def load(self, ecg_file) -> ECGRecord:
if not os.path.isfile(ecg_file):
raise FileNotFoundError(f"{ecg_file} is not found")
record = Holter(ecg_file)
record.load_data()
def load_ann(ann_file, annheader):
filesize = os.path.getsize(ann_file)
headersize = 522 + annheader.var_block_size + 4
record.beat_anns = []
with open(ann_file, 'rb') as f:
f.seek(headersize - 4, os.SEEK_SET)
first_sample = np.fromfile(f, dtype=np.uint32, count=1)[0]
current_sample = first_sample
timeout = False # was there a gap in the annotations?
for beat in range(int((filesize - headersize) / 4)):
# note, the beat at first_sample isn't annotated. so the first beat
# in beat_anns is actually the second beat of the recording.
ann = chr(np.fromfile(f, dtype=np.uint8, count=1)[0])
internal = chr(np.fromfile(f, dtype=np.uint8, count=1)[0])
toc = np.fromfile(f, dtype=np.int16, count=1)[0]
current_sample += toc
if ann == '!':
timeout = True # there was a few minutes gap in the anns; don't
# know how to line them up to rest of recording
record.beat_anns.append({'ann': ann, 'internal': internal, 'toc': toc})
if not timeout:
record.beat_anns[-1]['samp_num'] = current_sample
ann_file = os.path.splitext(ecg_file)[0] + '.ann'
ann_header = Holter(ann_file, check_valid=False, annfile=True)
load_ann(ann_file, ann_header)
time = Time.from_fs_samples(record.sr, len(record.lead[0].data))
record_name = os.path.split(ecg_file)[1]
record_name = ".".join(record_name.split(".")[:-1])
new_record = ECGRecord(name=record_name, time=time)
for leadi in record.lead:
new_record.add_signal(Signal(leadi.data, str(leadi)))
ecg_annotation = ECGAnnotation([ECGAnnotationSample(i["samp_num"], i["ann"]) for i in record.beat_anns])
new_record.annotations = ecg_annotation
new_record.info = SubjectInfo()
new_record.info.race = record.race
new_record.info.sex = record.sex
new_record.info.birth_date = record.birth_date
new_record.info.record_date = record.record_date
new_record.info.file_date = record.file_date
new_record.info.start_time = record.start_time
new_record.info.pm = record.pm
return new_record
def load(self, hea_file) -> ECGRecord:
base_path = os.path.splitext(hea_file)[0]
def load_annotation(ann_ext):
return wfdb.rdann(base_path, ann_ext)
hea_file = base_path + ".hea"
if not os.path.isfile(hea_file):
raise FileNotFoundError(f"{hea_file} is not found")
record = wfdb.rdrecord(base_path)
time = Time.from_fs_samples(record.fs, record.sig_len)
new_record = ECGRecord(name=record.record_name, time=time)
for signal, lead_name in zip(record.p_signal.T, record.sig_name):
new_record.add_signal(Signal(signal, lead_name))
ann = load_annotation("atr")
ecg_annotation = ECGAnnotation([
ECGAnnotationSample(samp, symbol)
for samp, symbol in zip(ann.sample, ann.symbol)
])
new_record.annotations = ecg_annotation
return new_record
def test_len(fs, samples):
time = Time.from_fs_samples(fs, samples)
assert len(time) == samples
def test_from_time_stamp_not_monotonic(time_stamps):
with pytest.raises(ValueError):
Time.from_timestamps(time_stamps)
def test_from_time_stamp(time_stamps):
time = Time.from_timestamps(time_stamps)
assert np.array_equal(time.time, time_stamps)
def test_slicing_single_element(time_stamps):
time = Time.from_timestamps(time_stamps)
assert time[0] == time_stamps[0]
def test_slicing(time_stamps):
time = Time.from_timestamps(time_stamps)
assert np.array_equal(time[0:1], time_stamps[0:1])
def test_from_fs_samples(fs, samples):
time = Time.from_fs_samples(fs, samples)
time_expected = (1 / fs) * np.arange(0, samples)
assert np.array_equal(time.time, time_expected)
def test_duration(fs, samples):
record = ECGRecord("record_100", time=Time.from_fs_samples(fs, samples))
assert record.duration == (samples - 1) / fs
def test_inconsistent_signal_type():
record = ECGRecord("record_100", time=Time.from_fs_samples(360, 10))
with pytest.raises(TypeError):
record.add_signal(electrocardiogram())
def test_inconsistent_signal_len():
record = ECGRecord("record_100", time=Time.from_fs_samples(360, 10))
with pytest.raises(ValueError):
record.add_signal(Signal(electrocardiogram(), "MLII"))
def test_length(fs, samples):
record = ECGRecord("record_100", time=Time.from_fs_samples(fs, samples))
assert len(record) == samples