Root Processing

This is the root processing suite, rhizotools (rhizo means "root related"), for images at the ORNL MARS (formerly CG-1D) beamline.

Quick Start

Installation

Using Pip

pip install rhizotools

Using Pixi (Recommended)

# Install pixi if you don't have it already
curl -fsSL https://pixi.sh/install.sh | bash

# Create a new environment with rhizotools
pixi init --name my-rhizo-project
cd my-rhizo-project
pixi add rhizotools

# Activate the environment
pixi shell

Using Conda

conda install -c conda-forge rhizotools

Development Guide

Setting Up Development Environment

# Clone the repository
git clone https://github.com/ornlneutronimaging/RootPlantProcessing.git
cd RootPlantProcessing

# Set up development environment with pixi
pixi install

# Activate the environment
pixi shell

Development Workflow

# Run tests
pixi run test

# Run linting checks
pixi run ruff check .

# Format code
pixi run ruff format .

# Build the package
pixi run build-pypi

# Build documentation
pixi run build-docs

Adding Dependencies

To add new dependencies:

1. Add Python dependencies to [project.dependencies] in pyproject.toml
2. Add pixi/conda dependencies to [tool.pixi.dependencies] in pyproject.toml
3. Run pixi install to update your environment

How to Use

# Importing sample dataset
wd = '/Users/...'  # Specify where you saved your sample data
from rhizotools.sampledata import sampledata
sampledata(wd)

# Running Code - Default Settings
from rhizotools.RP_run import RP_run
analysis_list = [
    'RP_stitch',
    'RP_crop',
    'RP_wc',
    'RP_mask',
    'RP_imagefilter',
    'RP_distmap',
    'RP_radwc',
    'RP_thickness',
    'RP_rootimage',
]
wd_userconfig = wd+'/Sample_Data'  # Specify where you saved your user_config file
RP_run(wd, wd_userconfig, analysis_list)

Known issue

1. When using pixi install for the first time, you might see the following error messages. The solutions is to increase your file limit with ulimit -n 65535 and then run pixi install again.

Too many open files (os error 24) at path