def test_homemade_expect_success(self):
filename = 'test_homemade_expect_success.txt'
sample_data = [(-65, -65, -65, 0.5), (-64.8, -64.5, -64.0, 0.6),
(-64.6, -64.2, -77.0, 0.7), (-64.3, -64.0, -99.9, 0.8)]
with open(filename, 'w') as datafile:
datafile.write("# a comment\n")
for row in sample_data:
datafile.write("\t ".join(map(str, row)) + "\t\n")
io = AsciiSignalIO(filename,
usecols=(0, 1, 3),
timecolumn=2,
skiprows=1,
time_units="ms",
delimiter='\t',
units="mV",
method='homemade',
signal_group_mode='all-in-one',
t_start=0.5)
block = io.read_block()
signal = block.segments[0].analogsignals[0]
self.assertEqual(signal.shape,
(4, 2)) # two columns remaining after usecols
# and timecolumn applied
assert_array_almost_equal(signal[:, 1].reshape(-1).magnitude,
np.array(sample_data)[:, 1],
decimal=5)
self.assertAlmostEqual(signal.sampling_period, 0.1 * pq.ms)
os.remove(filename)
def test_multichannel_with_negative_timecolumn(self):
sample_data = np.random.uniform(size=(200, 3))
sampling_period = 0.5
time_data = sampling_period * np.arange(sample_data.shape[0])
combined_data = np.hstack((sample_data, time_data[:, np.newaxis]))
filename = "test_multichannel.txt"
np.savetxt(filename, combined_data, delimiter=' ')
io = AsciiSignalIO(filename,
delimiter=' ',
units='mV',
method='genfromtxt',
timecolumn=-1,
time_units='ms',
signal_group_mode='all-in-one')
block = io.read_block()
signal = block.segments[0].analogsignals[0]
assert_array_almost_equal(signal.magnitude, sample_data, decimal=6)
self.assertEqual(signal.sampling_period, sampling_period * pq.ms)
self.assertEqual(len(block.segments[0].analogsignals), 1)
self.assertEqual(signal.t_stop,
sample_data.shape[0] * sampling_period * pq.ms)
self.assertEqual(signal.units, pq.mV)
os.remove(filename)
def test_irregular_multichannel(self):
sample_data = np.random.uniform(size=(200, 3))
sample_data[:, 0] = np.sort(
sample_data[:, 0]) # make column 0 the time column
filename = "test_irregular_multichannel.txt"
np.savetxt(filename, sample_data, delimiter=' ')
io = AsciiSignalIO(filename,
delimiter=' ',
timecolumn=0,
units='mV',
method='genfromtxt',
signal_group_mode='all-in-one')
block = io.read_block()
signal = block.segments[0].irregularlysampledsignals[0]
assert_array_almost_equal(signal.magnitude,
sample_data[:, 1:3],
decimal=6)
self.assertEqual(len(block.segments[0].analogsignals), 0)
self.assertEqual(len(block.segments[0].irregularlysampledsignals), 1)
self.assertEqual(signal.shape, (200, 2))
self.assertEqual(signal.units, pq.mV)
os.remove(filename)
def test_roundtrip_with_json_metadata(self):
sample_data = np.random.uniform(size=(200, 3))
filename = "test_roundtrip_with_json_metadata.txt"
metadata_filename = "test_roundtrip_with_json_metadata_about.json"
signal1 = AnalogSignal(sample_data,
units="pA",
sampling_rate=2 * pq.kHz)
seg1 = Segment()
block1 = Block()
seg1.analogsignals.append(signal1)
seg1.block = block1
block1.segments.append(seg1)
iow = AsciiSignalIO(filename, metadata_filename=metadata_filename)
iow.write_block(block1)
self.assert_(os.path.exists(metadata_filename))
ior = AsciiSignalIO(filename)
block2 = ior.read_block()
assert len(block2.segments[0].analogsignals) == 3
signal2 = block2.segments[0].analogsignals[1]
assert_array_almost_equal(signal1.magnitude[:, 1],
signal2.magnitude.reshape(-1),
decimal=7)
self.assertEqual(signal1.units, signal2.units)
self.assertEqual(signal1.sampling_rate, signal2.sampling_rate)
assert_array_equal(signal1.times, signal2.times)
os.remove(filename)
os.remove(metadata_filename)
def test_callable_expect_success(self):
sample_data = np.random.uniform(size=(200, 3))
filename = "test_genfromtxt_expect_success.txt"
np.savetxt(filename, sample_data, delimiter=' ')
sampling_rate = 1 * pq.kHz
def reader(filename, comment_rows):
return np.genfromtxt(filename,
delimiter=' ',
usecols=None,
skip_header=comment_rows or 0,
dtype='f')
io = AsciiSignalIO(filename,
sampling_rate=sampling_rate,
delimiter=' ',
units='mV',
method=reader)
block = io.read_block()
signal1 = block.segments[0].analogsignals[1]
assert_array_almost_equal(signal1.reshape(-1).magnitude,
sample_data[:, 1],
decimal=6)
self.assertEqual(len(block.segments[0].analogsignals), 3)
