diff --git a/core/functions/tracks.py b/core/functions/tracks.py
index bff48680a3ab1f46f656865270fdcc6d5e7722ee..ecc4e0f56742b720ffb01e7d9ac79c325983a72f 100644
--- a/core/functions/tracks.py
+++ b/core/functions/tracks.py
@@ -214,13 +214,12 @@ def get_joinable(tracks, smooth=False, tol=0.1, window=5, degree=3) -> dict:
"""
tracks.index.names = [
- "pos",
"trap",
"cell",
] # TODO remove this once it is integrated in the tracker
# contig=tracks.groupby(['pos','trap']).apply(tracks2contig)
clean = clean_tracks(tracks, min_len=window + 1, min_gr=0.9) # get useful tracks
- contig = clean.groupby(["pos", "trap"]).apply(get_contiguous_pairs)
+ contig = clean.groupby(["trap"]).apply(get_contiguous_pairs)
contig = contig.loc[contig.apply(len) > 0]
# candict = {k:v for d in contig.values for k,v in d.items()}
diff --git a/core/merger.py b/core/merger.py
index 6000a2b5467629e0d9a3097db60a3262e1d48f17..7659a6807cb3183ea02852df59f1a979639b7ecc 100644
--- a/core/merger.py
+++ b/core/merger.py
@@ -1,5 +1,36 @@
-# Classes in charge of merging tracks
+class Parameters:
+ """
+ :param tol: float or int threshold of average (prediction error/std) necessary
+ to consider two tracks the same. If float is fraction of first track,
+ if int it is absolute units.
+ :param window: int value of window used for savgol_filter
+ :param degree: int value of polynomial degree passed to savgol_filter
+ """
-class Merger(BasePicker):
+ def __init__(
+ self,
+ smooth: bool = False,
+ tolerance: float = 0.1,
+ window: int = 5,
+ degree: int = 3,
+ min_avg_delta: float = 0.9,
+ ):
+
+ self.smooth = smooth
+
+ self.tolerance = tolerance
+
+ self.window = window
+
+ self.degree = degree
+
+ self.min_avg_delta = min_avg_delta
+
+
+class Merger:
+ # Class in charge of merging tracks
def __init__(self, parameters):
- pass
+ self.parameters = parameters
+
+ def run(self, signal):
+ merged, joint_pairs = merge_tracks(signal, min_len=self.window + 1)
diff --git a/core/picker.py b/core/picker.py
index 0a4ed16652354581ca4c59a31c8517e50220c135..2618ae99a99b307918eebec00a1c8fb4b10dc728 100644
--- a/core/picker.py
+++ b/core/picker.py
@@ -1,11 +1,10 @@
-# from abc import ABC, abstractmethod
from typing import Tuple, Union, List
import numpy as np
import pandas as pd
from core.cells import CellsHDF
-from postprocessor.core.functions.tracks import max_ntps, max_nonstop_ntps
+from postprocessor.core.functions.signals import max_ntps, max_nonstop_ntps
# def BasePicker(ABC):
@@ -18,24 +17,24 @@ from postprocessor.core.functions.tracks import max_ntps, max_nonstop_ntps
class Picker:
"""
- :tracks: pd.DataFrame
+ :signals: pd.DataFrame of data used for selection, such as area or GFP/np.max/mean
:cells: Cell object passed to the constructor
:condition: Tuple with condition and associated parameter(s), conditions can be
"present", "nonstoply_present" or "quantile".
- Determines the thersholds or fractions of tracks/signals to use.
- :lineage: str {"mothers", "daughters", "families", "orphans"}. Mothers/daughters picks cells with those tags, families pick the union of both and orphans the difference between the total and families.
+ Determines the thersholds or fractions of signals/signals to use.
+ :lineage: str {"mothers", "daughters", "families" (mothers AND daughters), "orphans"}. Mothers/daughters picks cells with those tags, families pick the union of both and orphans the difference between the total and families.
"""
def __init__(
self,
- tracks: pd.DataFrame,
+ signals: pd.DataFrame,
cells: CellsHDF,
condition: Tuple[str, Union[float, int]] = None,
lineage: str = None,
sequence: List[str] = ["lineage", "condition"],
):
- self.tracks = tracks
- self._index = tracks.index
+ self.signals = signals
+ self._index = signals.index
self._cells = cells
self.condition = condition
self.lineage = lineage
@@ -57,7 +56,7 @@ class Picker:
return mb_matrix
def pick_by_lineage(self):
- idx = self.tracks.index
+ idx = self.signals.index
if self.lineage:
ma = self._cells["mother_assign"]
@@ -75,18 +74,18 @@ class Picker:
idx = idx[list(set(range(len(idx))).difference(families))]
idx = self._index[idx]
- idx = list(set(idx).intersection(self.tracks.index))
+ idx = list(set(idx).intersection(self.signals.index))
- return self.tracks.loc[idx]
+ return self.signals.loc[idx]
def pick_by_condition(self):
- idx = switch_case(self.condition[0], self.tracks, self.condition[1])
- return self.tracks.loc[idx]
+ idx = switch_case(self.condition[0], self.signals, self.condition[1])
+ return self.signals.loc[idx]
def run(self):
for alg in self.sequence:
- self.tracks = getattr(self, "pick_by" + alg)()
- return self.tracks
+ self.signals = getattr(self, "pick_by" + alg)()
+ return self.signals
def as_int(threshold: Union[float, int], ntps: int):
@@ -97,13 +96,13 @@ def as_int(threshold: Union[float, int], ntps: int):
def switch_case(
condition: str,
- tracks: pd.DataFrame,
+ signals: pd.DataFrame,
threshold: Union[float, int],
):
- threshold_asint = as_int(threshold, tracks.shape[1])
+ threshold_asint = as_int(threshold, signals.shape[1])
case_mgr = {
- "present": tracks.apply(max_ntps, axis=1) > threshold_asint,
- "nonstoply_present": tracks.apply(max_nonstop_ntps, axis=1) > threshold_asint,
- "quantile": [np.quantile(tracks.values[tracks.notna()], threshold)],
+ "present": signals.apply(max_ntps, axis=1) > threshold_asint,
+ "nonstoply_present": signals.apply(max_nonstop_ntps, axis=1) > threshold_asint,
+ "quantile": [np.quantile(signals.values[signals.notna()], threshold)],
}
return case_mgr[condition]
diff --git a/core/processor.py b/core/processor.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..917b951773a11d0b4d591be8951993382f824bbb 100644
--- a/core/processor.py
+++ b/core/processor.py
@@ -0,0 +1,13 @@
+class PostProcessor:
+ def __init__(self, parameters):
+ self.parameters = parameters
+
+ self.merger = Merger(parameters["merger"])
+ self.picker = Picker(parameters["picker"])
+ self.processes, self.branches = [
+ (self.get_process(process), branch)
+ for process, branch in parameters["processes"]
+ ]
+
+ def run(self):
+ pass