% pop_micro_smooth() - Temporally smooths microstate labels
%
% Temporally smooths microstate labels obtained either from segmentation or
% from backfitting. The labels should be stored in either
% EEG.microstate.labels or EEG.microstate.fit.labels, correspondingly.
%
% Usage:
% >> EEG = pop_micro_smooth ( EEG ); % pop up window
% >> EEG = pop_micro_smooth ( EEG, 'key1', 'val1')
%
% Please cite this toolbox as:
% Poulsen, A. T., Pedroni, A., Langer, N., & Hansen, L. K. (2018).
% Microstate EEGlab toolbox: An introductionary guide. bioRxiv.
%
% Inputs:
% EEG - EEGlab EEG structure with microstate field.
%
% Optional input:
% 'label_type' - Smooth labels obtained from: 'segmentation' (default)
% or 'backfit'.
% 'smooth_type' - Smoothing type: 'reject segments' (default) or
% 'windowed'.
%
% Method-specific inputs:
% * Reject segments:
% 'minTime' - Redristibute segments smaller than minTime (in ms) to
% the next best fitting microstate (default = 20 ms).
% 'polarity' - Account for polarity when calculating the global map
% dissimilarity. Typically off for spontaneous EEG and on
% for ERP data (default = 0).
% * Windowed smoothing:
% 'smooth_width' - Temporal smoothing width. Integer denoting the
% number of samples on each side of current sample
% (default: 3).
% 'smooth_weight' - Temporal smoothing weight (default: 5).
% 'max_iterations' - Maximum number of iterations of algorithm
% (default: 1000).
% 'threshold' - Threshold of convergence based on relative change
% in noise variance (default: 1e-6).
%
% Output:
% EEG - EEGlab struct with updated microstate labels.
%
% Authors:
% Andreas Trier Poulsen, atpo@dtu.dk
% Technical University of Denmark, DTU Compute, Cognitive systems.
%
% Andreas Pedroni, andreas.pedroni@uzh.ch
% University of Zürich, Psychologisches Institut, Methoden der
% Plastizitätsforschung.
%
% September 2017.
%
% See also: eeglab pop_micro_segment pop_micro_fit
% Copyright (C) 2017 Andreas Trier Poulsen, atpo@dtu.dk
%
% This program 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 2 of the License, or
% (at your option) any later version.
%
% This program 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 this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [EEG, com] = pop_micro_smooth(EEG, varargin)
%% Error check and initialisation
if nargin < 1
help pop_micro_smooth;
return;
end
% check whether microstate substruct exists.
if ~isfield(EEG,'microstate')
error('No microstate data present. Run microstate segmentation first.')
end
com = '';
%% pop-up window in case no further input is given
if nargin < 2
settings = smooth_popup();
if strcmp(settings,'cancel')
return
end
if strcmp(settings.smooth_type,'reject segments')
disp('Smoothing microstate labels using reject small segments...')
else
disp('Smoothing microstate labels using windowed smoothing...')
end
else
settings = check_settings(varargin);
end
%% Select data
if strcmp(settings.label_type,'segmentation')
if ischar(EEG.microstate.data)
data = EEG.data;
else
data = EEG.microstate.data;
end
else
data = EEG.data;
end
% Prototypes
A = EEG.microstate.prototypes;
%% Ready smoothing-specific settings
if strcmp(settings.smooth_type,'windowed')
opts.b = settings.smooth_width;
opts.lambda = settings.smooth_weight;
opts.max_iterations = settings.max_iterations;
opts.thresh = settings.threshold;
else
opts.polarity = settings.polarity;
% converting minTime from ms to samples
minTime_ms = settings.minTime;
minTime_samples = round( minTime_ms * EEG.srate/1000 );
opts.minTime = minTime_samples;
end
%% Run smoothing
labels = MicroSmooth(data, A, settings.smooth_type, opts);
%% Save smoothed labels
if strcmp(settings.label_type,'segmentation')
EEG.microstate.labels = labels;
else
EEG.microstate.fit.labels = labels;
end
%% Define command string
com = sprintf('%s = pop_micro_smooth( %s', inputname(1), inputname(1));
com = settings_to_string(com,settings);
com = [com ' );'];
end
% ------------------------------ Pop-ups ---------------------------------%
function settings = smooth_popup()
% Function for creating popup window to input settings
%
%% Create Inputs for popup
% Select labels to smooth
style.label_type = 'popupmenu';
dropdown_label = {'Microstate segmentation' 'Backfitting prototypes to EEG'}; % For dropdown menu
popmenu.label_type = {'segmentation' 'backfit'}; % Corresponding calls for pop-function
label_str = dropdown_label{1}; %string for popupmenu
for l = 2:length(dropdown_label); label_str = [label_str '|' dropdown_label{l}]; end
line.label_type = { {'Style' 'text' 'string' 'Smooth labels obtained from:'}, ...
