petfit-docker 0.1.4

A wrapper for generating Docker commands using regular PETFit syntax

petfit-docker

petfit-docker is a lightweight Python wrapper that turns a BIDS-App-like command line into the matching docker run invocation for PETFit. Interactive Shiny mode is the default; use --automatic or --mode automatic to run a non-interactive pipeline.

petfit-docker /path/to/bids /path/to/derivatives participant \
  --app modelling_plasma \
  --blood-dir /path/to/blood \
  --analysis-foldername Primary_Analysis

The command above runs:

docker run --rm -it \
  -p 3838:3838 \
  -v /path/to/bids:/data/bids_dir:ro \
  -v /path/to/derivatives:/data/derivatives_dir:rw \
  -v /path/to/blood:/data/blood_dir:ro \
  mathesong/petfit:latest \
  --func modelling_plasma --mode interactive

Install for development

cd wrapper
python -m pip install -e .

Examples

Launch the default region definition app:

petfit-docker /path/to/bids /path/to/derivatives/petfit participant

The three positional arguments follow the BIDS App convention:

petfit-docker <bids_dir> <output_dir> participant

Launch region definition:

petfit-docker /path/to/bids /path/to/derivatives participant --app regiondef

The positional output_dir can be either the derivatives root or the final PETFit output directory. These are equivalent with the default output folder name:

petfit-docker /path/to/bids /path/to/derivatives/petfit participant
petfit-docker /path/to/bids /path/to/derivatives participant --app regiondef
petfit-docker /path/to/bids /path/to/derivatives/petfit participant --app regiondef

Launch plasma-input modelling:

petfit-docker /path/to/bids /path/to/derivatives participant \
  --app modelling_plasma \
  --blood-dir /path/to/blood

Run plasma-input modelling automatically:

petfit-docker /path/to/bids /path/to/derivatives participant \
  --app modelling_plasma \
  --blood-dir /path/to/blood \
  --automatic

Open a shell in the image:

petfit-docker --shell -i mathesong/petfit:latest

Patching a local petfit

Use --patch (or -f) to point the wrapper at a local petfit checkout and test your local changes without rebuilding the image. The wrapper bind-mounts the source into the container, where it is reinstalled from source at startup so it overrides the petfit baked into the image:

petfit-docker /path/to/bids /path/to/derivatives participant \
  --app modelling_ref \
  --patch /path/to/your/petfit/checkout

This mirrors the --patch option of the PETPrep Docker wrapper. Because petfit is an R package it is reinstalled (not run directly from source), so the first few seconds of startup are spent installing the patched package. The patch works with every mode, including --shell.

Apple Silicon

The published PETFit Docker images are currently linux/amd64 only. The wrapper therefore requests --platform linux/amd64 by default, which avoids Docker's platform-mismatch warning on Apple Silicon while running under emulation. If a native or multi-architecture image is published later, override the platform with --platform linux/arm64 or disable the explicit platform with --platform "".