From 05843ad28af4f487c183403487b3f982f07d2ea4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Sun, 10 Oct 2021 23:48:34 +0100
Subject: [PATCH] adjust parameters and bugfixes
Former-commit-id: 0669c9f294dcb76451ce6700f3f946cfcfae3d33
---
core/processes/picker.py | 43 +++++++++++++++++++++++-----------------
1 file changed, 25 insertions(+), 18 deletions(-)
diff --git a/core/processes/picker.py b/core/processes/picker.py
index ec0814f3..23be1f70 100644
--- a/core/processes/picker.py
+++ b/core/processes/picker.py
@@ -1,3 +1,6 @@
+import seaborn as sns
+from matplotlib import pyplot as plt # TODO DELETE THIS
+
from typing import Tuple, Union, List
from abc import ABC, abstractmethod
@@ -27,9 +30,9 @@ class pickerParameters(ParametersABC):
"sequence": [
# ("lineage", "intersection", "families"),
("condition", "intersection", "any_present", 0.8),
- ("condition", "intersection", "growing", 50),
- ("condition", "intersection", "present", 5),
- ("condition", "intersection", "mother_buds", 5, 0.5),
+ ("condition", "intersection", "growing", 40),
+ ("condition", "intersection", "present", 8),
+ ("condition", "intersection", "mother_buds", 5, 0.8),
# ("lineage", "full_families", "intersection"),
],
}
@@ -162,9 +165,6 @@ class picker(ProcessABC):
return idx
- def pick_by_custom(self, signals, condition, thresh):
- pass
-
def pick_by_condition(self, signals, condition, thresh):
idx = self.switch_case(signals, condition, thresh)
return idx
@@ -201,14 +201,18 @@ class picker(ProcessABC):
for alg, op, *params in self.sequence:
if alg is "lineage":
param1 = params[0]
- new_indices = getattr(self, "pick_by_" + alg)(signals, param1)
+ new_indices = getattr(self, "pick_by_" + alg)(
+ signals.loc[list(indices)], param1
+ )
else:
param1, *param2 = params
- new_indices = getattr(self, "pick_by_" + alg)(signals, param1, param2)
+ new_indices = getattr(self, "pick_by_" + alg)(
+ signals.loc[list(indices)], param1, param2
+ )
if op is "union":
- new_indices = new_indices.intersection(set(signals.index))
- new_indices = indices.union(set(new_indices))
+ # new_indices = new_indices.intersection(set(signals.index))
+ new_indices = indices.union(new_indices)
indices = indices.intersection(new_indices)
@@ -224,12 +228,9 @@ class picker(ProcessABC):
threshold = [_as_int(*threshold, signals.shape[1])]
case_mgr = {
"any_present": lambda s, thresh: any_present(s, thresh),
- "present": lambda s, thresh: signals.notna().sum(axis=1) > thresh,
- "nonstoply_present": lambda s, thresh: signals.apply(
- max_nonstop_ntps, axis=1
- )
- > thresh_asint,
- "growing": lambda s, thresh: signals.diff(axis=1).sum(axis=1) > thresh,
+ "present": lambda s, thresh: s.notna().sum(axis=1) > thresh,
+ "nonstoply_present": lambda s, thresh: s.apply(thresh, axis=1) > thresh,
+ "growing": lambda s, thresh: s.diff(axis=1).sum(axis=1) > thresh,
"mother_buds": lambda s, p1, p2: mother_buds_wrap(s, p1, p2)
# "quantile": [np.quantile(signals.values[signals.notna()], threshold)],
}
@@ -306,10 +307,16 @@ def mother_buds(df, min_budgrowth_t, min_mobud_ratio):
size_filter = d_to_mother[
d_to_mother.apply(lambda x: x.dropna().iloc[0], axis=1) < 0
]
- cols_sorted = size_filter.sort_index(axis=1)
+ cols_sorted = (
+ size_filter.sort_index(axis=1)
+ .apply(pd.Series.first_valid_index, axis=1)
+ .sort_values()
+ )
if not len(cols_sorted):
return []
- bud_candidates = start[[True, *(np.diff(cols_sorted.columns) > min_budgrowth_t)]]
+ bud_candidates = cols_sorted.loc[
+ [True, *(np.diff(cols_sorted.values) > min_budgrowth_t)]
+ ]
return [mother_id] + [int(i) for i in bud_candidates.index.tolist()]
--
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