Fix for `no package called pandas` in SlicerMorph ALPACA k-means template selection - Apple ARM

Community SlicerMorph
1

Hi community,

I’ve run into a problem with k-means template selection on 2 different mac machines. One is a 2020 MacBook Pro M1, and the second is a 2023 MacBook Pro M3 Max. Working through the tutorial here, I can run steps 1 & 2, generating the reference point cloud, and generating the point clouds for the rest of my samples that match the reference, without error. Everything looks fine.

When I go to the next step called K-means based template selection, I set my number of templates, my # of iterations, then push the button and nothing happens. Changing the settings doesn’t help. A red stop sign with an error message pops up in the corner. The python console it says:

no package called pandas found

anaconda is built correctly on both computers, and pandas is installed. Error still received.

I found that following the steps outlined in this discourse post from 2019 from @pieper fixes the problem.

Go to the python terminal in Slicer, then:

>>> import os
>>> os.system('PythonSlicer -m pip install pandas')
0
>>> import pandas

(This is @pieper 's work, not mine :slight_smile: )

Restart, and everything works like normal! It took me a while to figure out a fix for this. I am hoping that anyone who has this problem will run across this post.

Cheers!

2

This is interesting, thanks for sharing.

ALPACA itself doesn’t use Pandas, but it calls GPA module, which uses. But I thought pandas is bundled with core SlicerPython. So you shouldn’t have to manually install it.

So I am not sure why this is happening. Is this a apple silicon specific issue?

3

I don’t think pandas is bundled with Slicer core. Any module that needs it should pip install it.

4

Is this a apple silicon specific issue?

In my experience, k-means template selection and all the other SlicerMorph tools have worked out of the box on Windows machines. I found it interesting that no one else has reported this problem. Maybe the k-means selection isn’t commonly on Macs.

I should report that I’m using 3DSlicer 5.6.2, and I installed SlicerMorph on this machine within the past 2 days. The older M1 machine that had this same issue was using the stable 3DSlicer build from January 2024.