Document organization

some-test/ECG_read_by_wfdb.py

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+import wfdb
+import numpy as np
+
+
+def getDataset(number, X_data):
+    # get ECG from mit-bih-arrhythmia-database-1.0.0
+    print("get data:" + number + " ECG")
+    record = wfdb.rdrecord('./mit-bih-arrhythmia-database-1.0.0/' + number, channel_names=['MLII'])
+    data = record.p_signal.flatten()
+
+    # get R sample and symbol
+    annotation = wfdb.rdann('mit-bih-arrhythmia-database-1.0.0/' + number, 'atr')
+    Rlocatation = annotation.sample
+    Rclass = annotation.symbol
+
+    X_data.append(data)
+    wfdb.plot_wfdb(record=record, annotation=annotation, time_units='seconds')
+    return
+
+
+def loadData():
+    numberSet = ['100', '101', '103', '105', '106', '107', '108', '109', '111', '112', '113', '114', '115',
+                 '116', '117', '119', '121', '122', '123', '124', '200', '201', '202', '203', '205', '208',
+                 '210', '212', '213', '214', '215', '217', '219', '220', '221', '222', '223', '228', '230',
+                 '231', '232', '233', '234']
+    dataSet = []
+    for n in numberSet:
+        getDataset(n, dataSet)
+
+    return dataSet
+
+
+def main():
+    dataSet = loadData()
+    dataSet = np.array(dataSet)
+    print(dataSet)
+    print(dataSet.__sizeof__())
+    print(dataSet.shape)
+    print("get ECG data")
+
+
+if __name__ == '__main__':
+    main()

some-test/ECG_read_weiyuqing_without_wfdb.py

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+import numpy as np
+import matplotlib.pyplot as plt
+from numpy import reshape
+
+# arr =
+ECGDATAPATH = "mit-bih-arrhythmia-database-1.0.0/"
+HEADERFILE = "100.hea"
+ATRFILE = '100.atr'
+DATAFILE = "100.dat"
+
+# Obtain the information of each part from the hea file and fill in
+f = open(ECGDATAPATH + HEADERFILE, "r")
+z = f.readline().split()
+nosig, sfreq = int(z[1]), int(z[2])  # single number,samp number
+SAMPLES2READ = 10 * sfreq  # number of data points
+
+dformat, gain, bitres, zerovalue, firstvalue = [], [], [], [], []
+
+for i in range(nosig):
+    z = f.readline().split()
+    dformat.append(int(z[1]))
+    gain.append(int(z[2]))
+    bitres.append(int(z[3]))
+    zerovalue.append(int(z[4]))
+    firstvalue.append(int(z[5]))
+f.close()
+
+# Obtain the information of each part from the dat file and fill in
+f=open(ECGDATAPATH + DATAFILE, "rb")
+b = f.read()
+f.close()
+
+A_init = np.frombuffer(b, dtype=np.uint8)
+A_shape0 = int(A_init.shape[0] / 3)
+A = A_init.reshape(A_shape0, 3)[:SAMPLES2READ]
+
+M = np.zeros((SAMPLES2READ, 2))
+
+M2H = A[:, 1] >> 4
+M1H = A[:, 1] & 15
+
+PRL = (A[:, 1] & 8) * (2 ** 9)
+PRR = A[:, 1] & 128 << 5
+
+M1H = M1H * (2 ** 8)
+M2H = M2H * (2 ** 8)
+
+M[:, 0] = A[:, 0] + M1H - PRL
+M[:, 1] = A[:, 2] + M2H - PRR
+
+if ((M[1, :] != firstvalue).any()):
+    print("inconsistent in the first bit value")
+
+if nosig == 2:
+    M[:, 0] = (M[:, 0] - zerovalue[0]) / gain[0]
+    M[:, 1] = (M[:, 1] - zerovalue[1]) / gain[1]
+    TIME = np.linspace(0, SAMPLES2READ - 1, SAMPLES2READ) / sfreq
+elif nosig == 1:
+    M2 = []
+    M[:, 0] = M[:, 0] - zerovalue[0]
+    M[:, 1] = M[:, 1] - zerovalue[1]
+    for i in range(M.shape[0]):
+        M2.append(M[:, 0][i])
+        M2.append(M[:, 1][i])
+    M2.append(0)
+    del M2[0]
+    M2 = np.array(M2) / gain[0]
+    TIME = np.linspace(0, 2 * SAMPLES2READ - 1, 2 * SAMPLES2READ) / sfreq
+else:
+    print("Sorting algorithm for more than 2 signals not programmed yet")
+
+# atr  deal
+f = open(ECGDATAPATH + ATRFILE, "rb")
+b = f.read()
+f.close()
+A_init = np.frombuffer(b, dtype=np.uint8)
+A_shape0 = int(A_init.shape[0] / 2)
+A = A_init.reshape(A_shape0, 2)
+
+ANNOT, ATRTIME = [], []
+i = 0
+while i < A.shape[0]:
+    annoth = A[i, 1] >> 2
+    if annoth == 59:
+        ANNOT.append(A[i + 3, 1] >> 2)
+        ATRTIME.append(A[i + 2, 0] + A[i + 2, 1] * (2 ** 8) + A[i + 1, 0] * (2 ** 16) + A[i + 1, 1] * (2 ** 24))
+        i += 3
+    elif annoth == 60:
+        pass
+    elif annoth == 61:
+        pass
+    elif annoth == 62:
+        pass
+    elif annoth == 63:
+        hilfe = (A[i, 1] & 3) * (2 * 8) + A[i, 0]
+        hilfe = hilfe + hilfe % 2
+        i += int(hilfe / 2)
+    else:
+        ATRTIME.append((A[i, 1] & 3) * (2 * 8) + A[i, 0])
+        ANNOT.append((A[i,1]>>2))
+    i+=1
+del ANNOT[len(ANNOT)-1]
+del ATRTIME[len(ATRTIME)-1]
+
+ATRTIME=np.array(ATRTIME)
+ATRTIME=np.cumsum(ATRTIME)/sfreq
+
+ind=np.where(ATRTIME<=TIME[-1])[0]
+ATRTIMED=ATRTIME[ind]
+
+ANNOT=np.round(ANNOT)
+ANNOTD=ANNOT[ind]
+
+print(M)
+print(ANNOT)
+print(ATRTIME)