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‎README.rst

Lines changed: 328 additions & 141 deletions
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‎demo.ipynb

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@@ -11,7 +11,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
@@ -94,8 +94,8 @@
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"source": [
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"# Demo 4 - Read part of a WFDB annotation file into a wfdb.Annotation object, and plot the samples\n",
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"annotation = wfdb.rdann('sampledata/100', 'atr', sampfrom = 100000, sampto = 110000)\n",
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"#annotation.fs = 360\n",
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"#wfdb.plotann(annotation, timeunits = 'minutes')\n",
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"annotation.fs = 360\n",
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"wfdb.plotann(annotation, timeunits = 'minutes')\n",
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"\n",
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"# Can also read the same file hosted on PhysioBank \n",
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"annotation2 = wfdb.rdann('100', 'atr', sampfrom = 100000, sampto = 110000, pbdir = 'mitdb')"
@@ -215,7 +215,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": null,
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"metadata": {
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"collapsed": false
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},
@@ -237,7 +237,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": null,
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"metadata": {
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"collapsed": true
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},

‎devtests.ipynb

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@@ -4,7 +4,9 @@
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"<h2>This script is for internal developer testing.</h2>"
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"<h2>This script is for internal developer testing.</h2>\n",
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"\n",
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"This is different from the unit tests located in the `tests` directory."
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]
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},
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{

‎setup.py

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@@ -20,7 +20,7 @@
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# Versions should comply with PEP440. For a discussion on single-sourcing
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# the version across setup.py and the project code, see
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# https://packaging.python.org/en/latest/single_source_version.html
23-
version='0.2.0',
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version='1.0.0',
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description='The WFDB Python Toolbox',
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long_description=long_description,

‎wfdb/annotations.py

Lines changed: 24 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -25,11 +25,21 @@ class Annotation():
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- aux: The auxiliary information string for the annotation.
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- fs: The sampling frequency of the record if contained in the annotation file.
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Constructor function:
29+
def __init__(self, recordname, annotator, annsamp, anntype, subtype = None,
30+
chan = None, num = None, aux = None, fs = None)
31+
2832
Call 'showanncodes()' to see the list of standard annotation codes. Any text used to label
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annotations that are not one of these codes should go in the 'aux' field rather than the
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'anntype' field.
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36+
Example usage:
37+
import wfdb
38+
ann1 = wfdb.Annotation(recordname='ann1', annotator='atr', annsamp=[10,20,400],
39+
anntype = ['N','N','['], aux=[None, None, 'Serious Vfib'])
3140
"""
32-
def __init__(self, recordname, annotator, annsamp, anntype, subtype = None, chan = None, num = None, aux = None, fs = None):
41+
def __init__(self, recordname, annotator, annsamp, anntype, subtype = None,
42+
chan = None, num = None, aux = None, fs = None):
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self.recordname = recordname
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self.annotator = annotator
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@@ -358,18 +368,24 @@ def wrann(recordname, annotator, annsamp, anntype, subtype = None, chan = None,
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Input arguments:
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- recordname (required): The string name of the WFDB record to be written (without any file extensions).
361-
- annsamp (required): The annotation location in samples relative to the beginning of the record.
362-
- anntype (required): The annotation type according the the standard WFDB codes.
363-
- subtype (default=None): The marked class/category of the annotation.
364-
- chan (default=None): The signal channel associated with the annotations.
365-
- num (default=None): The labelled annotation number.
366-
- aux (default=None): The auxiliary information string for the annotation.
371+
- annotator (required): The string annotation file extension.
372+
- annsamp (required): The annotation location in samples relative to the beginning of the record. List or numpy array.
373+
- anntype (required): The annotation type according the the standard WFDB codes. List or numpy array.
374+
- subtype (default=None): The marked class/category of the annotation. List or numpy array.
375+
- chan (default=None): The signal channel associated with the annotations. List or numpy array.
376+
- num (default=None): The labelled annotation number. List or numpy array.
377+
- aux (default=None): The auxiliary information string for the annotation. List or numpy array.
367378
- fs (default=None): The numerical sampling frequency of the record to be written to the file.
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369380
Note: This gateway function was written to enable a simple way to write WFDB annotation files without
370381
needing to explicity create an Annotation object beforehand.
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You may also create an Annotation object, manually set its attributes, and call its wrann() instance method.
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Note: Each annotation stored in a WFDB annotation file contains an annsamp and an anntype field. All other fields
386+
may or may not be present. Therefore in order to save space, when writing additional features such
387+
as 'aux' that are not present for every annotation, it is recommended to make the field a list, with empty
388+
indices set to None so that they are not written to the file.
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Example Usage:
375391
import wfdb
@@ -426,7 +442,7 @@ def rdann(recordname, annotator, sampfrom=0, sampto=None, pbdir=None):
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427443
Example usage:
428444
import wfdb
429-
ann = wfdb.rdann('100', 'atr', sampto = 300000)
445+
ann = wfdb.rdann('sampledata/100', 'atr', sampto = 300000)
430446
"""
431447

