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Refactor quality metrics tests to use fixture #3249

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merged 10 commits into from
Sep 12, 2024
Merged

Refactor quality metrics tests to use fixture #3249

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c61378e
simplify qm tests and wrap for multiprocessing
chrishalcrow Jul 24, 2024
df1564b
try -1 instead of 2
chrishalcrow Jul 24, 2024
b5d896d
delete print statement
chrishalcrow Jul 24, 2024
9d3aa2a
go back to n_jobs=1
chrishalcrow Jul 25, 2024
79f0206
Respond to Joe review
chrishalcrow Jul 25, 2024
5d5afd2
Put main stuff back
chrishalcrow Sep 11, 2024
f3aac42
oups
chrishalcrow Sep 11, 2024
de2ade6
Merge branch 'main' into simplify-qm-tests
chrishalcrow Sep 11, 2024
b35873c
compute pcs for sortinganalyzer again
chrishalcrow Sep 11, 2024
41f73ed
re-remove pcs
chrishalcrow Sep 12, 2024
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51 changes: 51 additions & 0 deletions src/spikeinterface/qualitymetrics/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
create_sorting_analyzer,
)

job_kwargs = dict(n_jobs=-1, progress_bar=True, chunk_duration="1s")


def _small_sorting_analyzer():
recording, sorting = generate_ground_truth_recording(
Expand Down Expand Up @@ -35,3 +37,52 @@ def _small_sorting_analyzer():
@pytest.fixture(scope="module")
def small_sorting_analyzer():
return _small_sorting_analyzer()


def _sorting_analyzer_simple():
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# we need high firing rate for amplitude_cutoff
recording, sorting = generate_ground_truth_recording(
durations=[
120.0,
],
sampling_frequency=30_000.0,
num_channels=6,
num_units=10,
generate_sorting_kwargs=dict(firing_rates=10.0, refractory_period_ms=4.0),
generate_unit_locations_kwargs=dict(
margin_um=5.0,
minimum_z=5.0,
maximum_z=20.0,
),
generate_templates_kwargs=dict(
unit_params=dict(
alpha=(200.0, 500.0),
)
),
noise_kwargs=dict(noise_levels=5.0, strategy="tile_pregenerated"),
seed=1205,
)

sorting_analyzer = create_sorting_analyzer(sorting, recording, format="memory", sparse=True)

sorting_analyzer.compute("random_spikes", max_spikes_per_unit=300, seed=1205)
sorting_analyzer.compute("noise_levels")
sorting_analyzer.compute("waveforms", **job_kwargs)
sorting_analyzer.compute("templates")
sorting_analyzer.compute("spike_amplitudes", **job_kwargs)

return sorting_analyzer


@pytest.fixture(scope="module")
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def sorting_analyzer_simple():
sorting_analyzer = get_sorting_analyzer(seed=2205)
return sorting_analyzer

return sorting_analyzer
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@pytest.fixture(scope="module")
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def sorting_analyzer_simple():
return _sorting_analyzer_simple()
85 changes: 32 additions & 53 deletions src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -135,36 +135,6 @@ def test_unit_id_order_independence(small_sorting_analyzer):
assert quality_metrics_2[metric][1] == metric_1_data["#4"]


def _sorting_analyzer_simple():
recording, sorting = generate_ground_truth_recording(
durations=[
50.0,
],
sampling_frequency=30_000.0,
num_channels=6,
num_units=10,
generate_sorting_kwargs=dict(firing_rates=6.0, refractory_period_ms=4.0),
noise_kwargs=dict(noise_levels=5.0, strategy="tile_pregenerated"),
seed=2205,
)

sorting_analyzer = create_sorting_analyzer(sorting, recording, format="memory", sparse=True)

sorting_analyzer.compute("random_spikes", max_spikes_per_unit=300, seed=2205)
sorting_analyzer.compute("noise_levels")
sorting_analyzer.compute("waveforms", **job_kwargs)
sorting_analyzer.compute("templates")
sorting_analyzer.compute("principal_components", n_components=5, mode="by_channel_local", **job_kwargs)
sorting_analyzer.compute("spike_amplitudes", **job_kwargs)

return sorting_analyzer


@pytest.fixture(scope="module")
def sorting_analyzer_simple():
return _sorting_analyzer_simple()


def _sorting_violation():
max_time = 100.0
sampling_frequency = 30000
Expand Down Expand Up @@ -570,27 +540,36 @@ def test_calculate_sd_ratio(sorting_analyzer_simple):

if __name__ == "__main__":
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I agree I think this is essential for certain Windows run. But it is super inconsistent which Windows. (for example I haven't needed to do if name == main yet, but others have.... So weird.

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no way! 🤯 so it depends on the Windows version?

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I think it is less "version" and more like version + sub-version + python version + CPU-type + IDE. Who knows what magic determines this.... But one of my co-workers has to do the if name == main, but I don't on my workstation.

