release 1.0.1 support for non-standard channel layout waveforms

extraction

README.md

@@ -40,13 +40,13 @@ https://doi.org/10.6084/m9.figshare.19705522
 ## Contribution
 
 Pypi Release checklist:
-Edit the version number in `setup.py`, and add release notes in `release_notes.md`
+- Edit the version number in `setup.py`, and add release notes in `release_notes.md`
 
 ```shell
 flake8
-tag=vX.Y.Z
+tag=X.Y.Z
 git tag -a $tag 
 git push origin %tag
 ```
 
-Create new release with tag vX.Y.Z (will automatically publish to PyPI)
+Create new release with tag X.Y.Z (will automatically publish to PyPI)

release_notes.md

@@ -1,4 +1,7 @@
 # 1.0.0
+## 1.0.1 2024-05-29: support for waveform extraction on non-standard electrode layouts
+  - bugfix waveform extraction: the probe channel layout is inferred from the spikeglx metadata by default
+  - bugfix waveform extraction: the channel neighnourhood fill value is the last channel index + 1 by default instead of 384
 ## 1.0.0 2024-04-22
 - Functionalities to check and mitigate saturation in neuropixel recordings
   - `spikeglx.Reader` has a `range_volts` method to get the saturating voltage value for a given type of probe

setup.py

@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="ibl-neuropixel",
-    version="1.0.0",
+    version="1.0.1",
     author="The International Brain Laboratory",
     description="Collection of tools for Neuropixel 1.0 and 2.0 probes data",
     long_description=long_description,

src/ibldsp/waveform_extraction.py

@@ -6,7 +6,6 @@
 from numpy.lib.format import open_memmap
 from joblib import Parallel, delayed, cpu_count
 
-import neuropixel
 import spikeglx
 from ibldsp.voltage import detect_bad_channels, interpolate_bad_channels, car
 from ibldsp.fourier import fshift

src/spikeglx.py

@@ -70,7 +70,7 @@ def __init__(
         """
         self.ignore_warnings = ignore_warnings
         sglx_file = Path(sglx_file)
-        meta_file = meta_file or  _get_companion_file(sglx_file, '.meta')
+        meta_file = meta_file or _get_companion_file(sglx_file, '.meta')
         # only used if MTSCOMP compressed
         self.ch_file = ch_file
 

src/tests/unit/cpu/test_spikeglx.py

@@ -629,14 +629,13 @@ def test_get_companion_file(self):
             self.assertEqual(meta_file, spikeglx._get_companion_file(sglx_file, '.meta'))
 
         with tempfile.TemporaryDirectory() as td:
-            sglx_file = Path(td) / f"sample3A_g0_t0.imec.ap.bin"
-            meta_file_ok = Path(td) / f"sample3A_g0_t0.imec.ap.meta"
+            sglx_file = Path(td) / "sample3A_g0_t0.imec.ap.bin"
+            meta_file_ok = Path(td) / "sample3A_g0_t0.imec.ap.meta"
             meta_file = Path(td) / f"sample3A_g0_t0.imec.ap.{str(uuid.uuid4())}.meta"
             meta_file.touch()
             meta_file_ok.touch()
             self.assertEqual(meta_file_ok, spikeglx._get_companion_file(sglx_file, '.meta'))
 
-
     def test_read_flat_binary_float32(self):
         # here we expect no scaling to V applied and no sync trace as the format is float32
         kwargs = dict(ns=60000, nc=384, fs=30000, dtype=np.float32)