mascaf.validation¶

Validation module for SWC models.

Provides the Validation class to compare SWC models against original mesh and skeleton data.

class mascaf.validation.Validation(mesh, skeleton, morphology)[source]¶

Bases: object

Validation of MorphologyGraph models against original mesh and skeleton.

This class provides methods to validate a MorphologyGraph by comparing it to the original mesh (geometry and surface) and the original skeleton (topology and centerline).

Parameters:

mesh (Union[Trimesh, MeshManager]) – The original mesh to validate against. Can be either a trimesh.Trimesh object or a MeshManager instance.
skeleton (SkeletonGraph) – The original skeleton graph used to generate the morphology.
morphology (Union[MorphologyGraph, str, Path]) – Either a MorphologyGraph instance to validate, or a path to an SWC file which will be loaded as a MorphologyGraph.

mesh¶

The mesh object (extracted from MeshManager if needed).

Type:: trimesh.Trimesh

mesh_manager¶

The MeshManager instance if provided, otherwise None.

Type:: MeshManager or None

skeleton¶

The original skeleton graph.

Type:: SkeletonGraph

morphology¶

The morphology graph to validate.

Type:: MorphologyGraph

swc_path¶

Path to the SWC file if loaded from file, otherwise None.

Type:: Path or None

Examples

>>> from mascaf import MeshManager, SkeletonGraph, Validation
>>> mesh_mgr = MeshManager(mesh_path="neuron.obj")
>>> skeleton = SkeletonGraph.from_polylines(polylines)
>>> # Option 1: Validate from SWC file
>>> validator = Validation(mesh_mgr, skeleton, "output.swc")
>>> # Option 2: Validate existing MorphologyGraph
>>> graph = MorphologyGraph.from_swc_file("output.swc")
>>> validator = Validation(mesh_mgr, skeleton, graph)
>>> volume_ratio = validator.compare_volumes()
>>> radius_errors = validator.validate_radii()

__init__(mesh, skeleton, morphology)[source]¶

Parameters:

mesh (Trimesh | MeshManager)
skeleton (SkeletonGraph)
morphology (MorphologyGraph | str | Path)

compare_volumes(account_for_overlaps=False)[source]¶

Compare total volume between mesh and morphology model.

Computes the mesh volume using trimesh and the morphology volume by summing truncated cone volumes for each edge segment.

Parameters:: account_for_overlaps (bool) – If True, subtract branch-point overlap corrections in the morphology volume (see MorphologyGraph.compute_volume()).
Returns:: Dictionary containing: - ‘mesh_volume’: float, volume of the mesh - ‘morphology_volume’: float, volume of the morphology model - ‘ratio’: float, morphology_volume / mesh_volume - ‘absolute_difference’: float, abs(morphology_volume - mesh_volume) - ‘relative_error’: float, abs difference / mesh_volume
Return type:: dict

Examples

>>> result = validator.compare_volumes()
>>> print(f"Volume ratio: {result['ratio']:.3f}")

compare_surface_areas(account_for_overlaps=False)[source]¶

Compare total surface area between mesh and morphology model.

Computes the mesh surface area using trimesh and the morphology surface area by summing lateral surface areas of truncated cones for each edge segment.

Parameters:: account_for_overlaps (bool) – If True, subtract branch-point overlap corrections in the morphology surface area (see MorphologyGraph.compute_surface_area()).
Returns:: Dictionary containing: - ‘mesh_area’: float, surface area of the mesh - ‘morphology_area’: float, surface area of the morphology model - ‘ratio’: float, morphology_area / mesh_area - ‘error’: float, morphology_area - mesh_area - ‘relative_error’: float, error / mesh_area
Return type:: dict

Examples

>>> result = validator.compare_surface_areas()
>>> print(f"Surface area ratio: {result['ratio']:.3f}")

full_validation()[source]¶

Run all validation checks and log comprehensive results.

Compares volumes and surface areas (with and without branch-point overlap correction when branch vertices are present) and logs each result via the module logger at INFO level.

Returns:: Results are emitted via logging rather than returned.
Return type:: None