io

The input/output subpackage contains classes used to represent WFDB objects, and functions to read, write, and download WFDB files.

WFDB Records

wfdb.io.rdrecord(record_name, sampfrom=0, sampto=None, channels=None, physical=True, pb_dir=None, m2s=True, smooth_frames=True, ignore_skew=False, return_res=64, force_channels=True, channel_names=None, warn_empty=False)

Read a WFDB record and return the signal and record descriptors as attributes in a Record or MultiRecord object.

record_name : str

The name of the WFDB record to be read, without any file extensions. If the argument contains any path delimiter characters, the argument will be interpreted as PATH/BASE_RECORD. Both relative and absolute paths are accepted. If the pb_dir parameter is set, this parameter should contain just the base record name, and the files fill be searched for remotely. Otherwise, the data files will be searched for in the local path.

sampfrom : int, optional

The starting sample number to read for all channels.

sampto : int, or ‘end’, optional

The sample number at which to stop reading for all channels. Reads the entire duration by default.

channels : list, optional

List of integer indices specifying the channels to be read. Reads all channels by default.

physical : bool, optional

Specifies whether to return signals in physical units in the p_signal field (True), or digital units in the d_signal field (False).

pb_dir : str, optional

Option used to stream data from Physiobank. The Physiobank database directory from which to find the required record files. eg. For record ‘100’ in ‘http://physionet.org/physiobank/database/mitdb’ pb_dir=’mitdb’.

m2s : bool, optional

Used when reading multi-segment records. Specifies whether to directly return a wfdb MultiRecord object (False), or to convert it into and return a wfdb Record object (True).

smooth_frames : bool, optional

Used when reading records with signals having multiple samples per frame. Specifies whether to smooth the samples in signals with more than one sample per frame and return an (MxN) uniform numpy array as the d_signal or p_signal field (True), or to return a list of 1d numpy arrays containing every expanded sample as the e_d_signal or e_p_signal field (False).

ignore_skew : bool, optional

Used when reading records with at least one skewed signal. Specifies whether to apply the skew to align the signals in the output variable (False), or to ignore the skew field and load in all values contained in the dat files unaligned (True).

return_res : int, optional

The numpy array dtype of the returned signals. Options are: 64, 32, 16, and 8, where the value represents the numpy int or float dtype. Note that the value cannot be 8 when physical is True since there is no float8 format.

force_channels : bool, optional

Used when reading multi-segment variable layout records. Whether to update the layout specification record, and the converted Record object if m2s is True, to match the input channels argument, or to omit channels in which no read segment contains the signals.

channel_names : list, optional

List of channel names to return. If this parameter is specified, it takes precedence over channels.

warn_empty : bool, optional

Whether to display a warning if the specified channel indices or names are not contained in the record, and no signal is returned.

record : Record or MultiRecord

The wfdb Record or MultiRecord object representing the contents of the record read.

If a signal range or channel selection is specified when calling this function, the resulting attributes of the returned object will be set to reflect the section of the record that is actually read, rather than necessarily the entire record. For example, if channels=[0, 1, 2] is specified when reading a 12 channel record, the ‘n_sig’ attribute will be 3, not 12.

The rdsamp function exists as a simple alternative to rdrecord for the common purpose of extracting the physical signals and a few important descriptor fields.

>>> record = wfdb.rdrecord('sample-data/test01_00s', sampfrom=800,
                           channels=[1, 3])

wfdb.io.rdsamp(record_name, sampfrom=0, sampto=None, channels=None, pb_dir=None, channel_names=None, warn_empty=False)

Read a WFDB record, and return the physical signals and a few important descriptor fields.

record_name : str

The name of the WFDB record to be read (without any file extensions). If the argument contains any path delimiter characters, the argument will be interpreted as PATH/baserecord and the data files will be searched for in the local path.

sampfrom : int, optional

The starting sample number to read for all channels.

sampto : int, or ‘end’, optional

The sample number at which to stop reading for all channels. Reads the entire duration by default.

channels : list, optional

List of integer indices specifying the channels to be read. Reads all channels by default.

pb_dir : str, optional

Option used to stream data from Physiobank. The Physiobank database directory from which to find the required record files. eg. For record ‘100’ in ‘http://physionet.org/physiobank/database/mitdb’ pb_dir=’mitdb’.

channel_names : list, optional

List of channel names to return. If this parameter is specified, it takes precedence over channels.

warn_empty : bool, optional

Whether to display a warning if the specified channel indices or names are not contained in the record, and no signal is returned.

signals : numpy array

A 2d numpy array storing the physical signals from the record.

fields : dict

A dictionary containing several key attributes of the read record:

• fs: The sampling frequency of the record
• units: The units for each channel
• sig_name: The signal name for each channel
• comments: Any comments written in the header

If a signal range or channel selection is specified when calling this function, the resulting attributes of the returned object will be set to reflect the section of the record that is actually read, rather than necessarily the entire record. For example, if channels=[0, 1, 2] is specified when reading a 12 channel record, the ‘n_sig’ attribute will be 3, not 12.

