A program that calculates head circumference from MRI data (.nii, .nii.gz, .nrrd).
Reason this release was yanked:
Wrong version number
Project description
NeuroRuler
A program that calculates head circumference from MRI data (
.nii
,.nii.gz
,.nrrd
).
Cite this tool
If you want 😉 format is bibtex.
@misc{neuroruler,
title={NeuroRuler},
author={Wei, Jesse and Lester, Madison and He, Peifeng and Schneider, Eric and Styner, Martin},
howpublished={\url{https://github.com/COMP523TeamD/HeadCircumferenceTool}},
year={2023}
}
Install
Your Python version needs to be 3.8+. Check with python --version
. Clone this repo, and install the Python dependencies.
pip install -r requirements.txt
pip install -i https://test.pypi.org/simple/ NeuroRuler
If pip
doesn't work, try pip3
or python3 -m pip
.
If contributing to this repo, please also run pre-commit install
to run pre-commit actions (i.e., autoformat) on your code before commits.
Start GUI
Run these commands in a Python terminal:
from GUI import gui
gui()
Note: If you make changes to the repo, then use the gui.py
script to run the GUI. Changes you make will not be reflected in the package from pip until uploaded to PyPi.
Configure settings
Edit config.json
.
You can also supply CLI arguments, which override settings in config.json
.
usage: gui.py [-h] [-d] [-e] [-t THEME] [-c COLOR]
options:
-h, --help show this help message and exit
-d, --debug print debug info
-e, --export-index exported file names use the index displayed in the GUI instead of the original file name
-t THEME, --theme THEME
configure theme, options are dark, dark-green, dark-hct, dark-purple, light, light-green, light-hct, or
light-purple
-c COLOR, --color COLOR
contour color as name (e.g. red) or hex color code rrggbb
Run tests
pytest
Documentation
https://headcircumferencetool.readthedocs.io
See .readthedocs.yaml
and docs/
.
Pre-commit actions
Run pre-commit install
to enable pre-commit actions.
Before each commit, the actions in .pre-commit-config.yaml
will be run. Specifically, code will be reformatted with black
. Note that some file names are excluded, so don't name any source code files those names.
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