def test_neoviewer():
#TODO make autorun neo tdtrawio test before
from neo.rawio.tdtrawio import TdtRawIO
dirname = '/tmp/files_for_testing_neo/tdt/aep_05/'
neorawio = TdtRawIO(dirname=dirname)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
app = ephyviewer.mkQApp()
win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
for i, sig_source in enumerate(sources['signal']):
view = ephyviewer.TraceViewer(source=sig_source, name='signal {}'.format(i))
win.add_view(view)
for i, ep_source in enumerate(sources['epoch']):
view = ephyviewer.EpochViewer(source=ep_source, name='epochs')
win.add_view(view)
win.show()
app.exec_()
def test_neoviewer(interactive=False):
from neo.rawio.tdtrawio import TdtRawIO
local_test_dir = get_tdt_test_files()
dirname = os.path.join(local_test_dir, 'aep_05')
neorawio = TdtRawIO(dirname=dirname)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
app = ephyviewer.mkQApp()
win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
for i, sig_source in enumerate(sources['signal']):
view = ephyviewer.TraceViewer(source=sig_source,
name='signal {}'.format(i))
win.add_view(view)
for i, ep_source in enumerate(sources['epoch']):
view = ephyviewer.EpochViewer(source=ep_source, name='epochs')
win.add_view(view)
if interactive:
win.show()
app.exec_()
else:
# close thread properly
win.close()
def test_neo_rawio_sources():
from neo.rawio.tdtrawio import TdtRawIO
local_test_dir = get_tdt_test_files()
dirname = os.path.join(local_test_dir, 'aep_05')
neorawio = TdtRawIO(dirname=dirname)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
#~ print(sources)
for s in sources['signal']:
print(s.t_start, s.nb_channel, s.sample_rate)
print(s.get_chunk(i_start=0, i_stop=1024).shape)
for s in sources['epoch']:
print(s.t_start, s.nb_channel)
#~ print(s.get_chunk(i_start=0, i_stop=1024).shape)
print(s.get_chunk_by_time(chan=0, t_start=None, t_stop=None))
for s in sources['spike']:
print(s.t_start, s.nb_channel)
print(s.get_chunk_by_time(chan=0, t_start=None, t_stop=None))
def test_neo_rawio_sources():
#TODO make autorun neo tdtrawio test before
from neo.rawio.tdtrawio import TdtRawIO
dirname = '/tmp/files_for_testing_neo/tdt/aep_05/'
neorawio = TdtRawIO(dirname=dirname)
neorawio.parse_header()
print(neorawio)
sources = ephyviewer.get_sources_from_neo_rawio(neorawio)
#~ print(sources)
for s in sources['signal']:
print(s.t_start, s.nb_channel, s.sample_rate)
print(s.get_chunk(i_start=0, i_stop=1024).shape)
for s in sources['epoch']:
print(s.t_start, s.nb_channel)
#~ print(s.get_chunk(i_start=0, i_stop=1024).shape)
print(s.get_chunk_by_time(chan=0, t_start=None, t_stop=None))
for s in sources['spike']:
print(s.t_start, s.nb_channel)
print(s.get_chunk_by_time(chan=0, t_start=None, t_stop=None))
def __init__(self, dirname):
TdtRawIO.__init__(self, dirname=dirname)
BaseFromRaw.__init__(self, dirname)
def __init__(self, dirname):
TdtRawIO.__init__(self, dirname=dirname)
BaseFromRaw.__init__(self, dirname)
def test_compare_load_multi_single_block(self):
dirname = self.get_local_path('tdt/aep_05')
filename = self.get_local_path('tdt/aep_05/Block-1/aep_05_Block-1.Tdx')
io_single = TdtRawIO(filename)
io_multi = TdtRawIO(dirname)
io_single.parse_header()
io_multi.parse_header()
self.assertEqual(io_single.tdt_block_mode, 'single')
self.assertEqual(io_multi.tdt_block_mode, 'multi')
self.assertEqual(io_single.block_count(), 1)
self.assertEqual(io_multi.block_count(), 1)
self.assertEqual(io_single.segment_count(0), 1)
self.assertEqual(io_multi.segment_count(0), 2)
# compare header infos
assert_array_equal(io_single.header['signal_streams'], io_multi.header['signal_streams'])
assert_array_equal(io_single.header['signal_channels'], io_multi.header['signal_channels'])
assert_array_equal(io_single.header['event_channels'], io_multi.header['event_channels'])
# not all spiking channels are present in first tdt block (segment)
for spike_channel in io_single.header['spike_channels']:
self.assertIn(spike_channel, io_multi.header['spike_channels'])
# check that extracted signal chunks are identical
assert_array_equal(io_single.get_analogsignal_chunk(0, 0, 0, 100, 0),
io_multi.get_analogsignal_chunk(0, 0, 0, 100, 0))
def test_invalid_dirname(self):
invalid_name = 'random_non_existant_tdt_filename'
assert not Path(invalid_name).exists()
with self.assertRaises(ValueError):
TdtRawIO(invalid_name)