data type for run_sorter in spikeinterface.sorters

[cfshang-maker]

Hi guys, I have suffered for several hours before posting this issue. I have been warned that "Can't interpolate_motion with dtype int16" when I tried to run_sorter on my recording, which has passed interpolate_motion. I even got this warning when I tried to save the motion-corrected recording. Should I return to the position before motion estimation and change my recording to float32 there so as to use run_sorter?

Best regards,
Chun-feng

[alejoe91]

Hi!

You don't have to suffer that long ;) just go ahead and ask!

You can simply do:

recording = spre.astype(recording, "float32")

prior to spike sorting

[cfshang-maker]

Thank you, Alessio,
I have tried that and confirmed the dtype (recording) as float32. However, I still got a batch of warnings as follows, ending with "ValueError: Can't interpolate_motion with dtype int16."

The whole batch is
File "", line 1, in
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\sorters\runsorter.py", line 210, in run_sorter
return run_sorter_local(**common_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\sorters\runsorter.py", line 300, in run_sorter_local
SorterClass.setup_recording(recording, folder, verbose=verbose)
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\sorters\basesorter.py", line 242, in setup_recording
cls._setup_recording(recording, sorter_output_folder, sorter_params, verbose)
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\sorters\external\kilosortbase.py", line 155, in _setup_recording
write_binary_recording(
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\core\recording_tools.py", line 140, in write_binary_recording
executor.run()
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\core\job_tools.py", line 494, in run
res = self.func(segment_index, frame_start, frame_stop, worker_dict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\core\recording_tools.py", line 157, in _write_binary_chunk
traces = recording.get_traces(start_frame=start_frame, end_frame=end_frame, segment_index=segment_index)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\core\baserecording.py", line 340, in get_traces
traces = rs.get_traces(start_frame=start_frame, end_frame=end_frame, channel_indices=channel_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\preprocessing\astype.py", line 76, in get_traces
traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\sortingcomponents\motion\motion_interpolation.py", line 509, in get_traces
traces = interpolate_motion_on_traces(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DELL\miniforge3\envs\dredge\Lib\site-packages\spikeinterface\sortingcomponents\motion\motion_interpolation.py", line 146, in interpolate_motion_on_traces
raise ValueError(f"Can't interpolate_motion with dtype {dtype}.")
ValueError: Can't interpolate_motion with dtype int16.

[chrishalcrow]

Hi @cfshang-maker make sure that you're doing the astype step before motion correction. If you are, please share your code and we can try to debug :)

[cfshang-maker]

Hi @cfshang-maker make sure that you're doing the astype step before motion correction. If you are, please share your code and we can try to debug :)

Hi Chris, I performed the astype after motion correction and before kilosort. Does the error imply that I cannot change the motion-corrected recording to float32? Should I do it before motion correction?

[chrishalcrow]

Yes, the motion interpolation relies on the recording before float32, so you need to give the motion correction a float32 recording => do it before motion correction.

[cfshang-maker]

Thank you for your instruction, Chris. I am following it.

[chrishalcrow]

Let me know if it works :)