From d43d57101761cba2d692916316d70cdf5ed1537d Mon Sep 17 00:00:00 2001
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Fri, 27 Oct 2023 15:13:42 +0100
Subject: [PATCH] renamed dunder routines in indexing
---
src/agora/utils/indexing.py | 24 ++++++++++++------------
src/postprocessor/core/postprocessing.py | 10 +++++-----
2 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/src/agora/utils/indexing.py b/src/agora/utils/indexing.py
index 23f3a533..371a69e6 100644
--- a/src/agora/utils/indexing.py
+++ b/src/agora/utils/indexing.py
@@ -73,7 +73,7 @@ def validate_lineage(
"""
if lineage.ndim == 2:
# [trap, mother, daughter] becomes [[trap, mother], [trap, daughter]]
- lineage = _assoc_indices_to_3d(lineage)
+ lineage = assoc_indices_to_3d(lineage)
if how == "mothers":
c_index = 0
elif how == "daughters":
@@ -123,7 +123,7 @@ def index_isin(x: np.ndarray, y: np.ndarray) -> np.ndarray:
return x_bool
-def _assoc_indices_to_3d(ndarray: np.ndarray):
+def assoc_indices_to_3d(ndarray: np.ndarray):
"""
Convert the last column to a new row and repeat first column's values.
@@ -153,6 +153,16 @@ def _assoc_indices_to_3d(ndarray: np.ndarray):
return result
+def assoc_indices_to_2d(array: np.ndarray):
+ """Convert indices to 2d."""
+ result = array
+ if len(array):
+ result = np.concatenate(
+ (array[:, 0, :], array[:, 1, 1, np.newaxis]), axis=1
+ )
+ return result
+
+
###################################################################
@@ -250,16 +260,6 @@ def validate_association(
return valid_association, valid_indices
-def _3d_index_to_2d(array: np.ndarray):
- """Revert _assoc_indices_to_3d."""
- result = array
- if len(array):
- result = np.concatenate(
- (array[:, 0, :], array[:, 1, 1, np.newaxis]), axis=1
- )
- return result
-
-
def compare_indices(x: np.ndarray, y: np.ndarray) -> np.ndarray:
"""
Fetch two 2-D indices and return a binary 2-D matrix
diff --git a/src/postprocessor/core/postprocessing.py b/src/postprocessor/core/postprocessing.py
index 33a6ebe1..2b13b68c 100644
--- a/src/postprocessor/core/postprocessing.py
+++ b/src/postprocessor/core/postprocessing.py
@@ -10,8 +10,8 @@ from agora.io.cells import Cells
from agora.io.signal import Signal
from agora.io.writer import Writer
from agora.utils.indexing import (
- _3d_index_to_2d,
- _assoc_indices_to_3d,
+ assoc_indices_to_2d,
+ assoc_indices_to_3d,
)
from agora.utils.merge import merge_lineage
from postprocessor.core.abc import get_parameters, get_process
@@ -133,19 +133,19 @@ class PostProcessor(ProcessABC):
record = self.signal.get_raw(self.targets["merging_picking"]["merger"])
merges = self.merger.run(record)
# get lineages from cells object attached to picker
- lineage = _assoc_indices_to_3d(self.picker.cells.mothers_daughters)
+ lineage = assoc_indices_to_3d(self.picker.cells.mothers_daughters)
if merges.any():
# update lineages and merges after merging
new_lineage, new_merges = merge_lineage(lineage, merges)
else:
new_lineage = lineage
new_merges = merges
- self.lineage = _3d_index_to_2d(new_lineage)
+ self.lineage = assoc_indices_to_2d(new_lineage)
self.writer.write(
"modifiers/merges", data=[np.array(x) for x in new_merges]
)
self.writer.write(
- "modifiers/lineage_merged", _3d_index_to_2d(new_lineage)
+ "modifiers/lineage_merged", assoc_indices_to_2d(new_lineage)
)
# run picker
picked_indices = self.picker.run(
--
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