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I/O of WFDB-compatible signal & header files from EP recording systems

Source: R/wfdb-io.R
wfdb_io.Rd

This function allows for WFDB files to be read from any WFDB-compatible system, and also allows writing out WFDB-compatible files from specific EP recording systems, as indicated in the details section. Writing WFDB leads to creation of both a dat (signal) and hea (header) file. These are both required for reading in files as well.

Usage

write_wfdb(
  data,
  record,
  record_dir,
  wfdb_path = getOption("wfdb_path"),
  header = list(frequency = 250, gain = 200L, label = character()),
  info_strings = list(),
  ...
)

read_wfdb(
  record,
  record_dir = ".",
  annotator = NA_character_,
  wfdb_path = getOption("wfdb_path"),
  begin = 0,
  end = NA_integer_,
  interval = NA_integer_,
  units = "digital",
  channels = character(),
  ...
)

read_signal(
  record,
  record_dir = ".",
  wfdb_path = getOption("wfdb_path"),
  begin = 0L,
  end = NA_integer_,
  interval = NA_integer_,
  units = "digital",
  channels = character(),
  ...
)

read_header(record, record_dir = ".", wfdb_path = getOption("wfdb_path"), ...)

Arguments

data

Can either be an egm object, or a data.frame (or similar) object. The function will appropriately set defaults based on the type.

  • egm = Will extract signal and header data directly from object, and thus is simplest to convert to a WFDB format

  • signal_table = This is a customized data.table class that has an invariant column containing sample information.

  • data.frame or data.table = Must have a column that represents a time point or index, and columns that represent signal values (preferably integers)

record

String that will be used to name the WFDB record. Cannot include extensions, and is not a filepath. alphanumeric characters are acceptable, as well as hyphens (-) and underscores (_)

record_dir

File path of directory that should be used read and write files. Defaults to current directory.

wfdb_path

Path that leads to installed wfdb software package on device. Needs to be directly set using set_wfdb_path(). Obtained from the system options on loading of the package, getOption('wfdb_path')

header

A header file is an optional named list of parameters that will be used to organize and describe the signal input from the data argument. If the type is given, specific additional elements will be searched for, such as the low or high pass filters, colors, or other signal attributes. At minimum, the following elements are required (as cannot be calculated):

  • frequency = sample frequency in Hertz as integer

  • label = vector of names for each channel as character

  • start_time = date/time object

info_strings

A list of strings that will be written as an appendix to the header file, usually containing information about the channels, (e.g. list of colors, extra labels, etc).

...

Additional arguments to be passed to the function

annotator

String that is the name of a WFDB-compatible annotation type, serving as the extension for the file that is written containing that annotation. Please see read_annotation() and write_annotation() for further details.

begin, end, interval

Timepoint as an integer (representing seconds), which is converted to an index position based on sampling frequency. The default is to start at the beginning of the record. If end or interval are given, the earlier of the two will be returned. The end argument gives a time index to read until. The interval argument is the length of time past the start point.

units

A character string representing either digital (DEFAULT) or physical units that should be used, if available.

  • digital = Index in sample number, signal in integers (A/D units)

  • physical = Index in elapsed time, signal in decimal voltage (e.g. mV). This will include 1 additional row over the header/column names that describes units

channels

Either the signal/channel in a character vector as a name or number. Allows for duplication of signal or to re-order signal if needed. If nothing is given, will default to all channels available.

Value

Depends on if it is a reading or writing function. For writing, will output an WFDB-based object reflecting the function. For reading, will output an extension of a data.table object reflecting the underlying function (e.g. signal_table() will return an object of class).

Functions

  • write_wfdb(): Writes out signal and header data into a WFDB-compatible format from R.

  • read_wfdb(): Reads a multicomponent WFDB-formatted set of files directly into an egm object. This serves to pull together read_signal(), read_header(), and read_annotation() for simplicity.

  • read_signal(): Specifically reads the signal data from the WFDB binary format, returning a signal_table object for evaluation in the R environment

  • read_header(): Specifically reads the header data from the WFDB header text format, returning a header_table object for evaluation in the R environment

Recording systems

Type of signal data, as specified by the recording system, that are currently supported.