def test_in_polygon():
polygon = [[0, 0], [1, 0], [1, 1], [0, 1], [0, 0]]
points = np.random.uniform(size=(100, 2), low=-1, high=1)
idx_expected = np.nonzero((points[:, 0] > 0) & (points[:, 1] > 0)
& (points[:, 0] < 1) & (points[:, 1] < 1))[0]
idx = np.nonzero(_in_polygon(points, polygon))[0]
ae(idx, idx_expected)
def test_regular_subset():
spikes = [2, 3, 5, 7, 11, 13, 17]
ae(regular_subset(spikes), spikes)
ae(regular_subset(spikes, 100), spikes)
ae(regular_subset(spikes, 100, offset=2), spikes)
ae(regular_subset(spikes, 3), [2, 7, 17])
ae(regular_subset(spikes, 3, offset=1), [3, 11])
def test_select_spikes_2():
n_spikes = 1000
n_clusters = 10
spike_times = artificial_spike_samples(n_spikes)
spike_times = 10. * spike_times / spike_times.max()
chunk_bounds = np.linspace(0.0, 10.0, 11)
n_chunks_kept = 3
chunks_kept = [0., 1., 4., 5., 8., 9.]
spike_clusters = artificial_spike_clusters(n_spikes, n_clusters)
spc = _spikes_per_cluster(spike_clusters)
ss = SpikeSelector(
get_spikes_per_cluster=lambda cl: spc.get(cl, np.array([], dtype=np.int64)),
spike_times=spike_times, chunk_bounds=chunk_bounds, n_chunks_kept=n_chunks_kept)
ae(ss.chunks_kept, chunks_kept)
def _check_chunks(sid):
chunk_ids = np.searchsorted(chunk_bounds, spike_times[sid], 'right') - 1
ae(np.unique(chunk_ids), [0, 4, 8])
# Select all spikes belonging to the kept chunks.
sid = ss(n_spikes, np.arange(n_clusters), subset_chunks=True)
_check_chunks(sid)
# Select 10 spikes from each cluster.
sid = ss(10, np.arange(n_clusters), subset_chunks=True)
assert np.all(np.diff(sid) > 0)
_check_chunks(sid)
ae(np.bincount(spike_clusters[sid]), [10] * 10)
def test_select_spikes_2():
spc = lambda c: {2: [2, 7, 11], 3: [3, 5], 5: []}.get(c, None)
sel = Selector(spc)
assert sel.select_spikes() is None
ae(sel.select_spikes([2, 5]), spc(2))
ae(sel.select_spikes([2, 5], 2), [2])
def test_select_spikes_3():
s = select_spikes(
[0],
max_n_spikes_per_cluster=4,
spikes_per_cluster=lambda x: np.arange(10),
batch_size=2,
)
ae(s, [0, 1, 8, 9])
def test_read_write(tempdir):
arr = np.arange(10).astype(np.float32)
path = Path(tempdir) / 'test.npy'
write_array(path, arr)
ae(read_array(path), arr)
ae(read_array(path, mmap_mode='r'), arr)
def test_unique():
"""Test _unique() function"""
_unique([])
n_spikes = 300
n_clusters = 3
spike_clusters = artificial_spike_clusters(n_spikes, n_clusters)
ae(_unique(spike_clusters), np.arange(n_clusters))
def test_get_padded():
arr = np.array([1, 2, 3])[:, np.newaxis]
with raises(RuntimeError):
ae(_get_padded(arr, -2, 5).ravel(), [1, 2, 3, 0, 0])
ae(_get_padded(arr, 1, 2).ravel(), [2])
ae(_get_padded(arr, 0, 5).ravel(), [1, 2, 3, 0, 0])
ae(_get_padded(arr, -2, 3).ravel(), [0, 0, 1, 2, 3])
def test_spikes_in_clusters():
"""Test _spikes_in_clusters()."""
n_spikes = 100
n_clusters = 5
spike_clusters = artificial_spike_clusters(n_spikes, n_clusters)
ae(_spikes_in_clusters(spike_clusters, []), [])
for i in range(n_clusters):
assert np.all(spike_clusters[_spikes_in_clusters(spike_clusters, [i])] == i)
clusters = [1, 2, 3]
assert np.all(np.in1d(
spike_clusters[_spikes_in_clusters(spike_clusters, clusters)], clusters))
def test_as_array():
ae(_as_array(3), [3])
ae(_as_array([3]), [3])
ae(_as_array(3.), [3.])
ae(_as_array([3.]), [3.])
with raises(ValueError):
_as_array(map)
def test_spikes_per_cluster():
"""Test _spikes_per_cluster()."""
