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…tional changes

triggered by bids-standard/bids-specification#1003 I checked how merging of JSON (and other) structures happens in FieldTrip. I figured that making the function names slightly more consistent would be a good step towards potential future improvements.
8 contributors

Users who have contributed to this file

@robertoostenveld @Spaak @ThreeFive-O @schoffelen @nno @roemervandermeij @apjanke @bmjstau
function ft_defaults
% FT_DEFAULTS (ending with "s") sets some general settings in the global variable
% ft_default (without the "s") and takes care of the required path settings. You can
% call this function in your startup.m script. This function is also called at the
% begin of all FieldTrip functions.
%
% The global configuration defaults are stored in the global "ft_default" structure.
% The ft_checkconfig function that is called by many FieldTrip functions will merge
% these global configuration defaults with the cfg ctructure that you pass to
% the FieldTrip function that you are calling.
%
% The global options and their default values are
% ft_default.checkconfig = string, can be 'pedantic', 'loose', 'silent' (default = 'loose')
% ft_default.checkpath = string, can be 'pedantic', 'once', 'no' (default = 'pedantic')
% ft_default.checksize = number in bytes, can be inf (default = 1e5)
% ft_default.showlogo = string, can be 'yes' or 'no' (default = 'yes')
% ft_default.showcallinfo = string, can be 'yes' or 'no' (default = 'yes')
% ft_default.trackcallinfo = string, can be 'yes' or 'no' (default = 'yes')
% ft_default.trackconfig = string, can be 'cleanup', 'report', 'off' (default = 'off')
% ft_default.trackusage = false, or string with salt for one-way encryption of identifying information (by default this is enabled and an automatic salt is created)
% 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.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
% ft_defaults
% global ft_default
% ft_default.option1 = value1
% 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.
%
% See also FT_HASTOOLBOX, FT_CHECKCONFIG, FT_TRACKUSAGE
% undocumented options
% ft_default.siunits = 'yes' or 'no'
% Copyright (C) 2009-2022, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip 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.
%
% FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
global ft_default
persistent initialized
persistent checkpath
if isempty(initialized)
initialized = false;
end
if isempty(checkpath)
checkpath = false;
end
% ft_warning is located in fieldtrip/utilities, which may not be on the path yet
if ~exist('ft_warning', 'file')
ft_warning = @warning;
end
% locate the file with the persistent FieldTrip preferences
fieldtripprefs = fullfile(prefdir, 'fieldtripprefs.mat');
if exist(fieldtripprefs, 'file')
prefs = load(fieldtripprefs); % the file contains multiple fields
ft_default = mergestruct(ft_default, prefs);
end
% Set the defaults in a global variable, ft_checkconfig will copy these over into the local configuration.
% NOTE ft_getopt might not be available on the path at this moment and can therefore not yet be used.
% NOTE all options here should be explicitly listed as allowed in ft_checkconfig
if ~isfield(ft_default, 'trackconfig'), ft_default.trackconfig = 'off'; end % cleanup, report, off
if ~isfield(ft_default, 'checkconfig'), ft_default.checkconfig = 'loose'; end % pedantic, loose, silent
if ~isfield(ft_default, 'checkpath'), ft_default.checkpath = 'pedantic'; end % pedantic, once, no
if ~isfield(ft_default, 'checksize'), ft_default.checksize = 1e5; end % number in bytes, can be inf
if ~isfield(ft_default, 'showlogo'), ft_default.showlogo = 'yes'; end % yes or no, this is relevant for SPM and EEGLAB
if ~isfield(ft_default, 'showcallinfo'), ft_default.showcallinfo = 'yes'; end % yes or no, this is used in ft_pre/postamble_provenance
if ~isfield(ft_default, 'debug'), ft_default.debug = 'no'; end % no, save, saveonerror, display, displayonerror, this is used in ft_pre/postamble_debug
if ~isfield(ft_default, 'outputfilepresent'), ft_default.outputfilepresent = 'overwrite'; end % can be keep, overwrite, error
% These options allow to disable parts of the provenance
if ~isfield(ft_default, 'trackcallinfo'), ft_default.trackcallinfo = 'yes'; end % yes or no
if ~isfield(ft_default, 'trackdatainfo'), ft_default.trackdatainfo = 'no'; end % yes or no
if ~isfield(ft_default, 'tracktimeinfo'), ft_default.tracktimeinfo = 'yes'; end % yes or no
if ~isfield(ft_default, 'trackmeminfo')
if ispc()
% don't track memory usage info under Windows; this does not work (yet)
ft_default.trackmeminfo = 'no';
else
ft_default.trackmeminfo = 'yes';
end
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
% 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
switch ft_default.checkpath
case 'pedantic'
% check every time
checkIncorrectPath();
case 'once'
% check only once
if ~checkpath
checkIncorrectPath();
checkpath = true;
end
case 'no'
% do not check
end % case
% Check whether this ft_defaults function has already been executed. Note that we
% should not use ft_default itself directly, because the user might have set stuff
% in that struct already prior to ft_defaults being called for the first time.