The rdrecord function is the base function upon which this one is built. It returns all attributes present, along with the signals, as attributes in a Record object. The function, along with the returned data type, has more options than rdsamp for users who wish to more directly manipulate WFDB content.

>>> signals, fields = wfdb.rdsamp('sample-data/test01_00s',
                                  sampfrom=800,
                                  channel =[1,3])

wfdb.io.wrsamp(record_name, fs, units, sig_name, p_signal=None, d_signal=None, fmt=None, adc_gain=None, baseline=None, comments=None, base_time=None, base_date=None, write_dir='')

Write a single segment WFDB record, creating a WFDB header file and any associated dat files.

record_name : str

The string name of the WFDB record to be written (without any file extensions). Must not contain any “.” since this would indicate an EDF file which is not compatible at this point.

fs : int, or float

The sampling frequency of the record.

units : list

A list of strings giving the units of each signal channel.

sig_name :

A list of strings giving the signal name of each signal channel.

p_signal : numpy array, optional

An (MxN) 2d numpy array, where M is the signal length. Gives the physical signal values intended to be written. Either p_signal or d_signal must be set, but not both. If p_signal is set, this method will use it to perform analogue-digital conversion, writing the resultant digital values to the dat file(s). If fmt is set, gain and baseline must be set or unset together. If fmt is unset, gain and baseline must both be unset.

d_signal : numpy array, optional

An (MxN) 2d numpy array, where M is the signal length. Gives the digital signal values intended to be directly written to the dat file(s). The dtype must be an integer type. Either p_signal or d_signal must be set, but not both. In addition, if d_signal is set, fmt, gain and baseline must also all be set.

fmt : list, optional

A list of strings giving the WFDB format of each file used to store each channel. Accepted formats are: ‘80’,‘212”,‘16’,‘24’, and ‘32’. There are other WFDB formats as specified by: https://www.physionet.org/physiotools/wag/signal-5.htm but this library will not write (though it will read) those file types.

adc_gain : list, optional

A list of numbers specifying the ADC gain.

baseline : list, optional

A list of integers specifying the digital baseline.

comments : list, optional

A list of string comments to be written to the header file.

base_time : str, optional

A string of the record’s start time in 24h ‘HH:MM:SS(.ms)’ format.

base_date : str, optional

A string of the record’s start date in ‘DD/MM/YYYY’ format.

write_dir : str, optional

The directory in which to write the files.

This is a gateway function, written as a simple method to write WFDB record files using the most common parameters. Therefore not all WFDB fields can be set via this function.

For more control over attributes, create a Record object, manually set its attributes, and call its wrsamp instance method. If you choose this more advanced method, see also the set_defaults, set_d_features, and set_p_features instance methods to help populate attributes.

>>> # Read part of a record from Physiobank
>>> signals, fields = wfdb.rdsamp('a103l', sampfrom=50000, channels=[0,1],
                               pb_dir='challenge/2015/training')
>>> # Write a local WFDB record (manually inserting fields)
>>> wfdb.wrsamp('ecgrecord', fs = 250, units=['mV', 'mV'],
                sig_name=['I', 'II'], p_signal=signals, fmt=['16', '16'])

class wfdb.io.Record(p_signal=None, d_signal=None, e_p_signal=None, e_d_signal=None, record_name=None, n_sig=None, fs=None, counter_freq=None, base_counter=None, sig_len=None, base_time=None, base_date=None, file_name=None, fmt=None, samps_per_frame=None, skew=None, byte_offset=None, adc_gain=None, baseline=None, units=None, adc_res=None, adc_zero=None, init_value=None, checksum=None, block_size=None, sig_name=None, comments=None)

The class representing single segment WFDB records.

Record objects can be created using the initializer, by reading a WFDB header with rdheader, or a WFDB record (header and associated dat files) with rdrecord.

The attributes of the Record object give information about the record as specified by: https://www.physionet.org/physiotools/wag/header-5.htm

In addition, the d_signal and p_signal attributes store the digital and physical signals of WFDB records with at least one channel.