{'Style' style.label_type 'string' label_str 'tag' 'label_type' 'value' 1} };
geo.label_type = {[1 1]};
% Smoothing type
style.smooth_type = 'popupmenu';
dropdown_smooth = {'Reject small segments' 'Windowed smoothing'}; % For dropdown menu
popmenu.smooth_type = {'reject segments' 'windowed'}; % Corresponding calls for pop-function
smooth_str = dropdown_smooth{1}; %string for popupmenu
for s = 2:length(dropdown_smooth); smooth_str = [smooth_str '|' dropdown_smooth{s}]; end
line.smooth_type = { {'Style' 'text' 'string' 'Choose smoothing method:'}, ...
{'Style' style.smooth_type 'string' smooth_str 'tag' 'smooth_type' 'value' 1} };
geo.smooth_type = {[1 1]};
%% Order inputs for GUI
geometry = [geo.label_type geo.smooth_type];
uilist = [line.label_type line.smooth_type];
%% Create Popup
[~,~,~,pop_out] = inputgui( geometry, uilist, ...
'pophelp(''pop_micro_smooth'');', 'Smooths microstate labels -- pop_micro_smooth()');
%% Interpret output from popup
if isstruct(pop_out)
settings = struct;
settings = interpret_popup(pop_out, settings, style, popmenu);
else
settings = 'cancel';
end
%% Create popup for smoothing specific settings
if ~strcmp(settings,'cancel')
switch settings.smooth_type
case 'reject segments'
settings = reject_popup(settings);
case 'windowed'
settings = window_popup(settings);
otherwise
error(['selected smooth type,''' settings.smooth_type ''' not available'])
end
end
end
function settings = reject_popup(settings)
% Popup for unique input for reject small segments
%
%% Create Inputs for popup
% Title string
info_str = 'Input parameters specific for ''Reject small segments''.';
line.info = { {'Style' 'text' 'string' info_str} {} };
geo.info = {1 1};
% Redristibute segments (minTime)
style.minTime = 'edit';
line.minTime = { {'Style' 'text' 'string' 'Redistribute segments smaller than (in ms):'}, ...
{'Style' style.minTime 'string' ' 30 ' 'tag' 'minTime'} };
geo.minTime = {[1 .2]};
% Polarity
style.polarity = 'checkbox';
pol_tipstr = 'Spontaneous EEG typically ignore polarity (off). Typically on for ERP data.';
line.polarity = { {'Style' 'text' 'string' 'Account for polarity when fitting.' ...
'tooltipstring' pol_tipstr}, ...
{'Style' style.polarity 'value' 0 'tag' 'polarity'} };
geo.polarity = {[1 .2]};
%% Order inputs for GUI
geometry = [geo.info geo.minTime geo.polarity];
uilist = [line.info line.minTime line.polarity];
%% Create Popup
[~,~,~,pop_out] = inputgui( geometry, uilist, ...
'pophelp(''pop_micro_smooth'');', 'Extra input for reject small segments -- pop_micro_smooth()');
%% Interpret output from popup
if isstruct(pop_out)
settings = interpret_popup(pop_out, settings, style);
else
settings = 'cancel';
end
end
function settings = window_popup(settings)
% Popup for unique input for windowed smoothing
%
%% Create Inputs for popup
% Title string
info_str = 'Input parameters specific for ''Windowed smoothing''.';
line.info = { {'Style' 'text' 'string' info_str} {} };
geo.info = {1 1};
% Smoothing width
style.smooth_width = 'edit';
line.smooth_width = { {'Style' 'text' 'string' 'Width of smoothing windows (in samples):'}, ...
{'Style' style.smooth_width 'string' ' 3 ' 'tag' 'smooth_width'} };
geo.smooth_width = {[1 .2]};
% Smoothing weight
style.smooth_weight = 'edit';
line.smooth_weight = { {'Style' 'text' 'string' 'Smoothing weight:'}, ...
{'Style' style.smooth_weight 'string' ' 5 ' 'tag' 'smooth_weight'} };
geo.smooth_weight = {[1 .2]};
% Max iterations
style.max_iterations = 'edit';
line.max_iterations = { {'Style' 'text' 'string' 'Max. no. of iterations:'}, ...
