pycivet 0.0.1a5

Object-oriented CIVET bindings for Python

pycivet

Object-oriented Python bindings for CIVET binaries like transform_objects and mincreshape.

Overview

pycivet provides helper methods which lazily invoke CIVET binaries with object-oriented syntax. Intermediate files are written to temporary locations and then unlinked immediately.

This Perl code snippet from marching_cubes.pl can be expressed in Python as such:

https://github.com/aces/surface-extraction/blob/7c9c5987a2f8f5fdeb8d3fd15f2f9b636401d9a1/scripts/marching_cubes.pl.in#L125-L134

from civet import MNI_DATAPATH
from civet.surface import ObjFile

starting_model = ObjFile(MNI_DATAPATH / 'surface-extraction' / 'white_model_320.obj')
starting_model.flip_x().slide_right().save('./output.obj')

Installation

It is recommended you install this package in a container image, e.g.

FROM docker.io/fnndsc/mni-conda-base:civet2.1.1-python3.10.2
RUN pip install pycivet