>>> record = wfdb.Record(record_name='r1', fs=250, n_sig=2, sig_len=1000,
                     file_name=['r1.dat','r1.dat'])

adc(expanded=False, inplace=False)

Performs analogue to digital conversion of the physical signal stored in p_signal if expanded is False, or e_p_signal if expanded is True.

The p_signal/e_p_signal, fmt, gain, and baseline fields must all be valid.

If inplace is True, the adc will be performed inplace on the variable, the d_signal/e_d_signal attribute will be set, and the p_signal/e_p_signal field will be set to None.

expanded : bool, optional

Whether to transform the e_p_signal attribute (True) or the p_signal attribute (False).

inplace : bool, optional

Whether to automatically set the object’s corresponding digital signal attribute and set the physical signal attribute to None (True), or to return the converted signal as a separate variable without changing the original physical signal attribute (False).

d_signal : numpy array, optional

The digital conversion of the signal. Either a 2d numpy array or a list of 1d numpy arrays.

>>> import wfdb
>>> record = wfdb.rdsamp('sample-data/100')
>>> d_signal = record.adc()
>>> record.adc(inplace=True)
>>> record.dac(inplace=True)

dac(expanded=False, return_res=64, inplace=False)

Performs the digital to analogue conversion of the signal stored in d_signal if expanded is False, or e_d_signal if expanded is True.

The d_signal/e_d_signal, fmt, gain, and baseline fields must all be valid.

If inplace is True, the dac will be performed inplace on the variable, the p_signal/e_p_signal attribute will be set, and the d_signal/e_d_signal field will be set to None.

expanded : bool, optional

Whether to transform the e_d_signal attribute (True) or the d_signal attribute (False).

inplace : bool, optional

Whether to automatically set the object’s corresponding physical signal attribute and set the digital signal attribute to None (True), or to return the converted signal as a separate variable without changing the original digital signal attribute (False).

p_signal : numpy array, optional

The physical conversion of the signal. Either a 2d numpy array or a list of 1d numpy arrays.

>>> import wfdb
>>> record = wfdb.rdsamp('sample-data/100', physical=False)
>>> p_signal = record.dac()
>>> record.dac(inplace=True)
>>> record.adc(inplace=True)

wrsamp(expanded=False, write_dir='')

Write a wfdb header file and any associated dat files from this object.

expanded : bool, optional

Whether to write the expanded signal (e_d_signal) instead of the uniform signal (d_signal).

write_dir : str, optional

The directory in which to write the files.

class wfdb.io.MultiRecord(segments=None, layout=None, record_name=None, n_sig=None, fs=None, counter_freq=None, base_counter=None, sig_len=None, base_time=None, base_date=None, seg_name=None, seg_len=None, comments=None, sig_name=None, sig_segments=None)

The class representing multi-segment WFDB records.

MultiRecord objects can be created using the initializer, or by reading a multi-segment WFDB record using ‘rdrecord’ with the m2s (multi to single) input parameter set to False.

The attributes of the MultiRecord object give information about the entire record as specified by: https://www.physionet.org/physiotools/wag/header-5.htm

In addition, the segments parameter is a list of Record objects representing each individual segment, or None representing empty segments, of the entire multi-segment record.

Notably, this class has no attribute representing the signals as a whole. The ‘multi_to_single’ instance method can be called on MultiRecord objects to return a single segment representation of the record as a Record object. The resulting Record object will have its ‘p_signal’ field set.

>>> record_m = wfdb.MultiRecord(record_name='rm', fs=50, n_sig=8,
                                sig_len=9999, seg_name=['rm_1', '~', rm_2'],
                                seg_len=[800, 200, 900])
>>> # Get a MultiRecord object
>>> record_s = wfdb.rdsamp('s00001-2896-10-10-00-31', m2s=False)
>>> # Turn it into a
>>> record_s = record_s.multi_to_single()

record_s initially stores a MultiRecord object, and is then converted into a Record object.

multi_to_single(physical, return_res=64)

Create a Record object from the MultiRecord object. All signal segments will be combined into the new object’s p_signal or d_signal field. For digital format, the signals must have the same storage format, baseline, and adc_gain in all segments.

physical : bool

Whether to convert the physical or digital signal.

return_res : int, optional

The return resolution of the p_signal field. Options are: 64, 32, and 16.

record : wfdb Record

The single segment record created.

