flatironinstitute
PermissionError: [WinError 32]
Hello,
I'm using spikeInterface to run MS5 on Windows 11 and Python 3.8, but I got the following error when creating the sorting object. Thanks in advance for your help.
filtering whitening write_binary_recording: 100%|███████████████████████████████████████████████████████████████████████████████████| 49/49 [00:02<00:00, 20.12it/s] Using training recording of duration 300 sec with the sampling mode uniform *** MS5 Elapsed time for SCHEME2 get_sampled_recording_for_training: 0.000 seconds *** Running phase 1 sorting Number of channels: 1 Number of timepoints: 7329960 Sampling frequency: 30000.0 Hz Channel 0: [ 0. -3.1] Loading traces *** MS5 Elapsed time for load_traces: 0.000 seconds *** Detecting spikes
Adjacency for detect spikes with channel radius 200 [[0]]
m = 0 (nbhd size: 1) Detected 193 spikes *** MS5 Elapsed time for detect_spikes: 0.020 seconds *** Removing duplicate times *** MS5 Elapsed time for remove_duplicate_times: 0.000 seconds *** Extracting 193 snippets *** MS5 Elapsed time for extract_snippets: 0.001 seconds *** Computing PCA features with npca=3 *** MS5 Elapsed time for compute_pca_features: 0.002 seconds *** Isosplit6 clustering with npca_per_subdivision=10 Found 1 clusters *** MS5 Elapsed time for isosplit6_subdivision_method: 0.001 seconds *** Computing templates *** MS5 Elapsed time for compute_templates: 0.001 seconds *** Determining optimal alignment of templates Template alignment converged. Align templates offsets: [0] *** MS5 Elapsed time for align_templates: 0.000 seconds *** Aligning snippets *** MS5 Elapsed time for align_snippets: 0.000 seconds *** Clustering aligned snippets Computing PCA features with npca=3 *** MS5 Elapsed time for compute_pca_features: 0.002 seconds *** Isosplit6 clustering with npca_per_subdivision=10 *** MS5 Elapsed time for isosplit6_subdivision_method: 0.001 seconds *** Found 1 clusters after alignment Computing templates *** MS5 Elapsed time for compute_templates: 0.001 seconds *** Offsetting times to peak Offsets to peak: [0] *** MS5 Elapsed time for determine_offsets_to_peak: 0.000 seconds *** Sorting times *** MS5 Elapsed time for sorting times: 0.000 seconds *** Removing out of bounds times *** MS5 Elapsed time for removing out of bounds times: 0.000 seconds *** Reordering units *** MS5 Elapsed time for reordering units: 0.000 seconds *** Creating sorting object *** MS5 Elapsed time for creating sorting object: 0.000 seconds *** *** MS5 Elapsed time for SCHEME2 sorting_scheme1: 0.041 seconds *** *** MS5 Elapsed time for SCHEME2 get_times_labels_from_sorting: 0.000 seconds *** Loading training traces *** MS5 Elapsed time for SCHEME2 training_recording.get_traces: 0.000 seconds *** Training classifier *** MS5 Elapsed time for SCHEME2 training classifier step 1: 0.001 seconds *** Adding snippets from phase 1 sorting Fitting models *** MS5 Elapsed time for SCHEME2 fitting models: 0.006 seconds *** Chunk size: 3333.3333333333335 sec Time chunk 1 of 1 Loading traces *** MS5 Elapsed time for SCHEME2 loading traces: 0.000 seconds *** Detecting spikes
Adjacency for detect spikes with channel radius 50 [[0]]
Scheme 2 detected 193 spikes in chunk 1 of 1
*** MS5 Elapsed time for SCHEME2 detecting spikes: 0.030 seconds ***
Extracting and classifying snippets
*** MS5 Elapsed time for SCHEME2 extracting and classifying snippets: 0.000 seconds ***
Updating events
Removing duplicates
*** MS5 Elapsed time for SCHEME2 updating events: 0.001 seconds ***
Concatenating results
*** MS5 Elapsed time for SCHEME2 concatenating results: 0.000 seconds ***
Perorming label mapping
*** MS5 Elapsed time for SCHEME2 label mapping: 0.000 seconds ***
Creating sorting object
*** MS5 Elapsed time for SCHEME2 creating sorting object: 0.000 seconds ***
Error running mountainsort5
Traceback (most recent call last):
