wfdb-python

Introduction

Native python scripts for reading and writing WFDB signals and annotations.

Usage

See the wfdbdemo.ipynb file for example scripts on how to call the functions.

Reading Signals

rdsamp - Read a WFDB file and return the signal as a numpy array and the metadata as a dictionary.

sig, fields = rdsamp(recordname, sampfrom=0, sampto=[], channels=[], physical=1, stacksegments=1, pbdl=0, dldir=os.cwd(), keepfiles=0)

Example Usage:

import wfdb
sig, fields = wfdb.rdsamp('mitdb/100', sampto=2000, pbdl=1)

Input Arguments:

• recordname (mandatory) - The name of the WFDB record to be read (without any file extensions).
• sampfrom (default=0) - The starting sample number to read for each channel.
• sampto (default=length of entire signal)- The final sample number to read for each channel.
• channels (default=all channels) - Indices specifying the channel to be returned.
• physical (default=1) - Flag that specifies whether to return signals in physical (1) or digital (0) units.
• stacksegments (default=1) - Flag used only for multi-segment files. Specifies whether to return the signal as a single stacked/concatenated numpy array (1) or as a list of one numpy array for each segment (0).
• pbdl (default=0): If this argument is set, the function will assume that the user is trying to download a physiobank file. Therefore the 'recordname' argument will be interpreted as a physiobank record name including the database subdirectory, rather than a local directory.
• dldir (default=os.getcwd()): The directory to download physiobank files to.
• keepfiles (default=0): Flag specifying whether to keep physiobank files newly downloaded through the function call.

Output Arguments:

• sig - An nxm numpy array where n is the signal length and m is the number of channels. If the input record is a multi-segment record, depending on the input stacksegments flag, sig will either be a single stacked/concatenated numpy array (1) or a list of one numpy array for each segment (0). For empty segments, stacked format will contain Nan values, and non-stacked format will contain a single integer specifying the length of the empty segment.
• fields - A dictionary of metadata about the record extracted or deduced from the header/signal file. If the input record is a multi-segment record, the output argument will be a list of dictionaries:
  • The first list element will be a dictionary of metadata about the master header.
  • If the record is in variable layout format, the next list element will be a dictionary of metadata about the layout specification header.
  • The last list element will be a list of dictionaries of metadata for each segment. For empty segments, the dictionary will be replaced by a single string: 'Empty Segment'

Reading Annotations

rdann - Read a WFDB annotation file recordname.annot and return the fields as lists or arrays.

annsamp, anntype, subtype, chan, num, aux, annfs = wfdb.rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1)

Example Usage:

import wfdb
annsamp, anntype, subtype, chan, num, aux, annfs = wfdb.rdann('100', 'atr')

Input Arguments:

• recordname (required) - The record name of the WFDB annotation file. ie. for file 100.atr recordname='100'.
• annot (required) - The annotator extension of the annotation file. ie. for file 100.atr annot='atr'.
• sampfrom (default=0)- The minimum sample number for annotations to be returned.
• sampto (default=the final annotation sample) - The maximum sample number for annotations to be returned.
• anndisp (default=1) - The annotation display flag that controls the data type of the anntype output parameter. anntype will either be an integer key(0), a shorthand display symbol(1), or a longer annotation code(2).

Output arguments:

• annsamp - The annotation location in samples relative to the beginning of the record.
• anntype - The annotation type according the the standard WFDB keys.
• subtype - The marked class/category of the annotation.
• chan - The signal channel associated with the annotations.
• num - The marked annotation number. This is not equal to the index of the current annotation.
• aux - The auxiliary information string for the annotation.
• annfs - The sampling frequency written in the beginning of the annotation file if present.

*NOTE: Every annotation contains the 'annsamp' and 'anntype' field. All other fields default to 0 or empty if not present.

Plotting Data

plotwfdb - Subplot and label each channel of an nxm signal on a graph. Also subplot annotation locations on selected channels if present.

plotwfdb(sig, fields, annsamp=[], annch=[0], title=[], plottime=1)

Example Usage:

import wfdb
sig, fields = wfdb.rdsamp('100')
annsamp=wfdb.rdann('100', 'atr')[0]
wfdb.plotwfdb(sig, fields, annsamp, 'mitdb record 100'): 
 

Input Arguments:

• sig (required)- An nxm numpy array containing the signal to be plotted - the first output argument of readsignal.rdsamp.
• fields (required) - A dictionary of metadata about the record - the second output argument of readsignal.rdsamp.
• annsamp (optional) - A 1d numpy array of annotation locations to be plotted on top of selected channels - first output argument of rdann.
• annch (default=[0]) - A list of channels on which to plot the annotations.
• title (optional)- A string containing the title of the graph.
• plottime (default=1) - Flag that specifies whether to plot the x axis as time (1) or samples (0). Defaults to samples if the input fields dictionary does not contain a value for fs.

Based on the original WFDB software package specifications

WFDB Software Package
WFDB Applications Guide
WFDB Header File Specifications