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Write to 'EDF' format

Source: R/edf.R
write_edf.Rd

Currently supports continuous 'EDF+' format with annotations

Usage

as_edf_channel(
  x,
  channel_num,
  sample_rate,
  label = sprintf("Ch%d", channel_num),
  physical_min = NA,
  physical_max = NA,
  is_annotation = NA,
  transducer_type = "",
  unit = "uV",
  filter = "",
  comment = ""
)

write_edf(
  channels,
  con,
  patient_id = "anomymous",
  recording_id = NULL,
  record_duration = NA,
  physical_min = NA,
  physical_max = NA,
  start_time = Sys.time()
)

Arguments

x

channel signals or annotations; for signals, x is a numeric vector; for annotations, x is a data frame with 'timestamp', 'comments', and optionally 'duration' (case sensitive) columns

channel_num

channel number, integer

sample_rate

sampling frequency

label

channel label, default is 'Ch' followed by the channel number for signal channels, or "EDF Annotation" for annotations

physical_min, physical_max

range of the channel values when converting from physical unit to digital; default is the range of x

is_annotation

whether the channel is annotation

transducer_type

transducer type

unit

physical unit or dimension; default is 'uV'

filter

preliminary filters applied to the signals

comment

additional comments (maximum 32 bytes)

channels

list of channel data, each element should be generated from as_edf_channel

con

file path or binary connection

patient_id

patient identifier; default is 'anomymous'

recording_id

recording identifier

record_duration

duration of each recording chunk: 'EDF' format slices the data into equal-length chunks and writes the data (interleave channels) to file; this is the duration for each chunk, not the entire recording length

start_time

start time of the recording; see as.POSIXct

Value

as_edf_channel returns a channel wrapper (with metadata); write_edf writes to the connection and returns nothing

Examples



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

channels <- list(

  # signal
  as_edf_channel(channel_num = 1, signal,
                 sample_rate = 375.5),

  as_edf_channel(channel_num = 2, signal,
                 sample_rate = 200),

  # annotation
  as_edf_channel(channel_num = 3, data.frame(
    timestamp = c(0, 1, 2),
    comments = c("Start", "half to go", "Finish!")
  ))

)

# write to file
path <- tempfile(fileext = ".edf")
write_edf(con = path, channels = channels)
#> Recording duration for each chunk is set to `2 sec`

edf <- read_edf(con = path, extract_path = tempdir())

annot <- edf$get_annotations()
annot
#> <fst file>
#> 3 rows, 4 columns (annot.fst)
#> 
#>   timestamp duration    comments   channel
#>    <double> <double> <character> <integer>
#> 1         0       NA       Start         3
#> 2         1       NA  half to go         3
#> 3         2       NA     Finish!         3


ch1 <- edf$get_channel(1)

# around 1e-5 due to digitization
range(ch1$value[seq_along(signal)] - signal)
#> [1] -1.777197e-05  1.545796e-05

ch2 <- edf$get_channel(2)
range(ch2$value[seq_along(signal)] - signal)
#> [1] -1.777197e-05  1.545796e-05


plot(ch1$time, ch1$value, type = "l",
     main = "Toy-example")
lines(ch2$time, ch2$value, col = "red")
abline(v = annot$timestamp, col = "gray", lty = 2)


edf$delete()
unlink(path)