import re
import numpy as np
import wfdb
class test_annotation():
"""
Testing read and write of WFDB annotations, including Physionet
streaming.
Target files created using the original WFDB Software Package
version 10.5.24
"""
def test_1(self):
"""
Target file created with:
rdann -r sample-data/100 -a atr > ann-1
"""
annotation = wfdb.rdann('sample-data/100', 'atr')
# This is not the fault of the script. The annotation file specifies a
# length 3
annotation.aux_note[0] = '(N'
# aux_note field with a null written after '(N' which the script correctly picks up. I am just
# getting rid of the null in this unit test to compare with the regexp output below which has
# no null to detect in the output text file of rdann.
# Target data from WFDB software package
lines = tuple(open('tests/target-output/ann-1', 'r'))
nannot = len(lines)
target_time = [None] * nannot
target_sample = np.empty(nannot, dtype='object')
target_symbol = [None] * nannot
target_subtype = np.empty(nannot, dtype='object')
target_chan = np.empty(nannot, dtype='object')
target_num = np.empty(nannot, dtype='object')
target_aux_note = [None] * nannot
RXannot = re.compile(
'[ \t]*(?P<time>[\[\]\w\.:]+) +(?P<sample>\d+) +(?P<symbol>.) +(?P<subtype>\d+) +(?P<chan>\d+) +(?P<num>\d+)\t?(?P<aux_note>.*)')
for i in range(0, nannot):
target_time[i], target_sample[i], target_symbol[i], target_subtype[i], target_chan[
i], target_num[i], target_aux_note[i] = RXannot.findall(lines[i])[0]
# Convert objects into integers
target_sample = target_sample.astype('int')
target_num = target_num.astype('int')
target_subtype = target_subtype.astype('int')
target_chan = target_chan.astype('int')
# Compare
comp = [np.array_equal(annotation.sample, target_sample),
np.array_equal(annotation.symbol, target_symbol),
np.array_equal(annotation.subtype, target_subtype),
np.array_equal(annotation.chan, target_chan),
np.array_equal(annotation.num, target_num),
annotation.aux_note == target_aux_note]
# Test file streaming
pn_annotation = wfdb.rdann('100', 'atr', pn_dir='mitdb', return_label_elements=['label_store', 'symbol'])
pn_annotation.aux_note[0] = '(N'
pn_annotation.create_label_map()
# Test file writing
annotation.wrann(write_fs=True)
write_annotation = wfdb.rdann('100', 'atr', return_label_elements=['label_store', 'symbol'])
write_annotation.create_label_map()
assert (comp == [True] * 6)
assert annotation.__eq__(pn_annotation)
assert annotation.__eq__(write_annotation)
def test_2(self):
"""
Annotation file with many aux_note strings.
Target file created with:
rdann -r sample-data/100 -a atr > ann-2
"""
annotation = wfdb.rdann('sample-data/12726', 'anI')
# Target data from WFDB software package
lines = tuple(open('tests/target-output/ann-2', 'r'))
nannot = len(lines)
target_time = [None] * nannot
target_sample = np.empty(nannot, dtype='object')
target_symbol = [None] * nannot
target_subtype = np.empty(nannot, dtype='object')
target_chan = np.empty(nannot, dtype='object')
target_num = np.empty(nannot, dtype='object')
target_aux_note = [None] * nannot
RXannot = re.compile(
'[ \t]*(?P<time>[\[\]\w\.:]+) +(?P<sample>\d+) +(?P<symbol>.) +(?P<subtype>\d+) +(?P<chan>\d+) +(?P<num>\d+)\t?(?P<aux_note>.*)')
for i in range(0, nannot):
target_time[i], target_sample[i], target_symbol[i], target_subtype[i], target_chan[
i], target_num[i], target_aux_note[i] = RXannot.findall(lines[i])[0]
# Convert objects into integers
target_sample = target_sample.astype('int')
target_num = target_num.astype('int')
target_subtype = target_subtype.astype('int')
target_chan = target_chan.astype('int')
# Compare
comp = [np.array_equal(annotation.sample, target_sample),
np.array_equal(annotation.symbol, target_symbol),
np.array_equal(annotation.subtype, target_subtype),
np.array_equal(annotation.chan, target_chan),
np.array_equal(annotation.num, target_num),
annotation.aux_note == target_aux_note]
# Test file streaming
pn_annotation = wfdb.rdann('12726', 'anI', pn_dir='prcp', return_label_elements=['label_store', 'symbol'])
pn_annotation.create_label_map()
# Test file writing
annotation.wrann(write_fs=True)
write_annotation = wfdb.rdann('12726', 'anI', return_label_elements=['label_store', 'symbol'])
write_annotation.create_label_map()
assert (comp == [True] * 6)
assert annotation.__eq__(pn_annotation)
assert annotation.__eq__(write_annotation)
def test_3(self):
"""
Annotation file with custom annotation types
Target file created with:
rdann -r sample-data/1003 -a atr > ann-3
"""
annotation = wfdb.rdann('sample-data/1003', 'atr')
# Target data from WFDB software package
lines = tuple(open('tests/target-output/ann-3', 'r'))
nannot = len(lines)
target_time = [None] * nannot
target_sample = np.empty(nannot, dtype='object')
target_symbol = [None] * nannot
target_subtype = np.empty(nannot, dtype='object')
target_chan = np.empty(nannot, dtype='object')
target_num = np.empty(nannot, dtype='object')
target_aux_note = [None] * nannot
RXannot = re.compile(
'[ \t]*(?P<time>[\[\]\w\.:]+) +(?P<sample>\d+) +(?P<symbol>.) +(?P<subtype>\d+) +(?P<chan>\d+) +(?P<num>\d+)\t?(?P<aux_note>.*)')
for i in range(0, nannot):
target_time[i], target_sample[i], target_symbol[i], target_subtype[i], target_chan[
i], target_num[i], target_aux_note[i] = RXannot.findall(lines[i])[0]
# Convert objects into integers
target_sample = target_sample.astype('int')
target_num = target_num.astype('int')
target_subtype = target_subtype.astype('int')
target_chan = target_chan.astype('int')
# Compare
comp = [np.array_equal(annotation.sample, target_sample),
np.array_equal(annotation.symbol, target_symbol),
np.array_equal(annotation.subtype, target_subtype),
np.array_equal(annotation.chan, target_chan),
np.array_equal(annotation.num, target_num),
annotation.aux_note == target_aux_note]
# Test file streaming
pn_annotation = wfdb.rdann('1003', 'atr', pn_dir='challenge-2014/set-p2', return_label_elements=['label_store', 'symbol'])
pn_annotation.create_label_map()
# Test file writing
annotation.wrann(write_fs=True)
write_annotation = wfdb.rdann('1003', 'atr', return_label_elements=['label_store', 'symbol'])
write_annotation.create_label_map()
assert (comp == [True] * 6)
assert annotation.__eq__(pn_annotation)
assert annotation.__eq__(write_annotation)