{'Style' style.max_iterations 'string' ' 1000 ' 'tag' 'max_iterations'} };
geo.max_iterations = {[1 .2]};
% Threshold
style.threshold = 'edit';
line.threshold = { {'Style' 'text' 'string' 'Relative threshold for convergence:'}, ...
{'Style' style.threshold 'string' ' 1e-6 ' 'tag' 'threshold'} };
geo.threshold = {[1 .2]};
%% Order inputs for GUI
geometry = [geo.info geo.smooth_width geo.smooth_weight geo.max_iterations geo.threshold];
uilist = [line.info line.smooth_width line.smooth_weight line.max_iterations line.threshold];
%% Create Popup
[~,~,~,pop_out] = inputgui( geometry, uilist, ...
'pophelp(''pop_micro_smooth'');', 'Extra input for windowed smoothing -- pop_micro_smooth()');
%% Interpret output from popup
if isstruct(pop_out)
settings = interpret_popup(pop_out, settings, style);
else
settings = 'cancel';
end
end
% ----------------------------------------------------------------------- %
% -------------------------- Helper functions --------------------------- %
function settings = check_settings(vargs)
% Checks settings given as optional inputs for pop_micro_smooth.
% The function checks and rearranges optional inputs to pop_micro_smooth.m
% struct. Undefined inputs is set to default values.
%% General inputs
varg_check = { 'label_type' 'string' [] 'segmentation'
'smooth_type' 'string' [] 'reject segments'};
%% Algorithm specifik inputs
smooth_type = find(strcmp('smooth_type',vargs)) + 1;
switch vargs{smooth_type}
case 'reject segments'
varg_check = [varg_check;
{'minTime' 'integer' [] 30;
'polarity' 'integer' [] 0 } ];
case 'windowed'
varg_check = [varg_check;
{ 'smooth_weight' 'integer' [] 5;
'smooth_width' 'integer' [] 3;
'max_iterations' 'integer' [] 1000;
'threshold' 'real' [] 1e-6 } ];
otherwise
error(['selected algorithm,''' vargs{smooth_type} ''' not available'])
end
settings = finputcheck( vargs, varg_check);
if ischar(settings), error(settings); end % check for error
end
function settings = interpret_popup(pop_out, settings, style, popmenu)
% Interpret output from pop_up window, "pop_out", and arrange it in
% "settings" struct. The fields in "style" should be the same as in "pop_out"
% (defined as tags in inputgui.m). The struct popmenu is optional and only
% needed if popmenus are used in the pop_up window.
names = fieldnames(style);
for i = 1:length(names)
switch style.(names{i})
case 'edit'
if isempty(pop_out.(names{i})) % empty?
settings.(names{i}) = [];
else
settings.(names{i}) = eval(pop_out.(names{i}));
end
case 'checkbox'
settings.(names{i}) = pop_out.(names{i});
case 'popupmenu'
settings.(names{i}) = popmenu.(names{i}){pop_out.(names{i})};
end
end
end
function com = settings_to_string(com,settings)
% Adds settings struct to existing com string in the form 'key1', 'val1',
% 'key2', 'val2' ... .
% Can handle structs, strings, vectors and scalars. I.e. not matrices.
names = fieldnames(settings);
for i = 1:length(names)
if isstruct(settings.(names{i})) % struct?
com = settings_to_string(com,settings.(names{i}));
elseif isempty(settings.(names{i})) % empty?
com = [ com sprintf(', ''%s'', []', names{i}) ];
elseif ischar(settings.(names{i})) % string?
com = [ com sprintf(', ''%s'', ''%s''', names{i}, settings.(names{i})) ];
elseif length(settings.(names{i})) > 1 % vector?
N_elements = length(settings.(names{i}));
range = max(settings.(names{i})) - min(settings.(names{i})) + 1;
if N_elements == range % write vetor as 'min_value:max_value'
com = [ com sprintf(', ''%s'', %g:%g', names{i}, ...
min(settings.(names{i})), max(settings.(names{i}))) ];
else % write vector with individual elements
com = [ com sprintf(', ''%s'', [%g', names{i}, ...
settings.(names{i})(1))];
for n = 2:N_elements
com = [ com sprintf(',%g', settings.(names{i})(n))];
end
com = [ com ']'];
end
else % scalar
com = [ com sprintf(', ''%s'', %g', names{i}, settings.(names{i})) ];
end
end
end