def test_experiment_channels():
with Experiment('myexperiment', dir=DIRPATH) as exp:
assert exp.name == 'myexperiment'
assert exp.application_data
# assert exp.user_data
assert exp.application_data.spikedetekt.nchannels == 3
assert exp.application_data.spikedetekt.waveforms_nsamples == 10
assert exp.application_data.spikedetekt.nfeatures == 3
# Channel group.
chgrp = exp.channel_groups[0]
assert chgrp.name == 'channel_group_0'
assert np.array_equal(chgrp.adjacency_graph, [[4, 6], [8, 4]])
assert chgrp.application_data
# assert chgrp.user_data
# Channels.
channels = chgrp.channels
assert list(sorted(channels.keys())) == [4, 6, 8]
# Channel.
ch = channels[4]
assert ch.name == 'channel_4'
ch.kwd_index
ch.ignored
assert np.allclose(ch.position, [.4, .6])
ch.voltage_gain
ch.display_threshold
assert ch.application_data
def test_experiment_setattr():
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
chgrp = exp.channel_groups[0]
color0 = chgrp.clusters.main[0].application_data.klustaviewa.color
# By default, the cluster's color is 1.
assert color0 == 1
# Set it to 0.
chgrp.clusters.main[0].application_data.klustaviewa.color = 0
# We check that the color has changed in the file.
assert chgrp.clusters.main[0].application_data.klustaviewa._f_getAttr('color') == 0
# Close and open the file.
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
chgrp = exp.channel_groups[0]
# Check that the change has been saved on disk.
assert chgrp.clusters.main[0].application_data.klustaviewa.color == 0
# Set back the field to its original value.
chgrp.clusters.main[0].application_data.klustaviewa.color = color0
def test_experiment_add_cluster():
with Experiment('myexperiment2', dir=DIRPATH, mode='a') as exp:
chgrp = exp.channel_groups[0]
chgrp.clusters.main.add_cluster(id=27, color=34)
assert 27 in chgrp.clusters.main.keys()
assert chgrp.clusters.main[27].application_data.klustaviewa.color == 34
assert np.allclose(chgrp.clusters.main.color[:], [1, 34])
chgrp.clusters.main.remove_cluster(id=27)
assert 27 not in chgrp.clusters.main.keys()
def test_experiment_add_cluster_group():
with Experiment('myexperiment2', dir=DIRPATH, mode='a') as exp:
chgrp = exp.channel_groups[0]
chgrp.cluster_groups.main.add_group(id=27, name='boo', color=34)
assert 27 in chgrp.cluster_groups.main.keys()
assert chgrp.cluster_groups.main[27].name == 'boo'
assert chgrp.cluster_groups.main[27].application_data.klustaviewa.color == 34
chgrp.cluster_groups.main.remove_group(id=27)
assert 27 not in chgrp.cluster_groups.main.keys()
def test_experiment_cluster_groups():
with Experiment('myexperiment', dir=DIRPATH) as exp:
chgrp = exp.channel_groups[0]
cluster_group = chgrp.cluster_groups.main[0]
assert cluster_group.name == 'Noise'
assert cluster_group.application_data
# assert cluster_group.user_data
assert np.array_equal(chgrp.cluster_groups.main.color[:], [1])
assert np.array_equal(chgrp.clusters.main.group[:], [0])
def test_experiment_repr_nokwd():
kwd = os.path.join(DIRPATH, 'myexperiment.raw.kwd')
kwd2 = os.path.join(DIRPATH, 'myexperiment2.raw.kwd')
# Move a KWD file and test if Experiment works without KWD.
os.rename(kwd, kwd2)
info("The following error message is expected (part of the unit test)")
with Experiment('myexperiment', dir=DIRPATH) as exp:
s = str(exp)
os.rename(kwd2, kwd)
def test_experiment_events():
with Experiment('myexperiment', dir=DIRPATH) as exp:
evtp = exp.event_types['myevents']
evtp.application_data
# evtp.user_data
samples = evtp.events.time_samples
assert isinstance(samples, tb.EArray)
assert samples.dtype == np.uint64
recordings = evtp.events.recording
assert isinstance(recordings, tb.EArray)
assert recordings.dtype == np.uint16
def test_experiment_recordings():
with Experiment('myexperiment', dir=DIRPATH) as exp:
rec = exp.recordings[0]
assert rec.name == 'recording_0'
assert rec.sample_rate == 20000.
assert rec.start_time == 10.
assert rec.start_sample == 200000.
assert rec.bit_depth == 16
assert rec.band_high == 100.
assert rec.band_low == 500.
