A program that calculates head circumference from MRI data (.nii, .nii.gz, .nrrd).
Reason this release was yanked:
Doesn't work
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/NeuroRuler}},
year={2023}
}
Install
Your Python version needs to be 3.8+. Check with python --version
. Install via pip.
python -m pip install NeuroRuler
If python
doesn't work, try python3
. Also, do not run pip install NeuroRuler
without python -m
, which may cause import issues.
If contributing to this repo, please also run python -m pip install -r requirements.txt
to install additional development dependencies (for code formatting, documentation, etc.). After installing additional dependencies, run pre-commit install
to enable pre-commit actions.
Run GUI
Run these commands in a Python terminal:
from NeuroRuler.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.
See release for how to upload to PyPI or Test 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://NeuroRuler.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.
Release
To publish to PyPI, edit the version number in setup.py
. If a branch named release-pypi
doesn't exist, create it. Push a tagged (use the version number) commit to the release-pypi
branch to publish to PyPI (these actions cause the pypi.yml
action to run).
The version number on PyPI will be the one in setup.py
, so make sure it's correct!
Follow a similar process to publish to TestPyPI, except the commit doesn't have to be tagged.
Project details
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Source Distribution
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Hashes for NeuroRuler-0.0.3-py3-none-any.whl
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