WIP on cleaning method
@@ -26,12 +26,13 @@ class PositionAndFeaturesClustering:
"peak_locations" : None,
"peak_localization_kwargs" : {"method" : "center_of_mass"},
"hdbscan_kwargs": {"min_cluster_size" : 100, "allow_single_cluster" : True, "core_dist_n_jobs" : -1, "cluster_selection_method" : "leaf"},
- "cleaning_kwargs" : {"method": "cosine", "similar_threshold" : 0.99, "sparsify_threshold" : 0.99},
+ "cleaning_kwargs" : {"similar_threshold" : 0.99, "sparsify_threshold" : 0.99},
"tmp_folder" : None,
"local_radius_um" : 50,
"max_spikes_per_unit" : 100,
"ms_before" : 1.5,
"ms_after": 2.5,
+ "cleaning": "cosine",
"waveform_mode" : "memmap",
"job_kwargs" : {"n_jobs" : -1, "chunk_memory" : "10M"},
}
@@ -185,7 +186,7 @@ class PositionAndFeaturesClustering:
wf_folder.mkdir()
- cleaning_method = params["cleaning_kwargs"].pop("method")
+ cleaning_method = params["cleaning"]
print("We found %d raw clusters, starting to clean with %s..." %(len(labels), cleaning_method))
