From 7b770b3f2e26e9539232883cef31fefddcb9da20 Mon Sep 17 00:00:00 2001
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Wed, 1 Nov 2023 10:57:02 +0000
Subject: [PATCH] feat(babysitter): added pixel_size to BabyParameters
---
src/aliby/baby_sitter.py | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/src/aliby/baby_sitter.py b/src/aliby/baby_sitter.py
index 064b374..386e312 100644
--- a/src/aliby/baby_sitter.py
+++ b/src/aliby/baby_sitter.py
@@ -15,24 +15,30 @@ class BabyParameters(ParametersABC):
def __init__(
self,
modelset_name,
+ pixel_size,
clogging_thresh,
min_bud_tps,
isbud_thresh,
+ session,
):
"""Initialise parameters for BABY."""
self.modelset_name = modelset_name
+ self.pixel_size = pixel_size
self.clogging_thresh = clogging_thresh
self.min_bud_tps = min_bud_tps
self.isbud_thresh = isbud_thresh
+ self.session = session
@classmethod
def default(cls, **kwargs):
"""Define default parameters; kwargs choose BABY model set."""
return cls(
modelset_name=get_modelset_name_from_params(**kwargs),
+ pixel_size=0.182,
clogging_thresh=0.75,
min_bud_tps=3,
isbud_thresh=0.5,
+ session=None,
)
def update_baby_modelset(self, path: t.Union[str, Path, t.Dict[str, str]]):
@@ -78,9 +84,11 @@ class BabyRunner(StepABC):
else:
brain = modelsets.get(
modelset_name,
+ pixel_size=parameters.pixel_size,
clogging_thresh=parameters.clogging_thresh,
min_bud_tps=parameters.min_bud_tps,
isbud_thresh=parameters.isbud_thresh,
+ session=parameters.session,
)
self.crawler = BabyCrawler(brain)
self.brightfield_channel = self.tiler.ref_channel_index
--
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