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 6828 2024-04-28 09:02:21Z bgrychtol $
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 % This was not an overload, but a function missing until 2017b
0105 %     if ~ver.isoctave && ver.ver < 9.0073
0106 %         addpath([HOMEDIR, '/overloads/vecnorm']);
0107 %     end
0108     if ver.isoctave 
0109         warning off Octave:shadowed-function
0110         addpath([HOMEDIR, '/overloads/octave']);
0111         warning on Octave:shadowed-function
0112     end
0113     warning on MATLAB:dispatcher:nameConflict
0114 
0115     %addpath([HOMEDIR, '/tests']);
0116 
0117     DEVDIR = [HOMEDIR(1:find(HOMEDIR == '/',1,'last')-1) '/dev'];
0118     for i = 1:length(path_array)
0119         p = genpath([DEVDIR, '/', path_array{i}]);
0120         addpath(p);
0121     end
0122 
0123     % We need to add an architecture specific directory for mex files
0124     if ver.isoctave
0125         archdir= strcat('/arch/octave/',computer);
0126 % Make sure that the archdir exists
0127         [status] = mkdir([HOMEDIR,archdir]);
0128     else
0129         % problem was that MSVC compiles depended on versions of MSVCRT1xx.dll.
0130     % which was not available with all windows/matlab versions.
0131     % New concept is to try building with MINGW compiler
0132         archdir= '/arch/matlab';
0133     end
0134     addpath([HOMEDIR, archdir]);
0135     fname = [HOMEDIR, archdir, '/eidors_var_id.', mexext];
0136     
0137     if ~exist(fname, 'file')
0138        eidors_msg('STARTUP: missing a required, pre-compiled mex file: eidors_var_id', 1);
0139        compile_mex(HOMEDIR,archdir,ver);
0140     end
0141 
0142     % check that the compiled mex file is newer than the source file
0143     srcf = strcat(HOMEDIR,'/arch/eidors_var_id.cpp');
0144     mexf = strcat(fname);
0145     if exist(srcf) == 2 && exist(mexf) == 3
0146         srcd=dir(srcf);
0147         mexd=dir(mexf);
0148 
0149 
0150         % We thank MATLAB for their version issues
0151         newer_src = false;
0152         try newer_src = datenum(srcd.date) > datenum(mexd.date);
0153         catch
0154            newer_src = srcd.datenum > mexd.datenum;
0155         end
0156 
0157         if newer_src
0158            warning('eidors_var_id.mex file is older than source file and should be recompiled.');
0159         end
0160 
0161         ok = eidors_var_id_ok;
0162         if newer_src || ~ok
0163            while 1
0164               if ~ok
0165                  resp = input('Would you like to compile now? [Y/n]: ','s');
0166               else
0167                  resp = input('Would you like to compile now? [y/N]: ','s');
0168                  if isempty(resp)
0169                     resp = 'n';
0170                  end
0171               end
0172               
0173               switch lower(resp)
0174                  case {'n', 'no'}
0175                     if ver.isoctave
0176                        eidors_msg([...
0177                           '  Please compile it using:\n'...
0178                           '    cd ',HOMEDIR,'/arch\n'...
0179                           '    mkoctfile -v --mex eidors_var_id.cpp\n'...
0180                           '    mkdir -p ..',archdir,'\n'...
0181                           '    mv *.mex ..',archdir ...
0182                           ],1);
0183                     else
0184                        eidors_msg([ ...
0185                           '  Please compile it using:\n'...
0186                           '     cd ',HOMEDIR,'/arch\n'...
0187                           '     mex "',HOMEDIR,'/arch/eidors_var_id.cpp"\n'...
0188                           '     mv *.mex* ',HOMEDIR,'/arch/matlab\n' ...
0189                           'If you have a 64 bit machine, please use "mex -largeArrayDims ..."' ...
0190                           ],1);
0191                     end
0192                     break;
0193                  case {'','y','yes'}
0194                    compile_mex(HOMEDIR,archdir,ver);
0195                    break;
0196               end
0197            end
0198         end
0199     end
0200 
0201 function compile_mex(HOMEDIR,archdir, ver)
0202     eidors_msg('Attempting to compile eidors_var_id',2);
0203     c = computer;
0204     flags = [];
0205 
0206     if ver.isoctave
0207          curdir = cd;
0208          cd(sprintf('%s/arch',HOMEDIR));
0209          mex eidors_var_id.cpp
0210 % We create the directory earlier
0211 %        system(sprintf('mkdir -p ..%s',archdir));
0212 %    Has to be absolute paths because Matlab coders are so stupid!!
0213          movefile(sprintf('%s/arch/*.mex',HOMEDIR), ...
