GrainMorph

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

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

Installation

GrainMorph requires Python 3.12+.

pip install grainmorph

For local development:

pip install -e ".[dev]"

Run the tests and code checks with the same Python environment:

python -m pytest -q
python -m ruff check --isolated .
python -m ruff format --isolated --check src tests

Releasing

Pushing a vX.Y.Z tag publishes that version to PyPI through .github/workflows/publish.yml, using PyPI trusted publishing (no API token):

1. Set the same version in pyproject.toml and src/grainmorph/__init__.py.
2. Commit, then tag and push: git tag -a vX.Y.Z -m "Release X.Y.Z" && git push origin main vX.Y.Z.

The workflow fails if the tag and the pyproject.toml version differ, then runs the tests before uploading. PyPI must list this repository as a trusted publisher for grainmorph (owner phykn, repository grainmorph, workflow publish.yml, environment pypi).

Quick Start

import grainmorph as gm

mask = gm.utils.create_circle_mask((256, 256), (128, 128), 60)
results = gm.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:

gm.utils.plot_analysis_results(mask, results)

API

gm.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,
)

roundness_params accepts these Wadell options. Defaults are defined in wadell/roundness.py and also apply to synthetic particle calibration:

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
• The largest 4-connected foreground component is selected and holes are filled
• Surrounding zero padding does not change the measured shape
• Downscaling is skipped if its output would have a one-pixel axis
• Shape, center, and rectangle corner arguments use image order: (height, width) and (y, x)
• Triangle vertices use Cartesian order (x, y), matching polygon coordinates

Project Layout

• analyzer.py: public analysis workflow and metric selection
• validation.py: public input normalization and analysis-option validation
• mask_ops.py: component selection, contours, and PreparedMask crop/resize transforms with result-coordinate restoration
• metrics.py: metric formulas and public result payloads
• fitting.py: circle and ellipse fitting plus oriented bounding boxes
• wadell/roundness.py: roundness options and the boundary-to-radius workflow
• wadell/boundary.py and smoothing.py: closed boundary extraction and periodic smoothing
• wadell/discretize.py: boundary approximation with (x, y) point arrays
• wadell/corner.py: convex corner selection, circle fitting, and accepted corner radii
• utils/: basic mask construction, parametric particle calibration and reporting, and visualization

Utilities

Mask constructors:

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

For example, a triangle in a non-square image uses (x, y) vertices:

mask = gm.utils.create_triangle_mask((20, 60), (30, 2), (40, 2), (30, 8))

create_particle_mask attempts to reach the requested roundness by calibrating surface roughness. Set seed for reproducible masks and return_info=True to receive (mask, info). The report measures the returned mask, including any clipping at the image bounds; target_met compares its roundness error with report_tol. A zero-radius particle reports roundness 0.0.

Visualization:

• gm.utils.plot_analysis_results(mask, results)

License

MIT