From f31d1b103b3b42f62881a84cb0ec88d2e909553d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Sun, 23 Oct 2022 17:58:23 +0100
Subject: [PATCH] feat(grouper): add mode "families" and "daughter"
---
src/agora/io/signal.py | 8 ++++---
src/agora/utils/kymograph.py | 42 ++++++++++++++++++++++++++++++++++++
src/postprocessor/grouper.py | 29 +++++++++++++++++++++----
3 files changed, 72 insertions(+), 7 deletions(-)
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 8349f201..797b8d99 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -41,11 +41,13 @@ class Signal(BridgeH5):
def __getitem__(self, dsets: t.Union[str, t.Collection]):
- if isinstance(dsets, str) and dsets.endswith("imBackground"):
+ if isinstance(
+ dsets, str
+ ): # or isinstance(Dsets,dsets.endswith("imBackground"):
df = self.get_raw(dsets)
- elif isinstance(dsets, str):
- df = self.apply_prepost(dsets)
+ # elif isinstance(dsets, str):
+ # df = self.apply_prepost(dsets)
elif isinstance(dsets, list):
is_bgd = [dset.endswith("imBackground") for dset in dsets]
diff --git a/src/agora/utils/kymograph.py b/src/agora/utils/kymograph.py
index 8d563de5..f19b77fa 100644
--- a/src/agora/utils/kymograph.py
+++ b/src/agora/utils/kymograph.py
@@ -2,8 +2,11 @@
import typing as t
from copy import copy
+import numpy as np
import pandas as pd
+index_row = t.Tuple[str, str, int, int]
+
def add_index_levels(
df: pd.DataFrame, additional_ids: t.Dict[str, pd.Series] = {}
@@ -16,3 +19,42 @@ def add_index_levels(
new_df[k] = srs
new_df.set_index(k, inplace=True, append=True)
return new_df
+
+
+def drop_level(
+ df: pd.DataFrame, name: str = "mother_label", as_list: bool = True
+) -> t.Union[t.List[index_row], pd.Index]:
+ """Drop index level
+
+ Parameters
+ ----------
+ df : pd.DataFrame
+ dataframe whose multiindex we will drop
+ name : str
+ name of index level to drop
+ as_list : bool
+ Whether to return as a list instead of an index
+
+ Examples
+ --------
+ FIXME: Add docs.
+
+ """
+ short_index = df.index.droplevel(name)
+ if as_list:
+ short_index = short_index.to_list()
+ return short_index
+
+
+def intersection_matrix(
+ index1: pd.MultiIndex, index2: pd.MultiIndex
+) -> np.ndarray:
+ """
+ Use casting to obtain the boolean mask of the intersection of two multiindices
+ """
+ if not isinstance(index1, np.ndarray):
+ index1 = np.array(index1.to_list())
+ if not isinstance(index2, np.ndarray):
+ index2 = np.array(index2.to_list())
+
+ return (index1[..., None] == index2.T).all(axis=1)
diff --git a/src/postprocessor/grouper.py b/src/postprocessor/grouper.py
index ebfd8f63..b4aac80f 100644
--- a/src/postprocessor/grouper.py
+++ b/src/postprocessor/grouper.py
@@ -13,9 +13,11 @@ import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
-from postprocessor.chainer import Chainer
from pathos.multiprocessing import Pool
+from agora.utils.kymograph import drop_level, intersection_matrix
+from postprocessor.chainer import Chainer
+
class Grouper(ABC):
"""Base grouper class."""
@@ -83,7 +85,7 @@ class Grouper(ABC):
standard: t.Optional[bool] = False,
**kwargs,
):
- """Concate
+ """Concatenate multiple signals
Parameters
----------
@@ -390,12 +392,31 @@ def concat_signal_ind(
raise (NotImplementedError)
elif mode == "raw":
combined = chainer.get_raw(path, **kwargs)
+ elif mode == "daughters":
+ combined = chainer.get_raw(path, **kwargs)
+ combined = combined.loc[
+ combined.index.get_level_values("mother_label") > 0
+ ]
elif mode == "families":
- combined = chainer[path]
+ combined = chainer.get_raw(path, **kwargs)
+ daughter_ids = combined.index[
+ combined.index.get_level_values("mother_label") > 0
+ ]
+ mother_id_mask = intersection_matrix(
+ daughter_ids.droplevel("cell_label"),
+ drop_level(combined, "mother_label", as_list=False),
+ ).any(axis=0)
+ combined = combined.loc[
+ combined.index[mother_id_mask].union(daughter_ids)
+ ]
+
combined["position"] = position
combined["group"] = group
combined.set_index(["group", "position"], inplace=True, append=True)
- combined.index = combined.index.swaplevel(-2, 0).swaplevel(-1, 1)
+ # combined.index = combined.index.swaplevel(-2, 0).swaplevel(-1, 1)
+ combined.index = combined.index.reorder_levels(
+ ("group", "position", "trap", "cell_label", "mother_label")
+ )
return combined
--
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