Description
Hello,
I managed to run deepinterpolation and the time series plot looks good. However, when I try to save it as a .dat binary file to run on my local installation of Kilosort3, I get the error message: TypeError: init() got an unexpected keyword argument 'recording'. I get the same error when running Kilosort3 on the denoised recording using the singularity container directly.
I run deepinterpolation via:
import spikeinterface.preprocessing as sp
rec5 = sp.deepinterpolate(sp.zero_channel_pad(rec4,384), model_path = '2020_02_29_15_28_unet_single_ephys_1024_mean_squared_error-1050.h5')
where rec4 is the output of filtering, removing bad channels and common average referencing, following the code of the Neuropixel tutorial. The zero channel padding is because I removed a bad channel (the reference channel). I have the model downloaded and the path is correct.
Regarding saving, I tried:
job_kwargs = dict(n_jobs=12, chunk_duration='1s', progress_bar=True)
rec = rec5.save(folder='myfolder', format='binary', **job_kwargs)
which gave the same TypeError: init() got an unexpected keyword argument 'recording'
as well as:
import spikeinterface.core as sc
job_kwargs = dict(chunk_duration='1s', progress_bar=True)
sc.write_binary_recording(rec5, file_paths = 'myfolder/deepinterpolation_denoised.dat', dtype='int16', n_jobs=12, **job_kwargs)
which again gave the same error.
May I know if I was running deepinterpolation wrongly? Also, is it recommended to save the output as a binary .dat file via the recording.save() method or the write_binary_recording() method? I attempted to save my filtered recording (without deepinterpolation denoising) via the .save() method but it gave a .raw file that my local installation of Kilosort3 did not accept (error message that the input was not binary).
Thank you!