Skip to content

Commit

Permalink
Merge commit '240fdf3' into release
Browse files Browse the repository at this point in the history
  • Loading branch information
@robertoostenveld
robertoostenveld committed Jul 29, 2022
2 parents 51cabc3 + 240fdf3 commit f1d1993
Showing 1 changed file with 48 additions and 32 deletions.
80 changes: 48 additions & 32 deletions ft_defaults.m
View file
Expand Up @@ -22,9 +22,9 @@
% ft_default.trackdatainfo = string, can be 'yes' or 'no' (default = 'no')
% ft_default.outputfilepresent = string, can be 'keep', 'overwrite', 'error' (default = 'overwrite')
% ft_default.debug = string, can be 'display', 'displayonerror', 'displayonsuccess', 'save', 'saveonerror', saveonsuccess' or 'no' (default = 'no')
% ft_default.toolbox.signal = string, can be 'compat' or 'matlab' (default = 'compat')
% ft_default.toolbox.stats = string, can be 'compat' or 'matlab' (default = 'compat')
% ft_default.toolbox.images = string, can be 'compat' or 'matlab' (default = 'compat')
% ft_default.toolbox.signal = string, can be 'compat' or 'matlab' (default is automatic, see below)
% ft_default.toolbox.stats = string, can be 'compat' or 'matlab' (default is automatic, see below)
% ft_default.toolbox.images = string, can be 'compat' or 'matlab' (default is automatic, see below)
% ft_default.reproducescript = string, directory to which the script and intermediate data are written (default = [])
%
% If you want to overrule these default settings, you can add something like this in your startup.m script
Expand All @@ -34,11 +34,15 @@
% ft_default.option2 = value2
%
% The toolbox option for signal, stats and images allows you to specify whether you
% want to use a compatible drop-in to be used for these MathWorks toolboxes, or the
% original version from MathWorks. The default is 'compat', which has the advantage
% that you do not need a license for these toolboxes.
% want to use the original version from MathWorks or a compatible drop-in to be used.
% When you use the Radboud University license server, i.e. at the Donders, the
% default is 'compat'. This has the advantage that you do not need a license for
% these toolboxes; we do not have that many licenses and parallel computations on our
% Donders compute cluster would otherwise use all licenses. In all other cases, the
% default is 'matlab' when the toolbox is available, and 'compat' when it is not
% available.
%
% See also FT_HASTOOLBOX, FT_CHECKCONFIG, FT_TRACKUSAGE
% See also FT_HASTOOLBOX, FT_CHECKCONFIG, FT_TRACKUSAGE, LICENSE

% undocumented options
% ft_default.siunits = 'yes' or 'no'
Expand Down Expand Up @@ -114,11 +118,23 @@
end
end

if strcmp(license(), '38957')
% within the Donders and Radboud University the default is compat, since we do not have that many licenses
default_images = 'compat';
default_stats = 'compat';
default_signal = 'compat';
else
% in this case it will still check whether the Mathworks toolbox is available and if not, the compatible version will be added
default_images = 'matlab';
default_stats = 'matlab';
default_signal = 'matlab';
end

% These options allow to prefer the MATLAB toolbox implementations ('matlab') over the drop-in replacements ('compat').
if ~isfield(ft_default, 'toolbox'), ft_default.toolbox = []; end
if ~isfield(ft_default.toolbox, 'images'), ft_default.toolbox.images = 'compat'; end % matlab or compat
if ~isfield(ft_default.toolbox, 'stats') , ft_default.toolbox.stats = 'compat'; end % matlab or compat
if ~isfield(ft_default.toolbox, 'signal'), ft_default.toolbox.signal = 'compat'; end % matlab or compat
if ~isfield(ft_default.toolbox, 'images'), ft_default.toolbox.images = default_images; end % matlab or compat
if ~isfield(ft_default.toolbox, 'stats') , ft_default.toolbox.stats = default_stats; end % matlab or compat
if ~isfield(ft_default.toolbox, 'signal'), ft_default.toolbox.signal = default_signal; end % matlab or compat

% Some people mess up their path settings and then have stuff on the path that should not be there.
% The following will issue a warning
Expand Down Expand Up @@ -189,13 +205,13 @@
end

if ~isdeployed

if isempty(which('ft_hastoolbox')) || isempty(which('ft_warning'))
% the fieldtrip/utilities directory contains the ft_hastoolbox and ft_warning
% functions, which are required for the remainder of this script
addpath(fullfile(fileparts(which('ft_defaults')), 'utilities'));
end