WFDB Anotations

wfdb.io.rdann(record_name, extension, sampfrom=0, sampto=None, shift_samps=False, pb_dir=None, return_label_elements=['symbol'], summarize_labels=False)

Read a WFDB annotation file record_name.extension and return an Annotation object.

record_name : str

The record name of the WFDB annotation file. ie. for file ‘100.atr’, record_name=‘100’.

extension : str

The annotatator extension of the annotation file. ie. for file ‘100.atr’, extension=’atr’.

sampfrom : int, optional

The minimum sample number for annotations to be returned.

sampto : int, optional

The maximum sample number for annotations to be returned.

shift_samps : bool, optional

Specifies whether to return the sample indices relative to sampfrom (True), or sample 0 (False).

pb_dir : str, optional

Option used to stream data from Physiobank. The Physiobank database directory from which to find the required annotation file. eg. For record ‘100’ in ‘http://physionet.org/physiobank/database/mitdb’: pb_dir=’mitdb’.

return_label_elements : list, optional

The label elements that are to be returned from reading the annotation file. A list with at least one of the following options: ‘symbol’, ‘label_store’, ‘description’.

summarize_labels : bool, optional

If True, assign a summary table of the set of annotation labels contained in the file to the ‘contained_labels’ attribute of the returned object. This table will contain the columns: [‘label_store’, ‘symbol’, ‘description’, ‘n_occurrences’]

annotation : Annotation

The Annotation object. Call help(wfdb.Annotation) for the attribute descriptions.

For every annotation sample, the annotation file explictly stores the ‘sample’ and ‘symbol’ fields, but not necessarily the others. When reading annotation files using this function, fields which are not stored in the file will either take their default values of 0 or None, or will be carried over from their previous values if any.

>>> ann = wfdb.rdann('sample-data/100', 'atr', sampto=300000)

wfdb.io.wrann(record_name, extension, sample, symbol=None, subtype=None, chan=None, num=None, aux_note=None, label_store=None, fs=None, custom_labels=None, write_dir='')

Write a WFDB annotation file.

Specify at least the following:

• The record name of the WFDB record (record_name)
• The annotation file extension (extension)
• The annotation locations in samples relative to the beginning of the record (sample)
• Either the numerical values used to store the labels (label_store), or more commonly, the display symbols of each label (symbol).

record_name : str

The string name of the WFDB record to be written (without any file extensions).

extension : str

The string annotation file extension.

sample : numpy array

A numpy array containing the annotation locations in samples relative to the beginning of the record.

symbol : list, or numpy array, optional

The symbols used to display the annotation labels. List or numpy array. If this field is present, label_store must not be present.

subtype : numpy array, optional

A numpy array containing the marked class/category of each annotation.

chan : numpy array, optional

A numpy array containing the signal channel associated with each annotation.

num : numpy array, optional

A numpy array containing the labelled annotation number for each annotation.

aux_note : list, optional

A list containing the auxiliary information string (or None for annotations without notes) for each annotation.

label_store : numpy array, optional

A numpy array containing the integer values used to store the annotation labels. If this field is present, symbol must not be present.

fs : int, or float, optional

The numerical sampling frequency of the record to be written to the file.

custom_labels : pandas dataframe, optional

The map of custom defined annotation labels used for this annotation, in addition to the standard WFDB annotation labels. Custom labels are defined by two or three fields:

• The integer values used to store custom annotation labels in the file (optional)
• Their short display symbols
• Their long descriptions.

This input argument may come in four formats:

1. A pandas.DataFrame object with columns: [‘label_store’, ‘symbol’, ‘description’]
2. A pandas.DataFrame object with columns: [‘symbol’, ‘description’] If this option is chosen, label_store values are automatically chosen.
3. A list or tuple of tuple triplets, with triplet elements representing: (label_store, symbol, description).
4. A list or tuple of tuple pairs, with pair elements representing: (symbol, description). If this option is chosen, label_store values are automatically chosen.

If the label_store field is given for this function, and custom_labels is defined, custom_labels must contain label_store in its mapping. ie. it must come in format 1 or 3 above.

write_dir : str, optional

The directory in which to write the annotation file

This is a gateway function, written as a simple way to write WFDB annotation files without needing to explicity create an Annotation object. You may also create an Annotation object, manually set its attributes, and call its wrann instance method.

Each annotation stored in a WFDB annotation file contains a sample field and a label field. All other fields may or may not be present.

>>> # Read an annotation as an Annotation object
>>> annotation = wfdb.rdann('b001', 'atr', pb_dir='cebsdb')
>>> # Write a copy of the annotation file
>>> wfdb.wrann('b001', 'cpy', annotation.sample, annotation.symbol)

wfdb.io.show_ann_labels()

Display the standard wfdb annotation label mapping.

