Errors about running example of surfdist

[DrChenziyan]

Hi~
When I test the example code in the readme, there is an error when I run sd.analysis.dist_calc

Here are my codes:

cmap = 'coolwarm'
base_dir = 'path/2/Applications/freesurfer/subjects/'
surf = nib.freesurfer.read_geometry(os.path.join(base_dir, 'bert/surf/lh.pial'))
cort = np.sort(nib.freesurfer.read_label(os.path.join(base_dir, 'bert/label/lh.cortex.label')))
sulc = nib.freesurfer.read_morph_data(os.path.join(base_dir, 'bert/surf/lh.sulc'))
src  = sd.load.load_freesurfer_label(os.path.join(base_dir, 'bert/label/lh.aparc.a2009s.annot'), 'S_central', cort)
## All codes above run successfully~~

# calculate distance
dist = sd.analysis.dist_calc(surf, cort, src)

AND Here are the errors:

NumbaNotImplementedError                  Traceback (most recent call last)
File [~/anaconda3/envs/d2l/lib/python3.9/site-packages/numba/core/typing/typeof.py:244](https://vscode-remote+ssh-002dremote-002bchenzy-005fsever1.vscode-resource.vscode-cdn.net/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/~/anaconda3/envs/d2l/lib/python3.9/site-packages/numba/core/typing/typeof.py:244), in _typeof_ndarray(val, c)
    243 try:
--> 244     dtype = numpy_support.from_dtype(val.dtype)
    245 except errors.NumbaNotImplementedError:

File [~/anaconda3/envs/d2l/lib/python3.9/site-packages/numba/np/numpy_support.py:114](https://vscode-remote+ssh-002dremote-002bchenzy-005fsever1.vscode-resource.vscode-cdn.net/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/~/anaconda3/envs/d2l/lib/python3.9/site-packages/numba/np/numpy_support.py:114), in from_dtype(dtype)
    112         return types.NestedArray(subtype, dtype.shape)
--> 114 raise errors.NumbaNotImplementedError(dtype)

NumbaNotImplementedError: >i4

During handling of the above exception, another exception occurred:

NumbaValueError                           Traceback (most recent call last)
[/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/test.ipynb](https://vscode-remote+ssh-002dremote-002bchenzy-005fsever1.vscode-resource.vscode-cdn.net/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/test.ipynb) Cell 4 in ()
      [1](vscode-notebook-cell://ssh-remote%2Bchenzy_sever1/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/test.ipynb#W3sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0) # calculate distance
----> [2](vscode-notebook-cell://ssh-remote%2Bchenzy_sever1/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/test.ipynb#W3sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1) dist = sd.analysis.dist_calc(surf, cort, src)

File [~/anaconda3/envs/d2l/lib/python3.9/site-packages/surfdist-0.15.5-py3.9.egg/surfdist/analysis.py:14](https://vscode-remote+ssh-002dremote-002bchenzy-005fsever1.vscode-resource.vscode-cdn.net/export/bioinfo-team/home/chenzy/Desktop/PythonTutorial/MedicalImages_Deeplearning/fmri_learning/~/anaconda3/envs/d2l/lib/python3.9/site-packages/surfdist-0.15.5-py3.9.egg/surfdist/analysis.py:14), in dist_calc(surf, cortex, source_nodes)
      6 def dist_calc(surf, cortex, source_nodes):
      8     """
      9     Calculate exact geodesic distance along cortical surface from set of source nodes.
     10     "dist_type" specifies whether to calculate "min", "mean", "median", or "max" distance values
...
--> 246     raise errors.NumbaValueError(f"Unsupported array dtype: {val.dtype}")
    247 layout = numpy_support.map_layout(val)
    248 readonly = not val.flags.writeable

NumbaValueError: Unsupported array dtype: >i4

The requirements of my computer:

python 3.9.10
numpy 1.23.5
numba 0.56.4
Cython 0.29.33
tvb-gist 2.2
nibabel 3.2.2

Could you please help me to solve the problem, Thank you~

[margulies]

Thanks for your interest in the code and for pointing out this error. I've discussed this with @neurabenn, and we've created a PR that only removed the numba requirement. Could you try running the code from this PR #18 , and let us know if it resolves the issue?