if initialized && exist('ft_hastoolbox', 'file')
return;
end
if isfield(ft_default, 'toolbox') && isfield(ft_default.toolbox, 'cleanup')
prevcleanup = ft_default.toolbox.cleanup;
else
prevcleanup = {};
end
if strcmp(ft_default.showlogo, 'yes')
% show a welcome message
fprintf([
'-------------------------------------------------------------------------------------------' ...
'\nFieldTrip is developed by members and collaborators of the Donders Institute for Brain,' ...
'\nCognition and Behaviour at Radboud University, Nijmegen, the Netherlands.' ...
'\n'...
'\n --------------------------'...
'\n / \\'...
'\n ------------------------------------'...
'\n / \\'...
'\n -------------------------------------------------'...
'\n / /\\/\\/\\/\\/\\ '...
'\n ---------------------------------------------------'...
'\n | F i e l d T r i p |'...
'\n ------------------------------------------'...
'\n \\ /'...
'\n ------------------------------------'...
'\n \\ /'...
'\n ----------'...
'\n' ...
'\nPlease cite the FieldTrip reference paper when you have used FieldTrip in your study.' ...
'\nRobert Oostenveld, Pascal Fries, Eric Maris, and Jan-Mathijs Schoffelen. FieldTrip: Open' ...
'\nSource Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data.' ...
'\nComputational Intelligence and Neuroscience, vol. 2011, Article ID 156869, 9 pages, 2011.' ...
'\ndoi:10.1155/2011/156869.' ...
'\n-------------------------------------------------------------------------------------------\n'
]);
end % if showlogo
% Ensure that the path containing ft_defaults is on the path.
% This allows people to do "cd path_to_fieldtrip; ft_defaults"
ftPath = fileparts(mfilename('fullpath')); % get the full path to this function, strip away 'ft_defaults'
ftPath = strrep(ftPath, '\', '\\');
if isempty(regexp(path, [ftPath pathsep '|' ftPath '$'], 'once'))
ft_warning('FieldTrip is not yet on your MATLAB path, adding %s', strrep(ftPath, '\\', '\'));
addpath(ftPath);
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');
checkMultipleToolbox('spm', 'spm.m');
checkMultipleToolbox('mne', 'fiff_copy_tree.m');
checkMultipleToolbox('eeglab', 'eeglab2fieldtrip.m');
checkMultipleToolbox('dipoli', 'write_tri.m');
checkMultipleToolbox('eeprobe', 'read_eep_avr.mexa64');
checkMultipleToolbox('yokogawa', 'GetMeg160ChannelInfoM.p');
checkMultipleToolbox('simbio', 'sb_compile_vista.m');
checkMultipleToolbox('fns', 'fns_region_read.m');
checkMultipleToolbox('bemcp', 'bem_Cii_cst.mexa64');
checkMultipleToolbox('bci2000', 'load_bcidat.m');
checkMultipleToolbox('openmeeg', 'openmeeg_helper.m');
checkMultipleToolbox('freesurfer', 'vox2ras_ksolve.m');
checkMultipleToolbox('fastica', 'fastica.m');
checkMultipleToolbox('besa', 'readBESAmul.m');
checkMultipleToolbox('neuroshare', 'ns_GetAnalogData.m');
checkMultipleToolbox('ctf', 'setCTFDataBalance.m');
checkMultipleToolbox('afni', 'WriteBrikHEAD.m');
checkMultipleToolbox('gifti', '@gifti/display.m');
checkMultipleToolbox('sqdproject', 'sqdread.m');
checkMultipleToolbox('xml4mat', 'xml2mat.m');
checkMultipleToolbox('cca', 'ccabss.m');
checkMultipleToolbox('bsmart', 'armorf.m');
checkMultipleToolbox('iso2mesh', 'iso2meshver.m');
checkMultipleToolbox('bct', 'degrees_und.m');
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')
addpath(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')
addpath(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')
addpath(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
if ft_platform_supports('matlabversion', -inf, '2008b'), ft_hastoolbox('compat/matlablt2009a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2009a'), ft_hastoolbox('compat/matlablt2009b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2009b'), ft_hastoolbox('compat/matlablt2010a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2010a'), ft_hastoolbox('compat/matlablt2010b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2010b'), ft_hastoolbox('compat/matlablt2011a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2011a'), ft_hastoolbox('compat/matlablt2011b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2011b'), ft_hastoolbox('compat/matlablt2012a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