def test_version_2(self):
"""Test reading a version 2 AxoGraph file"""
filename = self.get_filename_path('AxoGraph_Digitized_File')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(blk.annotations['format_ver'], 2)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Current', 'Voltage', 'Column4', 'Column5',
'Column6', 'Column7', 'Column8', 'Column9',
'Column10', 'Column11', 'Column12', 'Column13',
'Column14', 'Column15', 'Column16', 'Column17',
'Column18', 'Column19', 'Column20', 'Column21',
'Column22', 'Column23', 'Column24', 'Column25',
'Column26', 'Column27', 'Column28', 'Column29'])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('pA')
target = np.array([[0.3125],
[9.6875],
[9.6875],
[9.6875],
[9.3750]], dtype=np.float32)
assert_equal(arr, target)
assert_equal(sig.t_start, 0.00009999999747378752 * pq.s)
assert_equal(sig.sampling_period, 0.00009999999747378750 * pq.s)
def test_force_single_segment(self):
"""Test reading an episodic file into one Segment"""
filename = self.get_filename_path('episodic.axgd')
reader = AxographIO(filename=filename, force_single_segment=True)
blk = reader.read_block()
assert_equal(len(blk.segments), 1)
assert_equal(len(blk.channel_indexes), 60)
def test_multi_segment(self):
"""Test reading an episodic file into multiple Segments"""
filename = self.get_filename_path('episodic.axgd')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(len(blk.segments), 30)
assert_equal(len(blk.channel_indexes), 2)
def test_rec_datetime(self):
"""Test parsing the recording datetime from notes"""
# parsing of rec_datetime differs depending on acquisition mode
# file obtained in episodic acquisition mode has date and time on
# separate lines of notes
filename = self.get_filename_path('episodic.axgd')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(blk.rec_datetime, datetime(2018, 6, 7, 15, 11, 36))
# file obtained in continuous acquisition mode has date and time in
# single line of notes
filename = self.get_filename_path('events_and_epochs.axgx')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(blk.rec_datetime, datetime(2019, 5, 25, 20, 16, 25))
def test_events_and_epochs(self):
"""Test loading events and epochs"""
filename = self.get_filename_path('events_and_epochs.axgx')
reader = AxographIO(filename=filename)
blk = reader.read_block()
event = blk.segments[0].events[0]
assert_equal(event.times, [5999, 5999, 23499, 23499,
26499, 26499, 35999]
* blk.segments[0].analogsignals[0].sampling_period)
assert_equal(event.labels, ['Stop', 'Start', 'Stop', 'Start',
'Stop', 'Start', 'Stop'])
epoch = blk.segments[0].epochs[0]
assert_equal(epoch.times, np.array([0.1, 4]) * pq.s)
assert_equal(epoch.durations, np.array([1.4, 2]) * pq.s)
assert_equal(epoch.labels, ['test interval 1', 'test interval 2'])
def test_force_single_segment(self):
"""Test reading an episodic file into one Segment"""
filename = self.get_filename_path('episodic.axgd')
reader = AxographIO(filename=filename, force_single_segment=True)
blk = reader.read_block(signal_group_mode='split-all')
assert_equal(len(blk.segments), 1)
assert_equal(len(blk.groups), 60)
assert_equal(len(blk.segments[0].analogsignals), 60)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['CAP', 'STIM'] * 30)
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('V')
target = np.array([[1.37500e-06], [1.53125e-06], [1.34375e-06],
[1.09375e-06], [1.21875e-06]],
dtype=np.float32)
assert_equal(arr, target)
def test_version_5(self):
"""Test reading a version 5 AxoGraph file"""
filename = self.get_filename_path('AxoGraph_X_File.axgx')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(blk.annotations['format_ver'], 5)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Current', '', '', '', '', ''])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('pA')
target = np.array([[+3.0846775], [-2.5403225], [-1.2903225],
[+6.8346770], [-5.0403230]],
dtype=np.float32)
assert_equal(arr, target)
assert_equal(sig.t_start, 0.00005 * pq.s)
assert_equal(sig.sampling_period, 0.00005 * pq.s)
def test_version_1(self):
