Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

added lowpass parameter, fixed verbose option #3262

Merged
merged 2 commits into from
Jul 30, 2024
Merged

added lowpass parameter, fixed verbose option #3262

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
092c13c
added lowpass parameter, fixed verbose option
mhhennig Jul 27, 2024
0b7dc33
Update src/spikeinterface/sorters/external/herdingspikes.py
mhhennig Jul 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions src/spikeinterface/sorters/external/herdingspikes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ class HerdingspikesSorter(BaseSorter):
"chunk_size": None,
"rescale": True,
"rescale_value": -1280.0,
"lowpass": True,
"common_reference": "median",
"spike_duration": 1.0,
"amp_avg_duration": 0.4,
Expand Down Expand Up @@ -53,6 +54,7 @@ class HerdingspikesSorter(BaseSorter):
"out_file": "Path and filename to store detection and clustering results. (`str`, `HS2_detected`)",
"verbose": "Print progress information. (`bool`, `True`)",
"chunk_size": " Number of samples per chunk during detection. If `None`, a suitable value will be estimated. (`int`, `None`)",
"lowpass": "Enable internal low-pass filtering (simple two-step average). (`bool`, `True`)",
"common_reference": "Method for common reference filtering, can be `average` or `median` (`str`, `median`)",
"rescale": "Automatically re-scale the data. (`bool`, `True`)",
"rescale_value": "Factor by which data is re-scaled. (`float`, `-1280.0`)",
Expand Down Expand Up @@ -122,20 +124,21 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):

hs_version = version.parse(hs.__version__)

if hs_version >= version.parse("0.4.001"):
if hs_version >= version.parse("0.4.1"):
lightning_api = True
else:
lightning_api = False

assert (
lightning_api
), "HerdingSpikes version <0.4.001 is no longer supported. run:\n>>> pip install --upgrade herdingspikes"
), "HerdingSpikes version <0.4.1 is no longer supported. To upgrade, run:\n>>> pip install --upgrade herdingspikes"

recording = cls.load_recording_from_folder(sorter_output_folder.parent, with_warnings=False)

sorted_file = str(sorter_output_folder / "HS2_sorted.hdf5")
params["out_file"] = str(sorter_output_folder / "HS2_detected")
p = params
p.update({"verbose": verbose})

det = hs.HSDetectionLightning(recording, p)
det.DetectFromRaw()
Expand Down