);
0093     addpath([HOMEDIR, '/sample_data']);
0094     addpath([HOMEDIR, '/examples']);
0095     addpath([HOMEDIR, '/tools']);
0096     addpath([HOMEDIR, '/graphics/matlab']);
0097     addpath([HOMEDIR, '/graphics/vtk']);
0098     addpath(genpath([HOMEDIR, '/external'])); %add subdirectories
0099     addpath([HOMEDIR, '/deprecated']);
0100     addpath([HOMEDIR, '/overloads']);
0101     if ~ver.isoctave && ver.ver < 9.008
0102         addpath([HOMEDIR, '/overloads/sparse']);
0103     end
0104     if ~ver.isoctave && ver.ver < 9.0073
0105         addpath([HOMEDIR, '/overloads/vecnorm']);
0106     end
0107     if ver.isoctave 
0108         warning off Octave:shadowed-function
0109         addpath([HOMEDIR, '/overloads/octave']);
0110         warning on Octave:shadowed-function
0111     end
0112     warning on MATLAB:dispatcher:nameConflict
0113 
0114     %addpath([HOMEDIR, '/tests']);
0115 
0116     DEVDIR = [HOMEDIR(1:find(HOMEDIR == '/',1,'last')-1) '/dev'];
0117     for i = 1:length(path_array)
0118         p = genpath([DEVDIR, '/', path_array{i}]);
0119         addpath(p);
0120     end
0121 
0122     % We need to add an architecture specific directory for mex files
0123     if ver.isoctave
0124         archdir= strcat('/arch/octave/',computer);
0125 % Make sure that the archdir exists
0126         [status] = mkdir([HOMEDIR,archdir]);
0127     else
0128         % problem was that MSVC compiles depended on versions of MSVCRT1xx.dll.
0129     % which was not available with all windows/matlab versions.
0130     % New concept is to try building with MINGW compiler
0131         archdir= '/arch/matlab';
0132     end
0133     addpath([HOMEDIR, archdir]);
0134     fname = [HOMEDIR, archdir, '/eidors_var_id.', mexext];
0135     
0136     if ~exist(fname, 'file')
0137        eidors_msg('STARTUP: missing a required, pre-compiled mex file: eidors_var_id', 1);
0138        compile_mex(HOMEDIR,archdir,ver);
0139     end
0140 
0141     % check that the compiled mex file is newer than the source file
0142     srcf = strcat(HOMEDIR,'/arch/eidors_var_id.cpp');
0143     mexf = strcat(fname);
0144     if exist(srcf) == 2 && exist(mexf) == 3
0145         srcd=dir(srcf);
0146         mexd=dir(mexf);
0147 
0148 
0149         % We thank MATLAB for their version issues
0150         newer_src = false;
0151         try newer_src = datenum(srcd.date) > datenum(mexd.date);
0152         catch
0153            newer_src = srcd.datenum > mexd.datenum;
0154         end
0155 
0156         if newer_src
0157            warning('eidors_var_id.mex file is older than source file and should be recompiled.');
0158         end
0159 
0160         ok = eidors_var_id_ok;
0161         if newer_src || ~ok
0162            while 1
0163               if ~ok
0164                  resp = input('Would you like to compile now? [Y/n]: ','s');
0165               else
0166                  resp = input('Would you like to compile now? [y/N]: ','s');
0167                  if isempty(resp)
0168                     resp = 'n';
0169                  end
0170               end
0171               
0172               switch lower(resp)
0173                  case {'n', 'no'}
0174                     if ver.isoctave
0175                        eidors_msg([...
0176                           '  Please compile it using:\n'...
0177                           '    cd ',HOMEDIR,'/arch\n'...
0178                           '    mkoctfile -v --mex eidors_var_id.cpp\n'...
0179                           '    mkdir -p ..',archdir,'\n'...
0180                           '    mv *.mex ..',archdir ...
0181                           ],1);
0182                     else
0183                        eidors_msg([ ...
0184                           '  Please compile it using:\n'...
0185                           '     cd ',HOMEDIR,'/arch\n'...
0186                           '     mex "',HOMEDIR,'/arch/eidors_var_id.cpp"\n'...
0187                           '     mv *.mex* ',HOMEDIR,'/arch/matlab\n' ...
0188                           'If you have a 64 bit machine, please use "mex -largeArrayDims ..."' ...
0189                           ],1);
0190                     end
0191                     break;
0192                  case {'','y','yes'}
0193                    compile_mex(HOMEDIR,archdir,ver);
0194                    break;
0195               end
0196            end
0197         end
0198     end
0199 
0200 function compile_mex(HOMEDIR,archdir, ver)
0201     eidors_msg('Attempting to compile eidors_var_id',2);
0202     c = computer;
0203     flags = [];
0204 
0205     if ver.isoctave
0206          curdir = cd;
0207          cd(sprintf('%s/arch',HOMEDIR));
0208          mex eidors_var_id.cpp
0209 % We create the directory earlier
0210 %        system(sprintf('mkdir -p ..%s',archdir));
0211 %    Has to be absolute paths because Matlab coders are so stupid!!
