Colab Import Error

[Aaron Gonzalez]

Hello, I'm getting an error importing packages in colab. I'm trying to run a kinematics analysis through the colab scripts. I get this error: ImportError Traceback (most recent call last)
<ipython-input-2-297b6a014f0a> in <cell line: 6>()
4 import numpy as np
5 import matplotlib.pyplot as plt
----> 6 import utilsKinematics
7 from utils import download_kinematics

1 frames
/content/opencap-processing/utils.py in <module>
35 from utilsAuthentication import get_token
36 import matplotlib.pyplot as plt
---> 37 from scipy.signal import gaussian
38
39

ImportError: cannot import name 'gaussian' from 'scipy.signal' (/usr/local/lib/python3.10/site-packages/scipy/signal/__init__.py)

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Any help is appreciated, thank you!

[Antoine Falisse]

There was a bug in the latest version of scipy. I fixed the scipy version and it should work now. Let us know otherwise.

[Sam Hamner]

FYI

@Antoine I was running into a similar issue recently setting up a new computer to perform the Example.py following the readme on opencap-processing github, but I was having an issue with SciPy importing the gaussian function. Here is the error:

(opencap-processing) C:\Users\samner\OneDrive\Documents\samnerScripts\opencap-processing\opencap-processing>python example.py
Traceback (most recent call last):
File "C:\Users\samner\OneDrive\Documents\samnerScripts\opencap-processing\opencap-processing\example.py", line 22, in <module>
import utilsKinematics
File "C:\Users\samner\OneDrive\Documents\samnerScripts\opencap-processing\opencap-processing\utilsKinematics.py", line 23, in <module>
import utils
File "C:\Users\samner\OneDrive\Documents\samnerScripts\opencap-processing\opencap-processing\utils.py", line 37, in <module>
from scipy.signal import gaussian
ImportError: cannot import name 'gaussian' from 'scipy.signal' (C:\Users\samner\.conda\envs\opencap-processing\Lib\site-packages\scipy\signal\__init__.py)

I read online that there is an issue with SciPy 1.14 and ArViz, and downgrading to SciPy<1.13 would resolve the issue until a new version of SciPy is released (ArViz was to blame, apparently). I downgraded to 1.12 using the code below, and voila, it worked!

Code: Select all

pip install scipy==1.12

Here's the link to the blog re: SciPy and ArViz https://discourse.pymc.io/t/importerror ... gnal/14170

[Carmichael Ong]

There was a recent PR that updated this import: https://github.com/stanfordnmbl/opencap ... /132/files

The issue was that the import was deprecated and finally removed from SciPy, so we updated the import line in utils.py for the import. It should now work on current versions of SciPy (more info can be found in the related GitHub issue: https://github.com/stanfordnmbl/opencap ... issues/131).

Sam, since this was very recently merged (3 days ago), you'd have to pull the latest commit for opencap-processing to see if this would help your use case and avoid needing to downgrade SciPy.