% Some people mess up their path settings and then have different versions of certain toolboxes on the path.
% The following will issue a warning
checkMultipleToolbox('FieldTrip', 'ft_defaults.m');
Expand Down Expand Up @@ -226,7 +242,7 @@
checkMultipleToolbox('yokogawa_meg_reader', 'getYkgwHdrEvent.p');
checkMultipleToolbox('biosig', 'sopen.m');
checkMultipleToolbox('icasso', 'icassoEst.m');

try
% external/signal contains alternative implementations of some signal processing functions
if ~ft_platform_supports('signal') || ~strcmp(ft_default.toolbox.signal, 'matlab') || ~ft_hastoolbox('signal')
Expand All @@ -235,7 +251,7 @@
rmpath(fullfile(fileparts(which('ft_defaults')), 'external', 'signal'));
end
end

try
% external/stats contains alternative implementations of some statistics functions
if ~ft_platform_supports('stats') || ~strcmp(ft_default.toolbox.stats, 'matlab') || ~ft_hastoolbox('stats')
Expand All @@ -244,7 +260,7 @@
rmpath(fullfile(fileparts(which('ft_defaults')), 'external', 'stats'));
end
end

try
% external/images contains alternative implementations of some image processing functions
if ~ft_platform_supports('images') || ~strcmp(ft_default.toolbox.images, 'matlab') || ~ft_hastoolbox('images')
Expand All @@ -253,12 +269,12 @@
rmpath(fullfile(fileparts(which('ft_defaults')), 'external', 'images'));
end
end

try
% this directory contains various functions that were obtained from elsewere, e.g. MATLAB file exchange
ft_hastoolbox('fileexchange', 3, 1); % not required
end

try
% these directories deal with compatibility with older MATLAB versions
if ft_platform_supports('matlabversion', -inf, '2008a'), ft_hastoolbox('compat/matlablt2008b', 3, 1); end
Expand Down Expand Up @@ -298,7 +314,7 @@
% this deals with compatibility with all OCTAVE versions
if ft_platform_supports('octaveversion', -inf, +inf), ft_hastoolbox('compat/octave', 3, 1); end
end

try
% these contains template layouts, neighbour structures, MRIs and cortical meshes
ft_hastoolbox('template/layout', 1, 1);
Expand All @@ -308,75 +324,75 @@
ft_hastoolbox('template/neighbours', 1, 1);
ft_hastoolbox('template/sourcemodel', 1, 1);
end

try
% this is used in ft_statistics
ft_hastoolbox('statfun', 1, 1);
end

try
% this is used in ft_definetrial
ft_hastoolbox('trialfun', 1, 1);
end

try
% this contains the low-level reading functions
ft_hastoolbox('fileio', 1, 1);
end

try
% this is for filtering etc. on time-series data
ft_hastoolbox('preproc', 1, 1);
end

try
% this contains forward models for the EEG and MEG volume conductor
ft_hastoolbox('forward', 1, 1);
end

try
% this contains inverse source estimation methods
ft_hastoolbox('inverse', 1, 1);
end

try
% this contains intermediate-level plotting functions, e.g. multiplots and 3-d objects
ft_hastoolbox('plotting', 1, 1);
end

try
% this contains intermediate-level functions for spectral analysis
ft_hastoolbox('specest', 1, 1);
end

try
% this contains the functions to compute connectivity metrics
ft_hastoolbox('connectivity', 1, 1);
end

try
% this contains test scripts
ft_hastoolbox('test', 1, 1);
end

try
% this contains the functions for spike and spike-field analysis
ft_hastoolbox('contrib/spike', 1, 1);
end

try
% this contains user contributed functions
ft_hastoolbox('contrib/misc', 1, 1);
end

try
% this contains specific code and examples for realtime processing
ft_hastoolbox('realtime/example', 3, 1); % not required
ft_hastoolbox('realtime/online_mri', 3, 1); % not required
ft_hastoolbox('realtime/online_meg', 3, 1); % not required
ft_hastoolbox('realtime/online_eeg', 3, 1); % not required
end

end

% the toolboxes added by this function should not be removed by FT_POSTAMBLE_HASTOOLBOX
Expand Down

0 comments on commit f1d1993

Please sign in to comment.