Metadata-Version: 2.4
Name: pyellispeed
Version: 0.1.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Requires-Dist: numpy
Requires-Dist: pytest <=8.3.4 ; extra == 'test'
Requires-Dist: pytest-benchmark <=5.1.0 ; extra == 'test'
Provides-Extra: test
Summary: Ellipsoids drawing and analysis in 3D volumetric images.
Author-email: Guillaume Havard <guill.havard@gmail.com>
Requires-Python: >=3.8, <3.13
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Homepage, https://github.com/guillaume-havard/speedestpy
Project-URL: Issues, https://github.com/guillaume-havard/speedestpy/issues

# PyEllispeed

**PyEllispeed** is the package for drawing and analysis of ellipsoids in 3D volumetric images (3D arrays).
Forked from [PyEllipsoid](https://github.com/ashkarin/pyellipsoid). 

## How to use

To draw an ellipsoid:

```python

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:

```python

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:

```python

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

```bash
# Create a venv
virtualenv .venv

source .venv/bin/activate

# Install maturin
pip install maturin
```

```bash
# 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...)