>>> show_ann_labels()

wfdb.io.show_ann_classes()

Display the standard wfdb annotation classes

>>> show_ann_classes()

class wfdb.io.Annotation(record_name, extension, sample, symbol=None, subtype=None, chan=None, num=None, aux_note=None, fs=None, label_store=None, description=None, custom_labels=None, contained_labels=None)

The class representing WFDB annotations.

Annotation objects can be created using the initializer, or by reading a WFDB annotation file with rdann.

The attributes of the Annotation object give information about the annotation as specified by: https://www.physionet.org/physiotools/wag/annot-5.htm

Call show_ann_labels() to see the list of standard annotation codes. Any text used to label annotations that are not one of these codes should go in the ‘aux_note’ field rather than the ‘sym’ field.

>>> ann1 = wfdb.Annotation(record_name='rec1', extension='atr',
                           sample=[10,20,400], symbol=['N','N','['],
                           aux_note=[None, None, 'Serious Vfib'])

wrann(write_fs=False, write_dir='')

Write a WFDB annotation file from this object.

write_fs : bool, optional

Whether to write the fs attribute to the file.

Downloading

wfdb.io.get_dbs()

Get a list of all the Physiobank databases available.

>>> dbs = get_dbs()

wfdb.io.get_record_list(db_dir, records='all')

Get a list of records belonging to a database.

db_dir : str

The database directory, usually the same as the database slug. The location to look for a RECORDS file.

records : list, optional

A Option used when this function acts as a helper function. Leave as default ‘all’ to get all records.

>>> wfdb.get_record_list('mitdb')

wfdb.io.dl_database(db_dir, dl_dir, records='all', annotators='all', keep_subdirs=True, overwrite=False)

Download WFDB record (and optionally annotation) files from a Physiobank database. The database must contain a ‘RECORDS’ file in its base directory which lists its WFDB records.

db_dir : str

The Physiobank database directory to download. eg. For database: ‘http://physionet.org/physiobank/database/mitdb/’, db_dir=’mitdb’.

dl_dir : str

The full local directory path in which to download the files.

records : list, or ‘all’, optional

A list of strings specifying the WFDB records to download. Leave as ‘all’ to download all records listed in the database’s RECORDS file. eg. records=[‘test01_00s’, test02_45s] for database: https://physionet.org/physiobank/database/macecgdb/

annotators : list, ‘all’, or None, optional

A list of strings specifying the WFDB annotation file types to download along with the record files. Is either None to skip downloading any annotations, ‘all’ to download all annotation types as specified by the ANNOTATORS file, or a list of strings which each specify an annotation extension. eg. annotators = [‘anI’] for database: https://physionet.org/physiobank/database/prcp/

keep_subdirs : bool, optional

Whether to keep the relative subdirectories of downloaded files as they are organized in Physiobank (True), or to download all files into the same base directory (False).

overwrite : bool, optional

If True, all files will be redownloaded regardless. If False, existing files with the same name and relative subdirectory will be checked. If the local file is the same size as the online file, the download is skipped. If the local file is larger, it will be deleted and the file will be redownloaded. If the local file is smaller, the file will be assumed to be partially downloaded and the remaining bytes will be downloaded and appended.

>>> wfdb.dl_database('ahadb', os.getcwd())

wfdb.io.dl_files(db, dl_dir, files, keep_subdirs=True, overwrite=False)

Download specified files from a Physiobank database.

db : str

The Physiobank database directory to download. eg. For database: ‘http://physionet.org/physiobank/database/mitdb’, db=’mitdb’.

dl_dir : str

The full local directory path in which to download the files.

files : list

A list of strings specifying the file names to download relative to the database base directory.

keep_subdirs : bool, optional

Whether to keep the relative subdirectories of downloaded files as they are organized in Physiobank (True), or to download all files into the same base directory (False).

overwrite : bool, optional

If True, all files will be redownloaded regardless. If False, existing files with the same name and relative subdirectory will be checked. If the local file is the same size as the online file, the download is skipped. If the local file is larger, it will be deleted and the file will be redownloaded. If the local file is smaller, the file will be assumed to be partially downloaded and the remaining bytes will be downloaded and appended.

>>> wfdb.dl_files('ahadb', os.getcwd(),
                  ['STAFF-Studies-bibliography-2016.pdf', 'data/001a.hea',
                  'data/001a.dat'])

wfdb.io.set_db_index_url(db_index_url='http://physionet.org/physiobank/database/')

Set the database index url to a custom value, to stream remote files from another location.

db_index_url : str, optional

The desired new database index url. Leave as default to reset to the physiobank index url.