From eb00e2b2548b3551a5d081f882e0d4687fcec35e Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 21 Dec 2023 10:33:44 +0000
Subject: [PATCH] feature(signal): make check on lineage assignment by
validate_lineage optional
---
src/agora/io/signal.py | 16 ++++++++-----
src/agora/utils/indexing.py | 45 +++++++++++++++++++++----------------
2 files changed, 36 insertions(+), 25 deletions(-)
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 83907dc..e9b0dd1 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -142,15 +142,15 @@ class Signal(BridgeH5):
with h5py.File(self.filename, "r") as f:
if lineage_location not in f:
lineage_location = "postprocessing/lineage"
- tile_mo_da = f[lineage_location]
- if isinstance(tile_mo_da, h5py.Dataset):
- lineage = tile_mo_da[()]
+ traps_mothers_daughters = f[lineage_location]
+ if isinstance(traps_mothers_daughters, h5py.Dataset):
+ lineage = traps_mothers_daughters[()]
else:
lineage = np.array(
(
- tile_mo_da["trap"],
- tile_mo_da["mother_label"],
- tile_mo_da["daughter_label"],
+ traps_mothers_daughters["trap"],
+ traps_mothers_daughters["mother_label"],
+ traps_mothers_daughters["daughter_label"],
)
).T
return lineage
@@ -249,6 +249,7 @@ class Signal(BridgeH5):
dataset: str or t.List[str],
in_minutes: bool = True,
lineage: bool = False,
+ run_lineage_check: bool = True,
**kwargs,
) -> pd.DataFrame or t.List[pd.DataFrame]:
"""
@@ -262,6 +263,8 @@ class Signal(BridgeH5):
If True, convert column headings to times in minutes.
lineage: boolean
If True, add mother_label to index.
+ run_lineage_check: boolean
+ If True, raise exception if a likely error in the lineage assignment.
"""
try:
if isinstance(dataset, str):
@@ -279,6 +282,7 @@ class Signal(BridgeH5):
lineage,
indices=np.array(df.index.to_list()),
how="daughters",
+ run_lineage_check=run_lineage_check,
)
mother_label[valid_indices] = lineage[
valid_lineage, 1
diff --git a/src/agora/utils/indexing.py b/src/agora/utils/indexing.py
index faa8e25..1b20a71 100644
--- a/src/agora/utils/indexing.py
+++ b/src/agora/utils/indexing.py
@@ -5,7 +5,10 @@ i_dtype = {"names": ["trap_id", "cell_id"], "formats": [np.int64, np.int64]}
def validate_lineage(
- lineage: np.ndarray, indices: np.ndarray, how: str = "families"
+ lineage: np.ndarray,
+ indices: np.ndarray,
+ how: str = "families",
+ run_lineage_check: bool = True,
):
"""
Identify mother-bud pairs both in lineage and a Signal's indices.
@@ -28,6 +31,9 @@ def validate_lineage(
If "mothers", matches indicate mothers from mother-bud pairs;
If "daughters", matches indicate daughters from mother-bud pairs;
If "families", matches indicate mothers and daughters in mother-bud pairs.
+ run_lineage_check: bool
+ If True, check for errors in the lineage assignment such as a daughter
+ being assigned two mothers.
Returns
-------
@@ -85,24 +91,25 @@ def validate_lineage(
valid_indices = index_isin(indices, selected_lineages[:, c_index, :])
flat_valid_indices = valid_indices.flatten()
# test for mismatch
- if how == "families":
- test_mismatch = (
- indices[flat_valid_indices, :].size
- != np.unique(
- lineage[flat_valid_lineage, :].reshape(-1, 2), axis=0
- ).size
- )
- else:
- test_mismatch = (
- indices[flat_valid_indices, :].size
- != lineage[flat_valid_lineage, c_index, :].size
- )
- if test_mismatch:
- # all unique indices in valid_lineages should be in valid_indices
- raise Exception(
- "Error in validate_lineage: "
- "lineage information is likely not unique."
- )
+ if run_lineage_check:
+ if how == "families":
+ test_mismatch = (
+ indices[flat_valid_indices, :].size
+ != np.unique(
+ lineage[flat_valid_lineage, :].reshape(-1, 2), axis=0
+ ).size
+ )
+ else:
+ test_mismatch = (
+ indices[flat_valid_indices, :].size
+ != lineage[flat_valid_lineage, c_index, :].size
+ )
+ if test_mismatch:
+ # all unique indices in valid_lineages should be in valid_indices
+ raise Exception(
+ "Error in validate_lineage: "
+ "lineage information is likely not unique."
+ )
return flat_valid_lineage, flat_valid_indices
--
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