Regarding the issues of "si.read_openephys"

[TsungChihTsai]

Before I perform this way to analysis, it works. In the beginning, I found another issue about asking me to add "load_sync_channel= False". I tried it, but it remain the same issue. Therefore, I update my pip install spikeinterface to the lastest version. I analyzed the open ephys binary data, I encounter this issue. I also attempted to uninstall spikeinterface, and then install my original version I have ever used "pip install spikeinterface[full,widgets]==0.99.0" and "spikeinterface-gui>=0.4.1". And, it still show the same issue as below:

recording = si.read_openephys("D:/20240403_ASI/WT_iso_2024-04-03_11-12-01_001", stream_name="Record Node 105#File_Reader-100.Data",experiment_names ="experiment 1")

Could you please guide me to modify my path?

[alejoe91]

Hi,

What is the content of the folder? Can you print it also with subfolders? Did you delete any folder manually?

[TsungChihTsai]

Yes, I can show you. continuous subfolders D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\continuous.dat D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\input_flag.txt D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\timestamps.npy

recording1 subfolders D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\structure.oebin D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\sync_messages.txt D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\input_flag.txt D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\continuous.dat D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\input_flag.txt D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\continuous\File_Reader-100.Data\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\File_Reader-100.Data\TTL\full_words.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\File_Reader-100.Data\TTL\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\File_Reader-100.Data\TTL\states.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\File_Reader-100.Data\TTL\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\MessageCenter\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\MessageCenter\text.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\events\MessageCenter\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 1\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 1\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 1\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 1\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 1\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 10\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 10\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 10\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 10\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 10\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 11\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 11\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 11\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 11\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 11\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 12\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 12\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 12\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 12\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 12\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 13\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 13\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 13\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 13\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 13\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 14\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 14\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 14\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 14\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 14\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 15\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 15\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 15\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 15\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 15\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 16\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 16\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 16\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 16\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 16\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 17\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 17\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 17\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 17\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 17\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 18\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 18\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 18\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 18\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 18\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 19\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 19\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 19\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 19\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 19\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 2\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 2\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 2\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 2\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 2\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 20\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 20\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 20\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 20\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 20\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 21\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 21\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 21\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 21\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 21\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 22\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 22\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 22\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 22\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 22\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 23\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 23\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 23\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 23\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 23\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 24\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 24\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 24\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 24\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 24\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 25\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 25\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 25\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 25\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 25\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 26\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 26\electrode_indices.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 26\sample_numbers.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 26\timestamps.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 26\waveforms.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 27\clusters.npy D:\20240403_ASI\WT_iso_2024-04-03_11-12-01_001\Record Node 105\experiment1\recording1\spikes\Spike_Detector-104.Data\Electrode 27\electrode_indices.npy

No, I don't delete anything. It's the same folder I've ran spikeinterface.

[alejoe91]

Maybe experiment 1 should be experiment1 (no space)?

[TsungChihTsai]

I revised "recording = si.read_openephys("D:/20240403_ASI/WT_iso_2024-04-03_11-12-01_001", stream_name="Record Node 105#File_Reader-100.Data",experiment_names ="experiment1")", it still shows the same error.

[alejoe91]

Now the error is different. Can you add the load_sync_channel=False argument?

[TsungChihTsai]

I use another laptop at home now. I don't do any update for this laptop (I think it is not caused by update the module, but it happened today). This is different data. Because previous one is huge, I just keep a small one in my laptop. I encounter same issue, too. So, I added the load_sync_channel=False argument, but still shows an error shows. op.

---- laptop at home I ran a data is already sorted by kilosort3.

recording = si.read_openephys("D:\WT_ASI_2024-04-25_10-18-03_001", stream_name="Record Node 113#OE_FPGA_Acquisition_Board-119.Rhythm Data",experiment_names ="experiment1", load_sync_channel=False)

And, it works.

If I chose a new data I've never used before. It shows another issue which is due to "recording_saved = recording_sub.save(folder=output_folder / "preprocessed", **job_kwargs) "

====I also use "pip list" to check the version regarding to spikeinterface: spikeinterface 0.99.0 spikeinterface-gui 0.7.0 probeinterface 0.2.19 numpy 1.23.5 ( list this one, because I found I cannot ran this because the numpy version is higher than 2.0.0 in the beginning) ====For tracing the version I've used well before.

----I will check computer in the lab Tomorrow, I will check the desktop in the lab. Maybe, the new one data is a different issue (If I find this is true, I will raise another issue for that) , not the issue about this time.

And, I will let you know what happened. Thank a million.

[alejoe91]

Can you please upgrade to the latest spike interface? We fixed a bunch of issues in the recent releases!

[chrishalcrow]

If you keep getting errors about BrokenProcessPools and things like that, then the problem is related to multiprocessing. A good idea is to start with n_jobs=1, then move on to multiprocessing once everything is working with one job. But as @alejoe91 says, the multiprocessing has a better chance of working easily with the newest version of spikeinterface!

