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stk_init.m
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stk_init.m
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% STK_INIT initializes the STK
%
% CALL: stk_init ()
%
% STK_INIT sets paths and environment variables
% Copyright Notice
%
% Copyright (C) 2015-2018, 2019, 2022 CentraleSupelec
% Copyright (C) 2011-2014 SUPELEC
%
% Authors: Julien Bect <[email protected]>
% Emmanuel Vazquez <[email protected]>
% Copying Permission Statement
%
% This file is part of
%
% STK: a Small (Matlab/Octave) Toolbox for Kriging
% (https://github.com/stk-kriging/stk/)
%
% STK 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 3 of the License, or (at your
% option) any later version.
%
% STK 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 for more details.
%
% You should have received a copy of the GNU General Public License
% along with STK. If not, see <http://www.gnu.org/licenses/>.
%% PKG_ADD: stk_init ('pkg_load');
%% PKG_DEL: stk_init ('pkg_unload');
function output = stk_init (command)
if nargin == 0
command = 'pkg_load';
end
% Deduce the root of STK from the path to this function
root = fileparts (mfilename ('fullpath'));
switch command
case 'pkg_load'
stk_init__pkg_load (root);
case 'pkg_unload'
stk_init__pkg_unload (root);
case 'prune_mole'
stk_init__config_mole (root, false, true); % prune, but do not add to path
case 'clear_persistents'
% Note: this implies munlock
stk_init__clear_persistents ();
case 'munlock'
stk_init__munlock ();
case 'addpath'
% Add STK subdirectories to the search path
stk_init__addpath (root);
case 'rmpath'
% Remove STK subdirectories from the search path
stk_init__rmpath (root);
case 'genpath'
% Return the list of all STK "public" subdirectories
output = stk_init__genpath (root);
case 'build_mex'
% Compile all MEX-files in the STK
stk_init__build_mex (root, false);
case 'force_build_mex'
% Compile all MEX-files in the STK
stk_init__build_mex (root, true);
case 'get_make_info'
% Provide make information for STK's MEX-files
output = stk_init__get_make_info ();
case 'test_private_mex'
% Check if the MEX-files located in private dirs are found
stk_init__test_private_mex ();
otherwise
error ('Unknown command.');
end % switch
end % function
%#ok<*NODEF,*WNTAG,*SPERR,*SPWRN,*LERR,*CTCH,*SPERR>
function stk_init__pkg_load (root)
% Add STK's root directory to the path
addpath (root);
% Unlock all possibly mlock-ed STK files and clear all STK functions
% that contain persistent variables
stk_init__clear_persistents ();
% Build MEX-files "in-place"
stk_init__build_mex (root, false);
% Add STK subdirectories to the path
% (note: doing this ATFER building the MEX-files seems to solve
% the problem related to having MEX-files in private folders)
stk_init__addpath (root);
% Check that MEX-files located in private folders are properly detected (note:
% there are no MEX-files in private folders if STK is used as an Octave package)
if exist ('OCTAVE_VERSION', 'builtin') == 5 % Octave
stk_init__test_private_mex ();
end
% Set default options
stk_options_set ('default');
% Select default "parallelization engine"
stk_parallel_engine_set ();
% Hide some warnings about numerical accuracy
warning ('off', 'STK:stk_predict:NegativeVariancesSetToZero');
warning ('off', 'STK:stk_cholcov:AddingRegularizationNoise');
warning ('off', 'STK:stk_param_relik:NumericalAccuracyProblem');
% Uncomment this line if you want to see a lot of details about the internals
% of stk_dataframe and stk_factorialdesign objects:
% stk_options_set ('stk_dataframe', 'disp_format', 'verbose');
end % function
function stk_init__pkg_unload (root)
% Unlock all possibly mlock-ed STK files and clear all STK functions
% that contain persistent variables
stk_init__clear_persistents ();
% Remove STK subdirectories from the path
stk_init__rmpath (root);
% Remove STK root directory from the path
rmpath (root);
end % function
function stk_init__munlock ()
filenames = { ...
'stk_optim_fmincon', ...
'stk_options_set', ...
'stk_parallel_engine_set' };
for i = 1:(length (filenames))
name = filenames{i};
if mislocked (name)
munlock (name);
end
end
end % function
function stk_init__clear_persistents ()
stk_init__munlock ();
filenames = { ...
'stk_disp_progress', ...
'stk_disp_getformat', ...
'stk_expcov_iso', ...
'stk_expcov_aniso', ...
