itasc.contact_analysis.quantifiers.neighbor_count

Neighbor-count quantifier — per-cell adjacency degree from the contact graph.

A contacts-derived pooled quantity: compute_object_table() reads the position’s contact_analysis.h5 and returns the per (frame, cell_id) neighbor count in memory (no per-position artifact). The NLS subpopulation label is not stored here — it is left-joined by cell_id at pool time, exactly as the shape family does.

Classes

NeighborCountQuantifier()

Per (frame, cell_id) number of distinct cell-cell neighbors.

class itasc.contact_analysis.quantifiers.neighbor_count.NeighborCountQuantifier

Bases: Quantifier

Per (frame, cell_id) number of distinct cell-cell neighbors.

quantity_id: ClassVar[str] = 'neighbor_count'

Stable key; an empty value marks an intermediate (non-registered) base.

display_name: ClassVar[str] = 'Neighbor count'

Human-readable label shown wherever a quantity is selected.

requires: ClassVar[tuple[str, ...]] = ('contact_analysis_path',)

PositionInputs field names this quantifier needs to build.

table_keys: ClassVar[tuple[str, ...]] = ('frame', 'cell_id')

The index columns of this quantifier’s object_table — its natural grain (e.g. ("frame", "cell_id")). A non-empty value marks the quantity as aggregated: itasc.contact_analysis.shape_tables pools it across positions into a table named by quantity_id, keyed on these columns. Empty ⇒ not aggregated into an index-keyed table (e.g. contacts). Value columns are namespaced by quantity_id so a later joined view across tables never has colliding names.

compute_object_table(inputs, *, params=None)

The pooled tidy table for one position, computed directly from inputs.

A pooled quantifier (one that declares table_keys) implements this: it returns the same column-major table that object_table used to return after a disk round-trip, but never touches disk. None when this position yields no rows. Producers (contacts) are not pooled and do not implement it. params carries the shared build knobs (e.g. fov_area_mm2) for the quantifiers that opt in; per-position values (pixel size, frame interval) arrive via inputs.