Unexpected: AssertionError: 'inter_sample_shift' is not a property!

Hello!
Thank you for producing and maintaining such a fabulous piece of software!

Briefly, when I run Kilosort4 via runsorter.run_sorter_local, it complains that

AssertionError: 'inter_sample_shift' is not a property!

even though, on the line immediately preceding this run_sorter command, the following passes:

assert 'inter_sample_shift' in rec.get_property_keys().

I created a minimal example below to reproduce this behavior. The last section contains the error, and everything above is setup. For context, I originally encountered this assert error while preprocessing and motion correcting using spikeinterface, then passing this processed recording to Kilosort4 while skipping preprocessing and motion correction. In the example below, I run Kilosort4 on unprocessed data (which works) just to demonstrate the unexpected behavior.

Thanks for any advice!!

`

Load config file

config_file = '/mnt/lab/users/barnold/spike_sorting/package/spike_sort_config.yaml'
with open(config_file, 'r') as f:
config = yaml.safe_load(f)

Configure probe, specifying geometry of channels and other kwargs

positions = []
for i in range(config['probe']['n_row']):
# add channels by row, 2 channels per row
positions.append([0, i * config['probe']['pitch_row']])
positions.append([config['probe']['pitch_col'], i * config['probe']['pitch_row']])
positions = np.array(positions)

probe = Probe(ndim=config['probe']['n_dim'], si_units=config['probe']['units'])

probe.set_contacts(positions=positions,
shapes=config['probe']['shape'],
shape_params={'width': config['probe']['chan_width']})

probe.set_device_channel_indices(np.arange(config['probe']['n_chan']-1))

probe_kwargs = {'sampling_frequency': 30000.0561519867,
'num_channels': 385,
'dtype': 'int16',
'gain_to_uV': 2.3438,
'offset_to_uV': 0}

Load NP recording, assign probe

NP_file = '/mnt/mscratch1/Tarzan/2024-12-12_12-42-50/2024-12-12_12-43-01/NPElectrophysiology_2_2.bin'
rec = extractors.read_binary(file_paths = NP_file, **probe_kwargs)
rec = rec.select_channels([i for i in range(config['probe']['n_chan']-1)])
rec = rec.set_probe(probe)

set sample_shifts

sample_shifts = extractors.neuropixels_utils.get_neuropixels_sample_shifts(num_channels=rec.get_num_channels(), num_channels_per_adc=12)
rec.set_property('inter_sample_shift', sample_shifts)

take a small sample for testing

start_time_secs, duration_secs = 0,10
rec = rec.frame_slice(start_frame=int(start_time_secs * rec.sampling_frequency), end_frame=int((start_time_secs + duration_secs) * rec.sampling_frequency))

Unexpected AssertionError

this works like a charm

sorting = runsorter.run_sorter_local(sorter_name="kilosort4",
recording=rec,
folder=config['out_dir'],
**config['kilosort'])

do standard preprocessing using spikeinterface's preprocessing module

rec = preprocessing.bandpass_filter(recording=rec,
freq_min=config['ap_freqband']['lower'],
freq_max=config['ap_freqband']['upper'])

bad_channel_ids, channel_labels = preprocessing.detect_bad_channels(rec) # for this step, recording assumed to be filtered
rec = rec.remove_channels(remove_channel_ids=bad_channel_ids)
rec = preprocessing.phase_shift(recording=rec)
rec = preprocessing.common_reference(recording=rec, **config['common_reference'])

this passes

assert 'inter_sample_shift' in rec.get_property_keys()

this does NOT work and fails because of the assert error that just passed in previous line

sorting = runsorter.run_sorter_local(sorter_name="kilosort4",
recording=rec,
folder=config['out_dir'],
**config['kilosort']) `

This is the error message from the last command:

SpikeSortingError: Spike sorting error trace: ... File "/usr/local/lib/python3.9/dist-packages/spikeinterface/preprocessing/phase_shift.py", line 46, in __init__ assert "inter_sample_shift" in recording.get_property_keys(), "'inter_sample_shift' is not a property!" AssertionError: 'inter_sample_shift' is not a property!

Brian

Start with preprocessing/phase_shift.py and trace how the recording passed to runsorter.run_sorter_local retains properties after filtering, channel removal, and other preprocessing steps. Reproduce the minimal example and verify that the Kilosort4 run no longer raises the inter_sample_shift assertion while the property remains available.