def test_klusters_loader_1():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KlustersLoader(filename=xmlfile)
# Get full data sets.
features = l.get_features()
# features_some = l.get_some_features()
masks = l.get_masks()
waveforms = l.get_waveforms()
clusters = l.get_clusters()
spiketimes = l.get_spiketimes()
nclusters = len(Counter(clusters))
probe = l.get_probe()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
cluster_sizes = l.get_cluster_sizes()
# Check the shape of the data sets.
# ---------------------------------
assert check_shape(features, (nspikes, nchannels * fetdim + 1))
# assert features_some.shape[1] == nchannels * fetdim + 1
assert check_shape(masks, (nspikes, nchannels))
assert check_shape(waveforms, (nspikes, nsamples, nchannels))
assert check_shape(clusters, (nspikes,))
assert check_shape(spiketimes, (nspikes,))
assert check_shape(probe, (nchannels, 2))
assert check_shape(cluster_colors, (nclusters,))
assert check_shape(cluster_groups, (nclusters,))
assert check_shape(group_colors, (4,))
assert check_shape(group_names, (4,))
assert check_shape(cluster_sizes, (nclusters,))
# Check the data type of the data sets.
# -------------------------------------
assert check_dtype(features, np.float32)
assert check_dtype(masks, np.float32)
# HACK: Panel has no dtype(s) attribute
# assert check_dtype(waveforms, np.float32)
assert check_dtype(clusters, np.int32)
assert check_dtype(spiketimes, np.float32)
assert check_dtype(probe, np.float32)
assert check_dtype(cluster_colors, np.int32)
assert check_dtype(cluster_groups, np.int32)
assert check_dtype(group_colors, np.int32)
assert check_dtype(group_names, object)
assert check_dtype(cluster_sizes, np.int32)
l.close()
def test_klusters_loader_1():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KlustersLoader(filename=xmlfile)
# Get full data sets.
features = l.get_features()
# features_some = l.get_some_features()
masks = l.get_masks()
waveforms = l.get_waveforms()
clusters = l.get_clusters()
spiketimes = l.get_spiketimes()
nclusters = len(Counter(clusters))
probe = l.get_probe()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
cluster_sizes = l.get_cluster_sizes()
# Check the shape of the data sets.
# ---------------------------------
assert check_shape(features, (nspikes, nchannels * fetdim + 1))
# assert features_some.shape[1] == nchannels * fetdim + 1
assert check_shape(masks, (nspikes, nchannels))
assert check_shape(waveforms, (nspikes, nsamples, nchannels))
assert check_shape(clusters, (nspikes, ))
assert check_shape(spiketimes, (nspikes, ))
assert check_shape(probe, (nchannels, 2))
assert check_shape(cluster_colors, (nclusters, ))
assert check_shape(cluster_groups, (nclusters, ))
assert check_shape(group_colors, (4, ))
assert check_shape(group_names, (4, ))
assert check_shape(cluster_sizes, (nclusters, ))
# Check the data type of the data sets.
# -------------------------------------
assert check_dtype(features, np.float32)
assert check_dtype(masks, np.float32)
# HACK: Panel has no dtype(s) attribute
# assert check_dtype(waveforms, np.float32)
assert check_dtype(clusters, np.int32)
assert check_dtype(spiketimes, np.float32)
assert check_dtype(probe, np.float32)
assert check_dtype(cluster_colors, np.int32)
assert check_dtype(cluster_groups, np.int32)
assert check_dtype(group_colors, np.int32)
assert check_dtype(group_names, object)
assert check_dtype(cluster_sizes, np.int32)
l.close()
def test_klusters_loader_2():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KlustersLoader(filename=xmlfile)
# Get full data sets.
features = l.get_features()
masks = l.get_masks()
waveforms = l.get_waveforms()
clusters = l.get_clusters()
spiketimes = l.get_spiketimes()
nclusters = len(Counter(clusters))
probe = l.get_probe()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
cluster_sizes = l.get_cluster_sizes()
# Check selection.
# ----------------
index = nspikes / 2
waveform = select(waveforms, index)
cluster = clusters[index]
spikes_in_cluster = np.nonzero(clusters == cluster)[0]
nspikes_in_cluster = len(spikes_in_cluster)
l.select(clusters=[cluster])
# Check the size of the selected data.
# ------------------------------------
assert check_shape(l.get_features(), (nspikes_in_cluster,
nchannels * fetdim + 1))
assert check_shape(l.get_masks(full=True), (nspikes_in_cluster,
nchannels * fetdim + 1))
assert check_shape(l.get_waveforms(),
(nspikes_in_cluster, nsamples, nchannels))
assert check_shape(l.get_clusters(), (nspikes_in_cluster,))
assert check_shape(l.get_spiketimes(), (nspikes_in_cluster,))
# Check waveform sub selection.
# -----------------------------
waveforms_selected = l.get_waveforms()
assert np.array_equal(get_array(select(waveforms_selected, index)),
get_array(waveform))
l.close()
def test_klusters_loader_2():
# Open the mock data.
dir = TEST_FOLDER
xmlfile = os.path.join(dir, 'test.xml')
l = KlustersLoader(filename=xmlfile)
# Get full data sets.
features = l.get_features()
masks = l.get_masks()
waveforms = l.get_waveforms()
clusters = l.get_clusters()
spiketimes = l.get_spiketimes()
nclusters = len(Counter(clusters))
probe = l.get_probe()
cluster_colors = l.get_cluster_colors()
cluster_groups = l.get_cluster_groups()
group_colors = l.get_group_colors()
group_names = l.get_group_names()
cluster_sizes = l.get_cluster_sizes()
# Check selection.
# ----------------
index = nspikes / 2
waveform = select(waveforms, index)
cluster = clusters[index]
spikes_in_cluster = np.nonzero(clusters == cluster)[0]
nspikes_in_cluster = len(spikes_in_cluster)
l.select(clusters=[cluster])
# Check the size of the selected data.
# ------------------------------------
assert check_shape(l.get_features(),
(nspikes_in_cluster, nchannels * fetdim + 1))
assert check_shape(l.get_masks(full=True),
(nspikes_in_cluster, nchannels * fetdim + 1))
assert check_shape(l.get_waveforms(),
(nspikes_in_cluster, nsamples, nchannels))
assert check_shape(l.get_clusters(), (nspikes_in_cluster, ))
assert check_shape(l.get_spiketimes(), (nspikes_in_cluster, ))
# Check waveform sub selection.
# -----------------------------
waveforms_selected = l.get_waveforms()
assert np.array_equal(get_array(select(waveforms_selected, index)),
get_array(waveform))
l.close()
