From c9b1a9c6a4a06a934778d3369c55bf0956f7100b Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 22 May 2024 08:55:40 -0400 Subject: [PATCH 1/3] add docs WIP --- .../sorters/internal/simplesorter.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/spikeinterface/sorters/internal/simplesorter.py b/src/spikeinterface/sorters/internal/simplesorter.py index 7004514ec7..402c34d543 100644 --- a/src/spikeinterface/sorters/internal/simplesorter.py +++ b/src/spikeinterface/sorters/internal/simplesorter.py @@ -46,6 +46,23 @@ class SimpleSorter(ComponentsBasedSorter): "job_kwargs": {"n_jobs": -1, "chunk_duration": "1s"}, } + _params_descriptions = { + "apply_preprocessing": "whether to apply the preprocessing steps, default: False", + "waveforms": "A dictonary containing waveforms params: ms_before (peak of spike) default: 1.0, ms_after (peak of spike) deafult: 1.5", + "filtering": "A dictionary containing bandpass filter conditions, freq_min' default: 300 and 'freq_max' default:8000.0", + "detection": ( + "A dictionary for specifying the detection conditions of 'peak_sign' (pos or neg) default: 'neg', " + "'detect_threshold' (snr) default: 5.0, 'exclude_sweep_ms' default: 1.5, 'radius_um' default: 150.0" + ), + "features": "A dictionary for the PCA specifying the 'n_components, default: 3", + "clustering": ( + "A dictionary for specifying the clustering parameters: 'method' (to cluster) default: 'hdbscan', " + "'min_cluster_size' (min number of spikes per cluster) default: 25, 'allow_single_cluster' default: True, " + " 'core_dist_n_jobs' (parallelization) default: -1, cluster_selection_method (for hdbscan) default: leaf" + ), + "job_kwargs": "Spikeinterface job_kwargs (see job_kwargs documentation) default 'n_jobs': -1, 'chunk_duration': '1s'", + } + @classmethod def get_sorter_version(cls): return "1.0" From 08360fc4c7367a4f3868250695393fb126128992 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Wed, 22 May 2024 08:58:38 -0400 Subject: [PATCH 2/3] oops --- src/spikeinterface/sorters/internal/simplesorter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/spikeinterface/sorters/internal/simplesorter.py b/src/spikeinterface/sorters/internal/simplesorter.py index 402c34d543..7ead1b1626 100644 --- a/src/spikeinterface/sorters/internal/simplesorter.py +++ b/src/spikeinterface/sorters/internal/simplesorter.py @@ -46,7 +46,7 @@ class SimpleSorter(ComponentsBasedSorter): "job_kwargs": {"n_jobs": -1, "chunk_duration": "1s"}, } - _params_descriptions = { + _params_description = { "apply_preprocessing": "whether to apply the preprocessing steps, default: False", "waveforms": "A dictonary containing waveforms params: ms_before (peak of spike) default: 1.0, ms_after (peak of spike) deafult: 1.5", "filtering": "A dictionary containing bandpass filter conditions, freq_min' default: 300 and 'freq_max' default:8000.0", From 5d9b1e0c94699d2e3c33d7e1aa5a351c850c3105 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Thu, 23 May 2024 10:43:08 +0200 Subject: [PATCH 3/3] Update src/spikeinterface/sorters/internal/simplesorter.py --- src/spikeinterface/sorters/internal/simplesorter.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/spikeinterface/sorters/internal/simplesorter.py b/src/spikeinterface/sorters/internal/simplesorter.py index 7ead1b1626..314c552d6d 100644 --- a/src/spikeinterface/sorters/internal/simplesorter.py +++ b/src/spikeinterface/sorters/internal/simplesorter.py @@ -48,8 +48,8 @@ class SimpleSorter(ComponentsBasedSorter): _params_description = { "apply_preprocessing": "whether to apply the preprocessing steps, default: False", - "waveforms": "A dictonary containing waveforms params: ms_before (peak of spike) default: 1.0, ms_after (peak of spike) deafult: 1.5", - "filtering": "A dictionary containing bandpass filter conditions, freq_min' default: 300 and 'freq_max' default:8000.0", + "waveforms": "A dictonary containing waveforms params: 'ms_before' (peak of spike) default: 1.0, 'ms_after' (peak of spike) deafult: 1.5", + "filtering": "A dictionary containing bandpass filter conditions, 'freq_min' default: 300 and 'freq_max' default:8000.0", "detection": ( "A dictionary for specifying the detection conditions of 'peak_sign' (pos or neg) default: 'neg', " "'detect_threshold' (snr) default: 5.0, 'exclude_sweep_ms' default: 1.5, 'radius_um' default: 150.0"