From 091ca6511bccbd5869576f796dded3ecda97def7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 27 Feb 2023 10:42:09 +0000
Subject: [PATCH] [WIP]feat(cells): add cell sampling
---
src/agora/io/cells.py | 44 +++++++++++++++++++++++++++++++++++++++++--
1 file changed, 42 insertions(+), 2 deletions(-)
diff --git a/src/agora/io/cells.py b/src/agora/io/cells.py
index 182590b7..0e2891f3 100644
--- a/src/agora/io/cells.py
+++ b/src/agora/io/cells.py
@@ -409,14 +409,54 @@ class Cells:
# Stack all cells in a trap-wise manner
masks = self.at_time(frame)
return [
- stack_masks_in_trap(
+ stack_masks_in_tile(
masks.get(trap_id, np.array([], dtype=bool)), tile_shape
)
for trap_id in range(self.ntraps)
]
+ def _sample_occupied_tiles_tp(
+ self,
+ size=1,
+ min_ncells: int = 2,
+ min_consecutive_ntps: int = 5,
+ ):
+ cell_availability_matrix = self.matrix_trap_tp_where(
+ min_ncells=min_ncells, min_consecutive_tps=min_consecutive_ntps
+ )
+
+ # Find all valid tiles with min_ncells for at least min_tps
+ tile_ids, tps = np.where(cell_availability_matrix)
+
+ choices = np.random.choice(len(tile_ids), size=size)
+ return tile_ids[choices], tps[choices]
+
+ def _sample_masks(
+ self,
+ size=1,
+ min_ncells: int = 2,
+ min_consecutive_ntps: int = 5,
+ ):
+ """Sample a number of cells from different traps each."""
+ tile_ids, tps = self._sample_occupied_tiles_tp(
+ size=size,
+ min_ncells=min_ncells,
+ min_consecutive_ntps=min_consecutive_ntps,
+ )
+ # Sort sampled tiles to use automatic cache when possible
+ order = np.argsort(tps)
+ tile_ids = tile_ids[order]
+ tps = tps[order]
+
+ return (tile_ids, tps), np.array(
+ [
+ self.at_time(tp)[tile_ids[tile_id]]
+ for tp, tile_id in zip(tps, tile_ids)
+ ]
+ )
+
-def stack_masks_in_trap(
+def stack_masks_in_tile(
masks: t.List[np.ndarray], tile_shape: t.Tuple[int]
) -> np.ndarray:
# Stack all masks in a trap padding accordingly if no outlines found
--
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