wfdb使用说明

rdrecord的使用：

import matplotlib.pyplot as plt
import wfdb

record = wfdb.rdrecord('sample-data/a103l')
plt.plot(record.p_signal[0: 500, 0])
plt.plot(record.p_signal[500: 1000, 1])
plt.plot(record.p_signal[49500: 50000, 2])
plt.show()

rdsamp的使用：

from IPython.display import display
import matplotlib.pyplot as plt
import numpy as np
import os
import shutil

import wfdb

# Demo 2 - Read certain channels and sections of the WFDB record using the simplified 'rdsamp' function
# which returns a numpy array and a dictionary. Show the data.
signals, fields = wfdb.rdsamp('sample-data/s0010_re', channels=[14, 0, 5, 10], sampfrom=100, sampto=15000)
display(signals)
display(fields)

运行结果如下：

[[ 0.0335 -0.167  -0.237   0.1165]
 [ 0.0355 -0.1615 -0.2395  0.119 ]
 [ 0.0385 -0.168  -0.2465  0.116 ]
 ...
 [-0.0445  0.008   0.033   0.045 ]
 [-0.044   0.0175  0.042   0.052 ]
 [-0.044   0.0245  0.0365  0.05  ]]
{'comments': ['age: 81', 'sex: female', 'ECG date: 01/10/1990', 'Diagnose:', 'Reason for admission: Myocardial infarction', 'Acute infarction (localization): infero-latera', 'Former infarction (localization): no', 'Additional diagnoses: Diabetes mellitus', 'Smoker: no', 'Number of coronary vessels involved: 1', 'Infarction date (acute): 29-Sep-90', 'Previous infarction (1) date: n/a', 'Previous infarction (2) date: n/a', 'Hemodynamics:', 'Catheterization date: 16-Oct-90', 'Ventriculography: Akinesia inferior wall', 'Chest X-ray: Heart size upper limit of norm', 'Peripheral blood Pressure (syst/diast):  140/80 mmHg', 'Pulmonary artery pressure (at rest) (syst/diast): n/a', 'Pulmonary artery pressure (at rest) (mean): n/a', 'Pulmonary capillary wedge pressure (at rest): n/a', 'Cardiac output (at rest): n/a', 'Cardiac index (at rest): n/a', 'Stroke volume index (at rest): n/a', 'Pulmonary artery pressure (laod) (syst/diast): n/a', 'Pulmonary artery pressure (laod) (mean): n/a', 'Pulmonary capillary wedge pressure (load): n/a', 'Cardiac output (load): n/a', 'Cardiac index (load): n/a', 'Stroke volume index (load): n/a', 'Aorta (at rest) (syst/diast): 160/64 cmH2O', 'Aorta (at rest) mean: 106 cmH2O', 'Left ventricular enddiastolic pressure: 11 cmH2O', 'Left coronary artery stenoses (RIVA): RIVA 70% proximal to ramus diagonalis_2', 'Left coronary artery stenoses (RCX): No stenoses', 'Right coronary artery stenoses (RCA): No stenoses', 'Echocardiography: n/a', 'Therapy:', 'Infarction date: 29-Sep-90', 'Catheterization date: 16-Oct-90', 'Admission date: 29-Sep-90', 'Medication pre admission: Isosorbit-Dinitrate Digoxin Glibenclamide', 'Start lysis therapy (hh.mm): 19:45', 'Lytic agent: Gamma-TPA', 'Dosage (lytic agent): 30 mg', 'Additional medication: Heparin Isosorbit-Mononitrate ASA Diazepam', 'In hospital medication: ASA Isosorbit-Mononitrate Ca-antagonist Amiloride+Chlorothiazide Glibenclamide Insulin', 'Medication after discharge: ASA Isosorbit-Mononitrate Amiloride+Chlorothiazide Glibenclamide'], 'sig_len': 14900, 'sig_name': ['vz', 'i', 'avf', 'v5'], 'units': ['mV', 'mV', 'mV', 'mV'], 'n_sig': 4, 'base_time': None, 'fs': 1000, 'base_date': None}

Process finished with exit code 0

读header文件：

# Demo 3 - Read a WFDB header file only (without the signals)
record = wfdb.rdheader('sample-data/drive02')
display(record.__dict__)

# Can also read the same file hosted on Physiobank
record2 = wfdb.rdheader('drive02', pb_dir='drivedb')

rdann读取注释文件：

# Demo 4 - Read part of a WFDB annotation file into a wfdb.Annotation object, and plot the samples
annotation = wfdb.rdann('sample-data/100', 'atr', sampfrom=100000, sampto=110000)