'stk_gausscov_iso', ...
'stk_gausscov_aniso', ...
'stk_materncov_aniso', ...
'stk_materncov_iso', ...
'stk_materncov32_aniso', ...
'stk_materncov32_iso', ...
'stk_materncov52_aniso', ...
'stk_materncov52_iso', ...
'stk_sphcov_iso', ...
'stk_sphcov_aniso', ...
'stk_optim_fmincon', ...
'stk_options_set', ...
'stk_parallel_engine_set' ...
'stk_plot_shadedci' };
for i = 1:(length (filenames))
clear (filenames{i});
end
end % function
function stk_init__addpath (root)
path = stk_init__genpath (root);
% Check for missing directories
for i = 1:length (path)
if ~ exist (path{i}, 'dir')
error (sprintf (['Directory %s does not exist.\n' ...
'Is there a problem in stk_init__genpath ?'], path{i}));
end
end
% Add STK folders to the path
addpath (path{:});
% Selectively add MOLE subdirectories to compensate for missing functions
stk_init__config_mole (root, true, false); % (add to path, but do not prune)
end % function
function path = stk_init__genpath (root)
path = {};
% main function folders
path = [path { ...
fullfile(root, 'arrays' ) ...
fullfile(root, 'arrays', 'generic' ) ...
fullfile(root, 'core' ) ...
fullfile(root, 'covfcs' ) ...
fullfile(root, 'covfcs', 'rbf' ) ...
fullfile(root, 'lm' ) ...
fullfile(root, 'model' ) ...
fullfile(root, 'model', 'noise' ) ...
fullfile(root, 'model', 'prior_struct') ...
fullfile(root, 'param', 'classes' ) ...
fullfile(root, 'param', 'estim' ) ...
fullfile(root, 'sampling' ) ...
fullfile(root, 'utils' ) }];
% 'misc' folder and its subfolders
misc = fullfile (root, 'misc');
path = [path { ...
fullfile(misc, 'design' ) ...
fullfile(misc, 'dist' ) ...
fullfile(misc, 'distrib' ) ...
fullfile(misc, 'error' ) ...
fullfile(misc, 'optim' ) ...
fullfile(misc, 'options' ) ...
fullfile(misc, 'parallel') ...
fullfile(misc, 'pareto' ) ...
fullfile(misc, 'plot' ) ...
fullfile(misc, 'test' ) ...
fullfile(misc, 'text' ) }];
% IAGO
iago = fullfile (root, 'iago');
path = [path {iago ...
fullfile(iago, 'crit' ) ...
fullfile(iago, 'rep' ) ...
fullfile(iago, 'utils' ) }];
% folders that contain examples
path = [path { ...
fullfile(root, 'examples', '01_kriging_basics' ) ...
fullfile(root, 'examples', '02_design_of_experiments') ...
fullfile(root, 'examples', '03_miscellaneous' ) ...
fullfile(root, 'examples', 'datasets' ) ...
fullfile(root, 'examples', 'test_functions' ) }];
end % function
function stk_init__rmpath (root)
s = path ();
regex1 = strcat ('^', escape_regexp (root));
isoctave = (exist ('OCTAVE_VERSION', 'builtin') == 5);
if isoctave
try
% Use the modern name (__octave_config_info__) if possible
% NOTE: feval prevents Matlab from complaining about the underscores
apiver = feval ('__octave_config_info__', 'api_version');
assert (ischar (apiver));
catch
% Use the old name instead
apiver = octave_config_info ('api_version');
end
regex2 = strcat (escape_regexp (apiver), '$');
end
while ~ isempty (s)
[d, s] = strtok (s, pathsep); %#ok<STTOK>
if (~ isempty (regexp (d, regex1, 'once'))) ...
&& ((~ isoctave) || isempty (regexp (d, regex2, 'once'))) ...
&& (~ strcmp (d, root)) % Only remove subdirectories, not the root
rmpath (d);
end
end
end % function
function s = escape_regexp (s)
s = strrep (s, '\', '\\');
s = strrep (s, '+', '\+');
s = strrep (s, '.', '\.');
end % function
function stk_init__build_mex (root, force_recompile)
here = pwd ();
opts.force_recompile = force_recompile;
opts.include_dir = fullfile (root, 'misc', 'include');
% Get information about the MEX-files that need to be built
info = stk_init__get_make_info ();
% Matlab/Octave version info
if exist ('OCTAVE_VERSION', 'builtin') == 5
version_info = ['OCTAVE ' OCTAVE_VERSION];
else
version_info = ['MATLAB ' version];
end
for k = 1:(length (info))
gcc_version_warning = stk_init__compile ...