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I had responded but somehow dissapeared, "Haha lol the mysteries of multiprocessing, very interesting!"


sorting_analyzer = _sorting_analyzer_simple()
print(sorting_analyzer)

test_unit_structure_in_output(_small_sorting_analyzer())

# test_calculate_firing_rate_num_spikes(sorting_analyzer)
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# test_calculate_snrs(sorting_analyzer)
# test_calculate_amplitude_cutoff(sorting_analyzer)
# test_calculate_presence_ratio(sorting_analyzer)
# test_calculate_amplitude_median(sorting_analyzer)
# test_calculate_sliding_rp_violations(sorting_analyzer)
# test_calculate_drift_metrics(sorting_analyzer)
# test_synchrony_metrics(sorting_analyzer)
# test_synchrony_metrics_unit_id_subset(sorting_analyzer)
# test_synchrony_metrics_no_unit_ids(sorting_analyzer)
# test_calculate_firing_range(sorting_analyzer)
# test_calculate_amplitude_cv_metrics(sorting_analyzer)
# test_calculate_sd_ratio(sorting_analyzer)

# sorting_analyzer_violations = _sorting_analyzer_violations()
test_unit_structure_in_output(small_sorting_analyzer)
test_unit_id_order_independence(small_sorting_analyzer)

test_synchrony_counts_no_sync()
test_synchrony_counts_one_sync()
test_synchrony_counts_one_quad_sync()
test_synchrony_counts_not_all_units()

test_mahalanobis_metrics()
test_lda_metrics()
test_nearest_neighbors_metrics()
test_silhouette_score_metrics()
test_simplified_silhouette_score_metrics()

test_calculate_firing_rate_num_spikes(sorting_analyzer_simple)
test_calculate_snrs(sorting_analyzer)
test_calculate_amplitude_cutoff(sorting_analyzer)
test_calculate_presence_ratio(sorting_analyzer)
test_calculate_amplitude_median(sorting_analyzer)
test_calculate_sliding_rp_violations(sorting_analyzer)
test_calculate_drift_metrics(sorting_analyzer)
test_synchrony_metrics(sorting_analyzer)
test_synchrony_metrics_unit_id_subset(sorting_analyzer)
test_synchrony_metrics_no_unit_ids(sorting_analyzer)
test_calculate_firing_range(sorting_analyzer)
test_calculate_amplitude_cv_metrics(sorting_analyzer)
test_calculate_sd_ratio(sorting_analyzer)

sorting_analyzer_violations = _sorting_analyzer_violations()
# print(sorting_analyzer_violations)
# test_calculate_isi_violations(sorting_analyzer_violations)
# test_calculate_sliding_rp_violations(sorting_analyzer_violations)
# test_calculate_rp_violations(sorting_analyzer_violations)
test_calculate_isi_violations(sorting_analyzer_violations)
test_calculate_sliding_rp_violations(sorting_analyzer_violations)
test_calculate_rp_violations(sorting_analyzer_violations)
5 changes: 5 additions & 0 deletions src/spikeinterface/qualitymetrics/tests/test_pca_metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,3 +22,8 @@ def test_calculate_pc_metrics(small_sorting_analyzer):
assert not np.all(np.isnan(res2[metric_name].values))

assert np.array_equal(res1[metric_name].values, res2[metric_name].values)


if __name__ == "__main__":

test_calculate_pc_metrics(small_sorting_analyzer)
52 changes: 3 additions & 49 deletions src/spikeinterface/qualitymetrics/tests/test_quality_metric_calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
from pathlib import Path
import numpy as np


from spikeinterface.core import (
generate_ground_truth_recording,
create_sorting_analyzer,
Expand All @@ -15,51 +14,9 @@
compute_quality_metrics,
)


job_kwargs = dict(n_jobs=2, progress_bar=True, chunk_duration="1s")


def get_sorting_analyzer(seed=2205):
# we need high firing rate for amplitude_cutoff
recording, sorting = generate_ground_truth_recording(
durations=[
120.0,
],
sampling_frequency=30_000.0,
num_channels=6,
num_units=10,
generate_sorting_kwargs=dict(firing_rates=10.0, refractory_period_ms=4.0),
generate_unit_locations_kwargs=dict(
margin_um=5.0,
minimum_z=5.0,
maximum_z=20.0,
),
generate_templates_kwargs=dict(
unit_params=dict(
alpha=(200.0, 500.0),
)
),
noise_kwargs=dict(noise_levels=5.0, strategy="tile_pregenerated"),
seed=seed,
)

sorting_analyzer = create_sorting_analyzer(sorting, recording, format="memory", sparse=True)

sorting_analyzer.compute("random_spikes", max_spikes_per_unit=300, seed=seed)
sorting_analyzer.compute("noise_levels")
sorting_analyzer.compute("waveforms", **job_kwargs)
sorting_analyzer.compute("templates")
sorting_analyzer.compute("spike_amplitudes", **job_kwargs)

return sorting_analyzer


@pytest.fixture(scope="module")
def sorting_analyzer_simple():
sorting_analyzer = get_sorting_analyzer(seed=2205)
return sorting_analyzer


def test_compute_quality_metrics(sorting_analyzer_simple):
sorting_analyzer = sorting_analyzer_simple
print(sorting_analyzer)
Expand Down Expand Up @@ -291,9 +248,6 @@ def test_empty_units(sorting_analyzer_simple):

if __name__ == "__main__":

sorting_analyzer = get_sorting_analyzer()
print(sorting_analyzer)

test_compute_quality_metrics(sorting_analyzer)
test_compute_quality_metrics_recordingless(sorting_analyzer)
test_empty_units(sorting_analyzer)
test_compute_quality_metrics(sorting_analyzer_simple)
test_compute_quality_metrics_recordingless(sorting_analyzer_simple)
test_empty_units(sorting_analyzer_simple)