parallel rms, remove export to phy, clean up

Author: alejoe91

src/spikeinterface/exporters/tests/common.py

@@ -45,7 +45,10 @@ def make_sorting_analyzer(sparse=True, with_group=False):
     sorting_analyzer.compute("noise_levels")
     sorting_analyzer.compute("principal_components")
     sorting_analyzer.compute("template_similarity")
-    sorting_analyzer.compute("quality_metrics", metric_names=["snr"])
+    sorting_analyzer.compute(
+        "quality_metrics", metric_names=["snr", "amplitude_median", "isi_violation", "amplitude_cutoff"]
+    )
+    sorting_analyzer.compute(["spike_amplitudes", "spike_locations"])
 
     return sorting_analyzer
 

src/spikeinterface/exporters/tests/test_export_to_ibl.py

@@ -1,29 +1,115 @@
-import shutil
-
-import numpy as np
+import pytest
 
+from spikeinterface.preprocessing import bandpass_filter, decimate
 from spikeinterface.exporters import export_to_ibl
 
 from spikeinterface.exporters.tests.common import (
     make_sorting_analyzer,
     sorting_analyzer_sparse_for_export,
 )
 
+required_output_files = [
+    "spikes.times.npy",
+    "spikes.clusters.npy",
+    "spikes.depths.npy",
+    "spikes.amps.npy",
+    "clusters.waveforms.npy",
+    "clusters.peakToTrough.npy",
+    "clusters.channels.npy",
+    "clusters.metrics.csv",
+    "channels.localCoordinates.npy",
+    "channels.rawInd.npy",
+]
+ap_output_files = ["_iblqc_ephysTimeRmsAP.rms.npy", "_iblqc_ephysTimeRmsAP.timestamps.npy"]
+lfp_output_files = [
+    "_iblqc_ephysTimeRmsLF.rms.npy",
+    "_iblqc_ephysTimeRmsLF.timestamps.npy",
+    "_iblqc_ephysSpectralDensityLF.power.npy",
+    "_iblqc_ephysSpectralDensityLF.freqs.npy",
+]
+
+good_units_query = "amplitude_median < -30"
+
 
-def test_export_to_ibl(sorting_analyzer_sparse_for_export, create_cache_folder):
+def test_export_ap_to_ibl(sorting_analyzer_sparse_for_export, create_cache_folder):
     cache_folder = create_cache_folder
-    output_folder = cache_folder / "ibl_output"
-    for f in (output_folder,):
-        if f.is_dir():
-            shutil.rmtree(f)
+    output_folder = cache_folder / "ibl_ap_output"
 
+    sorting_analyzer = sorting_analyzer_sparse_for_export
+    # AP, but no LFP
     export_to_ibl(
-        sorting_analyzer_sparse_for_export,
+        sorting_analyzer,
         output_folder,
-        lfp_recording=sorting_analyzer_sparse_for_export.recording,
+        # good_units_query=good_units_query,
+        verbose=True,
+        n_jobs=-1,
     )
+    for f in required_output_files:
+        assert (output_folder / f).exists(), f"Missing file: {f}"
+    for f in ap_output_files:
+        assert (output_folder / f).exists(), f"Missing file: {f}"
+    for f in lfp_output_files:
+        assert not (output_folder / f).exists(), f"Unexpected file: {f}"
+
+
+def test_export_recordingless_to_ibl(sorting_analyzer_sparse_for_export, create_cache_folder):
+    cache_folder = create_cache_folder
+    output_folder = cache_folder / "ibl_recordingless_output"
+
+    sorting_analyzer = sorting_analyzer_sparse_for_export
+    recording = sorting_analyzer.recording
+    sorting_analyzer._recording = None
+
+    # AP, but no LFP
+    export_to_ibl(sorting_analyzer_sparse_for_export, output_folder, good_units_query=good_units_query, n_jobs=-1)
+    for f in required_output_files:
+        assert (output_folder / f).exists(), f"Missing file: {f}"
+    for f in ap_output_files:
+        assert not (output_folder / f).exists(), f"Missing file: {f}"
+    for f in lfp_output_files:
+        assert not (output_folder / f).exists(), f"Unexpected file: {f}"
+
+    sorting_analyzer._recording = recording
+
+
+def test_export_lfp_to_ibl(sorting_analyzer_sparse_for_export, create_cache_folder):
+    cache_folder = create_cache_folder
+    output_folder = cache_folder / "ibl_lfp_output"
+
+    sorting_analyzer = sorting_analyzer_sparse_for_export
+    recording = sorting_analyzer.recording
+    recording_lfp = bandpass_filter(recording, freq_min=0.5, freq_max=300)
+    recording_lfp = decimate(recording_lfp, 10)
+    # LFP, but no AP
+    export_to_ibl(
+        sorting_analyzer, output_folder, lfp_recording=recording_lfp, good_units_query=good_units_query, n_jobs=-1
+    )
+    for f in required_output_files:
+        assert (output_folder / f).exists(), f"Missing file: {f}"
+    for f in ap_output_files:
+        assert (output_folder / f).exists(), f"Unexpected file: {f}"
+    for f in lfp_output_files:
+        assert (output_folder / f).exists(), f"Missing file: {f}"
+
+
+def test_missing_info(sorting_analyzer_sparse_for_export, create_cache_folder):
+    cache_folder = create_cache_folder
+    output_folder = cache_folder / "ibl_missing_info_output"
+
+    sorting_analyzer = sorting_analyzer_sparse_for_export
+
+    # missing metrics
+    good_units_query = "rp_violations < 0.2"
+
+    with pytest.raises(ValueError, match="Missing required quality metrics"):
+        export_to_ibl(sorting_analyzer, output_folder, good_units_query=good_units_query, n_jobs=-1)
+
+    sorting_analyzer.delete_extension("spike_amplitudes")
+
+    with pytest.raises(ValueError, match="Missing required extension"):
+        export_to_ibl(sorting_analyzer, output_folder, n_jobs=-1)
 
 
 if __name__ == "__main__":
     sorting_analyzer = make_sorting_analyzer(sparse=True)
-    test_export_to_ibl(sorting_analyzer)
+    test_export_ap_to_ibl(sorting_analyzer)