def test_init(self):
with self.assertRaises(TaborException):
TaborSegment(None, None, None, None)
with self.assertRaises(TaborException):
TaborSegment(np.zeros(5), np.zeros(4), None, None)
with self.assertRaises(TaborException):
TaborSegment(np.zeros(4), np.zeros(4), np.zeros(4), None)
with self.assertRaises(TaborException):
TaborSegment(np.zeros(4), np.zeros(4), None, np.zeros(4))
ch_a = np.asarray(100 + np.arange(6), dtype=np.uint16)
ch_b = np.asarray(1000 + np.arange(6), dtype=np.uint16)
marker_a = np.ones(3, dtype=bool)
marker_b = np.arange(3, dtype=np.uint16)
ts = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_a,
marker_b=marker_b)
self.assertIs(ts.ch_a, ch_a)
self.assertIs(ts.ch_b, ch_b)
self.assertIs(ts.marker_a, marker_a)
self.assertIsNot(ts.marker_b, marker_b)
np.testing.assert_equal(ts.marker_b, marker_b != 0)
def setUp(self):
super().setUp()
ramp_up = np.linspace(0, 2**14 - 1, num=192, dtype=np.uint16)
ramp_down = ramp_up[::-1]
zero = np.ones(192, dtype=np.uint16) * 2**13
sine = ((np.sin(np.linspace(0, 2 * np.pi, 192 + 64)) + 1) / 2 *
(2**14 - 1)).astype(np.uint16)
self.segments = [
TaborSegment(ramp_up, ramp_up, None, None),
TaborSegment(ramp_down, zero, None, None),
TaborSegment(sine, sine, None, None)
]
self.zero_segment = TaborSegment(zero, zero, None, None)
# program 1
self.sequence_tables = [[(10, 0, 0), (10, 1, 0), (10, 0, 0),
(10, 1, 0)],
[(1, 0, 0), (1, 1, 0), (1, 0, 0), (1, 1, 0)]]
self.advanced_sequence_table = [(1, 1, 0), (1, 2, 0)]
self.channel_pair = TaborChannelPair(self.instrument, (1, 2),
'tabor_unit_test')
def test_data_a(self):
ch_a = np.asarray(100 + np.arange(32), dtype=np.uint16)
ch_b = np.asarray(1000 + np.arange(32), dtype=np.uint16)
marker_a = np.ones(16, dtype=bool)
marker_b = np.asarray(list(range(5)) + list(range(6)) + list(range(5)),
dtype=np.uint16)
on = 1 << 14
off = 0
marker_a_data = np.asarray([0] * 8 + [on] * 8 + [0] * 8 + [on] * 8,
dtype=np.uint16)
on = 1 << 15
off = 0
marker_b_data = np.asarray([0] * 8 + [off] + [on] * 4 + [off] +
[on] * 2 + [0] * 8 + [on] * 3 + [off] +
[on] * 4)
ts = TaborSegment(ch_a=ch_a, ch_b=ch_b, marker_a=None, marker_b=None)
self.assertIs(ts.data_a, ch_a)
ts = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_a,
marker_b=None)
expected_data = ch_a + marker_a_data
np.testing.assert_equal(ts.data_a, expected_data)
ts = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=None,
marker_b=marker_b)
expected_data = ch_a + marker_b_data
np.testing.assert_equal(ts.data_a, expected_data)
ts = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_a,
marker_b=marker_b)
expected_data = ch_a + marker_b_data + marker_a_data
np.testing.assert_equal(ts.data_a, expected_data)
with self.assertRaises(NotImplementedError):
TaborSegment(ch_a=None,
ch_b=ch_b,
marker_a=marker_a,
marker_b=marker_b).data_a
def exec_general(self, data_1, data_2, fill_value=None):
tabor_segments = [
TaborSegment(d1, d2, None, None) for d1, d2 in zip(data_1, data_2)
]
expected_length = (sum(segment.num_points
for segment in tabor_segments) + 16 *
(len(tabor_segments) - 1)) * 2
offset = 0
pyte_result = 15000 * np.ones(expected_length, dtype=np.uint16)