[TsungChihTsai]

Thanks for your suggestion.

I attempted to update spikeinterface in the lab desktop Successfully installed spikeinterface-0.101.0rc0

And, add load_sync_channel=False

But, it still have an issue,

I think maybe I update in a wrong way?

[alejoe91]

@TsungChihTsai can you send us the data? A google drive link will work!

[TsungChihTsai]

I save the original data without modified anything in google drive.

The link is as below: https://drive.google.com/drive/folders/1RFGTl8gtUbGqRShDMLPfM5rA5AOrzU6L?usp=sharing

If you find any problem, please let me know.

Thanks for your help.

---

I also create a new spikeinterface environment (https://github.com/SpikeInterface/spikeinterface/tree/main/installation_tips) as following steps: cd C:\code\spikeinterface_installation conda env create --file full_spikeinterface_environment_windows.yml conda activate spikeinterface_env

git clone https://github.com/SpikeInterface/spikeinterface.git cd spikeinterface pip install -e . cd ..

python cleanup_for_windows.py pip install notebook jupyter notebook

But, it still show the same error.

---

[TsungChihTsai]

@alejoe91 This data (https://drive.google.com/drive/folders/1RFGTl8gtUbGqRShDMLPfM5rA5AOrzU6L?usp=sharing) can run "recording = si.read_openephys("D:\WT_ASI_2024-04-25_10-18-03_001", stream_name="Record Node 113#OE_FPGA_Acquisition_Board-119.Rhythm Data",experiment_names ="experiment1", load_sync_channel=False)" on my laptop at home.

@chrishalcrow Yes, I change n_jobs=10 to n_jobs=1. And, it can continue the "recording_saved = recording_sub.save(folder=output_folder / "preprocessed", **job_kwargs) "!

When I ran the step of sorting, it show the original issue I met.

E=kilosort3 sorting = si.run_sorter(E, recording_saved, output_folder=output_folder/ E / 'results', docker_image=True,verbose=True, **sorter_params)

It show the original issue I met. AttributeError: np.issctype was removed in the NumPy 2.0 release. Use issubclass(rep, np.generic) instead.

When I face this situation in that time, I updated my numpy on the desktop. Then, it shows "keyerror=0"

---- (latest version of spikeinterface)

I also attempt to create a new environment and update the latest version of spikeinterface on my laptop, even though I added "load_sync_channel=False". Still have the issue for "ValueError: SYNC channel is not present in the recording. Set load_sync_channel to False"

[TsungChihTsai]

"ValueError: SYNC channel is not present in the recording. Set load_sync_channel to False" The issue is from "..\miniconda3\envs\si_env\Lib\site-packages\neo\rawio\openephysbinaryrawio.py" I revised it "Do not check this", and force it as "load_sync_channel=False" However, I am not sure if it will have an adverse effect? (I guess if someone have synchronized data, it still have an issue) Finally, I can run extractor. The version of neo is 0.12.0.. Do you suggest me update neo to which version?

When I ran kilosort3 in docker, it showed another issue: "AttributeError: np.issctype was removed in the NumPy 2.0 release. Use issubclass(rep, np.generic) instead.", it's related to "spikeinterface/kilosort3-compiled-base" in docker. Therefore, I update spikeinterface==0.100.8, docker.exe to v4.31.1 and change "job_kwargs = dict(n_jobs=20, chunk_duration="1s", progress_bar=True)"

When I ran kilosort4 in docker: I got "AttributeError: Bad parameters: ['n_jobs', 'chunk_duration', 'progress_bar']", I change parameters to "si.get_default_sorter_params("kilosort4")"

I've resolved these issues.

[alejoe91]

Let's still leave this open, since the open ephys error needs to be checked. I'll try to take a look at the data you shared on Monday.

[TsungChihTsai]

Thanks a million.

[alejoe91]

@TsungChihTsai I requested access to the drive folder

[TsungChihTsai]

I accept this request. Thanks!

[alejoe91]

@TsungChihTsai it works on my side:

This is with the current main version:

And this is with the latest stable release (0.100.8):

@zm711 maybe this could be a Windows problem?

[zm711]

Happy to test on Windows. But @TsungChihTsai you mentioned your neo version is 0.12.0. Could you update to 0.13.1? Or install from source. We've worked on this IO a bunch since the last release. If it is still not working with neo updated then I'll see if it is a Windows problem :)

[TsungChihTsai]

pip install neo==0.13.1

It still has this issue.

[alejoe91]

Can you just try the code from my screenshots here? https://github.com/SpikeInterface/spikeinterface/issues/3099#issuecomment-2202087760

This is using the folder you shared

[TsungChihTsai]

Yes, it works! Thanks!

[zm711]

Sorry, I missed this. I just requested access, but if it works then I'm not needed :)

[alejoe91]

Ok! closing then!