n_spikes = 100
n_clusters = 3
spike_clusters = artificial_spike_clusters(n_spikes, n_clusters)
assert not _spikes_per_cluster([])
spikes_per_cluster = _spikes_per_cluster(spike_clusters)
assert list(spikes_per_cluster.keys()) == list(range(n_clusters))
for i in range(n_clusters):
ae(spikes_per_cluster[i], np.sort(spikes_per_cluster[i]))
assert np.all(spike_clusters[spikes_per_cluster[i]] == i)
def test_accumulator_2():
acc = _accumulate([
{
'a': np.arange(3),
'b': np.arange(3) * 10,
'c': 0
},
{
'a': np.arange(3, 5),
'b': np.arange(3, 5) * 10,
'c': 1
},
])
ae(acc['a'], np.arange(5))
ae(acc['b'], np.arange(5) * 10)
# NOTE: in case of scalars, we take the first one and discard the others.
# We don't concatenate them.
assert acc['c'] == 0
def test_get_excerpts():
data = np.random.rand(100, 2)
subdata = get_excerpts(data, n_excerpts=10, excerpt_size=5)
assert subdata.shape == (50, 2)
ae(subdata[:5, :], data[:5, :])
ae(subdata[-5:, :], data[-10:-5, :])
data = np.random.rand(10, 2)
subdata = get_excerpts(data, n_excerpts=10, excerpt_size=5)
ae(subdata, data)
data = np.random.rand(10, 2)
subdata = get_excerpts(data, n_excerpts=1, excerpt_size=10)
ae(subdata, data)
assert len(get_excerpts(data, n_excerpts=0, excerpt_size=10)) == 0
def test_chunk():
data = np.random.randn(200, 4)
chunks = chunk_bounds(data.shape[0], 100, overlap=20)
with raises(ValueError):
data_chunk(data, (0, 0, 0))
assert data_chunk(data, (0, 0)).shape == (0, 4)
# Chunk 1.
ch = next(chunks)
d = data_chunk(data, ch)
d_o = data_chunk(data, ch, with_overlap=True)
ae(d_o, data[0:100])
ae(d, data[0:90])
# Chunk 2.
ch = next(chunks)
d = data_chunk(data, ch)
d_o = data_chunk(data, ch, with_overlap=True)
ae(d_o, data[80:180])
ae(d, data[90:170])
def test_concatenate_virtual_arrays_1():
arrs = [np.arange(5), np.arange(10, 12), np.array([0])]
c = _concatenate_virtual_arrays(arrs, scaling=1)
assert c.shape == (8,)
assert len(c) == 8
assert c._get_recording(3) == 0
assert c._get_recording(5) == 1
ae(c[:], [0, 1, 2, 3, 4, 10, 11, 0])
ae(c[0], [0])
ae(c[4], [4])
ae(c[5], [10])
ae(c[6], [11])
ae(c[4:6], [4, 10])
ae(c[:6], [0, 1, 2, 3, 4, 10])
ae(c[4:], [4, 10, 11, 0])
ae(c[4:-1], [4, 10, 11])
def test_select_spikes_1():
with raises(AssertionError):
select_spikes()
spikes = [2, 3, 5, 7, 11]
spc = lambda c: {2: [2, 7, 11], 3: [3, 5], 5: []}.get(c, None)
ae(select_spikes([], spikes_per_cluster=spc), [])
ae(select_spikes([2, 3, 5], spikes_per_cluster=spc), spikes)
ae(select_spikes([2, 5], spikes_per_cluster=spc), spc(2))
ae(select_spikes([2, 3, 5], 0, spikes_per_cluster=spc), spikes)
ae(select_spikes([2, 3, 5], None, spikes_per_cluster=spc), spikes)
ae(select_spikes([2, 3, 5], 1, spikes_per_cluster=spc), [2, 3])
ae(select_spikes([2, 5], 2, spikes_per_cluster=spc), [2])
def test_grouped_mean():
spike_clusters = np.array([2, 3, 2, 2, 5])
arr = [9, -3, 10, 11, -5]
ae(grouped_mean(arr, spike_clusters), [10, -3, -5])
def test_flatten_per_cluster():
spc = {2: [2, 7, 11], 3: [3, 5], 5: []}
arr = _flatten_per_cluster(spc)
ae(arr, [2, 3, 5, 7, 11])
def _check_chunks(sid):
chunk_ids = np.searchsorted(chunk_bounds, spike_times[sid], 'right') - 1
ae(np.unique(chunk_ids), [0, 4, 8])
def test_range_from_slice():
"""Test '_range_from_slice'."""
class _SliceTest(object):
"""Utility class to make it more convenient to test slice objects."""