File "m:/Monkey_Python/SIenv/test_SI.py", line 91, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\tempfile.py", line 803, in onerror _os.unlink(path) PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\josev\AppData\Local\Temp\tmp4kibvgq8\recording.dat'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "m:\Monkey_Python\SIenv\lib\site-packages\spikeinterface\sorters\basesorter.py", line 258, in run_from_folder SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose) File "m:\Monkey_Python\SIenv\lib\site-packages\spikeinterface\sorters\external\mountainsort5.py", line 203, in _run_from_folder raise ValueError(f"Invalid scheme: {scheme} given. scheme must be one of '1', '2' or '3'") File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\tempfile.py", line 828, in exit self.cleanup() File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\tempfile.py", line 832, in cleanup self._rmtree(self.name) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\tempfile.py", line 814, in _rmtree _shutil.rmtree(name, onerror=onerror) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\shutil.py", line 737, in rmtree return _rmtree_unsafe(path, onerror) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\shutil.py", line 615, in _rmtree_unsafe onerror(os.unlink, fullname, sys.exc_info()) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\tempfile.py", line 806, in onerror cls._rmtree(path) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\tempfile.py", line 814, in _rmtree _shutil.rmtree(name, onerror=onerror) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\shutil.py", line 737, in rmtree return _rmtree_unsafe(path, onerror) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\shutil.py", line 596, in _rmtree_unsafe onerror(os.scandir, path, sys.exc_info()) File "C:\Users\josev\AppData\Local\Programs\Python\Python38\lib\shutil.py", line 593, in _rmtree_unsafe with os.scandir(path) as scandir_it: NotADirectoryError: [WinError 267] The directory name is invalid: 'C:\Users\josev\AppData\Local\Temp\tmp4kibvgq8\recording.dat'
Spike sorting failed. You can inspect the runtime trace in M:\Monkey_Project\AlbusTesting\Albus-S1_TwoHands_5FR_NOpostchoice\sortMS5/spikeinterface_log.json.
Same as I met. Do you solve it now?
Not yet. and I didn't try anything to solve it. But, I was able to run MS5 using the Docker image method.
We updated the spikeinterface wrapper to try to help deal with some of these issues. If you reinstall spikeinterface from main (we haven't released a version with the fixes yet) we think we will prevent those issues on Windows. (I test on Windows myself and haven't run into this issue locally). Docker is also a potential solution.
Thanks @zm711
I have been running MS5 from docker and it works fine, but I think it will run a little faster if I run it directly. I will reinstall spikeinterface.
And just to confirm, when you said reinstall from main, did you mean do it like this?:
https://spikeinterface.readthedocs.io/en/latest/installation.html#from-source
Thanks again and I will update you on how it goes.
Yep that link explains. The only thing is that there is an API change (switching from waveform_extractor to sorting_analyzer), so if you're not ready for that switch then I just opened a PR to back port our MS5 patches into our 0.100.bug-fixes branch but that won't be ready for a little bit at least. Happy to help if you run into issues though! Just open an issue on the spikeinterface repo after the install.
OK¡ I'm just starting to implement a spikeinterface pipeline, so I will try to use sorting_analyzer instead of waveform_extractor. If I run into any issues I will post it on the spikeinterface repo (should I tag you on that repo? ). If I can't make the switch I will wait for the changes in the PR you opened, and in the meantime, I will keep using MS5 from docker.
Thank you so much and I will update how it goes.
Everyone is pretty responsive over there so up to you (you're welcome to tag me, but someone will definitely respond even if you don't :) ).
If you're just starting I would definitely recommend using the sorting_analyzer instead since that will be what is used going forward so I would hate for you to build a pipeline and then need to switch stuff over. And the analyzer is better :)