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if sampto and sampto <= sampfrom:

‎wfdb/downloads.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -87,9 +87,10 @@ def streamannotation(filename, pbdir):
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return annbytes
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90-
# Return a list of all the physiobank databases available
90+
9191
def getdblist():
92-
"""
92+
"""Return a list of all the physiobank databases available.
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Usage:
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dblist = getdblist()
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"""

‎wfdb/plots.py

Lines changed: 18 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -11,19 +11,27 @@ def plotrec(record=None, title = None, annotation = None, annch = [0], timeunits
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""" Subplot and label each channel of a WFDB Record.
1212
Optionally, subplot annotation locations over selected channels.
1313
14-
Usage: plotrec(record=None, title = None, annotation = None, annch = [0], timeunits='samples', returnfig=False)
14+
Usage:
15+
plotrec(record=None, title = None, annotation = None, annch = [0], timeunits='samples', returnfig=False)
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1617
Input arguments:
1718
- record (required): A wfdb Record object. The p_signals attribute will be plotted.
18-
- title (optional): A string containing the title of the graph.
19-
- annotation (optional): An Annotation object. The annsamp attribute locations will be overlaid on the signal.
19+
- title (default=None): A string containing the title of the graph.
20+
- annotation (default=None): An Annotation object. The annsamp attribute locations will be overlaid on the signal.
2021
- annch (default=[0]): A list of channels on which to plot the annotation samples.
2122
- timeunits (default='samples'): String specifying the x axis unit.
2223
Allowed options are: 'samples', 'seconds', 'minutes', and 'hours'.
2324
- returnfig (default=False): Specifies whether the figure is to be returned as an output argument
2425
2526
Output argument:
2627
- figure: The matplotlib figure generated. Only returned if the 'returnfig' option is set to True.
28+
29+
Example Usage:
30+
import wfdb
31+
record = wfdb.rdsamp('sampledata/100', sampto = 15000)
32+
annotation = wfdb.rdann('sampledata/100', 'atr', sampto = 15000)
33+
34+
wfdb.plotrec(record, annotation = annotation, title='Record 100 from MIT-BIH Arrhythmia Database', timeunits = 'seconds')
2735
"""
2836

2937
# Check the validity of items used to make the plot
@@ -154,7 +162,7 @@ def plotann(annotation, title = None, timeunits = 'samples', returnfig = False):
154162
155163
Input arguments:
156164
- annotation (required): An Annotation object. The annsamp attribute locations will be overlaid on the signal.
157-
- title (optional): A string containing the title of the graph.
165+
- title (default=None): A string containing the title of the graph.
158166
- timeunits (default='samples'): String specifying the x axis unit.
159167
Allowed options are: 'samples', 'seconds', 'minutes', and 'hours'.
160168
- returnfig (default=False): Specifies whether the figure is to be returned as an output argument
@@ -163,6 +171,12 @@ def plotann(annotation, title = None, timeunits = 'samples', returnfig = False):
163171
- figure: The matplotlib figure generated. Only returned if the 'returnfig' option is set to True.
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165173
Note: The plotrec function is useful for plotting annotations on top of signal waveforms.
174+
175+
Example Usage:
176+
import wfdb
177+
annotation = wfdb.rdann('sampledata/100', 'atr', sampfrom = 100000, sampto = 110000)
178+
annotation.fs = 360
179+
wfdb.plotann(annotation, timeunits = 'minutes')
166180
"""
167181

