victorgutemberg
commented
2 months ago hello @ttngu207 and @dimitri-yatsenko,
I'm running into another issue with the conversion to NWB. I think this might be related to different versions. Could you please export your pip/conda requirements on the environment you're using to run the code?
Great study by the way! 😄
32%|███▏ | 43/135 [41:24<1:42:31, 66.87s/it]Error adding roi_response_series: stimOffAl
ErrorMsg: 'stimOffAl'
33%|███▎ | 44/135 [42:16<1:34:34, 62.36s/it]Error adding roi_response_series: stimOffAl
ErrorMsg: 'stimOffAl'
53%|█████▎ | 72/135 [1:13:51<1:04:37, 61.55s/it]
Traceback (most recent call last):
File "/home/workstation/Projects/najafi-2018-nwb/scripts/convert_to_nwb.py", line 41, in <module>
moremat, postmat = (sio.loadmat(file_pair[x], struct_as_record=False, squeeze_me=True)
File "/home/workstation/Projects/najafi-2018-nwb/scripts/convert_to_nwb.py", line 41, in <genexpr>
moremat, postmat = (sio.loadmat(file_pair[x], struct_as_record=False, squeeze_me=True)
File "/home/workstation/anaconda3/envs/torch/lib/python3.10/site-packages/scipy/io/matlab/_mio.py", line 227, in loadmat
matfile_dict = MR.get_variables(variable_names)
File "/home/workstation/anaconda3/envs/torch/lib/python3.10/site-packages/scipy/io/matlab/_mio5.py", line 333, in get_variables
res = self.read_var_array(hdr, process)
File "/home/workstation/anaconda3/envs/torch/lib/python3.10/site-packages/scipy/io/matlab/_mio5.py", line 291, in read_var_array
return self._matrix_reader.array_from_header(header, process)
File "_mio5_utils.pyx", line 665, in scipy.io.matlab._mio5_utils.VarReader5.array_from_header
File "_mio5_utils.pyx", line 712, in scipy.io.matlab._mio5_utils.VarReader5.array_from_header
File "_mio5_utils.pyx", line 965, in scipy.io.matlab._mio5_utils.VarReader5.read_struct
File "_mio5_utils.pyx", line 663, in scipy.io.matlab._mio5_utils.VarReader5.read_mi_matrix
File "_mio5_utils.pyx", line 694, in scipy.io.matlab._mio5_utils.VarReader5.array_from_header
File "_mio5_utils.pyx", line 768, in scipy.io.matlab._mio5_utils.VarReader5.read_real_complex
File "_mio5_utils.pyx", line 445, in scipy.io.matlab._mio5_utils.VarReader5.read_numeric
File "_mio5_utils.pyx", line 350, in scipy.io.matlab._mio5_utils.VarReader5.read_element
File "_streams.pyx", line 171, in scipy.io.matlab._streams.ZlibInputStream.read_string
File "_streams.pyx", line 147, in scipy.io.matlab._streams.ZlibInputStream.read_into
File "_streams.pyx", line 134, in scipy.io.matlab._streams.ZlibInputStream._fill_buffer
zlib.error: Error -3 while decompressing data: incorrect data check
Running into an issue with converting NWB files.
I am working with Mac OSX Ventura for what it is worth. Working in the terminal and in the caiman environment.
Followed the instructions to download and unpack the Najafi 2018 dataset, which was done successfully. I'm running into issues with converting to nwb. My pynwb version is 2.3.2.
When running
% python3 scripts/convert_to_nwb.pyI run into the following error:
0%| | 0/135 [00:00<?, ?it/s]/Users/js0403/anaconda3/envs/caiman/lib/python3.10/site-packages/numpy/core/numeric.py:407: RuntimeWarning: invalid value encountered in cast multiarray.copyto(res, fill_value, casting='unsafe') /Users/js0403/najafi-2018-nwb/scripts/convert_to_nwb.py:156: RuntimeWarning: invalid value encountered in cast neuron_type[bad_roi_mask] = moremat['inhibitRois_pix'] 18%|███████▍ | 24/135 [03:45<22:53, 12.38s/it]Error adding roi_response_series: stimOffAl ErrorMsg: 'stimOffAl'
19%|███████▊ | 25/135 [04:00<24:18, 13.26s/it]Error adding roi_response_series: stimOffAl ErrorMsg: 'stimOffAl'
19%|████████ | 26/135 [04:08<21:24, 11.79s/it]Error adding roi_response_series: stimOffAl ErrorMsg: 'stimOffAl'
20%|████████▍ | 27/135 [04:25<23:52, 13.26s/it]Error adding roi_response_series: stimOffAl ErrorMsg: 'stimOffAl'
Each file is processed until it runs into 'stimOffAI' after which, the progress terminates.