[b48499]: / test / test_databases / test_afdb.py

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"""
methods from the base class, e.g. `load_data`, are comprehensively tested in this file
TestAFDB: accomplished
subsampling: accomplished
"""
import re
import shutil
from pathlib import Path
import numpy as np
import pandas as pd
import pytest
from torch_ecg.databases import AFDB, DataBaseInfo
from torch_ecg.utils.download import PHYSIONET_DB_VERSION_PATTERN
###############################################################################
# set paths
_CWD = Path(__file__).absolute().parents[2] / "tmp" / "test-db" / "afdb"
try:
shutil.rmtree(_CWD)
except FileNotFoundError:
pass
_CWD.mkdir(parents=True, exist_ok=True)
###############################################################################
with pytest.warns(RuntimeWarning):
reader = AFDB(_CWD, verbose=3)
if len(reader) == 0:
reader.download()
reader._update_db_list()
class TestAFDB:
def test_len(self):
assert len(reader) == 23
reader._ls_rec(local=False)
assert len(reader) == 23
def test_subsample(self):
ss_ratio = 0.3
reader_ss = AFDB(_CWD, subsample=ss_ratio, verbose=0)
assert len(reader_ss) == pytest.approx(len(reader) * ss_ratio, abs=1)
ss_ratio = 0.1 / len(reader)
reader_ss = AFDB(_CWD, subsample=ss_ratio)
assert len(reader_ss) == 1
with pytest.raises(AssertionError, match="`subsample` must be in \\(0, 1\\], but got `.+`"):
AFDB(_CWD, subsample=0.0)
with pytest.raises(AssertionError, match="`subsample` must be in \\(0, 1\\], but got `.+`"):
AFDB(_CWD, subsample=1.01)
with pytest.raises(AssertionError, match="`subsample` must be in \\(0, 1\\], but got `.+`"):
AFDB(_CWD, subsample=-0.1)
def test_load_data(self):
data = reader.load_data(0)
data_muv = reader.load_data(0, units="μv")
data_lead_last = reader.load_data(0, data_format="lead_last")
data_0 = reader.load_data(0, leads=0)
assert np.allclose(data, data_lead_last.T)
assert np.allclose(data, data_muv / 1000)
assert np.allclose(data[0], data_0)
assert reader.load_data(0, sampfrom=1000, sampto=2000).shape == (2, 1000)
assert reader.load_data(0, sampfrom=1000, sampto=2000, fs=reader.fs * 2).shape == (2, 2000)
assert reader.load_data(0, units=None).dtype == np.int32
with pytest.raises(
AssertionError,
match="`leads` should be a subset of .+ or non-negative integers less than",
):
reader.load_data(0, leads=3)
with pytest.raises(AssertionError, match="`data_format` should be one of `.+`, but got `.+`"):
reader.load_data(0, data_format="lead_last_first")
with pytest.raises(
AssertionError,
match=(
"`data_format` should be one of `\\['channel_first', 'lead_first', 'channel_last', 'lead_last'\\]` "
"when the passed number of `leads` is larger than 1"
),
):
reader.load_data(0, data_format="flat")
with pytest.raises(AssertionError, match="`units` should be one of `.+` or None, but got `.+`"):
reader.load_data(0, units="kV")
def test_load_ann(self):
ann = reader.load_ann(0)
assert isinstance(ann, dict) and ann.keys() == reader.class_map.keys()
ann = reader.load_ann(0, ann_format="mask")
assert isinstance(ann, np.ndarray) and ann.shape[0] == reader.load_data(0).shape[1]
ann = reader.load_ann(0, sampfrom=1000, sampto=2000)
ann_1 = reader.load_ann(0, sampfrom=1000, sampto=2000, keep_original=True)
for k, v in ann.items():
for idx, itv in enumerate(v):
assert len(ann_1[k][idx]) == len(itv) == 2
ann_1[k][idx] = [ann_1[k][idx][0] - 1000, ann_1[k][idx][1] - 1000]
assert ann == ann_1
ann = reader.load_ann(0, sampfrom=1000, sampto=2000, ann_format="mask")
ann_1 = reader.load_ann(0, sampfrom=1000, sampto=2000, ann_format="mask", keep_original=True)
assert ann.shape == ann_1.shape == (1000,)
assert np.allclose(ann, ann_1)
def test_load_beat_ann(self):
rec = reader.qrsc_records[0]
beat_ann = reader.load_beat_ann(rec)
assert isinstance(beat_ann, np.ndarray) and beat_ann.ndim == 1
beat_ann = reader.load_beat_ann(rec, use_manual=False)
assert isinstance(beat_ann, np.ndarray) and beat_ann.ndim == 1
beat_ann = reader.load_beat_ann(rec, sampfrom=1000, sampto=2000)
beat_ann_1 = reader.load_beat_ann(rec, sampfrom=1000, sampto=2000, keep_original=True)
assert beat_ann.shape == beat_ann_1.shape
assert np.allclose(beat_ann, beat_ann_1 - 1000)
def test_load_rpeak_indices(self):
# `load_rpeak_indices` is alias of `load_beat_ann`
rec = reader.qrsc_records[0]
beat_ann = reader.load_beat_ann(rec)
rpeak_indices = reader.load_rpeak_indices(rec)
assert np.allclose(beat_ann, rpeak_indices)
def test_meta_data(self):
assert isinstance(reader.version, str) and re.match(PHYSIONET_DB_VERSION_PATTERN, reader.version)
assert isinstance(reader.webpage, str) and len(reader.webpage) > 0
assert reader.get_citation() is None # printed
assert str(reader) == repr(reader)
assert isinstance(reader.df_all_db_info, pd.DataFrame)
assert len(reader.df_all_db_info) > 0
assert isinstance(reader.database_info, DataBaseInfo)
def test_plot(self):
reader.plot(0, leads=0, ticks_granularity=2, sampfrom=1000, sampto=2000)
reader.plot(0, ticks_granularity=0, sampfrom=1000, sampto=2000)
data = reader.load_data(0, leads=[0, 1], sampfrom=1000, sampto=2000)
reader.plot(0, data=data, ticks_granularity=1)