From 285bac72fc59847ab812f2057b99f3f495cf2351 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 19 Dec 2022 18:34:07 +0000
Subject: [PATCH] fix(postprocessor): cover empty cases
---
src/postprocessor/core/processor.py | 43 ++++++++++++++++++-----------
1 file changed, 27 insertions(+), 16 deletions(-)
diff --git a/src/postprocessor/core/processor.py b/src/postprocessor/core/processor.py
index 1bd5b262..37efd0d4 100644
--- a/src/postprocessor/core/processor.py
+++ b/src/postprocessor/core/processor.py
@@ -201,16 +201,20 @@ class PostProcessor(ProcessABC):
self._signal[self.targets["prepost"]["picker"][0]]
)
- mothers, daughters = np.array(self.picker.mothers), np.array(
- self.picker.daughters
- )
+ combined_idx = ([], [], [])
+ trap, mother, daughter = combined_idx
+
+ lineage = self.picker.cells.mothers_daughters
+
+ if lineage.any():
+ trap, mother, daughter = lineage.T
+ combined_idx = np.vstack((trap, mother, daughter))
+
+ trap_mother = np.vstack((trap, mother)).T
+ trap_daughter = np.vstack((trap, daughter)).T
multii = pd.MultiIndex.from_arrays(
- (
- np.append(mothers, daughters[:, 1].reshape(-1, 1), axis=1).T
- if daughters.any()
- else [[], [], []]
- ),
+ combined_idx,
names=["trap", "mother_label", "daughter_label"],
)
self._writer.write(
@@ -219,9 +223,9 @@ class PostProcessor(ProcessABC):
overwrite="overwrite",
)
- # apply merge to mother-daughter
- moset = set([tuple(x) for x in mothers])
- daset = set([tuple(x) for x in daughters])
+ # apply merge to mother-trap_daughter
+ moset = set([tuple(x) for x in trap_mother])
+ daset = set([tuple(x) for x in trap_daughter])
picked_set = set([tuple(x) for x in indices])
with h5py.File(self._filename, "a") as f:
merge_events = f["modifiers/merges"][()]
@@ -231,6 +235,7 @@ class PostProcessor(ProcessABC):
names=["trap", "mother_label", "daughter_label"],
)
self.lineage_merged = multii
+
if merge_events.any():
def search(a, b):
@@ -245,19 +250,25 @@ class PostProcessor(ProcessABC):
if (
tuple(source) in moset
): # update mother to lowest positive index among the two
- mother_ids = search(mothers, source)
- mothers[mother_ids] = (
+ mother_ids = search(trap_mother, source)
+ trap_mother[mother_ids] = (
target[0],
- self.pick_mother(mothers[mother_ids][0][1], target[1]),
+ self.pick_mother(
+ trap_mother[mother_ids][0][1], target[1]
+ ),
)
if tuple(source) in daset:
- daughters[search(daughters, source)] = target
+ trap_daughter[search(trap_daughter, source)] = target
if tuple(source) in picked_set:
indices[search(indices, source)] = target
self.lineage_merged = pd.MultiIndex.from_arrays(
np.unique(
- np.append(mothers, daughters[:, 1].reshape(-1, 1), axis=1),
+ np.append(
+ trap_mother,
+ trap_daughter[:, 1].reshape(-1, 1),
+ axis=1,
+ ),
axis=0,
).T,
names=["trap", "mother_label", "daughter_label"],
--
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