numpyradiomics 0.0.3

A light-weight python-native implementation of pyradiomics

NumpyRadiomics

A lightweight, pure-Python implementation of radiomic shape features, fully compatible with PyRadiomics definitions. Built on top of numpy, scipy, and skimage to minimize heavy dependencies while maintaining accuracy.

Features

• Standard Compliance: Implements the official PyRadiomics definitions for 2D and 3D shape features.
• Lightweight: No heavy C++ extensions or SimpleITK dependencies required—just standard scientific Python stacks.

Installation

pip install numpyradiomics

Usage

1. Basic Shape Extraction

The shape() function automatically dispatches to 2D or 3D logic based on the input mask dimensions.

import numpy as np
from numpyradiomics import shape, dro

# 1. Create a synthetic 3D mask (e.g., a 20x10x5 mm cuboid)
spacing = (1.0, 1.0, 1.0)
mask = dro.cuboid(radii_mm=(10.0, 5.0, 2.5), spacing=spacing)

# 2. Extract features
# extend=True (default) adds advanced metrics like Solidity and ConvexHullVolume
features = shape(mask, spacing, extend=True)

print(f"Volume:     {features['VoxelVolume']} mm^3")
print(f"Sphericity: {features['Sphericity']:.4f}")
print(f"Solidity:   {features['Solidity']:.4f}")

2. Working with Units

You can retrieve a dictionary mapping every feature to its physical unit (e.g., mm, mm^2, mm^3 or dimensionless).

from numpyradiomics import shape_units

# Get units for 3D features in centimeters
units = shape_units(dim=3, base_unit='cm')

print(f"MeshVolume unit: {units['MeshVolume']}")    # Output: cm^3
print(f"Elongation unit: {units['Elongation']}")    # Output: (empty string for dimensionless)

Supported Features

3D Shape (Standard)

• Volume: Mesh Volume, Voxel Volume
• Surface: Surface Area, Surface-to-Volume Ratio
• Dimensions: Max 3D Diameter, Max 2D Diameter (Slice, Column, Row)
• Shape Descriptors: Sphericity, Elongation, Flatness
• Axes: Major, Minor, and Least Axis Lengths

3D Shape (Extended)

• Advanced Volume: Convex Hull Volume, Bounding Box Volume
• Ratios: Solidity, Extent
• Inertia: Moments of Inertia, Fractional Anisotropy
• Other: Maximum Depth (Chebyshev Radius), Longest Caliper Diameter

2D Shape

• Area: Mesh Surface, Pixel Surface
• Perimeter: Perimeter, Perimeter-Surface Ratio
• Shape Descriptors: Sphericity, Spherical Disproportion, Elongation
• Axes: Major Axis, Minor Axis, Max Diameter

Texture

All standard texture metrics are available:

• GLCM: Gray Level Co-occurrence Matrix
• GLRLM: Gray Level Run Length Matrix
• GLSZM: Gray Level Size Zone Matrix
• GLDM: Gray Level Dependence Matrix
• NGTDM: Neighbouring Gray Tone Difference Matrix

License

Apache 2.0 License