2012a'), ft_hastoolbox('compat/matlablt2012b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2012b'), ft_hastoolbox('compat/matlablt2013a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2013a'), ft_hastoolbox('compat/matlablt2013b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2013b'), ft_hastoolbox('compat/matlablt2014a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2014a'), ft_hastoolbox('compat/matlablt2014b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2014d'), ft_hastoolbox('compat/matlablt2015a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2015a'), ft_hastoolbox('compat/matlablt2015b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2015b'), ft_hastoolbox('compat/matlablt2016a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2016a'), ft_hastoolbox('compat/matlablt2016b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2016b'), ft_hastoolbox('compat/matlablt2017a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2017a'), ft_hastoolbox('compat/matlablt2017b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2017b'), ft_hastoolbox('compat/matlablt2018a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2018a'), ft_hastoolbox('compat/matlablt2018b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2018b'), ft_hastoolbox('compat/matlablt2019a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2019a'), ft_hastoolbox('compat/matlablt2019b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2019b'), ft_hastoolbox('compat/matlablt2020a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2020a'), ft_hastoolbox('compat/matlablt2020b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2020b'), ft_hastoolbox('compat/matlablt2021a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2021a'), ft_hastoolbox('compat/matlablt2021b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2021b'), ft_hastoolbox('compat/matlablt2022a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2022a'), ft_hastoolbox('compat/matlablt2022b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2022b'), ft_hastoolbox('compat/matlablt2023a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2023a'), ft_hastoolbox('compat/matlablt2023b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2023b'), ft_hastoolbox('compat/matlablt2024a', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2024a'), ft_hastoolbox('compat/matlablt2024b', 3, 1); end
if ft_platform_supports('matlabversion', -inf, '2024b'), ft_hastoolbox('compat/matlablt2025a', 3, 1); end
% 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);
ft_hastoolbox('template/anatomy', 1, 1);
ft_hastoolbox('template/headmodel', 1, 1);
ft_hastoolbox('template/electrode', 1, 1);
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
ft_default.toolbox.cleanup = prevcleanup;
% track the usage of this function, this only happens once at startup
ft_trackusage('startup');
% remember that the function has executed in a persistent variable
initialized = true;
end % function ft_default
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function checkMultipleToolbox(toolbox, keyfile)
persistent warned
if isempty(warned)
warned = false;
end
if ~ft_platform_supports('which-all')
return;
end
list = which(keyfile, '-all');
if length(list)>1
ft_warning('Multiple versions of %s on your path will confuse FieldTrip', toolbox);
if ~warned % only throw the following warnings once
warned = true;
for i=1:length(list)
ft_warning('one version of %s is found here: %s', toolbox, list{i});
end
end
ft_warning('You probably used addpath(genpath(''path_to_fieldtrip'')), this can lead to unexpected behavior. See http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path');
end
end % function checkMultipleToolbox
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function checkIncorrectPath
p = fileparts(mfilename('fullpath'));
incorrect = fullfile(p, 'compat', 'incorrect');
if ~isempty(strfind(path, incorrect))
ft_warning('Your path is set up incorrectly. You probably used addpath(genpath(''path_to_fieldtrip'')), this can lead to unexpected behavior. See http://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path');
end
end % function checkIncorrectPath