0212          movefile(sprintf('%s/arch/*.mex',HOMEDIR), ...
0213                   sprintf('%s%s/',HOMEDIR,archdir));
0214          cd(curdir)
0215          return
0216     end
0217     
0218     if strcmp(c(end-1:end),'64')
0219        flags = '-largeArrayDims';
0220     end  
0221     cmd = sprintf('mex %s "%s/arch/eidors_var_id.cpp"', flags, HOMEDIR);
0222 % it seems to be better to use matlabs mex, especially since
0223 % there is a latex derivative called mex to interfere with us
0224     eval(cmd);
0225 
0226 % the assholes at matlab don"t respect the 'f' flag in their own
0227 % documentation. this means we need to rewrite the whole file move.
0228 % after 60 years of pcs you would think that copying files is
0229 % understood technology!
0230     targ = sprintf('%s%s/eidors_var_id.%s',HOMEDIR,archdir,mexext);
0231     try
0232     delete( targ );
0233     end
0234     movefile(sprintf('%s/eidors_var_id.%s',HOMEDIR, mexext), targ)
0235 
0236     ok = eidors_var_id_ok; % test it
0237     if ~ok
0238        fprintf([ ...
0239     'After compilation, eidors_var_id does not seem to be working.' ...
0240     'Sorry, you will need to debug this yourself. Some ideas are:\n\n' ...
0241     'On windows, try "mex -setup". You may need to install a compiler.' ...
0242     'For your matlab version (ie R2013a), see:' ...
0243     'http://www.mathworks.com/support/compilers/R2013a\n\n' ...
0244     'On linux, you may need to install older compilers like gcc-4.4.' ...
0245     'These can be used by writing\n' ...
0246     '   mex CC=gcc-4.4 CXX=g++-4.4 -largeArrayDims eidors_var_id.cpp\n']);
0247     end
0248 
0249 function print_welcome(HOMEDIR,archdir,ver)
0250     eidors_ver = eidors_obj('eidors_version');
0251     if eidors_ver(end) == '+' % post release version
0252        % THIS IS HORRIBLE, HORRIBLE CRAP IN SVN. LOTS OF USERS WANT GlobalRev
0253        % BUT THE ARROGANT SVN AUTHORS REFUSE TO PROVIDE IT!!!!
0254        % If available, we could write it into each checkin without having
0255        % to rely on a broken system call.
0256        [status, result] = system('svnversion');
0257        if status==0;
0258           eidors_ver = [eidors_ver, ' SVN_ID=', result(1:end-1)];
0259        else
0260           eidors_ver = [eidors_ver, ' SVN_ID=unknown'];
0261        end
0262     end
0263     eidors_msg('Installed EIDORS (Ver: %s)', eidors_ver,1);
0264 
0265     eidors_msg('Parameter: cache_size=%.0f MB',eidors_cache('cache_size')/(1024*1024),1);
0266     eidors_msg('Parameter: mapped_colour=%d',calc_colours('mapped_colour'),1);
0267     if calc_colours('greylev')>=0
0268         eidors_msg('Default background colour: black',1);
0269     else
0270         eidors_msg('Default background colour: white',1);
0271     end
0272     eidors_msg('EIDORS mex folder: %s%s',HOMEDIR,archdir,1);
0273     eidors_msg('EIDORS cache folder: %s (must be writable)', ...
0274          eidors_cache('cache_path'),1);
0275     eidors_msg('EIDORS model cache: %s', mk_library_model('LIBRARY_PATH'),1);
0276 
0277 
0278     % helpful messages
0279     % TODO: test if desktop is available
0280     if ver.isoctave
0281         canwritehtml=0;
0282     else try
0283             mf = com.mathworks.mde.desk.MLDesktop.getInstance.getMainFrame;
0284             if isempty(mf)
0285                 canwritehtml=0;
0286             else
0287                 canwritehtml=1;
0288             end
0289         catch
0290             canwritehtml=0;
0291         end
0292     end
0293     if canwritehtml
0294         tutorials = '<a href="http://eidors3d.sf.net/tutorial/tutorial.shtml">Tutorials</a>';
0295     else
0296         tutorials = 'Tutorials';
0297     end
0298     eidors_msg(['New to EIDORS? Have a look at the ',tutorials,'.'],1);
0299 
0300 function ok = eidors_var_id_ok;
0301     id0 = '';
0302     try id0 = eidors_var_id([]); end
0303     if strcmp(id0, ...
0304       'id_DA39A3EE5E6B4B0D3255BFEF95601890AFD80709')  % SHA1 of nothing
0305        ok = 1;
0306     else
0307        ok = 0;
0308     end
0309     if ok==0
0310        warning('caching (function eidors_var_id) is not working');
0311     else
0312        eidors_msg('tested function eidors_var_id: OK',1);
0313     end
eidors_startup

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
