Getting skippedcaipi_sampling.py to work

[StevenWhitaker]

I haven't used Python on my computer before, so I had to set it up basically from scratch in order to use skippedcaipi_sampling.py, specifically when calling Python from MATLAB using MATLAB's system command. There were some snags along the way, so I figured I would document my experience in case others experience the same thing.

System Information

I run Kubuntu 20.04 (so what I write here will largely be applicable to any Debian-based Linux distribution, particularly Ubuntu and its derivatives). It comes with Python 3.8.10 by default, but I had never used it.

Installing Necessary Packages

At first, I ran into error messages about missing modules, such as

ModuleNotFoundError: No module named 'numpy'

I installed the proper packages with

python3 -m pip install numpy matplotlib scipy

After this, I got the following error:

ImportError: /usr/local/MATLAB/R2022b/bin/glnxa64/libtiff.so.5: version `LIBTIFF_4.0' not found (required by /usr/lib/python3/dist-packages/PIL/_imaging.cpython-38-x86_64-linux-gnu.so)

After digging around StackOverflow, I determined I needed to run

sudo apt install libssl-dev

Upgrading Python

But even that wasn't enough, so I decided to try the most recent Python version (3.10.7). I had to install it from source, but it was relatively straightforward. Fortunately, running skippedcaipi_sampling.py from MATLAB worked after this (after installing numpy, matplotlib, and scipy again on the new Python version).

Conclusion

Getting skippedcaipi_sampling.py to work when called using MATLAB's system command was not as straightforward as I was hoping. Fortunately, the internet is full of knowledge, and I was able to get it working. Hopefully my experience can be helpful to someone else.

[StevenWhitaker]

I'll note here that I tried

python3 caipitest.py

and got

.../HarmonizedMRI/3DEPI/caipi/caipitest.py:26: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.

To get around this, I ran

python3 -m pip install pyqt5

and then the test worked.