from __future__ import annotations from dataclasses import dataclass, fields from multiprocessing import shared_memory from typing import Any import numpy as np from .empirical_maps import EmpiricalMapStore, PiecewiseRateMap @dataclass(frozen=True) class SharedArraySpec: offset: int shape: tuple[int, ...] dtype: str @dataclass(frozen=True) class SharedPiecewiseRateMapSpec: attributes: dict[str, Any] position: SharedArraySpec rate: SharedArraySpec @dataclass(frozen=True) class SharedEmpiricalMapStoreSpec: memory_name: str | None memory_size: int rec_maps: dict[str, SharedPiecewiseRateMapSpec] mut_maps: dict[str, SharedPiecewiseRateMapSpec] metadata: dict[str, dict] common_span_cache: dict[str, tuple[float, float]] usable_chrom_cache: dict[float, tuple[str, ...]] def _piecewise_attributes(rate_map: PiecewiseRateMap) -> dict[str, Any]: return { field.name: getattr(rate_map, field.name) for field in fields(PiecewiseRateMap) if field.name not in {"position", "rate"} } def _layout_array(array: np.ndarray, offset: int) -> tuple[SharedArraySpec, int]: value = np.asarray(array) if value.dtype.hasobject: raise TypeError("empirical map arrays must not use object dtype") alignment = max(1, int(value.dtype.alignment)) aligned_offset = ((offset + alignment - 1) // alignment) * alignment spec = SharedArraySpec( offset=aligned_offset, shape=tuple(int(size) for size in value.shape), dtype=value.dtype.str, ) return spec, aligned_offset + int(value.nbytes) def _layout_maps( maps: dict[str, PiecewiseRateMap], offset: int, ) -> tuple[dict[str, SharedPiecewiseRateMapSpec], int]: out: dict[str, SharedPiecewiseRateMapSpec] = {} for chrom, rate_map in maps.items(): position_spec, offset = _layout_array(rate_map.position, offset) rate_spec, offset = _layout_array(rate_map.rate, offset) out[chrom] = SharedPiecewiseRateMapSpec( attributes=_piecewise_attributes(rate_map), position=position_spec, rate=rate_spec, ) return out, offset def _copy_array( array: np.ndarray, spec: SharedArraySpec, shm: shared_memory.SharedMemory, ) -> None: source = np.ascontiguousarray(array) view = np.ndarray( spec.shape, dtype=np.dtype(spec.dtype), buffer=shm.buf, offset=spec.offset, ) view[...] = source def _copy_maps( maps: dict[str, PiecewiseRateMap], specs: dict[str, SharedPiecewiseRateMapSpec], shm: shared_memory.SharedMemory, ) -> None: for chrom, rate_map in maps.items(): spec = specs[chrom] _copy_array(rate_map.position, spec.position, shm) _copy_array(rate_map.rate, spec.rate, shm) def create_shared_empirical_map_store( store: EmpiricalMapStore, ) -> tuple[SharedEmpiricalMapStoreSpec, list[shared_memory.SharedMemory]]: """Copy all empirical arrays into one shared-memory segment.""" rec_specs, offset = _layout_maps(store.rec_maps, 0) mut_specs, memory_size = _layout_maps(store.mut_maps, offset) if memory_size == 0: return ( SharedEmpiricalMapStoreSpec( memory_name=None, memory_size=0, rec_maps=rec_specs, mut_maps=mut_specs, metadata=store.metadata, common_span_cache=dict(store._common_span_cache), usable_chrom_cache=dict(store._usable_chrom_cache), ), [], ) shm = shared_memory.SharedMemory(create=True, size=memory_size) try: _copy_maps(store.rec_maps, rec_specs, shm) _copy_maps(store.mut_maps, mut_specs, shm) spec = SharedEmpiricalMapStoreSpec( memory_name=shm.name, memory_size=memory_size, rec_maps=rec_specs, mut_maps=mut_specs, metadata=store.metadata, common_span_cache=dict(store._common_span_cache), usable_chrom_cache=dict(store._usable_chrom_cache), ) except Exception: shm.close() shm.unlink() raise return spec, [shm] def _attach_array( spec: SharedArraySpec, shm: shared_memory.SharedMemory, ) -> np.ndarray: array = np.ndarray( spec.shape, dtype=np.dtype(spec.dtype), buffer=shm.buf, offset=spec.offset, ) array.flags.writeable = False return array def _attach_piecewise_map( spec: SharedPiecewiseRateMapSpec, shm: shared_memory.SharedMemory, ) -> PiecewiseRateMap: return PiecewiseRateMap( position=_attach_array(spec.position, shm), rate=_attach_array(spec.rate, shm), **spec.attributes, ) def attach_shared_empirical_map_store( spec: SharedEmpiricalMapStoreSpec, ) -> tuple[EmpiricalMapStore, list[shared_memory.SharedMemory]]: """Attach read-only NumPy views to a shared empirical map store.""" if spec.memory_name is None: if spec.memory_size != 0 or spec.rec_maps or spec.mut_maps: raise ValueError("shared empirical map specification is missing its memory segment") return ( EmpiricalMapStore( metadata=spec.metadata, _common_span_cache=dict(spec.common_span_cache), _usable_chrom_cache=dict(spec.usable_chrom_cache), ), [], ) shm = shared_memory.SharedMemory(name=spec.memory_name) try: store = EmpiricalMapStore( rec_maps={ chrom: _attach_piecewise_map(map_spec, shm) for chrom, map_spec in spec.rec_maps.items() }, mut_maps={ chrom: _attach_piecewise_map(map_spec, shm) for chrom, map_spec in spec.mut_maps.items() }, metadata=spec.metadata, _common_span_cache=dict(spec.common_span_cache), _usable_chrom_cache=dict(spec.usable_chrom_cache), ) except Exception: shm.close() raise return store, [shm] def release_shared_memory( handles: list[shared_memory.SharedMemory], *, unlink: bool = False, ) -> None: for shm in handles: try: shm.close() except FileNotFoundError: pass if unlink: try: shm.unlink() except FileNotFoundError: pass