for i, segment in enumerate(tabor_segments):
offset = pytabor.make_combined_wave(segment.ch_a,
segment.ch_b,
dest_array=pyte_result,
dest_array_offset=offset,
add_idle_pts=i > 0)
self.assertEqual(expected_length, offset)
result = make_combined_wave(tabor_segments, fill_value=15000)
np.testing.assert_equal(pyte_result, result)
dest_array = 15000 * np.ones(expected_length, dtype=np.uint16)
result = make_combined_wave(tabor_segments,
destination_array=dest_array)
np.testing.assert_equal(pyte_result, result)
# test that the destination array data is not copied
self.assertEqual(dest_array.__array_interface__['data'],
result.__array_interface__['data'])
with self.assertRaises(ValueError):
make_combined_wave(tabor_segments, destination_array=np.ones(16))
def test_from_binary_segment(self):
ch_a = np.asarray(100 + np.arange(32), dtype=np.uint16)
ch_b = np.asarray(1000 + np.arange(32), dtype=np.uint16)
marker_a = np.ones(16, dtype=bool)
marker_b = np.asarray(list(range(5)) + list(range(6)) + list(range(5)),
dtype=np.uint16)
segment = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_a,
marker_b=marker_b)
binary = segment.get_as_binary()
reconstructed = TaborSegment.from_binary_segment(binary)
self.assertEqual(segment, reconstructed)
def test_from_binary_data(self):
ch_a = np.asarray(100 + np.arange(32), dtype=np.uint16)
ch_b = np.asarray(1000 + np.arange(32), dtype=np.uint16)
marker_a = np.ones(16, dtype=bool)
marker_b = np.asarray(list(range(5)) + list(range(6)) + list(range(5)),
dtype=np.uint16)
segment = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_a,
marker_b=marker_b)
data_a = segment.data_a
data_b = segment.data_b
reconstructed = TaborSegment.from_binary_data(data_a, data_b)
self.assertEqual(segment, reconstructed)
def test_eq(self):
ch_a = np.asarray(100 + np.arange(32), dtype=np.uint16)
ch_b = np.asarray(1000 + np.arange(32), dtype=np.uint16)
marker_ones = np.ones(16, dtype=bool)
marker_random = np.asarray(list(range(5)) + list(range(6)) +
list(range(5)),
dtype=np.uint16)
marker_zeros = np.zeros(16, dtype=bool)
segment_1 = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_ones,
marker_b=marker_random)
segment_2 = TaborSegment(ch_a=ch_a,
ch_b=ch_a,
marker_a=marker_ones,
marker_b=marker_random)
segment_a0 = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_zeros,
marker_b=marker_random)
segment_anone = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=None,
marker_b=marker_random)
segment_none = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=None,
marker_b=None)
self.assertEqual(segment_1, segment_1)
self.assertNotEqual(segment_1, segment_2)
self.assertEqual(segment_a0, segment_anone)
self.assertEqual(segment_anone, segment_a0)
self.assertEqual(segment_anone, segment_anone)
self.assertNotEqual(segment_anone, segment_none)
self.assertEqual(segment_none, segment_none)
self.assertNotEqual(segment_a0, segment_1)
def test_invalid_segment_length(self):
gen = itertools.count()
data_1 = [
np.fromiter(gen, count=32, dtype=np.uint16),
np.fromiter(gen, count=15, dtype=np.uint16),
np.fromiter(gen, count=192, dtype=np.uint16)
]
data_2 = [
np.fromiter(gen, count=32, dtype=np.uint16),