self.assertEqual(signal1.t_stop, sample_data.shape[0] / sampling_rate)
self.assertEqual(signal1.units, pq.mV)
os.remove(filename)
def test_csv_expect_success(self):
filename = 'test_csv_expect_success.csv'
sample_data = [
(-65, -65, -65, 0.5),
(-64.8, -64.5, -64.0, 0.6),
(-64.6, -64.2, -77.0, 0.7),
(-64.3, -64.0, -99.9, 0.8)
]
with open(filename, 'w') as csvfile:
writer = csv.writer(csvfile, delimiter=',',
quotechar='|', quoting=csv.QUOTE_MINIMAL)
for row in sample_data:
writer.writerow(row)
io = AsciiSignalIO(filename, usecols=(0, 1, 3), timecolumn=2,
# note that timecolumn applies to the remaining columns after applying usecols
time_units="ms", delimiter=',', units="mV", method='csv',
signal_group_mode='all-in-one', t_start=0.5)
block = io.read_block()
signal = block.segments[0].analogsignals[0]
self.assertEqual(signal.shape, (4, 2)) # two columns remaining after usecols and timecolumn applied
assert_array_almost_equal(signal[:, 1].reshape(-1).magnitude,
np.array(sample_data)[:, 1],
decimal=5)
self.assertAlmostEqual(signal.sampling_period, 0.1 * pq.ms)
os.remove(filename)
def test_genfromtxt_expect_success(self):
sample_data = np.random.uniform(size=(200, 3))
filename = "test_genfromtxt_expect_success.txt"
np.savetxt(filename, sample_data, delimiter=' ')
sampling_rate = 1 * pq.kHz
io = AsciiSignalIO(filename, sampling_rate=sampling_rate, delimiter=' ',
units='mV', method='genfromtxt')
block = io.read_block()
signal1 = block.segments[0].analogsignals[1]
assert_array_almost_equal(signal1.reshape(-1).magnitude, sample_data[:, 1],
decimal=6)
self.assertEqual(len(block.segments[0].analogsignals), 3)
self.assertEqual(signal1.t_stop, sample_data.shape[0] / sampling_rate)
self.assertEqual(signal1.units, pq.mV)
os.remove(filename)
def test_multichannel(self):
sample_data = np.random.uniform(size=(200, 3))
filename = "test_multichannel.txt"
np.savetxt(filename, sample_data, delimiter=' ')
sampling_rate = 1 * pq.kHz
io = AsciiSignalIO(filename, sampling_rate=sampling_rate, delimiter=' ',
units='mV', method='genfromtxt',
signal_group_mode='all-in-one')
block = io.read_block()
signal = block.segments[0].analogsignals[0]
assert_array_almost_equal(signal.magnitude, sample_data,
decimal=6)
self.assertEqual(len(block.segments[0].analogsignals), 1)
self.assertEqual(signal.t_stop, sample_data.shape[0] / sampling_rate)
self.assertEqual(signal.units, pq.mV)
os.remove(filename)
def test_read_with_json_metadata(self):
sample_data = np.random.uniform(size=(200, 3))
filename = "test_read_with_json_metadata.txt"
metadata_filename = "test_read_with_json_metadata_about.json"
np.savetxt(filename, sample_data, delimiter=' ')
metadata = {
"filename": filename,
"delimiter": " ",
"timecolumn": None,
"units": "mV",
"time_units": "ms",
"sampling_rate": {
"value": 1.0,
"units": "kHz"
},
"method": "genfromtxt",
"signal_group_mode": 'split-all'
}
with open(metadata_filename, "w") as fp:
json.dump(metadata, fp)
expected_sampling_rate = 1 * pq.kHz
io = AsciiSignalIO(filename)
block = io.read_block()
signal1 = block.segments[0].analogsignals[1]
assert_array_almost_equal(signal1.reshape(-1).magnitude,
sample_data[:, 1],
decimal=6)
self.assertEqual(len(block.segments[0].analogsignals), 3)
self.assertEqual(signal1.sampling_rate, expected_sampling_rate)
self.assertEqual(signal1.t_stop,
sample_data.shape[0] / signal1.sampling_rate)
self.assertEqual(signal1.units, pq.mV)
os.remove(filename)
os.remove(metadata_filename)
def test_genfromtxt_irregular_expect_success(self):
sample_data = np.random.uniform(size=(200, 3))
sample_data[:, 0] = np.sort(
sample_data[:, 0]) # make column 0 the time column
filename = "test_genfromtxt_irregular_expect_success.txt"
np.savetxt(filename, sample_data, delimiter=' ')
io = AsciiSignalIO(filename,
delimiter=' ',
timecolumn=0,
units='mV',
method='genfromtxt',
signal_group_mode='split-all')
block = io.read_block()
signal1 = block.segments[0].irregularlysampledsignals[1]
assert_array_almost_equal(signal1.reshape(-1).magnitude,
sample_data[:, 2],
decimal=6)
self.assertEqual(len(block.segments[0].analogsignals), 0)
self.assertEqual(len(block.segments[0].irregularlysampledsignals), 2)
self.assertEqual(signal1.units, pq.mV)
os.remove(filename)
