From 01adfb23806779a95796f2aaad4a239295a50811 Mon Sep 17 00:00:00 2001
From: Swainlab <peter.swain@ed.ac.uk>
Date: Fri, 21 Jul 2023 12:56:54 +0100
Subject: [PATCH] added and verified validate_lineage, now used by picker
---
src/agora/utils/indexing_new.py | 89 ++++++++++++++++++----
src/postprocessor/core/reshapers/picker.py | 21 ++++-
2 files changed, 94 insertions(+), 16 deletions(-)
diff --git a/src/agora/utils/indexing_new.py b/src/agora/utils/indexing_new.py
index 0f7b4a26..aca8667c 100644
--- a/src/agora/utils/indexing_new.py
+++ b/src/agora/utils/indexing_new.py
@@ -12,31 +12,90 @@ import typing as t
def validate_lineage(
- lineage: np.ndarray,
- indices: np.ndarray,
- match_column: t.Optional[int] = None,
-) -> t.Tuple[np.ndarray, np.ndarray]:
+ lineage: np.ndarray, indices: np.ndarray, how: str = "families"
+):
"""
Identify mother-bud pairs that exist both in lineage and a Signal's indices.
+
+ Parameters
+ ----------
+ lineage : np.ndarray
+ 2D array of lineage associations where columns are
+ (trap, mother, daughter)
+ or
+ a 3D array, which is an array of 2 X 2 arrays comprising
+ [[trap_id, mother_label], [trap_id, daughter_label]].
+ indices : np.ndarray
+ A 2D array of cell indices from a Signal, (trap_id, cell_label).
+ This array should not include mother_label.
+ how: str
+ 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.
+
+ Returns
+ -------
+ valid_lineage: boolean np.ndarray
+ 1D array indicating matched elements in lineage.
+ valid_indices: boolean np.ndarray
+ 1D array indicating matched elements in indices.
+
+ Examples
+ --------
+ >>> import numpy as np
+ >>> from agora.utils.indexing import validate_lineage
+
+ >>> lineage = np.array([ [[0, 1], [0, 3]], [[0, 1], [0, 4]], [[0, 1], [0, 6]], [[0, 4], [0, 7]] ])
+ >>> indices = np.array([ [0, 1], [0, 2], [0, 3]])
+
+ >>> valid_lineage, valid_indices = validate_lineage(lineage, indices)
+
+ >>> print(valid_lineage)
+ array([ True, False, False, False])
+ >>> print(valid_indices)
+ array([ True, False, True])
+
+ and
+
+ >>> lineage = np.array([[[0,3], [0,1]], [[0,2], [0,4]]])
+ >>> indices = np.array([[0,1], [0,2], [0,3]])
+ >>> valid_lineage, valid_indices = validate_lineage(lineage, indices)
+ >>> print(valid_lineage)
+ array([ True, False])
+ >>> print(valid_indices)
+ array([ True, False, True])
"""
if lineage.ndim == 2:
# [trap, mother, daughter] becomes [[trap, mother], [trap, daughter]]
lineage = _assoc_indices_to_3d(lineage)
+ if how == "mothers":
+ c_index = 0
+ elif how == "daughters":
+ c_index = 1
# dtype links together trap and cell ids
- dtype = {
- "names": ["trap_id", "cell_id"],
- "formats": [np.int64, np.int64],
- }
+ dtype = {"names": ["trap_id", "cell_id"], "formats": [np.int64, np.int64]}
lineage = np.ascontiguousarray(lineage, dtype=np.int64)
# find (trap, cell_ids) in intersection
inboth = np.intersect1d(lineage.view(dtype), indices.view(dtype))
- # both mother and bud must be in indices
- valid_lineage = np.isin(lineage.view(dtype), inboth).all(axis=1).flatten()
- # select only pairs of mother and bud indices
- valid_indices = np.isin(
- indices.view(dtype), lineage[valid_lineage.flatten(), ...].view(dtype)
- ).flatten()
- return valid_lineage, valid_indices
+ # find valid lineage
+ valid_lineage = np.isin(lineage.view(dtype), inboth)
+ if how == "families":
+ # both mother and bud must be in indices
+ valid_lineage = valid_lineage.all(axis=1)
+ else:
+ valid_lineage = valid_lineage[:, c_index, :]
+ # find valid indices
+ possible_indices = lineage[valid_lineage.flatten(), ...]
+ if how == "families":
+ # select only pairs of mother and bud indices
+ valid_indices = np.isin(
+ indices.view(dtype), possible_indices.view(dtype)
+ )
+ else:
+ valid_indices = np.isin(
+ indices.view(dtype), possible_indices.view(dtype)[:, c_index, :]
+ )
+ return valid_lineage.flatten(), valid_indices.flatten()
def validate_association(
diff --git a/src/postprocessor/core/reshapers/picker.py b/src/postprocessor/core/reshapers/picker.py
index 2b5414b0..c05d4279 100644
--- a/src/postprocessor/core/reshapers/picker.py
+++ b/src/postprocessor/core/reshapers/picker.py
@@ -5,7 +5,8 @@ import pandas as pd
from agora.abc import ParametersABC
from agora.io.cells import Cells
-from agora.utils.indexing_new import validate_association
+from agora.utils.indexing import validate_association
+from agora.utils.indexing_new import validate_lineage
from agora.utils.cast import _str_to_int
from agora.utils.kymograph import drop_mother_label
from postprocessor.core.lineageprocess import LineageProcess
@@ -52,6 +53,23 @@ class Picker(LineageProcess):
signal: pd.DataFrame,
how: str,
mothers_daughters: t.Optional[np.ndarray] = None,
+ ) -> pd.MultiIndex:
+ """
+ Return rows of a signal corresponding to either mothers, daughters,
+ or mother-daughter pairs using lineage information.
+ """
+ cells_present = drop_mother_label(signal.index)
+ mothers_daughters = self.get_lineage_information(signal)
+ _, valid_indices = validate_lineage(
+ mothers_daughters, cells_present, how
+ )
+ return signal.index[valid_indices]
+
+ def pick_by_lineage_original(
+ self,
+ signal: pd.DataFrame,
+ how: str,
+ mothers_daughters: t.Optional[np.ndarray] = None,
) -> pd.MultiIndex:
"""
Return rows of a signal corresponding to either mothers, daughters,
@@ -60,6 +78,7 @@ class Picker(LineageProcess):
cells_present = drop_mother_label(signal.index)
mothers_daughters = self.get_lineage_information(signal)
#: might be better if match_column defined as a string to make everything one line
+ breakpoint()
if how == "mothers":
_, valid_indices = validate_association(
mothers_daughters, cells_present, match_column=0
--
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