Install

Create conda environment (Recommended)

git pull https://github.com/lukemshepherd/PCA_2.git

conda env create -f environment.yml

conda activate PCA2

With pip

pip install PCA2

Editable install

git pull https://github.com/lukemshepherd/PCA_2.git

pip install -e .

How to use

from PCA2.core import *
from mayavi import mlab # for calling the plots

Set custom filter level (optional)

bone.filter_level = 0.3

Load the data that you want to use

tibia_f2 = bone.from_matlab_path(matlab_file='data/tibia_f2.mat')
tibia_f1 = bone.from_matlab_path(matlab_file='data/phantom_tibia_f1.mat')

Set custom colour for bone (optional)

tibia_f1.default_color = (0.8, 0.3, 0)

Rotate the bone

rotate(tibia_f1, tibia_f2)

0.17471680699860007 no invert
0.5819453559235347 no invert
3.906788298496456e-16 no invert

Plotting the rotation

Plotting with mayavi is very similar to matplotplib where you build a scene and call it with show()

You can plot bones by calling the .plot() method and then mlab.show()

# tibia_f2.plot()
# mlab.show()

Table of angles

df_angles(tibia_f1, tibia_f2, name='tibia')

1.7785780651003298e-16 no invert
1.2719202621569003e-16 no invert
3.906788298496456e-16 no invert

	tibia f2: pc1	tibia f2: pc2	tibia f2: pc3
tibia f1: pc1	1.778578e-16	NaN	NaN
tibia f1: pc2	NaN	1.271920e-16	NaN
tibia f1: pc3	NaN	NaN	3.906788e-16