Read `ephys` data

ieegio supports reading from multiple data formats, such as EDF(+)/BDF(+), BrainVision, BCI2000, BlackRock NEV/NSx. Most of these readers have similar interface.

To start, please load ieegio. This vignette uses sample data. Please feel free to replace the sample path with your own data path.

library(ieegio)
edf_path <- ieegio_sample_data("edfPlusD.edf")

Here is a basic example that reads in the sample EDF data and creates a FileCache object that stores the signals channel-by-channel for fast access:

edf <- read_edf(edf_path, verbose = FALSE)
print(edf)

You can check header, channel table, and annotations via the following methods:

header <- edf$get_header()
str(header)

chan_tbl <- edf$get_channel_table()
print(chan_tbl, nrows = 2, topn = 2)

annot <- edf$get_annotations()
annot

You can also query a channel by calling the get_channel method.

# get Channel 1
channel <- edf$get_channel(1)
channel

A channel can also be looked up by its label instead of its number, which saves a round trip through the channel table:

edf$get_channel("squarewave")

The channel contains the following elements:

type: a character indicating the original file type;
info: list of basic information such as Channel number, Label, acquisition SampleRate, and Unit of the signals;
continuous: a logical value whether the time frames are continuous;
time: a numeric vector of time in seconds for each point;
value: a numeric vector of the signal value, often converted from digital to analog trace.

Using such information, it is straightforward to plot the channel data:

plot(
  x = channel$time, y = channel$value,
  xlab = "Time", ylab = channel$info$Unit,
  main = channel$info$Label,
  type = "p", pch = ".", col = "green", lwd = 2
)

Writing `EDF` files

To save signals back out, build each channel with as_edf_channel and hand the list to write_edf. A channel is either a signal vector or an annotation table:

signal <- sin(seq(0, 10, by = 0.01))

channels <- list(
  as_edf_channel(signal, channel_num = 1,
                 sample_rate = 200, label = "sine"),

  as_edf_channel(
    data.frame(
      timestamp = c(0, 5),
      comments = c("start", "end")
    ),
    channel_num = 2
  )
)

out_path <- tempfile(fileext = ".edf")
write_edf(channels = channels, con = out_path)

Reading it back gives the signal and the annotations:

written <- read_edf(out_path, extract_path = tempfile(), verbose = FALSE)
written$get_channel("sine")
written$get_annotations()

Read ephys data

Writing EDF files

Read `ephys` data

Writing `EDF` files