np.fromiter(gen, count=16, dtype=np.uint16),
np.fromiter(gen, count=193, dtype=np.uint16)
]
tabor_segments = [TaborSegment(d, d, None, None) for d in data_1]
with self.assertRaises(ValueError):
make_combined_wave(tabor_segments)
tabor_segments = [TaborSegment(d, d, None, None) for d in data_2]
with self.assertRaises(ValueError):
make_combined_wave(tabor_segments)
def test_data_b(self):
ch_a = np.asarray(100 + np.arange(6), dtype=np.uint16)
ch_b = np.asarray(1000 + np.arange(6), dtype=np.uint16)
marker_a = np.ones(3, dtype=bool)
marker_b = np.arange(3, dtype=np.uint16)
ts = TaborSegment(ch_a=ch_a,
ch_b=ch_b,
marker_a=marker_a,
marker_b=marker_b)
self.assertIs(ts.data_b, ch_b)
def test_read_waveforms(self):
self.channel_pair._amend_segments(self.segments)
waveforms = self.channel_pair.read_waveforms()
segments = [
TaborSegment.from_binary_segment(waveform)
for waveform in waveforms
]
expected = [self.zero_segment, *self.segments]
for ex, r in zip(expected, segments):
ex1, ex2 = ex.data_a, ex.data_b
r1, r2 = r.data_a, r.data_b
np.testing.assert_equal(ex1, r1)
np.testing.assert_equal(ex2, r2)
self.assertEqual(expected, segments)
def exec_general(self, data_1, data_2, fill_value=None):
tabor_segments = [
TaborSegment(d1, d2, None, None) for d1, d2 in zip(data_1, data_2)
]
expected_length = (sum(segment.num_points
for segment in tabor_segments) + 16 *
(len(tabor_segments) - 1)) * 2
result = make_combined_wave(tabor_segments, fill_value=fill_value)
self.assertEqual(len(result), expected_length)
validate_result(tabor_segments, result, fill_value=fill_value)
destination_array = np.empty(expected_length, dtype=np.uint16)
result = make_combined_wave(tabor_segments,
fill_value=fill_value,
destination_array=destination_array)
validate_result(tabor_segments, result, fill_value=fill_value)
self.assertEqual(destination_array.__array_interface__['data'],
result.__array_interface__['data'], 'Data was copied')
def setUp(self):
self.ch_a = [
np.arange(16, dtype=np.uint16),
np.arange(32, 64, dtype=np.uint16)
]
self.ch_b = [
1000 + np.arange(16, dtype=np.uint16),
1000 + np.arange(32, 64, dtype=np.uint16)
]
self.marker_a = [np.ones(8, bool), np.array([0, 1] * 8, dtype=bool)]
self.marker_b = [
np.array([0, 0, 0, 1] * 2, bool),
np.array([1, 0, 1, 1] * 4, dtype=bool)
]
self.segments = [
TaborSegment(ch_a, ch_b, marker_a, marker_b)
for ch_a, ch_b, marker_a, marker_b in zip(
self.ch_a, self.ch_b, self.marker_a, self.marker_b)
]
self.sequencer_tables = [[(1, 1, 0), (1, 2, 0)],
[(1, 1, 0), (2, 2, 0), (1, 1, 0)]]
self.adv_sequencer_table = [(1, 1, 0), (1, 2, 0), (2, 1, 0)]
self.read_segments = [
segment.get_as_binary() for segment in self.segments
]
self.read_sequencer_tables = [
(np.array([1, 1]), np.array([1, 2]), np.array([0, 0])),
(np.array([1, 2, 1]), np.array([1, 2, 1]), np.array([0, 0, 0]))
]
self.read_adv_sequencer_table = (np.array([1, 1,
2]), np.array([1, 2, 1]),
np.array([0, 0, 0]))
self.selection_order = [0, 1, 0, 1, 1, 0, 0, 1, 0, 1]
self.selection_order_without_repetition = [0, 1, 0, 1, 0, 0, 1, 0, 1]
def test_num_points(self):
self.assertEqual(
TaborSegment(np.zeros(6), np.zeros(6), None, None).num_points, 6)