From 54a7513159f0a8f264faa870167766fbf677e6a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 7 Sep 2022 11:38:41 +0100
Subject: [PATCH] style(extractor): Improve typing
---
extraction/core/extractor.py | 21 ++++++++++-----------
1 file changed, 10 insertions(+), 11 deletions(-)
diff --git a/extraction/core/extractor.py b/extraction/core/extractor.py
index bce0ef85..fca1e1e8 100644
--- a/extraction/core/extractor.py
+++ b/extraction/core/extractor.py
@@ -46,7 +46,7 @@ class ExtractorParameters(ParametersABC):
def __init__(
self,
- tree: t.Dict[str, t.Dict[reduction_method, t.Collection[str]]],
+ tree: extraction_tree,
sub_bg: set = set(),
multichannel_ops: t.Dict = {},
):
@@ -260,12 +260,11 @@ class Extractor(ProcessABC):
# a subset of channels was specified
channel_ids = [self.tiler.get_channel_index(ch) for ch in channels]
else:
- # oh oh
+ # a list of the indices of the z stacks
channel_ids = None
- # a list of the indices of the z stacks
if z is None:
- z = list(range(self.tiler.shape[-1]))
- # gets the data via tiler
+ # gets the tiles data via tiler
+ z: t.List[int] = list(range(self.tiler.shape[-1]))
tiles = (
self.tiler.get_tiles_timepoint(
tp, channels=channel_ids, z=z, **kwargs
@@ -456,7 +455,7 @@ class Extractor(ProcessABC):
"""
if tree is None:
# use default
- tree = self.params.tree
+ tree: extraction_tree = self.params.tree
# dictionary with channel: {reduction algorithm : metric}
ch_tree = {ch: v for ch, v in tree.items() if ch != "general"}
# tuple of the channels
@@ -484,10 +483,10 @@ class Extractor(ProcessABC):
# find image data at the time point
# stored as an array arranged as (traps, channels, timepoints, X, Y, Z)
- # Alan: traps does not appear the best name here!
- traps = self.get_tiles(tp, tile_shape=tile_size, channels=tree_chs)
+ tiles = self.get_tiles(tp, tile_shape=tile_size, channels=tree_chs)
# generate boolean masks for background as a list with one mask per trap
+ bgs = []
if self.params.sub_bg:
bgs = [
~np.sum(m, axis=2).astype(bool)
@@ -501,10 +500,10 @@ class Extractor(ProcessABC):
self.img_bgsub = {}
for ch, red_metrics in tree.items():
# NB ch != is necessary for threading
- if ch != "general" and traps is not None and len(traps):
+ if ch != "general" and tiles is not None and len(traps):
# image data for all traps and z sections for a particular channel
# as an array arranged as (no traps, X, Y, no Z channels)
- img = traps[:, tree_chs.index(ch), 0]
+ img = tiles[:, tree_chs.index(ch), 0]
else:
img = None
# apply metrics to image data
@@ -516,7 +515,7 @@ class Extractor(ProcessABC):
**kwargs,
)
# apply metrics to image data with the background subtracted
- if ch in self.params.sub_bg and img is not None:
+ if bgs and ch in self.params.sub_bg and img is not None:
# calculate metrics with subtracted bg
ch_bs = ch + "_bgsub"
self.img_bgsub[ch_bs] = []
--
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