Feat/physicell microenvironment - #6
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Implement the previously-empty microenvironment/ stub with three composed, domain-framed analyses of tissue microenvironment structure: - niches: identify_niches clusters neighborhood-composition vectors (k-means) into spatial niches — recurring local cell-type mixtures. Returns NicheResult with per-cell labels and per-niche profiles. - boundaries: detect_boundaries scores each cell's neighborhood "foreignness" and flags interface cells. Generalizes the pairwise spatial.interface_cells to any grouping; accepts niche labels to find niche interfaces. Returns BoundaryResult. - gradients: spatial_gradient estimates a scalar field's gradient by local linear regression (grid-agnostic); substrate_gradient wraps it over the voxel substrate field (dropping constant axes), and density_gradient over local cell density. Returns GradientField with magnitude and direction. Validated against a finite-difference reference on the regular voxel grid (corr > 0.97 interior). Adds tests/test_microenvironment.py (24 tests), including known-answer checks (linear field recovers exact gradient; two composition regions split into two niches).
A pair-review of the substrate access and microenvironment module surfaced one real bug and two hardening items: - HIGH: internalized_substrates() hardcoded '_0.._n' column suffixes, but the parser names a size-1 vector with the bare field name and a size-3 vector with _x/_y/_z. So single- and triple-substrate models (the two most common PhysiCell setups) raised a misleading "not recorded" error even though the data was present. The 5-substrate example fixture never exercised it. Now derive the column names from the field's own <labels> entry via expand_cell_labels. - MEDIUM: spatial_gradient returned a silent minimum-norm gradient for under-determined local fits (fewer than ndim+1 points, or collinear neighbors). Now clamp k to at least ndim+1 and return NaN for rank-deficient fits rather than a plausible-but-wrong vector. - LOW: substrate_at flattened multi-dimensional queries despite documenting shape preservation. Now broadcast the inputs and reshape the result to match, so a grid of points in yields a grid out. Adds regression tests: internalized mapping for 1/3/5 substrates, substrate_at output-shape and broadcasting, and gradient NaN on degenerate neighbor sets.
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