From 287db15d7995fa98d9a42e3b7670d34e43acea51 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Thu, 23 Mar 2023 16:39:46 +0000
Subject: [PATCH] fix(pp): squash typo bugs and indexing
---
src/agora/io/signal.py | 2 +-
src/agora/utils/indexing.py | 19 +++++++++++++++----
src/postprocessor/core/lineageprocess.py | 2 +-
3 files changed, 17 insertions(+), 6 deletions(-)
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 1da5ab10..42b5c9d5 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -139,7 +139,7 @@ class Signal(BridgeH5):
# if lineage_location not in f:
# lineage_location = lineage_location.split("_")[0]
if lineage_location not in f:
- lineage_location = "postprocessor/lineage"
+ lineage_location = "postprocessing/lineage"
tile_mo_da = f[lineage_location]
if isinstance(tile_mo_da, h5py.Dataset):
diff --git a/src/agora/utils/indexing.py b/src/agora/utils/indexing.py
index 5ca4494d..789ca5a0 100644
--- a/src/agora/utils/indexing.py
+++ b/src/agora/utils/indexing.py
@@ -114,10 +114,21 @@ def _assoc_indices_to_3d(ndarray: np.ndarray):
"""
result = ndarray
if len(ndarray) and ndarray.ndim > 1:
- result = np.transpose(
- np.hstack((ndarray[:, [0]], ndarray)).reshape(-1, 2, 2),
- axes=[0, 2, 1],
- )
+ if ndarray.shape[1] == 3: # Faster indexing for single positions
+ result = np.transpose(
+ np.hstack((ndarray[:, [0]], ndarray)).reshape(-1, 2, 2),
+ axes=[0, 2, 1],
+ )
+ else: # 20% slower but more general indexing
+ columns = np.arange(ndarray.shape[1])
+
+ result = np.stack(
+ (
+ ndarray[:, np.delete(columns, -1)],
+ ndarray[:, np.delete(columns, -2)],
+ ),
+ axis=1,
+ )
return result
diff --git a/src/postprocessor/core/lineageprocess.py b/src/postprocessor/core/lineageprocess.py
index 8c2874e2..ff332fab 100644
--- a/src/postprocessor/core/lineageprocess.py
+++ b/src/postprocessor/core/lineageprocess.py
@@ -60,7 +60,7 @@ class LineageProcess(PostProcessABC):
elif hasattr(self, "lineage"):
lineage = self.lineage
elif hasattr(self, "cells"):
- with h5py.File(self.cells.filename, "a") as f:
+ with h5py.File(self.cells.filename, "r") as f:
if (lineage_loc := "modifiers/lineage_merged") in f and merged:
lineage = f.get(lineage_loc)[()]
elif (lineage_loc := "modifiers/lineage)") in f:
--
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