https://gitlab.gbar.dtu.dk/heliaib/PUPILS-preprocessing-pipeline
Tip revision: 222e578ec8659484520836c194f88738f51d58d9 authored by heliaib on 22 February 2022, 20:27:11 UTC
Adjust indexing for multiple blinks end of the trace
Adjust indexing for multiple blinks end of the trace
Tip revision: 222e578
processPupilData.m
function [data_out, info] = processPupilData(data, options)
% processPupilData is the main function of the PUPILS preprocessing
% pipeline, it calls the different event detection algorithms and producess
% a dataframe with event information and interpolated data.
%
% Inputs:
% - data : dataframe (samples x categories) minimum dataframe should
% include [time stamps, x-coordinate, y-coordinate,
% pupilsize] in that order. In addition, x and y velocity
% values might be included.
% - options : structure defining the options for the event detection
% algorithms, missing data interpolation and noise removal.
%
% Outputs:
% - data_out : dataframe that contains the original data with appended
% information, in the following order: [blink information,
% saccade information, interpolated data, denoised data]
%
% - info : structure containing metadata regarding events and
% quality of the pre-processed data
%
% ----------------------------------------------------------------------- %
%% Check that data stamps are equally spaced
if ~checkSampleSpacing(data)
error('Time samples are not equally spaced - Check your data for missing samples')
end
%% Check options and define default values
if nargin == 1 % Defaults
options.fs = 500; % sampling frequency (Hz)
options.vel_threshold = 30; % velocity threshold for saccade detection
options.pre_blink_t = 100; % region to interpolate before blink (ms)
options.post_blink_t = 200; % region to interpolate after blink (ms)
options.low_pass_fc = 10; % Low-pass filter cut-off frequency (Hz)
options.min_sacc_duration = 10; % Minimum saccade duration in (ms)
options.xy_units = 'px'; % Input units for the x-y coordinates (pixels)
warning('No processing options were definded. The pipeline will work with default values only');
end
info = initializeInformationStructure();
%% Event detections
% Blinks
[data_out info_blinks] = detectBlinks(data, options);
bf = fieldnames(info_blinks); % Add metadata to main info structure
for i = 1:length(bf)
info.(bf{i}) = info_blinks.(bf{i});
end
% Sacaddes
[data_out info_saccades] = detectSaccades(data_out, options);
sf = fieldnames(info_saccades);
for i = 1:length(sf)
info.(sf{i}) = info_saccades.(sf{i});
end
% Fixations
[data_out info_fixations] = generateFixationInfo(data_out, options);
sf = fieldnames(info_fixations);
for i = 1:length(sf)
info.(sf{i}) = info_fixations.(sf{i});
end
%% Data interpolation
[data_out info_interp] = interpolatePupilData(data_out, info, options);
intf = fieldnames(info_interp);
for i = 1:length(intf)
info.(intf{i}) = info_interp.(intf{i});
end
%% De-noising
data_out = denoisePupilData(data_out, info, options);
end