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Linter/type checking fixes

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This commit is contained in:
Richard Bowman 2022-04-20 13:31:33 +01:00
parent 18145d4b67
commit e356d11e7e
1 changed files with 49 additions and 29 deletions
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78
openflexure_microscope/api/default_extensions/scan.py
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@ -2,7 +2,7 @@ import datetime
import logging
import time
import uuid
from typing import Dict, List, Optional, Tuple, Callable
from typing import Callable, Dict, List, Optional, Tuple
import marshmallow
import numpy as np
@ -29,6 +29,7 @@ XyzCoordinate = Tuple[int, int, int]
### Grid construction
class FocusManager:
"""Manage axial motion during a series of XY moves
@ -36,21 +37,22 @@ class FocusManager:
It currently uses the regular autofocus method, and has support
for background detection.
"""
initial_position: XyzCoordinate = None
focused_positions: List[XyzCoordinate] = None
current_image_is_background: Optional[Callable] = None
autofocus: Optional[Callable] = None
microscope: Microscope = None
initial_position: XyzCoordinate = None # type: ignore[assignment]
focused_positions: List[XyzCoordinate] = None # type: ignore[assignment]
microscope: Microscope = None # type: ignore[assignment]
current_image_is_background_function: Optional[Callable] = None
autofocus_function: Optional[Callable] = None
axial_jump_threshold: Optional[float] = None
def __init__(
self,
self,
microscope: Microscope,
initial_position: XyzCoordinate,
autofocus_function: Optional[Callable],
current_image_is_background_function: Optional[Callable] = None,
axial_jump_threshold: Optional[float] = 0.4
):
axial_jump_threshold: Optional[float] = 0.4,
):
"""Set up management of axial motion.
The `FocusManager` keeps track of previous positions where the
@ -74,19 +76,19 @@ class FocusManager:
use background estimation.
"""
self.initial_position = initial_position
self.focused_positions = []
self.microscope = microscope
self.autofocus_function = autofocus_function
if not autofocus_function:
logging.info("Setting up FocusManager with autofocus disabled.")
self.current_image_is_background_function = current_image_is_background_function
self.axial_jump_threshold = axial_jump_threshold
self.focused_positions = []
def record_focused_point(self, position: XyzCoordinate):
"""Add a position to the list of successfully-focused points"""
self.focused_positions.append(position)
def closest_focused_point(self, position: XyCoordinate) -> XyzCoordinate:
def closest_focused_point(self, position: XyCoordinate) -> Optional[XyzCoordinate]:
"""The closest point in our list of focused points to a given XY position."""
return closest_point_in_xy(position, self.focused_positions)
@ -122,9 +124,11 @@ class FocusManager:
"""
if not self.axial_jump_threshold:
return False
closest_focused_point = self.closest_focused_point(position)
closest_focused_point = self.closest_focused_point(position[:2])
if not closest_focused_point:
return False
move = np.array(position) - np.array(closest_focused_point)
lateral_move = np.sqrt(np.sum(move[:2]**2))
lateral_move = np.sqrt(np.sum(move[:2] ** 2))
axial_move = np.abs(move[2])
return axial_move > lateral_move * self.axial_jump_threshold
@ -160,7 +164,6 @@ class FocusManager:
self.record_focused_point(here)
def construct_grid(
initial: XyCoordinate,
step_sizes: XyCoordinate,
@ -225,6 +228,7 @@ def construct_grid(
return arr
def construct_grid_1d(
initial: XyCoordinate,
step_sizes: XyCoordinate,
@ -237,7 +241,9 @@ def construct_grid_1d(
but the list-of-lists is flattened to a simple list.
"""
path = []
grid = construct_grid(initial=initial, step_sizes=step_sizes, n_steps=n_steps, style=style)
grid = construct_grid(
initial=initial, step_sizes=step_sizes, n_steps=n_steps, style=style
)
for line in grid:
path += line # concatenate the lists
return path
@ -340,38 +346,49 @@ class ScanExtension(BaseExtension):
# Locate the autofocus extension
autofocus_extension = find_extension("org.openflexure.autofocus")
if not autofocus_extension:
raise RuntimeError("The Autofocus extension is missing: select 'None' as your autofocus type to scan without autofocusing.")
raise RuntimeError(
"The Autofocus extension is missing: select 'None' as your autofocus "
"type to scan without autofocusing."
)
if not (microscope.has_real_stage() and microscope.has_real_camera()):
raise RuntimeError("A real stage and camera are needed in order to autofocus. You can still run a scan without autofocus.")
raise RuntimeError(
"A real stage and camera are needed in order to autofocus. You can "
"still run a scan without autofocus."
)
if use_fast_autofocus:
def autofocus():
# Run fast autofocus. Client should provide dz ~ 2000
autofocus_extension.fast_autofocus(microscope, dz=dz)
time.sleep(0.5)
return autofocus
else:
def autofocus():
# Run slow autofocus. Client should provide dz ~ 50
autofocus_extension.autofocus(
microscope,
range(-3 * dz, 4 * dz, dz),
)
autofocus_extension.autofocus(microscope, range(-3 * dz, 4 * dz, dz))
time.sleep(0.5)
return autofocus
def get_background_detect_function(self):
"""Return a function that returns true if we are looking at background"""
# Check for the background detect extension, raise an error now if it's missing.
background_detect_extension = find_extension("org.openflexure.background-detect")
background_detect_extension = find_extension(
"org.openflexure.background-detect"
)
if not background_detect_extension:
raise RuntimeError(
"Detecting background fields requires the background detect extension and it was not found."
)
def current_image_is_background():
verdict = background_detect_extension.grab_and_classify_image()
logging.debug(f"Background detection verdict: {verdict}")
return verdict["classification"] == "background"
return current_image_is_background
### Scanning
@ -428,10 +445,11 @@ class ScanExtension(BaseExtension):
}
# Perform set-up to be able to autofocus, if needed
autofocus: Optional[Callable] = None
if autofocus_dz:
autofocus = self.get_autofocus_function(dz=autofocus_dz, use_fast_autofocus=fast_autofocus)
else:
autofocus = None
autofocus = self.get_autofocus_function(
dz=autofocus_dz, use_fast_autofocus=fast_autofocus
)
if detect_empty_fields_and_skip_autofocus:
current_image_is_background = self.get_background_detect_function()
else:
@ -439,9 +457,11 @@ class ScanExtension(BaseExtension):
focus_manager = FocusManager(
microscope,
initial_position,
autofocus_function = autofocus,
current_image_is_background_function = current_image_is_background,
axial_jump_threshold = 0.4 if detect_empty_fields_and_skip_autofocus else None
autofocus_function=autofocus,
current_image_is_background_function=current_image_is_background,
axial_jump_threshold=0.4
if detect_empty_fields_and_skip_autofocus
else None,
)
# Now step through each point in the x-y coordinate array