Error when running CS BART example

I have been trying to run the cs example, but I keep getting the following error. I have looked upon BART’s documentation and GitHub page, but I couldn’t find much information about it. I am running this from inside a docker.

I am running in a docker with:

• BART 0.7.0
• Python 3.8
• Ubuntu 18.04
• No GPUs

my command:

python3.8 ./fastMRI/fastmri_examples/cs/run_bart.py \
    --challenge "singlecoil" \
    --data_path "data/FastMRI/knee/" \
    --out_path "pred-recons" \
    --reg_wt 0.01 \
    --mask_type "random" \
    --split val

If I try the advised steps

Once BART is installed, set the TOOLBOX_PATH environment variable and point PYTHONPATH to the python wrapper for BART:

export TOOLBOX_PATH=$(which bart) # here I have tried a bunch of different options like /usr/local/bin, /usr/local/bin/bart, etc
export PYTHONPATH=${TOOLBOX_PATH}/python:${PYTHONPATH}

BART still can’t be found via python even though I can call it from shell and I get:

Traceback (most recent call last):
  File "run_bart.py", line 15, in <module>
    import bart
ModuleNotFoundError: No module named 'bart'

My fix

I did manage to run the experiment by hardcoding the repository with sys.path.append inside run_bart.py

import sys
sys.path.append("./bart/python")      

What did I miss? I can probably fix this myself, but I am not aware of what exactly I missed.

EDIT: I forgot to mention that the correct argument for the script is out_path and not output_path as cited in the CS example README

[mmuckley]

I didn’t see any issues in PR #135 so I went ahead and merged it. If you find an issue feel free to open a new PR.

[mmuckley]

Yeah feel free to change both of them! I’ll comment over there when I get a chance to look.