From 792fb895ba99f36b6ae54372c9125e7ac06c5cf9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 28 Sep 2022 00:47:52 +0100
Subject: [PATCH] refactor(lineageprocess): add lineage requirements
---
.../core/processes/lineageprocess.py | 41 ++++++++++++++++---
1 file changed, 35 insertions(+), 6 deletions(-)
diff --git a/src/postprocessor/core/processes/lineageprocess.py b/src/postprocessor/core/processes/lineageprocess.py
index 2c0cc6a0..38565e18 100644
--- a/src/postprocessor/core/processes/lineageprocess.py
+++ b/src/postprocessor/core/processes/lineageprocess.py
@@ -1,7 +1,11 @@
+import typing as t
+from abc import abstractmethod
+
import numpy as np
import pandas as pd
-from agora.abc import ParametersABC
+from agora.abc import ParametersABC
+from agora.utils.lineage import group_matrix
from postprocessor.core.abc import PostProcessABC
@@ -21,11 +25,6 @@ class LineageProcess(PostProcessABC):
def __init__(self, parameters: LineageProcessParameters):
super().__init__(parameters)
- def run(
- self,
- ):
- pass
-
def filter_signal_cells(self, signal: pd.DataFrame):
"""
Use casting to filter cell ids in signal and lineage
@@ -44,3 +43,33 @@ class LineageProcess(PostProcessABC):
)
return self.lineage[mo_av & da_av]
+
+ @abstractmethod
+ def run(
+ self,
+ data: pd.DataFrame,
+ mother_bud_ids: t.Dict[t.Tuple[int], t.Collection[int]],
+ *args,
+ ):
+ pass
+
+ @classmethod
+ def as_function(
+ cls,
+ data: pd.DataFrame,
+ lineage: t.Union[t.Dict[t.Tuple[int], t.List[int]]],
+ *extra_data,
+ **kwargs,
+ ):
+ """
+ Overrides PostProcess.as_function classmethod.
+ Lineage functions require lineage information to be passed if run as function.
+ """
+ if isinstance(lineage, np.ndarray):
+ lineage = group_matrix(lineage, n_keys=2)
+
+ parameters = cls.default_parameters(**kwargs)
+ return cls(parameters=parameters).run(
+ data, mother_bud_ids=lineage, *extra_data
+ )
+ # super().as_function(data, *extra_data, lineage=lineage, **kwargs)
--
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