ibllib.tests.test_ephys

Functions

a_little_spike
make_synthetic_data
synthetic_with_bad_channels

Classes

TestDetectBadChannels
TestDetectSpikes
TestDriftmapSpikeSortingMemmap	Unit tests for ibllib.ephys.spikes.driftmap_spike_sorting_memmap.
TestEphysQC
TestFpgaTask
TestNeuropixel	Comprehensive tests about geometry are run as part of the spikeglx reader testing suite

a_little_spike(nsw=121, nc=1)

make_synthetic_data(ns=10000, nc=384, nss=121, ncs=21, nspikes=1200, tr=None, sample=None)

synthetic_with_bad_channels()

class TestNeuropixel(methodName='runTest')

Bases: TestCase

Comprehensive tests about geometry are run as part of the spikeglx reader testing suite

test_layouts()

tests_headers()

class TestFpgaTask(methodName='runTest')

Bases: TestCase

test_impeccable_dataset()

class TestEphysQC(methodName='runTest')

Bases: TestCase

tempdir = None

classmethod setUpClass() → None

Hook method for setting up class fixture before running tests in the class.

classmethod tearDownClass() → None

Hook method for deconstructing the class fixture after running all tests in the class.

setUp() → None

Hook method for setting up the test fixture before exercising it.

tearDown() → None

Hook method for deconstructing the test fixture after testing it.

test_ensure_data()

class TestDetectSpikes(methodName='runTest')

Bases: TestCase

test_spike_detection()

Test that creates a synthetic dataset with spikes and an amplitude decay function with the probe gemetry, and then pastes spikes all around the dataset and detects and de-duplicates The test is feeding the detections in a new round of simulation, and then computing the zero-lag cross-correlation between input and simulated output, and asserting on the similarity

class TestDetectBadChannels(methodName='runTest')

Bases: TestCase

test_channel_detections()

This test creates a synthetic dataset with voltage stripes and 3 types of bad channels 1) dead channels or low amplitude 2) noisy 3) out of the brain

class TestDriftmapSpikeSortingMemmap(methodName='runTest')

Bases: TestCase

Unit tests for ibllib.ephys.spikes.driftmap_spike_sorting_memmap.

rec_len = 300.0

firing_rate = 50

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_output_matches_brainbox_driftmap()

Chunked histogram is identical to the image produced by brainbox.plot.driftmap.

test_spike_count_conserved()

Sum of histogram bins equals n_spikes (no spikes lost or double-counted).

test_nan_depths_excluded()

Spikes with NaN depth are silently skipped and not counted in the histogram.

test_chunking_invariant()

Result is independent of chunk_size.