pyellispeed 0.1.0

Ellipsoids drawing and analysis in 3D volumetric images.

PyEllispeed

PyEllispeed is the package for drawing and analysis of ellipsoids in 3D volumetric images (3D arrays). Forked from PyEllipsoid.

How to use

To draw an ellipsoid:

import numpy as np
from pyellispeed import drawing

# Define an image shape, axis order is: Z, Y, X
image_shape = (128, 128, 128)

# Define an ellipsoid, axis order is: X, Y, Z
ell_center = (64, 64, 64)
ell_radii = (5, 50, 30)
ell_angles = np.deg2rad([80, 30, 20]) # Order of rotations is X, Y, Z

# Draw a 3D binary image containing the ellipsoid
image = drawing.make_ellipsoid_image(image_shape, ell_center, ell_radii, ell_angles)

To compute inertia ellipsoid for given ellipsoid image:

import numpy as np
from pyellispeed import drawing, analysis

# Draw a 3D binary image containing an ellipsoid
image_shape = (128, 128, 128)
ell_center = (64, 64, 64)
ell_radii = (5, 50, 30)
ell_angles = np.deg2rad([80, 30, 20])
image = drawing.make_ellipsoid_image(image_shape, ell_center, ell_radii, ell_angles)

# Compute inertia ellipsoid
points = analysis.sample_random_points(image)
inertia_ellipsoid = analysis.compute_inertia_ellipsoid(points)

To rotate axes and find relative rotation between the original and rotated axes:

import numpy as np
from pyellispeed import geometry

original_axes = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
rot_angles = np.deg2rad([0, 0, 45]) # Rotate around Z-axis by 45 deg

# Build rotation matrix and rotate the axes
rotm = geometry.build_rotation_matrix(*rot_angles)
rotated_axes = np.dot(rotm, np.transpose(original_axes)).T

# Find relative rotation
rel_rotm = geometry.find_relative_axes_rotation(original_axes, rotated_axes)

# Validate relative rotation matrix
rel_rotated_axes = np.dot(rel_rotm, np.transpose(original_axes)).T
assert(np.all(rotated_axes == rel_rotated_axes))

# Compute rotation angles
# Please note, that these angles might differ from rot_angles!
rel_rot_angles = geometry.rotation_matrix_to_angles(rel_rotm)
print(np.rad2deg(rel_rot_angles))

How to work on the project

# Create a venv
virtualenv .venv

source .venv/bin/activate

# Install maturin
pip install maturin

# To compile on your computer to do some work
maturin develop

# If you want to test
pip install pytest
pytest tests


# If you want to benchmark
pip install pytest-benchmark
pytest --benchmark-only test_benchmark
# It is recommended to compile in release mode with 
maturin develop --release

Next steps

• Add stub file for type annotation and documentation
• Use GPU with python libraries (cupy...)