def test_matplotlib_figure(self):
# Test figure drawing method (doesn't inspect output).
# Select matplotlib backend that doesn't require a screen
import matplotlib
matplotlib.use('template')
path = os.path.join(DIR_FORMATS, 'abf-v1.abf')
abf = axon.AbfFile(path)
abf.matplotlib_figure()
def test_read_protocol_v1(self):
# Test reading a v1 protocol file.
# Load file
path = os.path.join(DIR_FORMATS, 'abf-protocol.pro')
abf = axon.AbfFile(path)
# Check version info
self.assertIn('version 1.65', abf.info())
self.assertEqual(
abf.info(),
'Axon Protocol File: abf-protocol.pro\n'
'ABF Format version 1.65\n'
'Recorded on: 2005-06-17 14:33:02.160000\n'
'Acquisition mode: 5: Episodic stimulation mode\n'
'Protocol set for 1 trials, spaced 0.0s apart.\n'
' with 1 runs per trial, spaced 0.0s apart.\n'
' and 30 sweeps per run, spaced 5.0s apart.\n'
'Sampling rate: 20000.0 Hz'
)
# Test getting full header runs without crashing
abf.info(True)
# Load, force as protocol
path = os.path.join(DIR_FORMATS, 'abf-protocol.pro')
abf = axon.AbfFile(path, is_protocol_file=True)
# Check version info
self.assertIn('version 1.65', abf.info())
self.assertIn('Axon Protocol File', abf.info())
# Test protocol extraction
p = abf.myokit_protocol()
self.assertEqual(len(p), 60)
# Test step extraction
p = abf.protocol_steps()
self.assertEqual(len(p), 1)
self.assertEqual(len(p[0]), 30)
def test_read_v2(self):
# Test reading a version 2 file.
# Load file
path = os.path.join(DIR_FORMATS, 'abf-v2.abf')
abf = axon.AbfFile(path)
# Check version info
self.assertIn('version 2.0', abf.info())
self.assertEqual(
abf.info(),
'Axon Binary File: abf-v2.abf\n'
'ABF Format version 2.0\n'
'Recorded on: 2014-10-01 14:03:55.980999\n'
'Acquisition mode: 5: Episodic stimulation mode\n'
'Protocol set for 1 trials, spaced 0.0s apart.\n'
' with 1 runs per trial, spaced 0.0s apart.\n'
' and 1 sweeps per run, spaced 5.0s apart.\n'
'Sampling rate: 10000.0 Hz\n'
'Channel 0: "IN 0"\n'
' Unit: pA\n'
' Low-pass filter: 10000.0 Hz\n'
' Cm (telegraphed): 6.34765625 pF')
# Test getting full header runs without crashing
abf.info(True)
# Test len returns number of sweeps
self.assertEqual(len(abf), 1)
# Test data access
self.assertEqual(abf.data_channels(), 1) # 1 data channel
x = abf.extract_channel(0)
self.assertEqual(len(x), 1 + len(abf)) # sweeps + time
self.assertEqual(len(x[0]), len(x[1]))
y = abf.extract_channel_as_myokit_log(0)
self.assertEqual(len(y), 1 + len(abf)) # sweeps + time
z = abf.myokit_log()
self.assertEqual(len(z), 6) # time + channel + 4 protocol channels
sweep = abf[0]
self.assertEqual(len(sweep), 1) # 1 channel in sweep
channel = sweep[0]
self.assertEqual(len(abf) * len(channel.times()), len(z.time()))
self.assertEqual(len(abf) * len(channel.values()), len(z.time()))
# Test protocol extraction
self.assertEqual(abf.protocol_channels(), 4) # 4 protocol channels
p = abf.myokit_protocol()
self.assertEqual(len(p), 2) # 2 steps in this protocol
self.assertEqual(abf.protocol_holding_level(0), -120)
p = abf.myokit_protocol(0)
self.assertEqual(len(p), 2)
def test_read_v1(self):
# Test reading a version 1 file.
# Load file
path = os.path.join(DIR_FORMATS, 'abf-v1.abf')
abf = axon.AbfFile(path)
self.assertEqual(abf.filename(), path)
# Check version info
self.assertIn('version 1.65', abf.info())
self.assertEqual(
abf.info(),
'Axon Binary File: abf-v1.abf\n'
'ABF Format version 1.65\n'
'Recorded on: 2014-11-14 12:52:29.389999\n'
'Acquisition mode: 5: Episodic stimulation mode\n'
'Protocol set for 1 trials, spaced 0.0s apart.\n'
' with 1 runs per trial, spaced 0.0s apart.\n'
' and 9 sweeps per run, spaced 0.5s apart.\n'
'Sampling rate: 10000.0 Hz\n'
'Channel 0: "IN 0 "\n'
' Unit: pA'
)
# Test getting full header runs without crashing
abf.info(True)
# Test len returns number of sweeps
self.assertEqual(len(abf), 9)
# Test data access
self.assertEqual(abf.data_channels(), 1) # 1 data channel
x = abf.extract_channel(0)
self.assertEqual(len(x), 1 + len(abf)) # sweeps + time
self.assertEqual(len(x[0]), len(x[1]))
self.assertEqual(len(x[0]), len(x[2]))
self.assertEqual(len(x[0]), len(x[3]))
self.assertEqual(len(x[0]), len(x[4]))
self.assertEqual(len(x[0]), len(x[5]))
self.assertEqual(len(x[0]), len(x[6]))
self.assertEqual(len(x[0]), len(x[7]))
self.assertEqual(len(x[0]), len(x[8]))
self.assertEqual(len(x[0]), len(x[9]))
y = abf.extract_channel_as_myokit_log(0)
self.assertEqual(len(y), 1 + len(abf)) # sweeps + time
z = abf.myokit_log()
self.assertEqual(len(z), 6) # time + channel + 4 protocol channels
sweep = abf[0]
self.assertEqual(len(sweep), 1) # 1 channel in sweep
channel = sweep[0]
self.assertIsInstance(channel.number(), int)
self.assertIn('Channel', str(channel))
self.assertEqual(len(abf) * len(channel.times()), len(z.time()))
self.assertEqual(len(abf) * len(channel.values()), len(z.time()))
# Test reading of sweeps as one long array
x, y = abf.extract_channel(0, join=True)
z = abf.extract_channel(0)
self.assertEqual(len(x), len(y))
self.assertEqual(len(x), len(abf) * len(z[0]))
self.assertTrue(np.all(x[1:] > x[:-1]))
# Test protocol extraction
self.assertEqual(abf.protocol_channels(), 4) # 4 protocol channels
p = abf.myokit_protocol()
self.assertEqual(len(p), 18) # 18 steps in this protocol
self.assertEqual(abf.protocol_holding_level(0), 0)
p = abf.myokit_protocol(0)
self.assertEqual(len(p), 18)