From 1d82fe1188aacd53e234a5ff373e7997400bde6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Thu, 23 Jun 2022 13:57:51 +0100
Subject: [PATCH] add static typing and clean separators
---
aliby/tile/tiler.py | 61 ++++++---------------------------------------
1 file changed, 7 insertions(+), 54 deletions(-)
diff --git a/aliby/tile/tiler.py b/aliby/tile/tiler.py
index d22c7f77..de383b5a 100644
--- a/aliby/tile/tiler.py
+++ b/aliby/tile/tiler.py
@@ -30,8 +30,6 @@ class Trap:
self.half_size = size // 2
self.max_size = max_size
- ###
-
def padding_required(self, tp):
"""
Check if we need to pad the trap image for this time point.
@@ -51,8 +49,6 @@ class Trap:
drifts = self.parent.drifts
return self.centre - np.sum(drifts[: tp + 1], axis=0)
- ###
-
def as_tile(self, tp):
"""
Return trap in the OMERO tile format of x, y, w, h
@@ -65,8 +61,6 @@ class Trap:
y = int(y - self.half_size)
return x, y, self.size, self.size
- ###
-
def as_range(self, tp):
"""
Return trap in a range format: two slice objects that can
@@ -76,9 +70,6 @@ class Trap:
return slice(x, x + w), slice(y, y + h)
-###
-
-
class TrapLocations:
"""
Stores each trap as an instance of Trap.
@@ -105,8 +96,6 @@ class TrapLocations:
def __iter__(self):
yield from self.traps
- ###
-
@property
def shape(self):
"""
@@ -133,8 +122,6 @@ class TrapLocations:
res["drifts"] = np.expand_dims(self.drifts[tp], axis=0)
return res
- ###
-
@classmethod
def from_tiler_init(cls, initial_location, tile_size, max_size=1200):
"""
@@ -158,16 +145,10 @@ class TrapLocations:
return trap_locs
-###
-
-
class TilerParameters(ParametersABC):
_defaults = {"tile_size": 117, "ref_channel": "Brightfield", "ref_z": 0}
-####
-
-
class Tiler(ProcessABC):
"""
Remote Timelapse Tiler.
@@ -200,14 +181,17 @@ class Tiler(ProcessABC):
except Exception as e:
print(f"Warning:Tiler: No z_perchannel data: {e}")
- ###
-
@classmethod
def from_image(cls, image: Image, parameters: TilerParameters):
return cls(image.data, image.metadata, parameters)
@classmethod
- def from_hdf5(cls, image: Image, filepath, parameters=None):
+ def from_hdf5(
+ cls,
+ image: Union[Image, ImageLocal],
+ filepath: Union[str, PosixPath],
+ parameters: TilerParameters = None,
+ ):
trap_locs = TrapLocations.read_hdf5(filepath)
metadata = load_attributes(filepath)
metadata["channels"] = image.metadata["channels"]
@@ -227,16 +211,12 @@ class Tiler(ProcessABC):
tiler.n_processed = len(trap_locs.drifts)
return tiler
- ###
-
@lru_cache(maxsize=2)
def get_tc(self, t, c):
full = self.image[t, c].compute(scheduler="synchronous")
return full
- ###
-
@property
def shape(self):
"""
@@ -264,16 +244,7 @@ class Tiler(ProcessABC):
def n_traps(self):
return len(self.trap_locs)
- @property
- def finished(self):
- """
- Returns True if all channels have been processed
- """
- return self.n_processed == self.image.shape[0]
-
- ###
-
- def _initialise_traps(self, tile_size):
+ def _initialise_traps(self, tile_size: int):
"""
Find initial trap positions.
@@ -297,15 +268,11 @@ class Tiler(ProcessABC):
# store traps in an instance of TrapLocations
self.trap_locs = TrapLocations.from_tiler_init(trap_locs, tile_size)
- ###
-
def find_drift(self, tp):
"""
Find any translational drifts between two images at consecutive
time points using cross correlation
"""
- # TODO check that the drift doesn't move any tiles out of
- # the image, remove them from list if so
prev_tp = max(0, tp - 1)
# cross-correlate
drift, error, _ = phase_cross_correlation(
@@ -318,8 +285,6 @@ class Tiler(ProcessABC):
else:
self.trap_locs.drifts.append(drift.tolist())
- ###
-
def get_tp_data(self, tp, c):
traps = []
full = self.get_tc(tp, c)
@@ -330,16 +295,12 @@ class Tiler(ProcessABC):
traps.append(ndtrap)
return np.stack(traps)
- ###
-
def get_trap_data(self, trap_id, tp, c):
full = self.get_tc(tp, c)
trap = self.trap_locs.traps[trap_id]
ndtrap = self.ifoob_pad(full, trap.as_range(tp))
return ndtrap
- ###
-
def run_tp(self, tp):
"""
Find traps if they have not yet been found.
@@ -373,8 +334,6 @@ class Tiler(ProcessABC):
return None
- ###
-
# The next set of functions are necessary for the extraction object
def get_traps_timepoint(self, tp, tile_size=None, channels=None, z=None):
# FIXME we currently ignore the tile size
@@ -390,21 +349,15 @@ class Tiler(ProcessABC):
res.append(val)
return np.stack(res, axis=1)
- ###
-
def get_channel_index(self, item):
for i, ch in enumerate(self.channels):
if item in ch:
return i
- ###
-
def get_position_annotation(self):
# TODO required for matlab support
return None
- ###
-
@staticmethod
def ifoob_pad(full, slices): # TODO Remove when inheriting TilerABC
"""
--
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