From e602d557ff61c61e3747928d80b8733228d09244 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 29 Jun 2022 18:39:18 +0100
Subject: [PATCH] style(extractor): Blackify with new defaults
---
extraction/core/extractor.py | 72 +++++++++++++++++++++++++++---------
1 file changed, 55 insertions(+), 17 deletions(-)
diff --git a/extraction/core/extractor.py b/extraction/core/extractor.py
index 9f769eaa..6b7e0ca8 100644
--- a/extraction/core/extractor.py
+++ b/extraction/core/extractor.py
@@ -39,7 +39,7 @@ class ExtractorParameters(ParametersABC):
def __init__(
self,
- tree: Dict[Union[str, None], Dict[Union[Callable, None], List[str]]] = None,
+ tree: Dict[str, Dict[Callable, List[str]]] = None,
sub_bg: set = set(),
multichannel_ops: Dict = {},
):
@@ -63,7 +63,9 @@ class ExtractorParameters(ParametersABC):
"""
with h5py.open(store_name, "r") as f:
- microscope = f["/"].attrs.get("microscope") # TODO Check this with Arin
+ microscope = f["/"].attrs.get(
+ "microscope"
+ ) # TODO Check this with Arin
assert microscope, "No metadata found"
return "_".join((microscope, suffix))
@@ -95,7 +97,10 @@ class Extractor(ProcessABC):
default_meta = {"pixel_size": 0.236, "z_size": 0.6, "spacing": 0.6}
def __init__(
- self, parameters: ExtractorParameters, store: str = None, tiler: Tiler = None
+ self,
+ parameters: ExtractorParameters,
+ store: str = None,
+ tiler: Tiler = None,
):
self.params = parameters
if store:
@@ -108,11 +113,15 @@ class Extractor(ProcessABC):
self.load_funs()
@classmethod
- def from_tiler(cls, parameters: ExtractorParameters, store: str, tiler: Tiler):
+ def from_tiler(
+ cls, parameters: ExtractorParameters, store: str, tiler: Tiler
+ ):
return cls(parameters, store=store, tiler=tiler)
@classmethod
- def from_img(cls, parameters: ExtractorParameters, store: str, img_meta: tuple):
+ def from_img(
+ cls, parameters: ExtractorParameters, store: str, img_meta: tuple
+ ):
return cls(parameters, store=store, tiler=Tiler(*img_meta))
@property
@@ -154,14 +163,17 @@ class Extractor(ProcessABC):
)
funs = funs.intersection(CUSTOM_FUNS.keys())
ARG_VALS = {
- k: {k2: self.get_meta(k2) for k2 in v} for k, v in CUSTOM_ARGS.items()
+ k: {k2: self.get_meta(k2) for k2 in v}
+ for k, v in CUSTOM_ARGS.items()
}
# self._custom_funs = {trap_apply(CUSTOM_FUNS[fun],])
self._custom_funs = {}
for k, f in CUSTOM_FUNS.items():
def tmp(f):
- return lambda m, img: trap_apply(f, m, img, **ARG_VALS.get(k, {}))
+ return lambda m, img: trap_apply(
+ f, m, img, **ARG_VALS.get(k, {})
+ )
self._custom_funs[k] = tmp(f)
@@ -187,7 +199,9 @@ class Extractor(ProcessABC):
z = list(range(self.tiler.shape[-1]))
traps = (
- self.tiler.get_traps_timepoint(tp, channels=channel_ids, z=z, **kwargs)
+ self.tiler.get_traps_timepoint(
+ tp, channels=channel_ids, z=z, **kwargs
+ )
if channel_ids
else None
)
@@ -238,7 +252,11 @@ class Extractor(ProcessABC):
return (tuple(results), tuple(idx))
def extract_funs(
- self, traps: List[np.array], masks: List[np.array], metrics: List[str], **kwargs
+ self,
+ traps: List[np.array],
+ masks: List[np.array],
+ metrics: List[str],
+ **kwargs,
) -> dict:
"""
Extract multiple metrics from a timepoint
@@ -253,7 +271,11 @@ class Extractor(ProcessABC):
return d
def reduce_extract(
- self, traps: Union[np.array, None], masks: list, red_metrics: dict, **kwargs
+ self,
+ traps: np.array,
+ masks: list,
+ red_metrics: dict,
+ **kwargs,
) -> dict:
"""
Wrapper to apply reduction and then extraction.
@@ -274,7 +296,8 @@ class Extractor(ProcessABC):
if traps is not None:
for red_fun in red_metrics.keys():
reduced_traps[red_fun] = [
- self.reduce_dims(trap, method=RED_FUNS[red_fun]) for trap in traps
+ self.reduce_dims(trap, method=RED_FUNS[red_fun])
+ for trap in traps
]
d = {
@@ -326,7 +349,8 @@ class Extractor(ProcessABC):
if labels is None:
raw_labels = cells.labels_at_time(tp)
labels = {
- trap_id: raw_labels.get(trap_id, []) for trap_id in range(cells.ntraps)
+ trap_id: raw_labels.get(trap_id, [])
+ for trap_id in range(cells.ntraps)
}
# masks
@@ -368,7 +392,11 @@ class Extractor(ProcessABC):
img = traps[:, tree_chs.index(ch), 0]
d[ch] = self.reduce_extract(
- red_metrics=red_metrics, traps=img, masks=masks, labels=labels, **kwargs
+ red_metrics=red_metrics,
+ traps=img,
+ masks=masks,
+ labels=labels,
+ **kwargs,
)
if (
@@ -396,9 +424,15 @@ class Extractor(ProcessABC):
)
# Additional operations between multiple channels (e.g. pH calculations)
- for name, (chs, merge_fun, red_metrics) in self.params.multichannel_ops.items():
+ for name, (
+ chs,
+ merge_fun,
+ red_metrics,
+ ) in self.params.multichannel_ops.items():
if len(
- set(chs).intersection(set(self.img_bgsub.keys()).union(tree_chs))
+ set(chs).intersection(
+ set(self.img_bgsub.keys()).union(tree_chs)
+ )
) == len(chs):
imgs = [self.get_imgs(ch, traps, tree_chs) for ch in chs]
merged = MERGE_FUNS[merge_fun](*imgs)
@@ -435,7 +469,9 @@ class Extractor(ProcessABC):
"""
return self.run(tps=[tp], **kwargs)
- def run(self, tree=None, tps: List[int] = None, save=True, **kwargs) -> dict:
+ def run(
+ self, tree=None, tps: List[int] = None, save=True, **kwargs
+ ) -> dict:
if tree is None:
tree = self.params.tree
@@ -523,7 +559,9 @@ class Extractor(ProcessABC):
if not hasattr(flds, "__iter__"):
flds = [flds]
meta_short = {k.split("/")[-1]: v for k, v in self.meta.items()}
- return {f: meta_short.get(f, self.default_meta.get(f, None)) for f in flds}
+ return {
+ f: meta_short.get(f, self.default_meta.get(f, None)) for f in flds
+ }
### Helpers
--
GitLab