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Working environment (Python IDE/Jupyter Notebook/other): Jupyter Notebook
Which of the demo scripts you're using for your analysis (if applicable): demo_online_cnmfE.ipynb
CaImAn version*: 1.11.3
CaImAn installation process (pip install ./pip install -e ./conda): conda
- Describe the issue that you are experiencing
Trying to run cnm_online.fit_online() with the images with shape (26213, 608, 608) and get IndexError: too many indices for array.
- Copy error log below
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/user/anaconda3/envs/caiman/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/home/user/anaconda3/envs/caiman/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "/home/user/anaconda3/envs/caiman/lib/python3.11/site-packages/caiman/motion_correction.py", line 3044, in tile_and_correct_wrapper
imgs = imgs[(slice(None),) + indices]
~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: too many indices for array: array is 2-dimensional, but 3 were indexed
"""
The above exception was the direct cause of the following exception:
IndexError Traceback (most recent call last)
Cell In[29], line 2
1 # run online estimator
----> 2 cnm_online.fit_online()
- The Setup.
Operating system (Linux/macOS/Windows): Linux
Python version (3.x): 3.11.9
Working environment (Python IDE/Jupyter Notebook/other): Jupyter Notebook
Which of the demo scripts you're using for your analysis (if applicable): demo_online_cnmfE.ipynb
CaImAn version*: 1.11.3
CaImAn installation process (pip install ./pip install -e ./conda): conda
- Describe the issue that you are experiencing
Trying to run cnm_online.fit_online() with the images with shape (26213, 608, 608) and get IndexError: too many indices for array.
- Copy error log below
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/user/anaconda3/envs/caiman/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/home/user/anaconda3/envs/caiman/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "/home/user/anaconda3/envs/caiman/lib/python3.11/site-packages/caiman/motion_correction.py", line 3044, in tile_and_correct_wrapper
imgs = imgs[(slice(None),) + indices]
~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: too many indices for array: array is 2-dimensional, but 3 were indexed
"""
The above exception was the direct cause of the following exception:
IndexError Traceback (most recent call last)
Cell In[29], line 2
1 # run online estimator
----> 2 cnm_online.fit_online()
File ~/anaconda3/envs/caiman/lib/python3.11/site-packages/caiman/source_extraction/cnmf/online_cnmf.py:1152, in OnACID.fit_online(self, **kwargs)
...
772 return self._value
773 else:
--> 774 raise self._value
IndexError: too many indices for array: array is 2-dimensional, but 3 were indexed
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