From 5cf6da4620d23978e1d12751aee33feef2f654f4 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Tue, 23 May 2023 19:14:36 +0100
Subject: [PATCH] minor doc changes
---
src/postprocessor/core/lineageprocess.py | 10 ++---
src/postprocessor/core/reshapers/buddings.py | 40 ++++++++------------
2 files changed, 21 insertions(+), 29 deletions(-)
diff --git a/src/postprocessor/core/lineageprocess.py b/src/postprocessor/core/lineageprocess.py
index b8e3e76b..c359df89 100644
--- a/src/postprocessor/core/lineageprocess.py
+++ b/src/postprocessor/core/lineageprocess.py
@@ -12,7 +12,7 @@ from postprocessor.core.abc import PostProcessABC
class LineageProcessParameters(ParametersABC):
- """Parameters."""
+ """Parameters - none are necessary."""
_defaults = {}
@@ -21,7 +21,7 @@ class LineageProcess(PostProcessABC):
"""
To analyse lineage data.
- Currently bare bones, but extracts lineage information from a signal or a Cells object.
+ Currently bare bones, but extracts lineage information from a Signal or Cells object.
"""
def __init__(self, parameters: LineageProcessParameters):
@@ -35,7 +35,7 @@ class LineageProcess(PostProcessABC):
lineage: np.ndarray,
*args,
):
- """Implement method required by PostProcessABC."""
+ """Implement method required by PostProcessABC - undefined."""
pass
@classmethod
@@ -47,9 +47,9 @@ class LineageProcess(PostProcessABC):
**kwargs,
):
"""
- Override PostProcess.as_function classmethod.
+ Override PostProcesABC.as_function method.
- Lineage functions require lineage information to be passed if run as functions.
+ Lineage functions require lineage information to be run as functions.
"""
parameters = cls.default_parameters(**kwargs)
return cls(parameters=parameters).run(
diff --git a/src/postprocessor/core/reshapers/buddings.py b/src/postprocessor/core/reshapers/buddings.py
index acdf0165..4398b947 100644
--- a/src/postprocessor/core/reshapers/buddings.py
+++ b/src/postprocessor/core/reshapers/buddings.py
@@ -13,16 +13,10 @@ from postprocessor.core.lineageprocess import (
class buddingsParameters(LineageProcessParameters):
- """Parameter class to obtain budding events.
-
- Parameters
- ----------
- LineageProcessParameters : lineage_location
- Location of lineage matrix to be used for calculations.
+ """
+ Parameter class to obtain budding events.
- Examples
- --------
- FIXME: Add docs.
+ Define the location of lineage information in the h5 file.
"""
@@ -31,45 +25,44 @@ class buddingsParameters(LineageProcessParameters):
class buddings(LineageProcess):
"""
- Calculate buddings in a trap assuming one mother per trap
- returns a pandas series with the buddings.
+ Calculate buddings in a trap assuming one mother per trap.
+
+ Return a pandas series with the buddings.
- We define a budding event as the moment in which a bud was identified for
- the first time, even if the bud is not considered one until later
- in the experiment.
+ We define a budding event as when a bud is first identified.
+
+ This bud may not be considered a bud until later in the experiment.
"""
def __init__(self, parameters: buddingsParameters):
+ """Initialise buddings."""
super().__init__(parameters)
def run(
self, signal: pd.DataFrame, lineage: np.ndarray = None
) -> pd.DataFrame:
+ """TODO."""
lineage = lineage or self.lineage
-
- # Get time of first appearance for all cells
- fvi = signal.apply(lambda x: x.first_valid_index(), axis=1)
-
- # Select mother cells in a given dataset
+ # select traps and mother cells in a given signal
traps_mothers: t.Dict[tuple, list] = {
tuple(mo): [] for mo in lineage[:, :2] if tuple(mo) in signal.index
}
for trap, mother, daughter in lineage:
if (trap, mother) in traps_mothers.keys():
traps_mothers[(trap, mother)].append(daughter)
-
mothers = signal.loc[
set(signal.index).intersection(traps_mothers.keys())
]
- # Create a new dataframe with dimensions (n_mother_cells * n_timepoints)
+ # create a new dataframe with dimensions (n_mother_cells * n_timepoints)
buddings = pd.DataFrame(
np.zeros((mothers.shape[0], signal.shape[1])).astype(bool),
index=mothers.index,
columns=signal.columns,
)
buddings.columns.names = ["timepoint"]
-
- # Fill the budding events
+ # get time of first appearance for every cell using Pandas
+ fvi = signal.apply(lambda x: x.first_valid_index(), axis=1)
+ # fill the budding events
for mother_id, daughters in traps_mothers.items():
daughters_idx = set(
fvi.loc[
@@ -82,5 +75,4 @@ class buddings(LineageProcess):
mother_id,
daughters_idx,
] = True
-
return buddings
--
GitLab