(version_info, fullfile (root, info(k).relpath), ...
opts, info(k).mexname, info(k).other_src, info(k).includes);
end
% Matlab only: issue GCC version warning only once
if ~ isempty (gcc_version_warning)
warning (gcc_version_warning.id, gcc_version_warning.msg);
end
cd (here);
end % function
function gcc_version_warning = stk_init__compile ...
(version_info, d, opts, mexname, other_src, includes)
mex_filename = [mexname '.' mexext];
mex_fullpath = fullfile (d, mex_filename);
src_filename = [mexname '.c'];
% List of all source files (not counting include files)
src_files = [{src_filename} other_src];
compile = opts.force_recompile;
if ~ compile
% Compile if the MEX is not present or out-dated
dir_mex = dir (mex_fullpath);
compile = isempty (dir_mex);
% Compile if different version of Matlab/Octave (better safe than sorry)
try
fid = fopen ([mex_fullpath '.info']);
assert (strcmp (version_info, fgetl (fid)));
catch
compile = true;
end
if ~ compile
% Compile if one of the source files is more recent than the MEX
for k = 1:(length (src_files))
% Look for src file in current directory
dir_src = dir (fullfile (d, src_files{k}));
if isempty (dir_src)
error ('STK:stk_init__build_mex:FileNotFound', ...
sprintf ('Source file %s not found', src_files{k}));
end
if dir_mex.datenum < dir_src.datenum
compile = true;
break;
end
end
if (~ compile) && (~ isempty (includes))
% Compile if one of the include files is more recent than the MEX
for k = 1:(length (includes))
% Look for header file in current directory
dir_hdr = dir (fullfile (d, includes{k}));
if isempty (dir_hdr)
% Look for header file in include directory
dir_hdr = dir (fullfile (opts.include_dir, includes{k}));
if isempty (dir_hdr)
error ('STK:stk_init__build_mex:FileNotFound', ...
sprintf ('Header file %s not found', includes{k}));
end
end
if dir_mex.datenum < dir_hdr.datenum
compile = true;
break;
end
end
end
end
end
gcc_version_warning = [];
isoctave = (exist ('OCTAVE_VERSION', 'builtin') == 5);
persistent use_silent
if isoctave && (isempty (use_silent))
use_silent = false;
end
if compile
fprintf ('Compiling MEX-file %s... ', mexname);
here = pwd ();
try % Safely change directory
cd (d);
include = sprintf ('-I%s', opts.include_dir);
if isoctave
mex (src_files{:}, include);
else
warning_state = warning ('off', 'MATLAB:mex:GccVersion_link');
lastwarn ('');
if isempty (use_silent)
% Try with -silent (only supported in recent versions of Matlab)
try
mex ('-silent', src_files{:}, include);
use_silent = true;
catch
% Try without -silent
mex (src_files{:}, include);
use_silent = false;
end
elseif use_silent
mex ('-silent', src_files{:}, include);
else
mex (src_files{:}, include);
end
[lastmsg, lastid] = lastwarn ();
if ~ isempty (strfind (lastid, 'GccVersion')) %#ok<STREMP>
gcc_version_warning.msg = lastmsg;
gcc_version_warning.id = lastid;
end
warning (warning_state);
end
fid = fopen ([mex_fullpath '.info'], 'wt');
fprintf (fid, version_info);
fclose (fid);
fprintf ('ok.\n');
if isoctave
fflush (stdout);
end
cd (here);
catch
cd (here);
rethrow (lasterror ());
end
end
end % function
function info = stk_init__get_make_info ()
relpath = fullfile ('misc', 'dist', 'private');
info = register_mex ([], relpath, 'stk_dist_matrixx');
info = register_mex (info, relpath, 'stk_dist_matrixy');
info = register_mex (info, relpath, 'stk_dist_pairwise');
info = register_mex (info, relpath, 'stk_filldist_discr_mex');
info = register_mex (info, relpath, 'stk_mindist_mex');
info = register_mex (info, relpath, 'stk_gpquadform_matrixy');
info = register_mex (info, relpath, 'stk_gpquadform_matrixx');
info = register_mex (info, relpath, 'stk_gpquadform_pairwise');
relpath = fullfile ('misc', 'distrib', 'private');
info = register_mex (info, relpath, 'stk_distrib_bivnorm0_cdf');
