Merge pull request #1 from ttngu207/nei_nienborg

integrate with the latest version of SpikeInterface

CHANGELOG.md

@@ -3,6 +3,12 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.4.0] - 2024-05-28
+
++ Add - support for SpikeInterface version >= 0.101.0 (updated API)
++ Add - feature for memoization of spike sorting results (prevent duplicated runs)
+
+
 ## [0.3.4] - 2024-03-22
 
 + Add - pytest

element_array_ephys/__init__.py

@@ -1,22 +1 @@
-"""
-isort:skip_file
-"""
-
-import logging
-import os
-
-import datajoint as dj
-
-
-__all__ = ["ephys", "get_logger"]
-
-dj.config["enable_python_native_blobs"] = True
-
-
-def get_logger(name):
-    log = logging.getLogger(name)
-    log.setLevel(os.getenv("LOGLEVEL", "INFO"))
-    return log
-
-
 from . import ephys_acute as ephys

element_array_ephys/probe.py

@@ -1,12 +1,10 @@
-"""
-Neuropixels Probes
-"""
-
 import datajoint as dj
 
 from .readers import probe_geometry
 from .readers.probe_geometry import build_electrode_layouts
 
+log = dj.logger
+
 schema = dj.schema()
 
 
@@ -33,20 +31,6 @@ def activate(
         schema_name, create_schema=create_schema, create_tables=create_tables
     )
 
-    # Add neuropixels probes
-    for probe_type in (
-        "neuropixels 1.0 - 3A",
-        "neuropixels 1.0 - 3B",
-        "neuropixels UHD",
-        "neuropixels 2.0 - SS",
-        "neuropixels 2.0 - MS",
-    ):
-        if not (ProbeType & {"probe_type": probe_type}):
-            try:
-                ProbeType.create_neuropixels_probe(probe_type)
-            except dj.errors.DataJointError as e:
-                print(f"Unable to create probe-type: {probe_type}\n{str(e)}")
-
 
 @schema
 class ProbeType(dj.Lookup):
@@ -87,39 +71,10 @@ class Electrode(dj.Part):
 
     @staticmethod
     def create_neuropixels_probe(probe_type: str = "neuropixels 1.0 - 3A"):
-        """
-        Create `ProbeType` and `Electrode` for neuropixels probes:
-        + neuropixels 1.0 - 3A
-        + neuropixels 1.0 - 3B
-        + neuropixels UHD
-        + neuropixels 2.0 - SS
-        + neuropixels 2.0 - MS
-
-        For electrode location, the (0, 0) is the
-         bottom left corner of the probe (ignore the tip portion)
-        Electrode numbering is 0-indexing
-        """
-
-        npx_probes_config = probe_geometry.M
-        npx_probes_config["neuropixels 1.0 - 3A"] = npx_probes_config["3A"]
-        npx_probes_config["neuropixels 1.0 - 3B"] = npx_probes_config["NP1010"]
-        npx_probes_config["neuropixels UHD"] = npx_probes_config["NP1100"]
-        npx_probes_config["neuropixels 2.0 - SS"] = npx_probes_config["NP2000"]
-        npx_probes_config["neuropixels 2.0 - MS"] = npx_probes_config["NP2010"]
-
-        probe_type = {"probe_type": probe_type}
-        probe_params = dict(
-            zip(
-                probe_geometry.geom_param_names,
-                npx_probes_config[probe_type["probe_type"]],
-            )
+        log.warning(
+            "Class method `ProbeType.create_neuropixels_probe` is deprecated. Use `create_neuropixels_probe` instead.",
         )
-        electrode_layouts = probe_geometry.build_npx_probe(
-            **{**probe_params, **probe_type}
-        )
-        with ProbeType.connection.transaction:
-            ProbeType.insert1(probe_type, skip_duplicates=True)
-            ProbeType.Electrode.insert(electrode_layouts, skip_duplicates=True)
+        return create_neuropixels_probe(probe_type)
 
 
 @schema
@@ -171,3 +126,51 @@ class Electrode(dj.Part):
         -> master
         -> ProbeType.Electrode
         """
+
+
+def create_neuropixels_probe_types():
+    # Add neuropixels probes
+    for probe_type in (
+        "neuropixels 1.0 - 3A",
+        "neuropixels 1.0 - 3B",
+        "neuropixels UHD",
+        "neuropixels 2.0 - SS",
+        "neuropixels 2.0 - MS",
+    ):
+        if not (ProbeType & {"probe_type": probe_type}):
+            create_neuropixels_probe(probe_type)
+
+
+def create_neuropixels_probe(probe_type: str = "neuropixels 1.0 - 3A"):
+    """
+    Create `ProbeType` and `Electrode` for neuropixels probes:
+    + neuropixels 1.0 - 3A
+    + neuropixels 1.0 - 3B
+    + neuropixels UHD
+    + neuropixels 2.0 - SS
+    + neuropixels 2.0 - MS
+
+    For electrode location, the (0, 0) is the
+     bottom left corner of the probe (ignore the tip portion)
+    Electrode numbering is 0-indexing
+    """
+    npx_probes_config = probe_geometry.M
+    npx_probes_config["neuropixels 1.0 - 3A"] = npx_probes_config["3A"]
+    npx_probes_config["neuropixels 1.0 - 3B"] = npx_probes_config["NP1010"]
+    npx_probes_config["neuropixels UHD"] = npx_probes_config["NP1100"]
+    npx_probes_config["neuropixels 2.0 - SS"] = npx_probes_config["NP2000"]
+    npx_probes_config["neuropixels 2.0 - MS"] = npx_probes_config["NP2010"]
+
+    probe_type = {"probe_type": probe_type}
+    probe_params = dict(
+        zip(
+            probe_geometry.geom_param_names,
+            npx_probes_config[probe_type["probe_type"]],
+        )
+    )
+    electrode_layouts = probe_geometry.build_npx_probe(
+        **{**probe_params, **probe_type}
+    )
+    with ProbeType.connection.transaction:
+        ProbeType.insert1(probe_type)
+        ProbeType.Electrode.insert(electrode_layouts)

element_array_ephys/spike_sorting/ecephys_spike_sorting.py

@@ -22,7 +22,6 @@
 
 
 import datajoint as dj
-from element_array_ephys import get_logger
 from decimal import Decimal
 import json
 from datetime import datetime, timedelta
@@ -33,7 +32,7 @@
     kilosort_triggering,
 )
 
-log = get_logger(__name__)
+log = dj.logger
 
 schema = dj.schema()
 

element_array_ephys/spike_sorting/si_preprocessing.py

@@ -2,7 +2,7 @@
 from spikeinterface import preprocessing
 
 
-def catGT(recording):
+def CatGT(recording):
     recording = si.preprocessing.phase_shift(recording)
     recording = si.preprocessing.common_reference(
         recording, operator="median", reference="global"
@@ -35,3 +35,14 @@ def IBLdestriping_modified(recording):
         recording, operator="median", reference="global"
     )
     return recording
+
+
+def NienborgLab_preproc(recording):
+    """Preprocessing pipeline for 32chn ephys data from Trellis."""
+    recording = si.preprocessing.bandpass_filter(
+        recording=recording, freq_min=300, freq_max=6000
+    )
+    recording = si.preprocessing.common_reference(
+        recording=recording, operator="median"
+    )
+    return recording