SpikeInterface / SpikeInterface/spikeinterface
Extra neo kwarg for BioCAM's event-based compression not passed to SpykingCircus2
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Description
Recently, support for BioCAM's event-based compression was added to neo.
It requires the user to decide between filling the gaps in recordings with zeros or artificial noise, specified by fill_gaps_strategy in SI.
When running SpykingCircus2 on compressed data, it looks like this kwarg isn't passed properly to the internal filtering functions.
I'm running the following :
recording = se.read_biocam(data_path,
mea_pitch=60,
electrode_width=21,
fill_gaps_strategy="synthetic_noise",
)
recording = recording.remove_channels('1')
recording = spre.unsigned_to_signed(recording, bit_depth=12)
sorting = ss.run_sorter(
sorter_name="spykingcircus2", recording=recording,
folder=str(output_folder / "sc2_output"),verbose=True, **p,
)
HerdingSpikes2 runs just fine on the same file, so this seems to be sorter-specific.
Here's the full trace :
Error running spykingcircus2
Traceback (most recent call last):
File "/home/user/Documents/ephy/sc_si.py", line 60, in <module>
sorting = ss.run_sorter(
^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/sorters/runsorter.py", line 198, in run_sorter
return run_sorter_local(**common_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/sorters/runsorter.py", line 260, in run_sorter_local
SorterClass.run_from_folder(folder, raise_error, verbose)
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/sorters/basesorter.py", line 310, in run_from_folder
raise SpikeSortingError(
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/sorters/internal/spyking_circus2.py", line 172, in _run_from_folder
recording_w = whiten(recording_f, **whitening_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/core/core_tools.py", line 35, in source_class_or_dict_of_sources_classes
return source_class(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/preprocessing/whiten.py", line 93, in __init__
W, M = compute_whitening_matrix(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/preprocessing/whiten.py", line 192, in compute_whitening_matrix
data, cov, M = compute_covariance_matrix(recording, apply_mean, regularize, regularize_kwargs, random_chunk_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/preprocessing/whiten.py", line 244, in compute_covariance_matrix
random_data = get_random_data_chunks(recording, concatenated=True, return_in_uV=False, **random_chunk_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/core/recording_tools.py", line 608, in get_random_data_chunks
traces_chunk = recording.get_traces(
^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/core/baserecording.py", line 339, in get_traces
traces = rs.get_traces(start_frame=start_frame, end_frame=end_frame, channel_indices=channel_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/preprocessing/common_reference.py", line 183, in get_traces
traces = self.parent_recording_segment.get_traces(start_frame, end_frame, slice(None))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/preprocessing/filter.py", line 162, in get_traces
traces_chunk, left_margin, right_margin = get_chunk_with_margin(
^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/core/recording_tools.py", line 854, in get_chunk_with_margin
traces_chunk = rec_segment.get_traces(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/preprocessing/unsigned_to_signed.py", line 54, in get_traces
traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/core/channelslice.py", line 101, in get_traces
traces = self._parent_recording_segment.get_traces(start_frame, end_frame, parent_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/spikeinterface/src/spikeinterface/extractors/neoextractors/neobaseextractor.py", line 367, in get_traces
raw_traces = self.neo_reader.get_analogsignal_chunk(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/python-neo/neo/rawio/baserawio.py", line 1006, in get_analogsignal_chunk
raw_chunk = self._get_analogsignal_chunk(block_index, seg_index, i_start, i_stop, stream_index, channel_indexes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/Documents/GitHub/python-neo/neo/rawio/biocamrawio.py", line 148, in _get_analogsignal_chunk
raise ValueError(
ValueError: Please set `fill_gaps_strategy` to 'zeros' or 'synthetic_noise'.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in spikeinterface/sorters/internal/spyking_circus2.py at the whitening call, then trace the filtering and recording access shown in the traceback through preprocessing/filter.py and neobaseextractor.py. Verify how sorter recording options are propagated to the Neo reader. Done means SpykingCircus2 can read BioCAM compressed data with the requested fill_gaps_strategy and the existing failure is covered by a relevant test.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100