def main():
"""Outer shell that processes ECG by calling
GetData and PatientInfo
:param csv_file: user input of csv_path from
current directory
:raises ImportError: if module missing
"""
try:
import os
import numpy as np
import scipy.signal as sig
import logging as lg
from ReadECG import GetData
from PatientHeartRate import PatientInfo
except ImportError as e:
print('ImportError: %s module not found.' % e.name)
print('Activate virtual environment.')
print('Input file path (including extension):')
csv_file = input()
print('Beginning ECG Processing...')
try:
inter = GetData(csv_file)
final = PatientInfo(inter)
print('Finished ECG Processing.')
name = os.path.basename(csv_file)
name = os.path.splitext(name)[0]
json_name = name + '.json'
print('Results seen in %s file' % json_name)
except:
print('Processing failed.')
def test_write_json():
patient1 = PatientInfo(GetData('test_data/test_data1.csv'))
name = os.path.basename(patient1.path)
name = os.path.splitext(name)[0]
json_name = name + '.json'
with open(json_name) as json_data:
d = json.load(json_data)
assert (d['ECG Duration'] == patient1.duration)
assert (np.allclose(d['Voltage Extremes'],
np.array(patient1.voltage_extremes)))
assert (np.isclose(d['Number of Beats'], patient1.num_beats))
assert (np.isclose(d['Mean BPM'], patient1.mean_hr_bpm))
assert (np.allclose(d['Times of Beats'], patient1.beats))
def test_calc_beats():
patient1 = PatientInfo(GetData('test_data/test_data1.csv'))
assert pytest.approx(patient1.num_beats, 5) == 32
assert pytest.approx(patient1.mean_hr_bpm, 5) == 72
result1 = patient1.beats
actual1 = np.array([
0.108, 0.792, 1.636, 2.308, 3.311, 4.1, 4.903, 5.661, 6.556, 7.384,
8.253, 8.997, 9.769, 10.6, 11.47, 12.29, 13.01, 14, 14.73, 15.44,
16.33, 17.15, 18, 18.82, 19.64, 20.41, 21.18, 21.97, 22.78, 23.59,
24.43, 25.27, 26.77
])
diff1 = np.absolute(result1 - actual1)
assert (all(i <= 0.2 for i in diff1))
patient2 = PatientInfo(GetData('test_data/test_data18.csv'))
assert pytest.approx(patient2.num_beats, 5) == 18
assert pytest.approx(patient2.mean_hr_bpm, 5) == 62
result2 = patient2.beats
actual2 = np.array([
0, .749, 1.499, 2.249, 2.999, 3.746, 4.499, 5.249, 5.994, 6.749, 7.471,
8.224, 8.976, 9.729, 10.5, 11.25, 12, 12.69, 13.5
])
diff2 = np.absolute(result2 - actual2)
assert (all(i <= 0.2 for i in diff2))
def test_GetData():
with pytest.raises(TypeError):
GetData('test_data/test_data1.json')
with pytest.raises(OSError):
GetData('test_data/notreal.csv')
def test_get_data():
with pytest.raises(IOError):
GetData('test_data/empty.csv')
def test_check_interp():
intt = PatientInfo(GetData('test_data/test_data30.csv'))
v = intt.volt
t = intt.time
assert (not np.isnan(v).any())
assert (not np.isnan(t).any())
def test_calc_duration():
patient2 = PatientInfo(GetData('test_data/test_data1.csv'))
assert (np.isclose(patient2.duration, 27.775))
patient3 = PatientInfo(GetData('test_data/test_data30.csv'))
assert (np.isclose(patient3.duration, 39.996))
def test_check_volt_range():
with pytest.raises(ValueError):
PatientInfo(GetData('test_data/test_data32.csv'))
def test_calc_volt_ex():
patient1 = PatientInfo(GetData('test_data/test_data1.csv'))
assert (patient1.voltage_extremes == (-0.68, 1.05))
patient2 = PatientInfo(GetData('test_data/test_data9.csv'))
assert (patient2.voltage_extremes == (-1.07, 0.255))