def __init__(self, **kwargs):
self._kwargs = kwargs
def __getitem__(self, item):
if isinstance(item, slice):
return _range_from_slice(item, **self._kwargs)
with raises(ValueError):
_SliceTest()[:]
with raises(ValueError):
_SliceTest()[1:]
ae(_SliceTest()[:5], [0, 1, 2, 3, 4])
ae(_SliceTest()[1:5], [1, 2, 3, 4])
with raises(ValueError):
_SliceTest()[::2]
with raises(ValueError):
_SliceTest()[1::2]
ae(_SliceTest()[1:5:2], [1, 3])
with raises(ValueError):
_SliceTest(start=0)[:]
with raises(ValueError):
_SliceTest(start=1)[:]
with raises(ValueError):
_SliceTest(step=2)[:]
ae(_SliceTest(stop=5)[:], [0, 1, 2, 3, 4])
ae(_SliceTest(start=1, stop=5)[:], [1, 2, 3, 4])
ae(_SliceTest(stop=5)[1:], [1, 2, 3, 4])
ae(_SliceTest(start=1)[:5], [1, 2, 3, 4])
ae(_SliceTest(start=1, step=2)[:5], [1, 3])
ae(_SliceTest(start=1)[:5:2], [1, 3])
ae(_SliceTest(length=5)[:], [0, 1, 2, 3, 4])
with raises(ValueError):
_SliceTest(length=5)[:3]
ae(_SliceTest(length=5)[:10], [0, 1, 2, 3, 4])
ae(_SliceTest(length=5)[:5], [0, 1, 2, 3, 4])
ae(_SliceTest(start=1, length=5)[:], [1, 2, 3, 4, 5])
ae(_SliceTest(start=1, length=5)[:6], [1, 2, 3, 4, 5])
with raises(ValueError):
_SliceTest(start=1, length=5)[:4]
ae(_SliceTest(start=1, step=2, stop=5)[:], [1, 3])
ae(_SliceTest(start=1, stop=5)[::2], [1, 3])
ae(_SliceTest(stop=5)[1::2], [1, 3])
def test_concatenate_virtual_arrays_3():
arrs = [np.zeros((2, 2)), np.ones((3, 2))]
c = _concatenate_virtual_arrays(arrs, scaling=2)
ae(c[3], 2 * np.ones((1, 2)))
def test_select_spikes_1():
spike_times = np.array([0., 1., 2., 3.3, 4.4])
spike_clusters = np.array([1, 2, 1, 2, 4])
chunk_bounds = [0.0, 1.1, 2.2, 3.3, 4.4, 5.5, 6.6]
n_chunks_kept = 2
cluster_ids = [1, 2, 4]
spikes_ids_kept = [0, 1, 3]
spc = _spikes_per_cluster(spike_clusters)
ss = SpikeSelector(
get_spikes_per_cluster=lambda cl: spc.get(cl, np.array([], dtype=np.int64)),
spike_times=spike_times, chunk_bounds=chunk_bounds, n_chunks_kept=n_chunks_kept)
ae(ss.chunks_kept, [0.0, 1.1, 3.3, 4.4])
ae(ss(3, [], subset_chunks=True), [])
ae(ss(3, [0], subset_chunks=True), [])
ae(ss(3, [1], subset_chunks=True), [0])
ae(ss(None, cluster_ids, subset_chunks=True), spikes_ids_kept)
ae(ss(0, cluster_ids, subset_chunks=True), spikes_ids_kept)
ae(ss(3, cluster_ids, subset_chunks=True), spikes_ids_kept)
ae(ss(2, cluster_ids, subset_chunks=True), spikes_ids_kept)
assert list(ss(1, cluster_ids, subset_chunks=True)) in [[0, 1], [0, 3]]
ae(ss(2, cluster_ids, subset_spikes=[0, 1], subset_chunks=True), [0, 1])
ae(ss(2, cluster_ids, subset_chunks=False), np.arange(5))
def test_spikes_from_chunked():
chunk_bounds = [0, 4, 9, 12, 20] # noqa
spike_times = [ 1, 3, 4, 5, 7, 15] # noqa
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 0), [])
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 1), [4])
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 2), [4, 5])
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 3), [4, 5, 7])
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 4), [1, 4, 5, 7])
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 5), [1, 3, 4, 5, 7])
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 6), spike_times)
ae(select_spikes_from_chunked(spike_times, chunk_bounds, 10), spike_times)
def test_index_of():
"""Test _index_of."""
arr = [36, 42, 42, 36, 36, 2, 42]
lookup = _unique(arr)
ae(_index_of(arr, lookup), [1, 2, 2, 1, 1, 0, 2])
def test_pad():
arr = np.random.rand(10, 3)
ae(_pad(arr, 0, 'right'), arr[:0, :])
ae(_pad(arr, 3, 'right'), arr[:3, :])
ae(_pad(arr, 9), arr[:9, :])
ae(_pad(arr, 10), arr)
ae(_pad(arr, 12, 'right')[:10, :], arr)
ae(_pad(arr, 12)[10:, :], np.zeros((2, 3)))
ae(_pad(arr, 0, 'left'), arr[:0, :])
ae(_pad(arr, 3, 'left'), arr[7:, :])
ae(_pad(arr, 9, 'left'), arr[1:, :])
ae(_pad(arr, 10, 'left'), arr)
ae(_pad(arr, 12, 'left')[2:, :], arr)
ae(_pad(arr, 12, 'left')[:2, :], np.zeros((2, 3)))
with raises(ValueError):
_pad(arr, -1)
def test_concatenate_virtual_arrays_2():
arrs = [np.zeros((2, 2)), np.ones((3, 2))]
c = _concatenate_virtual_arrays(arrs)
assert c.shape == (5, 2)
ae(c[:, :], np.vstack((np.zeros((2, 2)), np.ones((3, 2)))))
ae(c[0:4, 0], [0, 0, 1, 1])