From 8ef3726cc4f980d8ac3c2ab3b67a10f905551245 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 3 Apr 2023 16:38:20 +0100
Subject: [PATCH] fix(pp): refresh bud_metric and merging
---
src/agora/utils/merge.py | 20 ++++++----
src/postprocessor/core/processor.py | 4 +-
.../core/reshapers/bud_metric.py | 37 +++++++++++++------
3 files changed, 40 insertions(+), 21 deletions(-)
diff --git a/src/agora/utils/merge.py b/src/agora/utils/merge.py
index e74a9a03..93669912 100644
--- a/src/agora/utils/merge.py
+++ b/src/agora/utils/merge.py
@@ -31,8 +31,11 @@ def apply_merges(data: pd.DataFrame, merges: np.ndarray):
"""
+ indices = data.index
+ if "mother_label" in indices.names:
+ indices = indices.droplevel("mother_label")
valid_merges, indices = validate_association(
- merges, np.array(list(data.index))
+ merges, np.array(list(indices))
)
# Assign non-merged
@@ -129,14 +132,15 @@ def merge_association(
valid_indices = comparison_mat.any(axis=0)
- replacement_d = {}
- for dataset in grouped_merges:
- for k in dataset:
- replacement_d[tuple(k[0])] = dataset[-1][1]
+ if valid_indices.any(): # Where valid, perform transformation
+ replacement_d = {}
+ for dataset in grouped_merges:
+ for k in dataset:
+ replacement_d[tuple(k[0])] = dataset[-1][1]
- flat_indices[valid_indices] = [
- replacement_d[tuple(i)] for i in flat_indices[valid_indices]
- ]
+ flat_indices[valid_indices] = [
+ replacement_d[tuple(i)] for i in flat_indices[valid_indices]
+ ]
merged_indices = flat_indices.reshape(-1, 2, 2)
return merged_indices
diff --git a/src/postprocessor/core/processor.py b/src/postprocessor/core/processor.py
index e0adac14..72bbf3f7 100644
--- a/src/postprocessor/core/processor.py
+++ b/src/postprocessor/core/processor.py
@@ -204,7 +204,9 @@ class PostProcessor(ProcessABC):
self._writer.write(
"modifiers/picks",
data=pd.MultiIndex.from_arrays(
- picked_indices, names=["trap", "cell_label"]
+ picked_indices.T,
+ # names=["trap", "cell_label", "mother_label"],
+ names=["trap", "cell_label"],
),
overwrite="overwrite",
)
diff --git a/src/postprocessor/core/reshapers/bud_metric.py b/src/postprocessor/core/reshapers/bud_metric.py
index d23ea115..bf813739 100644
--- a/src/postprocessor/core/reshapers/bud_metric.py
+++ b/src/postprocessor/core/reshapers/bud_metric.py
@@ -65,23 +65,36 @@ class BudMetric(LineageProcess):
mothers_mat = np.zeros((len(md), signal.shape[1]))
cells_were_dropped = 0 # Flag determines if mothers (1), daughters (2) or both were missing (3)
- md_index = signal.index.droplevel("mother_label")
- if md is not None: # Get intersection of lineage and current index
+ md_index = signal.index
+ if (
+ "mother_label" not in md_index.names
+ ): # Generate mother label from md dict if unavailable
+ d = {v: k for k, values in md.items() for v in values}
+ signal["mother_label"] = list(
+ map(lambda x: d.get(x, [0])[-1], signal.index)
+ )
+ signal.set_index("mother_label", append=True, inplace=True)
related_items = set(
[*md.keys(), *[y for x in md.values() for y in x]]
)
- intersection = md_index.intersection(related_items)
- if len(intersection) < len(signal):
- print("Dropped cells before bud_metric") # TODO log
-
- signal = (
- signal.reset_index("mother_label")
- .loc(axis=0)[intersection]
- .set_index("mother_label", append=True)
- )
+ md_index = md_index.intersection(related_items)
+ elif "mother_label" in md_index.names:
+ md_index = md_index.droplevel("mother_label")
+ else:
+ raise ("Unavailable relationship information")
+
+ if len(md_index) < len(signal):
+ print("Dropped cells before bud_metric") # TODO log
+
+ signal = (
+ signal.reset_index("mother_label")
+ .loc(axis=0)[md_index]
+ .set_index("mother_label", append=True)
+ )
names = list(signal.index.names)
del names[-2]
+
output_df = (
signal.loc[signal.index.get_level_values("mother_label") > 0]
.groupby(names)
@@ -101,7 +114,7 @@ def _combine_daughter_tracks(tracks: t.Collection[pd.Series]):
prioritising the most recent entity.
"""
sorted_da_ids = tracks.sort_index(level="cell_label")
- tp_fvt = sorted_da_ids.apply(lambda x: x.last_valid_index(), axis=0)
+ tp_fvt = sorted_da_ids.apply(lambda x: x.first_valid_index(), axis=1)
tp_fvt = sorted_da_ids.index.get_indexer(tp_fvt)
tp_fvt[tp_fvt < 0] = sorted_da_ids.shape[0] - 1
--
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