From c79c476d6f5a7f0ec43ba04942cf7c1626340684 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 26 Sep 2022 18:59:17 +0100
Subject: [PATCH] post(multisignal): optimise align using bottleneck
---
src/postprocessor/core/multisignal/align.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/postprocessor/core/multisignal/align.py b/src/postprocessor/core/multisignal/align.py
index 855ceccb..241736f3 100644
--- a/src/postprocessor/core/multisignal/align.py
+++ b/src/postprocessor/core/multisignal/align.py
@@ -1,9 +1,10 @@
#!/usr/bin/env python3
+import bottleneck as bn
import numpy as np
import pandas as pd
-from agora.abc import ParametersABC
+from agora.abc import ParametersABC
from postprocessor.core.abc import PostProcessABC
@@ -97,7 +98,7 @@ class align(PostProcessABC):
# i.e. if events_at_least = 1, then cells that have no birth events are
# deleted.
event_mask = mask_df.apply(
- lambda x: np.sum(x) >= self.events_at_least, axis=1
+ lambda x: bn.nansum(x) >= self.events_at_least, axis=1
)
mask_df = mask_df.iloc[event_mask.to_list()]
@@ -132,7 +133,7 @@ class align(PostProcessABC):
# Do not remove bits of traces before first event
else:
# Add columns to left, filled with NaNs
- max_shift = np.max(shift_list)
+ max_shift = bn.nanmax(shift_list)
mask_aligned = df_extend_nan(mask_aligned, max_shift)
trace_aligned = df_extend_nan(trace_aligned, max_shift)
# shift each
--
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