From 148d92c32ed250ff70def7430a03e94d7f9c8338 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 5 Oct 2022 17:40:48 +0100
Subject: [PATCH] refactor(picker): use shared function for indices
---
src/postprocessor/core/reshapers/picker.py | 41 ++++++++++++++--------
1 file changed, 27 insertions(+), 14 deletions(-)
diff --git a/src/postprocessor/core/reshapers/picker.py b/src/postprocessor/core/reshapers/picker.py
index 117b5d4b..4d8a6b2d 100644
--- a/src/postprocessor/core/reshapers/picker.py
+++ b/src/postprocessor/core/reshapers/picker.py
@@ -1,19 +1,23 @@
-from abc import ABC, abstractmethod
+# from abc import ABC, abstractmethod
# from copy import copy
-from itertools import groupby
-from typing import List, Tuple, Union
+# from itertools import groupby
+# from typing import List, Tuple, Union
+import typing as t
+from typing import Union
-import igraph as ig
+# import igraph as ig
import numpy as np
import pandas as pd
+
from agora.abc import ParametersABC
from agora.io.cells import Cells
-from utils_find_1st import cmp_equal, find_1st
-from postprocessor.core.lineageprocess import LineageProcess
-from postprocessor.core.functions.tracks import max_nonstop_ntps, max_ntps
+# from postprocessor.core.functions.tracks import max_nonstop_ntps, max_ntps
from agora.utils.association import validate_association
+from postprocessor.core.lineageprocess import LineageProcess
+
+# from utils_find_1st import cmp_equal, find_1st
class pickerParameters(ParametersABC):
@@ -47,11 +51,18 @@ class picker(LineageProcess):
self.cells = cells
- def pick_by_lineage(self, signal, how):
+ def pick_by_lineage(
+ self,
+ signal: pd.DataFrame,
+ how: str,
+ mothers_daughters: t.Optional[np.ndarray] = None,
+ ):
self.orig_signals = signal
idx = np.array(signal.index.to_list())
- mothers_daughters = self.cells.mothers_daughters
+
+ if mothers_daughters is None:
+ mothers_daughters = self.cells.mothers_daughters
valid_indices, valid_lineage = [slice(None)] * 2
if how == "mothers":
@@ -60,11 +71,11 @@ class picker(LineageProcess):
)
elif how == "daughters":
valid_lineage, valid_indices = validate_association(
- mothers_daughters, idx, match_column=0
+ mothers_daughters, idx, match_column=1
)
elif how == "families": # Mothers and daughters that are still present
valid_lineage, valid_indices = validate_association(
- mothers_daughters, idx, match_column=0
+ mothers_daughters, idx
)
idx = idx[valid_indices]
@@ -72,9 +83,11 @@ class picker(LineageProcess):
return mothers_daughters, idx
- def loc_lineage(self, signals: pd.DataFrame, how: str):
- _, valid_indices = self.pick_by_lineage(signals, how)
- return signals.loc[valid_indices]
+ def loc_lineage(self, kymo: pd.DataFrame, how: str, lineage=None):
+ _, valid_indices = self.pick_by_lineage(
+ kymo, how, mothers_daughters=lineage
+ )
+ return kymo.loc[[tuple(x) for x in valid_indices]]
def pick_by_condition(self, signals, condition, thresh):
idx = self.switch_case(signals, condition, thresh)
--
GitLab