Description
Hello,
I'm trying to add some labels ["good", "noise", "mua", "artifact"] to a sorting_analyzer, but when I wanted to do it by creating a dictionary with empty "removed_units" & "merge_units_groups" it throws an error saying that merge_unit_groups must contain at least two units. But I don't want to merge anything. I only want to add labels. Is there a way to do it by "curation_dict", The alternative I found was by setting a property to the "sorting_analyzer.sorting.set_property('quality', ['mua'])". I only have one unit, so it was not complicated, but it might be useful to allow "apply_curation" when there are no merge_units_groups.
A related question after I set the property is: What is the best practice for saving this change?
I did it by saving the sorting analyzer again:
"sorting_analyzer.save_as(format="binary_folder", folder=sorter_analyzer_folder+'_curated')"
Is there a way to avoid rewriting the folder?
Thanks in advance for your help.
Here is the dictionary that I created for curation:
# Sample Dictionary to be applied on the result to have a “clean” result
curation_dict = dict(
format_version = "1",
# Define LABELS
# For label category with exclusive=True : a column is created and values are the unique label.
# For label category with exclusive=False : one column per possible is created and values are boolean.
label_definitions = dict(
quality = dict(label_options = ["good", "noise", "mua", "artifact"], exclusive = True)
# Keep adding custom labels. Example:
# putative_type = dict(label_options = ["excitatory", "inhibitory", "pyramidal", "mitral"], exclusive = False)
),
#
unit_ids = sorting_analyzer.unit_ids,
removed_units = [], # List of units to remove. Example: [31, 42]
merge_unit_groups = [[], []], # List of Lists of units to merge (at least 2 units require). Example: [[3, 6], [10, 14, 20]]
manual_labels = [
dict(unit_id = 1, quality = ["mua"]),
# Keep adding neurons' labels. Example:
# dict(unit_id = 2, quality = ["noise"], putative_type = ["excitatory", "pyramidal"])
],
)Here is the error when trying "apply_curation" with that dictionary:
--> [343](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:343) analyzer, new_unit_ids = analyzer.merge_units(
[344](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:344) curation_dict["merge_unit_groups"],
[345](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:345) censor_ms=censor_ms,
[346](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:346) merging_mode=merging_mode,
[347](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:347) sparsity_overlap=sparsity_overlap,
[348](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:348) new_id_strategy=new_id_strategy,
[349](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:349) return_new_unit_ids=True,
[350](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:350) format="memory",
[351](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:351) verbose=verbose,
[352](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:352) **job_kwargs,
[353](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:353) )
[354](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:354) apply_curation_labels(analyzer.sorting, new_unit_ids, curation_dict)
[355](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/curation/curation_format.py:355) return analyzer
File m:\Monkey_Python\SIenv\Lib\site-packages\spikeinterface\core\sortinganalyzer.py:1101, in SortingAnalyzer.merge_units(self, merge_unit_groups, new_unit_ids, censor_ms, merging_mode, sparsity_overlap, new_id_strategy, return_new_unit_ids, format, folder, verbose, **job_kwargs)
[1098](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1098) for units in merge_unit_groups:
[1099](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1099) # TODO more checks like one units is only in one group
[1100](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1100) if len(units) < 2:
-> [1101](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1101) raise ValueError("Merging requires at least two units to merge")
[1103](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1103) # TODO : no this function did not exists before
[1104](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1104) if not isinstance(merge_unit_groups[0], (list, tuple)):
[1105](file:///M:/Monkey_Python/SIenv/Lib/site-packages/spikeinterface/core/sortinganalyzer.py:1105) # keep backward compatibility : the previous behavior was only one merge
ValueError: Merging requires at least two units to merge