"""Test reading a version 1 AxoGraph file"""
filename = self.get_filename_path('AxoGraph_Graph_File')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(blk.annotations['format_ver'], 1)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Current', 'Current'])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('pA')
target = np.array([[-5.5078130], [-3.1171880], [+1.6640626],
[+1.6640626], [+4.0546880]],
dtype=np.float32)
assert_equal(arr, target)
assert_equal(sig.t_start, 0.0005000000237487257 * pq.s)
assert_equal(sig.sampling_period, 0.0005000010132789612 * pq.s)
def test_version_6(self):
"""Test reading a version 6 AxoGraph file"""
filename = self.get_filename_path('File_axograph.axgd')
reader = AxographIO(filename=filename)
blk = reader.read_block()
assert_equal(blk.annotations['format_ver'], 6)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Membrane Voltage-1'])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('mV')
target = np.array([[-60.731834], [-60.701313], [-60.670795],
[-60.701313], [-60.731834]],
dtype=np.float32)
assert_equal(arr, target)
assert_equal(sig.t_start, 0.00002 * pq.s)
assert_equal(sig.sampling_period, 0.00002 * pq.s)
def test_file_with_corrupt_comment(self):
"""Test reading a file with a corrupt comment"""
filename = self.get_filename_path('corrupt-comment.axgx')
reader = AxographIO(filename=filename)
blk = reader.read_block(signal_group_mode='split-all')
assert_equal(blk.annotations['format_ver'], 6)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Data 1', 'Data 2'])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('mV')
target = np.array(
[[0.000000], [9.999833], [19.998667], [29.995500], [39.989334]],
dtype=np.float32)
assert_equal(arr, target)
assert_equal(sig.t_start, 0 * pq.s)
assert_equal(sig.sampling_period, 0.01 * pq.s)
def test_group_by_same_units(self):
"""Test reading with group-by-same-units"""
filename = self.get_filename_path('episodic.axgd')
reader = AxographIO(filename=filename)
blk = reader.read_block(signal_group_mode='group-by-same-units')
assert_equal(len(blk.segments), 30)
assert_equal(len(blk.groups), 1)
assert_equal(len(blk.segments[0].analogsignals), 1)
chan_names = blk.segments[0].analogsignals[0].array_annotations['channel_names']
assert_equal(chan_names, ['CAP', 'STIM'])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('V')
target = np.array([[1.37500e-06, 3.43750e-03],
[1.53125e-06, 2.81250e-03],
[1.34375e-06, 1.87500e-03],
[1.09375e-06, 1.56250e-03],
[1.21875e-06, 1.56250e-03]], dtype=np.float32)
assert_equal(arr, target)
def test_group_by_same_units(self):
"""Test reading with group-by-same-units"""
filename = self.get_filename_path('episodic.axgd')
reader = AxographIO(filename=filename)
blk = reader.read_block(signal_group_mode='group-by-same-units')
assert_equal(len(blk.segments), 30)
assert_equal(len(blk.channel_indexes), 1)
assert_equal(len(blk.segments[0].analogsignals), 1)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Channel bundle (CAP,STIM) '])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('V')
target = np.array([[1.37500e-06, 3.43750e-03],
[1.53125e-06, 2.81250e-03],
[1.34375e-06, 1.87500e-03],
[1.09375e-06, 1.56250e-03],
[1.21875e-06, 1.56250e-03]], dtype=np.float32)
assert_equal(arr, target)
def test_file_written_by_axographio_package_without_linearsequence(self):
"""Test reading file written by axographio package without linearsequence time column"""
filename = self.get_filename_path(
'written-by-axographio-without-linearsequence.axgx')
reader = AxographIO(filename=filename)
blk = reader.read_block(signal_group_mode='split-all')
assert_equal(blk.annotations['format_ver'], 6)
names = [sig.name for sig in blk.segments[0].analogsignals]
assert_equal(names, ['Data 1', 'Data 2'])
sig = blk.segments[0].analogsignals[0][:5]
arr = sig.as_array('mV')
target = np.array(
[[0.000000], [9.999833], [19.998667], [29.995500], [39.989334]],
dtype=np.float32)
assert_equal(arr, target)
assert_equal(sig.t_start, 0 * pq.s)
assert_equal(sig.sampling_period, 0.009999999999999787 * pq.s)