rd = rec.raw
assert isinstance(rd, tb.EArray)
assert rd.shape == (0, 3)
assert rd.dtype == np.int16
def test_experiment_add_spikes_nomasks():
with Experiment('myexperiment_nomasks', dir=DIRPATH, mode='a') as exp:
chgrp = exp.channel_groups[0]
spikes = chgrp.spikes
assert spikes.features_masks.shape == (0, 3)
assert isinstance(spikes.features, tb.Array)
assert spikes.features.shape == (0, 3)
spikes.add(time_samples=1000)
spikes.add(time_samples=2000)
assert len(spikes) == 2
assert spikes.features_masks.shape == (2, 3)
assert isinstance(spikes.features, tb.Array)
assert spikes.features.shape == (2, 3)
def test_experiment_features():
"""Test the wrapper around features implementing a custom cache."""
with Experiment('myexperiment', dir=DIRPATH) as exp:
chgrp = exp.channel_groups[0]
spikes = chgrp.spikes
assert isinstance(spikes.features_masks, tb.EArray)
assert spikes.features_masks.dtype == np.float32
assert spikes.features_masks.ndim == 3
assert isinstance(spikes.waveforms_raw, tb.EArray)
assert spikes.waveforms_raw.dtype == np.int16
assert spikes.waveforms_raw.ndim == 3
assert isinstance(spikes.waveforms_filtered, tb.EArray)
assert spikes.waveforms_filtered.dtype == np.int16
assert spikes.waveforms_filtered.ndim == 3
def test_experiment_spikes():
with Experiment('myexperiment', dir=DIRPATH) as exp:
chgrp = exp.channel_groups[0]
spikes = chgrp.spikes
assert isinstance(spikes.time_samples, tb.EArray)
assert spikes.time_samples.dtype == np.uint64
assert spikes.time_samples.ndim == 1
t = spikes.concatenated_time_samples
# assert isinstance(t, np.ndarray)
assert t.dtype == np.uint64
assert t.ndim == 1
assert isinstance(spikes.time_fractional, tb.EArray)
assert spikes.time_fractional.dtype == np.uint8
assert spikes.time_fractional.ndim == 1
assert isinstance(spikes.recording, tb.EArray)
assert spikes.recording.dtype == np.uint16
assert spikes.recording.ndim == 1
assert isinstance(spikes.clusters.main, tb.EArray)
assert spikes.clusters.main.dtype == np.uint32
assert spikes.clusters.main.ndim == 1
assert isinstance(spikes.clusters.original, tb.EArray)
assert spikes.clusters.original.dtype == np.uint32
assert spikes.clusters.original.ndim == 1
assert isinstance(spikes.features_masks, tb.EArray)
assert spikes.features_masks.dtype == np.float32
assert spikes.features_masks.ndim == 3
assert isinstance(spikes.waveforms_raw, tb.EArray)
assert spikes.waveforms_raw.dtype == np.int16
assert spikes.waveforms_raw.ndim == 3
assert isinstance(spikes.waveforms_filtered, tb.EArray)
assert spikes.waveforms_filtered.dtype == np.int16
assert spikes.waveforms_filtered.ndim == 3
def test_experiment_copy_clusters():
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
clusters = exp.channel_groups[0].spikes.clusters
# Adding spikes.
for i in range(10):
exp.channel_groups[0].spikes.add(time_samples=i*1000, cluster=10+i)
main = clusters.main[:]
original = clusters.original[:]
assert len(main) == 10
assert len(original) == 10
assert np.allclose(main, np.arange(10, 20))
assert np.allclose(original, np.zeros(10))
# Change original clusters on disk.
clusters.original[1:10:2] = 123
assert np.all(clusters.main[1:10:2] != 123)
# Copy clusters from original to main.
clusters.copy('original', 'main')
assert np.all(clusters.main[1:10:2] == 123)
def test_experiment_repr():
with Experiment('myexperiment', dir=DIRPATH) as exp:
s = str(exp)
def test_experiment_clusters():
with Experiment('myexperiment', dir=DIRPATH) as exp:
chgrp = exp.channel_groups[0]
cluster = chgrp.clusters.main[0]
def test_experiment_vectorizer():
with Experiment('myexperiment', dir=DIRPATH) as exp:
clustering = exp.channel_groups[0].clusters.main
dv = DictVectorizer(clustering, 'application_data.klustaviewa.color')
assert np.array_equal(dv[0], 1)
assert np.array_equal(dv[:], [1])
def test_recluster():
with Experiment('myexperiment', dir=DIRPATH) as exp:
spikes, clu = run_klustakwik(exp, channel_group=0, clusters=[5, 8])
assert 10 < len(clu) < 990