From cc84c443a7f0a3253a23f12761a18a3a6c185f75 Mon Sep 17 00:00:00 2001
From: Swainlab <peter.swain@ed.ac.uk>
Date: Mon, 17 Jul 2023 14:33:34 +0100
Subject: [PATCH] more docs; fixed Pandas warning for merge
---
src/agora/utils/merge.py | 2 +-
src/postprocessor/core/reshapers/bud_metric.py | 8 +++++---
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/agora/utils/merge.py b/src/agora/utils/merge.py
index 442bdf0e..b588871b 100644
--- a/src/agora/utils/merge.py
+++ b/src/agora/utils/merge.py
@@ -48,7 +48,7 @@ def apply_merges(data: pd.DataFrame, merges: np.ndarray):
# TODO Use matrices to perform merges in batch
# for efficiency
if valid_merges.any():
- to_merge = data.loc[indices]
+ to_merge = data.loc[indices].copy()
targets, sources = zip(*merges[valid_merges])
for source, target in zip(sources, targets):
target = tuple(target)
diff --git a/src/postprocessor/core/reshapers/bud_metric.py b/src/postprocessor/core/reshapers/bud_metric.py
index b5c9ab2c..57c01069 100644
--- a/src/postprocessor/core/reshapers/bud_metric.py
+++ b/src/postprocessor/core/reshapers/bud_metric.py
@@ -78,7 +78,9 @@ class BudMetric(LineageProcess):
else:
md_index = md_index.droplevel("mother_label")
if len(md_index) < len(signal):
- print("Dropped cells before applying bud_metric") # TODO log
+ print(
+ f"Dropped {len(signal) - len(md_index)} cells before applying bud_metric"
+ ) # TODO log
# restrict signal to the cells in md_index moving mother_label to do so
signal = (
signal.reset_index("mother_label")
@@ -90,7 +92,7 @@ class BudMetric(LineageProcess):
daughter_df = signal.loc[mother_labels > 0]
# join data for daughters with the same mother
output_df = daughter_df.groupby(["trap", "mother_label"]).apply(
- lambda x: _combine_daughter_tracks(x)
+ combine_daughter_tracks
)
output_df.columns = signal.columns
# daughter data is indexed by mothers, which themselves have no mothers
@@ -101,7 +103,7 @@ class BudMetric(LineageProcess):
return output_df
-def _combine_daughter_tracks(tracks: pd.DataFrame):
+def combine_daughter_tracks(tracks: pd.DataFrame):
"""
Combine multiple time series of daughter cells into one time series.
--
GitLab