Syntax error while importing

[caggursoy]

Hi,

I am receiving the following runtime error whenever I try to import the package. Here's how I try to import it

from mni_to_atlas import AtlasBrowser

Traceback (most recent call last):

  File ~/.conda/envs/nipype/lib/python3.10/site-packages/IPython/core/interactiveshell.py:3526 in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  Cell In[11], line 11
    from mni_to_atlas import AtlasBrowser

  File ~/.conda/envs/nipype/lib/python3.10/site-packages/mni_to_atlas/__init__.py:3
    from .atlas_browser import AtlasBrowser

  File ~/.conda/envs/nipype/lib/python3.10/site-packages/mni_to_atlas/atlas_browser.py:336
    region_id = int(self._atlas[*atlas_coords])
                    ^
SyntaxError: invalid syntax. Perhaps you forgot a comma?

And here's my system information:

• Ubuntu 22.04
• Python 3.9.13
• conda 22.9.0
• Running on JupyterLab, so:
  • IPython : 7.31.1
  • ipykernel : 6.15.2
  • ipywidgets : 7.6.5
  • jupyter_client : 7.3.4
  • jupyter_core : 4.11.1
  • jupyter_server : 1.18.1
  • jupyterlab : 3.4.4
  • nbclient : 0.5.13
  • nbconvert : 6.4.4
  • nbformat : 5.5.0
  • notebook : 6.4.12
  • qtconsole : 5.3.2
  • traitlets : 5.1.1

I would be glad if you can offer any help with this regard

[caggursoy]

Update

If I remove the character from line 336 of _atlasbrowser.py I encounter a completely different error. Original script `region_id = int(self._atlas[atlas_coords]) Edited script region_id = int(self._atlas[atlas_coords])`

Please see the error below, when the edited script is run with the following parameters: coord = np.array([0,40,-4]) atlas.find_regions(coord)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/zi/home/cagatay.guersoy/.conda/envs/nipype/lib/python3.10/site-packages/mni_to_atlas/atlas_browser.py", line 141, in find_regions
    region = self._find_region(atlas_coords)
  File "/zi/home/cagatay.guersoy/.conda/envs/nipype/lib/python3.10/site-packages/mni_to_atlas/atlas_browser.py", line 336, in _find_region
    region_id = int(self._atlas[atlas_coords])
TypeError: only length-1 arrays can be converted to Python scalars

[tsbinns]

Thanks for bringing this to my attention! I haven't touched this code in a while so I'll have to investigate what's going wrong, will try to have a solution in the coming days.

Cheers!

[tsbinns]

@caggursoy Please can you try updating your Python version to >= 3.11, that should stop this from happening.

Will try to release a new version in the coming days as a more permanent fix.