From 403b483d77d56aea0215eba19f88ff30b6ab95ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 4 Oct 2022 20:04:10 +0100
Subject: [PATCH] refactor(cells): make lineage consistent
---
src/agora/io/cells.py | 26 ++++++++++++++++----------
1 file changed, 16 insertions(+), 10 deletions(-)
diff --git a/src/agora/io/cells.py b/src/agora/io/cells.py
index 095b59c4..d1108691 100644
--- a/src/agora/io/cells.py
+++ b/src/agora/io/cells.py
@@ -3,7 +3,7 @@ import typing as t
from collections.abc import Iterable
from itertools import groupby
from pathlib import Path, PosixPath
-from functools import lru_cache
+from functools import lru_cache, cached_property
import h5py
import numpy as np
@@ -264,10 +264,11 @@ class Cells:
rand = np.random.randint(mat.sum())
return (traps[rand], tps[rand])
+ @lru_cache(20)
def mothers_in_trap(self, trap_id: int):
return self.mothers[trap_id]
- @property
+ @cached_property
def mothers(self):
"""
Return nested list with final prediction of mother id for each cell
@@ -279,24 +280,29 @@ class Cells:
self.ntraps,
)
- @property
- def mothers_daughters(self):
+ @cached_property
+ def mothers_daughters(self) -> np.ndarray:
+ """
+ Return mothers and daugters as a single array with three columns:
+ trap, mothers and daughters
+ """
nested_massign = self.mothers
if sum([x for y in nested_massign for x in y]):
- mothers, daughters = zip(
- *[
- ((tid, m), (tid, d))
+ mothers_daughters = np.array(
+ [
+ (tid, m, d)
for tid, trapcells in enumerate(nested_massign)
for d, m in enumerate(trapcells, 1)
if m
- ]
+ ],
+ dtype=np.uint16,
)
else:
- mothers, daughters = ([], [])
+ mothers_daughters = np.array([])
# print("Warning:Cells: No mother-daughters assigned")
- return mothers, daughters
+ return mothers_daughters
@staticmethod
def mother_assign_to_mb_matrix(ma: t.List[np.array]):
--
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