partimorph 0.1.6

Particle shape analysis and visualization library.

PartiMorph

PartiMorph analyzes a single 2D binary particle mask and returns geometric shape metrics.

Metric	Meaning
Wadell roundness	Corner curvature-based roundness
Circularity	4 * pi * area / perimeter^2
Sphericity	Inscribed circle radius divided by enclosing circle radius
Aspect ratio	Fitted ellipse major axis divided by minor axis

Roundness, circularity, and sphericity are clipped to 0..1. Aspect ratio is >= 1.

Installation

PartiMorph requires Python 3.12+.

pip install partimorph

For local development:

pip install -e ".[dev]"

Quick Start

import partimorph as pm

mask = pm.utils.create_circle_mask((256, 256), (128, 128), 60)
results = pm.analyze_mask(mask)

if results is None:
    raise ValueError("mask has no foreground pixels")

print(results["roundness"]["val"])
print(results["circularity"]["val"])
print(results["sphericity"]["val"])
print(results["aspect_ratio"]["val"])

Visualize the results:

pm.utils.plot_analysis_results(mask, results)

API

pm.analyze_mask(
    mask,
    use_aspect_ratio=True,
    use_roundness=True,
    use_circularity=True,
    use_sphericity=True,
    roundness_params=None,
    eps=0.001,
    target_dim=384,
)

Parameter	Description
mask	2D numpy.ndarray with bool or {0, 1} values
use_*	Toggle individual metrics on/off
roundness_params	Optional dict to override Wadell roundness parameters
eps	Tolerance for geometric computations
target_dim	Large masks are downscaled to this size for speed, then coordinates are rescaled

Returns None for an empty mask. Otherwise, returns an AnalysisResult dict. Disabled metrics are omitted; enabled metrics are present and may be None when the geometry cannot be measured.

Result Shape

{
  "roundness": {"val": float} | None,
  "circularity": {"val": float} | None,
  "sphericity": {
    "val": float,
    "inscribed": {"x": float, "y": float, "r": float},
    "enclosing": {"x": float, "y": float, "r": float},
  } | None,
  "aspect_ratio": {
    "val": float,
    "ellipse": {
      "major": float, "minor": float,
      "x": float, "y": float, "angle": float,
      "w": float, "h": float, "bbox": list[list[float]],
    },
  } | None,
}

Input Rules

• mask must be a 2D numpy.ndarray
• Allowed values are bool or numeric {0, 1}
• Floating masks must not contain NaN or inf
• Empty mask returns None
• Shape and center arguments use image order: (height, width) and (y, x)

Utilities

Mask constructors:

• pm.utils.create_circle_mask(...)
• pm.utils.create_ellipse_mask(...)
• pm.utils.create_rectangle_mask(...)
• pm.utils.create_square_mask(...)
• pm.utils.create_triangle_mask(...)
• pm.utils.create_pentagon_mask(...)
• pm.utils.create_star_mask(...)
• pm.utils.create_particle_mask(...)

Visualization:

• pm.utils.plot_analysis_results(mask, results)

License

MIT