168182
# Check the validity of items used to make the plot

‎wfdb/records.py

Lines changed: 31 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -310,6 +310,22 @@ class Record(BaseRecord, _headers.HeadersMixin, _signals.SignalsMixin):
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311311
In addition, the d_signals and p_signals attributes store the digital and physical
312312
signals of WFDB records with at least one channel.
313+
314+
Contructor function:
315+
def __init__(self, p_signals=None, d_signals=None,
316+
recordname=None, nsig=None,
317+
fs=None, counterfreq=None, basecounter=None,
318+
siglen=None, basetime=None, basedate=None,
319+
filename=None, fmt=None, sampsperframe=None,
320+
skew=None, byteoffset=None, adcgain=None,
321+
baseline=None, units=None, adcres=None,
322+
adczero=None, initvalue=None, checksum=None,
323+
blocksize=None, signame=None, comments=None)
324+
325+
Example Usage:
326+
import wfdb
327+
record1 = wfdb.Record(recordname='r1', fs=250, nsig=2, siglen=1000, filename=['r1.dat','r1.dat'])
328+
313329
"""
314330
# Constructor
315331
def __init__(self, p_signals=None, d_signals=None,
@@ -423,8 +439,20 @@ class MultiRecord(BaseRecord, _headers.MultiHeadersMixin):
423439
instance method can be called on MultiRecord objects to return a single segment representation
424440
of the record as a Record object. The resulting Record object will have its 'p_signals' field set.
425441
426-
eg. record1 = wfdb.rdsamp('s00001-2896-10-10-00-31', m2s = False)
427-
record1 = record1.multi_to_single()
442+
Contructor function:
443+
def __init__(self, segments = None, layout = None,
444+
recordname=None, nsig=None, fs=None,
445+
counterfreq=None, basecounter=None,
446+
siglen=None, basetime=None, basedate=None,
447+
segname = None, seglen = None, comments=None)
448+
449+
Example Usage:
450+
import wfdb
451+
recordM = wfdb.MultiRecord(recordname='rm', fs=50, nsig=8, siglen=9999,
452+
segname=['rm_1', '~', rm_2'], seglen=[800, 200, 900])
453+
454+
recordL = wfdb.rdsamp('s00001-2896-10-10-00-31', m2s = False)
455+
recordL = recordL.multi_to_single()
428456
"""
429457

430458
# Constructor
@@ -972,7 +1000,7 @@ def wrsamp(recordname, fs, units, signames, p_signals = None, d_signals = None,
9721000
# Write a local WFDB record (manually inserting fields)
9731001
wfdb.wrsamp('ecgrecord', fs = 250, units = ['mV', 'mV'], signames = ['I', 'II'], p_signals = sig, fmt = ['16', '16'])
9741002
"""
975-
1003+
9761004
# Check input field combinations
9771005
if p_signals is not None and d_signals is not None:
9781006
sys.exit('Must only give one of the inputs: p_signals or d_signals')
@@ -1229,9 +1257,6 @@ def dldatabasefiles(pbdb, dlbasedir, files, keepsubdirs = True, overwrite = Fals
12291257
- pbdb (required): The Physiobank database directory to download.
12301258
eg. For database 'http://physionet.org/physiobank/database/mitdb', pbdb = 'mitdb'.
12311259
- dlbasedir (required): The full local directory path in which to download the files.
1232-
- records (default='all'): Specifier of the WFDB records to download. Is either a list of strings
1233-
which each specify a record, or 'all' to download all records listed in the database's RECORDS file.
1234-
eg. records = ['test01_00s', test02_45s] for database https://physionet.org/physiobank/database/macecgdb/
12351260
- files (required): A list of strings specifying the file names to download relative to the database
12361261
base directory
12371262
- keepsubdirs (default=True): Whether to keep the relative subdirectories of downloaded files

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