Merge branch 'main' into agg-backend-in-tests

Author: alejoe91

.pre-commit-config.yaml

@@ -6,13 +6,13 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.3.1
     hooks:
     -   id: black
         files: ^src/|^tests/
 - repo: https://github.com/codespell-project/codespell
   # Configuration for codespell is in .pre-commit-config.yaml
-  rev: v2.4.1
+  rev: v2.4.2
   hooks:
   -    id: codespell
        additional_dependencies:

src/probeinterface/generator.py

@@ -12,7 +12,6 @@
 from .probegroup import ProbeGroup
 from .utils import combine_probes
 
-
 _default_shape_to_params = {"circle": "radius", "square": "width", "rect": "height"}
 
 

src/probeinterface/neuropixels_tools.py

@@ -18,7 +18,6 @@
 from .probe import Probe
 from .utils import import_safely
 
-
 global _np_probe_features
 _np_probe_features = None
 
@@ -28,7 +27,8 @@ def _load_np_probe_features():
     global _np_probe_features
     if _np_probe_features is None:
         probe_features_filepath = Path(__file__).absolute().parent / Path("resources/neuropixels_probe_features.json")
-        _np_probe_features = json.load(open(probe_features_filepath, "r"))
+        with open(probe_features_filepath, "r") as f:
+            _np_probe_features = json.load(f)
     return _np_probe_features
 
 
@@ -92,8 +92,7 @@ def _load_np_probe_features():
 
 def get_probe_length(probe_part_number: str) -> int:
     """
-    Returns the length of a given probe. We assume a length of
-    1cm (10_000 microns) by default.
+    Returns the length of a given probe from ProbeTable specifications.
 
     Parameters
     ----------
@@ -103,12 +102,16 @@ def get_probe_length(probe_part_number: str) -> int:
     Returns
     -------
     probe_length : int
-        Length of full probe (microns)
+        Length of full probe shank from tip to base (microns)
     """
+    np_features = _load_np_probe_features()
+    probe_spec = np_features["neuropixels_probes"].get(probe_part_number)
 
-    probe_length = 10_000
+    if probe_spec is not None and "shank_tip_to_base_um" in probe_spec:
+        return int(probe_spec["shank_tip_to_base_um"])
 
-    return probe_length
+    # Fallback for unknown probes or missing field
+    return 10_000
 
 
 def make_mux_table_array(mux_information) -> np.array:
@@ -1218,7 +1221,6 @@ def read_openephys(
                 "probe": sliced_probe,
             }
         else:
-
             channel_names = np.array(list(channels.attrib.keys()))
             channel_ids = np.array([int(ch[2:]) for ch in channel_names])
             channel_order = np.argsort(channel_ids)
@@ -1304,6 +1306,7 @@ def read_openephys(
             np_probe_dict = {
                 "shank_ids": shank_ids,
                 "elec_ids": elec_ids,
+                "channel_names": channel_names,
                 "pt_metadata": pt_metadata,
                 "slot": slot,
                 "port": port,
@@ -1426,6 +1429,9 @@ def read_openephys(
             pt_metadata, probe_part_number, elec_ids, shank_ids=shank_ids, mux_info=mux_info
         )
 
+    if "channel_names" in np_probe_info:
+        probe.annotate_contacts(channel_name=np_probe_info["channel_names"])
+
     chans_saved = get_saved_channel_indices_from_openephys_settings(settings_file, stream_name=stream_name)
     if chans_saved is not None:
         probe = probe.get_slice(chans_saved)

src/probeinterface/probe.py

@@ -570,14 +570,15 @@ def set_contact_ids(self, contact_ids: np.array | list):
             self._contact_ids = None
             return
 
-        assert np.unique(contact_ids).size == contact_ids.size, "Contact ids have to be unique within a Probe"
-
         if contact_ids.size != self.get_contact_count():
-            ValueError(
+            raise ValueError(
                 f"contact_ids {contact_ids.size} do not have the same size "
                 f"as number of contacts {self.get_contact_count()}"
             )
 
+        if np.unique(contact_ids).size != contact_ids.size:
+            raise ValueError("contact_ids must be unique within a Probe")
+
         if contact_ids.dtype.kind != "U":
             contact_ids = contact_ids.astype("U")
 

src/probeinterface/testing.py

@@ -4,7 +4,8 @@
 from probeinterface import __version__ as version
 
 json_schema_file = Path(__file__).absolute().parent / "schema" / "probe.json.schema"
-schema = json.load(open(json_schema_file, "r"))
+with open(json_schema_file, "r") as f:
+    schema = json.load(f)
 
 
 def validate_probe_dict(probe_dict):

src/probeinterface/wiring.py

@@ -5,7 +5,6 @@
 from __future__ import annotations
 import numpy as np
 
-
 # This code will not be formatted by Black
 # fmt: off
 pathways = {

tests/test_io/test_3brain.py

@@ -8,7 +8,6 @@
 
 from probeinterface.testing import validate_probe_dict
 
-
 data_path = Path(__file__).absolute().parent.parent / "data" / "3brain"
 brw_files = glob.glob(str(data_path / "*.brw"))
 

tests/test_io/test_io.py

@@ -14,7 +14,6 @@
 
 import pytest
 
-
 data_path = Path(__file__).absolute().parent.parent / "data"
 
 

tests/test_io/test_spikegadgets.py

@@ -5,7 +5,6 @@
 from probeinterface.io import parse_spikegadgets_header
 from probeinterface.testing import validate_probe_dict
 
-
 data_path = Path(__file__).absolute().parent.parent / "data" / "spikegadgets"
 test_file = "SpikeGadgets_test_data_2xNpix1.0_20240318_173658_header_only.rec"
 

tests/test_library.py

@@ -15,7 +15,6 @@
     clear_cache,
 )
 
-
 manufacturer = "neuronexus"
 probe_name = "A1x32-Poly3-10mm-50-177"