0214                   sprintf('%s%s/',HOMEDIR,archdir));
0215          cd(curdir)
0216          return
0217     end
0218     
0219     if strcmp(c(end-1:end),'64')
0220        flags = '-largeArrayDims';
0221     end  
0222     cmd = sprintf('mex %s "%s/arch/eidors_var_id.cpp"', flags, HOMEDIR);
0223 % it seems to be better to use matlabs mex, especially since
0224 % there is a latex derivative called mex to interfere with us
0225     eval(cmd);
0226 
0227 % the assholes at matlab don"t respect the 'f' flag in their own
0228 % documentation. this means we need to rewrite the whole file move.
0229 % after 60 years of pcs you would think that copying files is
0230 % understood technology!
0231     targ = sprintf('%s%s/eidors_var_id.%s',HOMEDIR,archdir,mexext);
0232     try
0233     delete( targ );
0234     end
0235     movefile(sprintf('%s/eidors_var_id.%s',HOMEDIR, mexext), targ)
0236 
0237     ok = eidors_var_id_ok; % test it
0238     if ~ok
0239        fprintf([ ...
0240     'After compilation, eidors_var_id does not seem to be working.' ...
0241     'Sorry, you will need to debug this yourself. Some ideas are:\n\n' ...
0242     'On windows, try "mex -setup". You may need to install a compiler.' ...
0243     'For your matlab version (ie R2013a), see:' ...
0244     'http://www.mathworks.com/support/compilers/R2013a\n\n' ...
0245     'On linux, you may need to install older compilers like gcc-4.4.' ...
0246     'These can be used by writing\n' ...
0247     '   mex CC=gcc-4.4 CXX=g++-4.4 -largeArrayDims eidors_var_id.cpp\n']);
0248     end
0249 
0250 function print_welcome(HOMEDIR,archdir,ver)
0251     eidors_ver = eidors_obj('eidors_version');
0252     if eidors_ver(end) == '+' % post release version
0253        % THIS IS HORRIBLE, HORRIBLE CRAP IN SVN. LOTS OF USERS WANT GlobalRev
0254        % BUT THE ARROGANT SVN AUTHORS REFUSE TO PROVIDE IT!!!!
0255        % If available, we could write it into each checkin without having
0256        % to rely on a broken system call.
0257        [status, result] = system('svnversion');
0258        if status==0;
0259           eidors_ver = [eidors_ver, ' SVN_ID=', result(1:end-1)];
0260        else
0261           eidors_ver = [eidors_ver, ' SVN_ID=unknown'];
0262        end
0263     end
0264     eidors_msg('Installed EIDORS (Ver: %s)', eidors_ver,1);
0265 
0266     eidors_msg('Parameter: cache_size=%.0f MB',eidors_cache('cache_size')/(1024*1024),1);
0267     eidors_msg('Parameter: mapped_colour=%d',calc_colours('mapped_colour'),1);
0268     if calc_colours('greylev')>=0
0269         eidors_msg('Default background colour: black',1);
0270     else
0271         eidors_msg('Default background colour: white',1);
0272     end
0273     eidors_msg('EIDORS mex folder: %s%s',HOMEDIR,archdir,1);
0274     eidors_msg('EIDORS cache folder: %s (must be writable)', ...
0275          eidors_cache('cache_path'),1);
0276     eidors_msg('EIDORS model cache: %s', mk_library_model('LIBRARY_PATH'),1);
0277 
0278 
0279     % helpful messages
0280     % TODO: test if desktop is available
0281     if ver.isoctave
0282         canwritehtml=0;
0283     else try
0284             mf = com.mathworks.mde.desk.MLDesktop.getInstance.getMainFrame;
0285             if isempty(mf)
0286                 canwritehtml=0;
0287             else
0288                 canwritehtml=1;
0289             end
0290         catch
0291             canwritehtml=0;
0292         end
0293     end
0294     if canwritehtml
0295         tutorials = '<a href="http://eidors3d.sf.net/tutorial/tutorial.shtml">Tutorials</a>';
0296     else
0297         tutorials = 'Tutorials';
0298     end
0299     eidors_msg(['New to EIDORS? Have a look at the ',tutorials,'.'],1);
0300 
0301 function ok = eidors_var_id_ok;
0302     id0 = '';
0303     try id0 = eidors_var_id([]); end
0304     if strcmp(id0, ...
0305       'id_DA39A3EE5E6B4B0D3255BFEF95601890AFD80709')  % SHA1 of []
0306        ok = 1;
0307     elseif strcmp(id0, ...
0308       'id_99AA06D3014798D86001C324468D497F8C010DD2')  % xxHash of []
0309        ok = 1;
0310     else
0311        ok = 0;
0312     end
0313     if ok==0
0314        warning('caching (function eidors_var_id) is not working');
0315     else
0316        eidors_msg('tested function eidors_var_id: OK',1);
0317     end
eidors_startup

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