relpath = fullfile ('arrays', '@stk_dataframe', 'private');
info = register_mex (info, relpath, 'get_column_number');
relpath = 'sampling';
info = register_mex (info, relpath, 'stk_sampling_vdc_rr2', {}, {'primes.h'});
relpath = fullfile ('sampling', 'private');
info = register_mex (info, relpath, 'stk_sampling_sobol_mex');
relpath = fullfile ('misc', 'pareto', 'private');
info = register_mex (info, relpath, 'stk_paretofind_mex', {}, {'pareto.h'});
info = register_mex (info, relpath, 'stk_isdominated_mex', {}, {'pareto.h'});
info = register_mex (info, relpath, 'stk_dominatedhv_mex', {'wfg.c'}, {'wfg.h'});
end % function
function info = register_mex (info, relpath, mexname, other_src, includes)
if nargin < 4
other_src = {};
end
if nargin < 5
includes = {};
end
k = 1 + length (info);
info(k).relpath = relpath;
info(k).mexname = mexname;
info(k).other_src = other_src;
info(k).includes = [{'stk_mex.h'} includes];
end % function
function stk_init__test_private_mex ()
try
n = 5; d = 2;
x = rand (n, d);
D = stk_dist (x); % calls a MEX-file internally
assert (isequal (size (D), [n n]));
catch
err = lasterror ();
if (~ isempty (regexp (err.message, 'stk_dist_matrixx', 'once'))) ...
&& (~ isempty (regexp (err.message, 'undefined', 'once')))
fprintf ('\n\n');
warning (sprintf (['\n\n' ...
'!>>>>>> PLEASE RESTART OCTAVE BEFORE USING STK <<<<<<!\n' ...
'! !\n' ...
'! Some STK functions implemented as MEX-files have !\n' ...
'! just been compiled, but will not be detected until !\n' ...
'! Octave is restarted. !\n' ...
'! !\n' ...
'! We apologize for this inconvenience, which is !\n' ...
'! related to a known Octave bug (bug #40824), that !\n' ...
'! will hopefully be fixed in the near future. !\n' ...
'! (see https://savannah.gnu.org/bugs/?40824) !\n' ...
'! !\n' ...
'!>>>>>> PLEASE RESTART OCTAVE BEFORE USING STK <<<<<<!\n' ...
'\n']));
else
rethrow (err);
end
end
end % function
function stk_init__config_mole (root, do_addpath, prune_unused)
mole_dir = fullfile (root, 'misc', 'mole');
isoctave = (exist ('OCTAVE_VERSION', 'builtin') == 5);
if isoctave
recursive_rmdir_state = confirm_recursive_rmdir (0);
end
opts = {root, mole_dir, do_addpath, prune_unused};
% Provide missing octave functions for Matlab users
% TODO: extract functions that are REALLY needed in separate directories
% and get rid of the others !
if (exist ('OCTAVE_VERSION', 'builtin') ~= 5) % if Matlab
if do_addpath
addpath (fullfile (mole_dir, 'matlab'));
end
elseif prune_unused
rmdir (fullfile (mole_dir, 'matlab'), 's');
end
% graphics_toolkit
% * For Octave users: available in Octave >= 4.0.0
% * For Matlab users: there is no function named graphics_toolkit in Matlab.
% Our implementation returns either 'matlab-jvm' or 'matlab-nojvm'.
install_mole_function ('graphics_toolkit', opts{:});
% quantile
% * For Octave users: available in Octave >= 4.0.0
% * For Matlab users: quantile is missing from Matlab itself, but it provided
% by the Statistics toolbox if you're rich enough to afford it.
install_mole_function ('quantile', opts{:});
% cleanup
if isoctave
confirm_recursive_rmdir (recursive_rmdir_state);
end
end % function
function install_mole_function (funct_name, ...
root, mole_dir, do_addpath, prune_unused)
function_dir = fullfile (mole_dir, funct_name);
w = which (funct_name);
if (isempty (w)) || (~ isempty (strfind (w, root))) %#ok<STREMP> % if the function is absent
function_mfile = fullfile (function_dir, [funct_name '.m']);
if exist (function_dir, 'dir') && exist (function_mfile, 'file')
% fprintf ('[MOLE] Providing function %s\n', function_name);
if do_addpath
addpath (function_dir);
end
else
warning (sprintf ('[MOLE] Missing function: %s\n', funct_name));
end
elseif prune_unused && (exist (function_dir, 'dir'))
rmdir (function_dir, 's');
end
end % function