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Py_get_data

Introduction

Getting data from anywave is getting channels. The function will return a list of Channel objects.

Channel object

import anywave
chan = anywave.Channel()

chan.name # name (electrode label or electrode label and reference label)
chan.type   # type of channel as a string.
chan.ref    # reference channel label, can be empty.
chan.sr     # Sampling Rate in Hz
chan.lp     # Low Pass filter value applied to data.
chan.hp     # High Pass filter value applied to data.
chan.notch  # notch filter value applied to data.
chan.data   # data is a numpy array of float32

Input channels policy

When a plugin is launched, depending on the input and modifiers flags defined, the default input channels may vary.
If no flags are specified, the default behavior is to pick the selected channels.
If no channels are selected within the AnyWave views, then the current montage channels are picked.

Default usage

import sys, anywave
anywave.init(sys.argv)

channels = anywave.get_data()

channels is the current list of channels AnyWave has set as input for the plugin. See the Input channels policy section.

Add an extra parameter to the function

In order to specify constraints or requirements on the data we want to access to, the function allows an extra parameter which must be a struct.

Change the default behavior when picking channels

Request the current montage channels:

import sys, anywave
anywave.init(sys.argv)

cfg['channels_source'] = 'montage'
channels = anywave.get_data(cfg)
# Here channels are the ones present in the current montage no matter the user selection.

Force to get as recorded channels (no matter the montage, we want channels present in the file):

import sys, anywave


anywave.init(sys.argv)
cfg = { 'channels_source' : 'raw' }
channels = anywave.get_data(cfg)

Get selected channels:

import sys, anywave


anywave.init(sys.argv)
cfg = { 'channels_source' : 'selection' }
channels = anywave.get_data(cfg)
# channels can be empty meaning there are no selected channels.

Select a time range for data

The example below will get all the data available in the file which could be a lot of data.
To get only a chunk of the data use the following syntax:

import sys, anywave


anywave.init(sys.argv)
# start at position 10s in the file
 # we want 5 seconds of data
cfg = { 'start' : 10, 'duration' : 5 } 
channels = anywave.get_data(cfg)

Get data marked by markers

Instead of specifying a time range, it also possible to get data using time ranges provided by markers.
A marker has a position and may have a duration hence it can be used to get data.

import sys, anywave
anywave.init(sys.argv)

cfg = { 'use_markers' : ['EI'] } 
channels = anywave.get_data(cfg)

This code will get data marked by the EI marker(s).
WARNING: if there are several EI markers on the data file the data chunks of every markers will be concatenated and returned by get_data.

If you need to get EI markers one by one, the solution is to use the get_markers function to have all markers in an array and then iterate over each markers requesting data with the get_data function.

Avoid data (artefacted)

It is also possible to get data specifying a time range and also make sure that bad data (mostly artefacted chunks) won't overlap the requested data.

import sys, anywave
anywave.init(sys.argv)
# we suppose artefact and seizure markers exist 
cfg = { 'skip_markers' : ['artefact', 'seizure']  } 

channels = anywave.get_data(cfg)

This code will get all the data from the default picked channels EXCEPT chunks marked artefact and seizure.

Get channels by their types

import sys, anywave


anywave.init(sys.argv)
cfg = { 'channels_source' : 'montage', 'types' : ['EEG']  } 
channels = anywave.get_data(cfg)
# Warning channels may  be empty if no EEG channels are present in the current montage.

Get channel by their names

import sys, anywave


anywave.init(sys.argv)

cfg = { 'channels_source' : 'montage', 'labels' : ['TP1', 'TP2'] } 
# get only TP1 and TP2 channels, we assume they exist in the current montage.
channels = anywave.get_data(cfg)

Specify a reference channel (bipolarity)

If you want a bipolar channels, just can specify the reference when setting the channel label :

import sys, anywave


anywave.init(sys.argv)
cfg = { 'channels_source' : 'montage', 'labels' : ['TP1 - TP2', 'TP2 - TP3'] } 
# We want bipolar channels TP1-TP2 and TP2-TP3
# We assume that the channels exist and their bipolar reference is possible.
channels = anywave.get_data(cfg)

Specifying how to filter or not the data

By default, the data came as AnyWave will process them in the GUI.

Force to get raw data (no filtering)

import sys, anywave


anywave.init(sys.argv)
cfg = { 'channels_source' : 'montage', 'raw_data' : True } 
channels = anywave('get_data', cfg);

Filter using low pass and high pass

import sys, anywave


anywave.init(sys.argv)
cfg = { 'channels_source' : 'montage', 'filters' : [1, 60, 0] } 
# apply 1-60Hz filter, no notch.  
# Note that the third value (notch) is optional.
channels = anywave.get_data(cfg)

Advanced usage

This function also allows to do more complicated things like request to load data from a specified file or skip some chunks of data (artefacted data for example).

Load data from a specified file

To get data from a file, the full path to the file must be specified as follow:

import sys, anywave


anywave.init(sys.argv)
cfg = { 'data_path' : 'd:\data\file.eeg'  } 
channels = anywave.get_data(cfg)

If the file cannot be opened an error will occur. It is a good practice to embed this code in a try catch section.

Channels picking policy when specifying a data file

If the file specified has an associated .mtg file, AnyWave will load it and apply this montage.
Thus, the channels picked by default will be the montage channels.
You can however change this policy as shown before by adding the field channels_source to the struct.

Specify a marker file

This feature allows using a custom marker file. The markers contained in that file can then be used with the following keys:
'use_markers'
'skip_markers'

import sys, anywave


anywave.init(sys.argv)
cfg = { 'marker_file' : 'd:\data\my_markers.mrk', 'skip_markers' : ['avoid', 'bad data']  } 
# full path must be set
 # we assume avoir and bad data are markers present in the my_markers.mrk file 
channels = anywave.get_data(cfg)