HabitatGraphFeatureOptions

Note

This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the Habitat Guide and Python API guide (v2.0) for usage.

class HabitatGraphFeatureOptions(include_single_habitat_graph: bool = True, include_pairwise_habitat_graph: bool = True, edge_method: Literal['centroid_distance', 'adjacency', 'min_distance'] = 'min_distance', distance_threshold: float = 5.0, adjacency_connectivity: str = 'corner', adjacency_min_voxels: int = 10, edge_weight: Literal['none', 'distance', 'inverse_distance', 'contact_voxels'] = 'none', min_region_voxels: int = 1, connectivity: str = 'full', erosion_radius: int = 0, node_method: Literal['uniform_grid', 'component'] = 'uniform_grid', subdivide_region_voxels: int = 1000, block_size: int = 8, block_min_coverage: float = 0.2, pairwise_include_intra_edges: bool = True, include_extended_metrics: bool = True, extended_min_nodes: int = 10, small_world_nrand: int = 100, small_world_niter: int = 100, rich_club_q: int = 100, graph_null_sampler: str = 'analytic', graph_null_device: str = 'auto')

Bases: object

Runtime options for graph-based habitat feature extraction.

Default node rule: node_method='uniform_grid' with block_size=8 (global VOI lattice; each kept cube emits one node per connected habitat subregion at that subregion’s voxel centroid; edge length in voxels, not millimetres). Default edge rule: edge_method='min_distance' with distance_threshold=5.0. Face-adjacent 8-cubes connect (closest voxels are one hop apart). One empty lattice cell between cubes is closest-voxel distance about 8, which is greater than 5, so those stay disconnected. adjacency and centroid_distance remain available. erosion_radius=0 measures the habitat labels as drawn.

__init__(include_single_habitat_graph: bool = True, include_pairwise_habitat_graph: bool = True, edge_method: Literal['centroid_distance', 'adjacency', 'min_distance'] = 'min_distance', distance_threshold: float = 5.0, adjacency_connectivity: str = 'corner', adjacency_min_voxels: int = 10, edge_weight: Literal['none', 'distance', 'inverse_distance', 'contact_voxels'] = 'none', min_region_voxels: int = 1, connectivity: str = 'full', erosion_radius: int = 0, node_method: Literal['uniform_grid', 'component'] = 'uniform_grid', subdivide_region_voxels: int = 1000, block_size: int = 8, block_min_coverage: float = 0.2, pairwise_include_intra_edges: bool = True, include_extended_metrics: bool = True, extended_min_nodes: int = 10, small_world_nrand: int = 100, small_world_niter: int = 100, rich_club_q: int = 100, graph_null_sampler: str = 'analytic', graph_null_device: str = 'auto') → None

Examples using habit.kernels.HabitatGraphFeatureOptions

/auto_examples/05_quantify/plot_04_graph_features

Graph features