显示label信息：

import wfdb

# View the standard WFDB annotation labels
wfdb.show_ann_labels()

运行结果如下：

    label_store symbol                                    description
0             0                              Not an actual annotation
1             1      N                                    Normal beat
2             2      L                  Left bundle branch block beat
3             3      R                 Right bundle branch block beat
4             4      a                Aberrated atrial premature beat
5             5      V              Premature ventricular contraction
6             6      F          Fusion of ventricular and normal beat
7             7      J              Nodal (junctional) premature beat
8             8      A                   Atrial premature contraction
9             9      S     Premature or ectopic supraventricular beat
10           10      E                        Ventricular escape beat
11           11      j                 Nodal (junctional) escape beat
12           12      /                                     Paced beat
13           13      Q                            Unclassifiable beat
14           14      ~                          Signal quality change
16           16      |                     Isolated QRS-like artifact
18           18      s                                      ST change
19           19      T                                  T-wave change
20           20      *                                        Systole
21           21      D                                       Diastole
22           22      "                             Comment annotation
23           23      =                         Measurement annotation
24           24      p                                    P-wave peak
25           25      B              Left or right bundle branch block
26           26      ^                      Non-conducted pacer spike
27           27      t                                    T-wave peak
28           28      +                                  Rhythm change
29           29      u                                    U-wave peak
30           30      ?                                       Learning
31           31      !                       Ventricular flutter wave
32           32      [      Start of ventricular flutter/fibrillation
33           33      ]        End of ventricular flutter/fibrillation
34           34      e                             Atrial escape beat
35           35      n                   Supraventricular escape beat
36           36      @  Link to external data (aux_note contains URL)
37           37      x             Non-conducted P-wave (blocked APB)
38           38      f                Fusion of paced and normal beat
39           39      (                                 Waveform onset
40           40      )                                   Waveform end
41           41      r       R-on-T premature ventricular contraction

Process finished with exit code 0

ECG Processing：

import matplotlib.pyplot as plt
import numpy as np
import wfdb
from wfdb import processing


# Use the gqrs detection algorithm and correct the peaks

def peaks_hr(sig, peak_inds, fs, title, figsize=(20, 10), saveto=None):
    "Plot a signal with its peaks and heart rate"
    # Calculate heart rate
    hrs = processing.compute_hr(sig_len=sig.shape[0], qrs_inds=peak_inds, fs=fs)

    N = sig.shape[0]

    fig, ax_left = plt.subplots(figsize=figsize)
    ax_right = ax_left.twinx()

    ax_left.plot(sig, color='#3979f0', label='Signal')
    ax_left.plot(peak_inds, sig[peak_inds], 'rx', marker='x', color='#8b0000', label='Peak', markersize=12)
    ax_right.plot(np.arange(N), hrs, label='Heart rate', color='m', linewidth=2)

    ax_left.set_title(title)

    ax_left.set_xlabel('Time (ms)')
    ax_left.set_ylabel('ECG (mV)', color='#3979f0')
    ax_right.set_ylabel('Heart rate (bpm)', color='m')
    # Make the y-axis label, ticks and tick labels match the line color.
    ax_left.tick_params('y', colors='#3979f0')
    ax_right.tick_params('y', colors='m')
    if saveto is not None:
        plt.savefig(saveto, dpi=600)
    plt.show()


# Load the wfdb record and the physical samples
record = wfdb.rdrecord('sample-data/100', sampfrom=0, sampto=10000, channels=[0])

# Use the gqrs algorithm to detect qrs locations in the first channel
qrs_inds = processing.gqrs_detect(sig=record.p_signal[:, 0], fs=record.fs)

# Plot results
peaks_hr(sig=record.p_signal, peak_inds=qrs_inds, fs=record.fs,
         title="GQRS peak detection on record 100")

# Correct the peaks shifting them to local maxima
min_bpm = 20
max_bpm = 230
# min_gap = record.fs * 60 / min_bpm
# Use the maximum possible bpm as the search radius
search_radius = int(record.fs * 60 / max_bpm)
corrected_peak_inds = processing.correct_peaks(record.p_signal[:, 0], peak_inds=qrs_inds,
                                               search_radius=search_radius, smooth_window_size=150)

# Display results
print('Corrected gqrs detected peak indices:', sorted(corrected_peak_inds))
peaks_hr(sig=record.p_signal, peak_inds=sorted(corrected_peak_inds), fs=record.fs,
         title="Corrected GQRS peak detection on sampledata/100")

Use the xqrs detection algorithm and compare results to reference annotations

import matplotlib.pyplot as plt
import numpy as np
import wfdb
from wfdb import processing


sig, fields = wfdb.rdsamp('sample-data/100', channels=[0], sampto=15000)
ann_ref = wfdb.rdann('sample-data/100','atr', sampto=15000)

# Run qrs detection on signal
xqrs = processing.XQRS(sig=sig[:,0], fs=fields['fs'])
xqrs.detect()
# Alternatively, use the gateway function to get the qrs indices directly
# qrs_inds = processing.xqrs_detect(sig=sig[:,0], fs=fields['fs'])

# Compare detected qrs complexes to reference annotation.
# Note, first sample in 100.atr is not a qrs.
comparitor = processing.compare_annotations(ref_sample=ann_ref.sample[1:],
                                            test_sample=xqrs.qrs_inds,
                                            window_width=int(0.1 * fields['fs']),
                                            signal=sig[:,0])

# Print and plot the results
comparitor.print_summary()
comparitor.plot(title='xqrs detected qrs vs reference annotations')

运行结果如下：