EDF/EDF+ file I/O

Functions for reading European Data Format (EDF/EDF+) files commonly used for EEG, PSG, and other physiological recordings. Read EDF/EDF+ file

Usage

readEDF(
  path,
  channels = NULL,
  start_time = NULL,
  end_time = NULL,
  resample = FALSE
)

Arguments

path: Path to the EDF file.
channels: Optional character vector of channel names to load. If NULL, all channels are loaded.
start_time: Optional start time in seconds for reading a subset.
end_time: Optional end time in seconds for reading a subset.
resample: Logical. If FALSE (default) and channels have differing native sampling rates, the native rates are preserved by returning a MultiRatePhysioExperiment (one stream per rate). If TRUE, all channels are resampled to the highest rate and a single PhysioExperiment is returned (legacy behaviour).

Value

A PhysioExperiment with the EDF signal data in the "raw" assay, or - when channels have differing native rates and resample = FALSE - a MultiRatePhysioExperiment. Channel metadata (label, transducer, physical dimensions, digital/physical min/max) are stored in colData, and recording metadata in metadata.

Details

Reads an EDF or EDF+ file and returns a PhysioExperiment object.

EDF (European Data Format) is a standard file format for storing multichannel physiological signals. EDF+ extends this with annotations and discontinuous recordings.

The function parses the EDF header to extract:

Channel labels and types
Sampling rates (may differ per channel)
Physical dimensions (units)
Recording start date/time

If channels have different native sampling rates, the rates are preserved by returning a MultiRatePhysioExperiment (one stream per rate); pass resample = TRUE for the legacy single-rate behaviour.

References

Kemp, B., et al. (1992). "A simple format for exchange of digitized polygraphic recordings." Electroencephalography and Clinical Neurophysiology, 82(5), 391-393. doi:10.1016/0013-4694(92)90009-7

Examples

# Round-trip a small recording through a temporary EDF file
pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(400), nrow = 100, ncol = 4)),
  colData = S4Vectors::DataFrame(label = c("Fp1", "Fp2", "C3", "C4")),
  samplingRate = 100
)
tmp <- tempfile(fileext = ".edf")
writeEDF(pe, tmp)

# Read the whole file back
pe_in <- readEDF(tmp)
dim(SummarizedExperiment::assay(pe_in, "raw"))
#> [1] 100   4

# Read only specific channels
pe_sub <- readEDF(tmp, channels = c("Fp1", "C3"))

unlink(tmp)