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Lint and type fixes

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This commit is contained in:
Richard Bowman 2022-04-06 23:36:55 +01:00
parent cfb1bb09a6
commit 7f66235cac
1 changed files with 39 additions and 19 deletions
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58
openflexure_microscope/api/default_extensions/scan.py
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@ -2,10 +2,10 @@ import datetime
import logging
import time
import uuid
from functools import reduce
from typing import Dict, List, Optional, Tuple
import marshmallow
import numpy as np
from labthings import (
current_action,
fields,
@ -15,7 +15,6 @@ from labthings import (
)
from labthings.extensions import BaseExtension
from labthings.views import ActionView
import numpy as np
from typing_extensions import Literal
from openflexure_microscope.api.v2.views.actions.camera import FullCaptureArgs
@ -36,7 +35,7 @@ def construct_grid(
step_sizes: XyCoordinate,
n_steps: XyCoordinate,
style: Literal["raster", "snake", "spiral"] = "raster",
):
) -> List[List[XyCoordinate]]:
"""
Given an initial position, step sizes, and number of steps,
construct a 2-dimensional list of scan x-y positions.
@ -96,7 +95,9 @@ def construct_grid(
return arr
def closest_point_in_xy(current_position: XyCoordinate, points: List[XyzCoordinate]):
def closest_point_in_xy(
current_position: XyCoordinate, points: List[XyzCoordinate]
) -> Optional[XyzCoordinate]:
"""Find the closest point in a list
Given a 2D position, find the 3D position that's closest in XY and return it.
@ -108,16 +109,14 @@ def closest_point_in_xy(current_position: XyCoordinate, points: List[XyzCoordina
return None
points_2d = np.asarray(points)[:, :2]
squared_distances = np.sum((points_2d - current_position)**2, axis=1)
squared_distances = np.sum((points_2d - current_position) ** 2, axis=1)
# We reverse the distances before searching, as argmin will return the first
# point in the event of there being multiple points with the same minimum,
# and we want to pick the last one.
reverse_min_index = np.argmin(squared_distances[::-1])
# of course, now we must convert the index to be the right way round
min_index = len(points) - 1 - reverse_min_index
if min_index != len(points) - 1:
logging.info(f"Using point {min_index} of {len(points)} for focus.")
return points[min_index]
return points[int(min_index)] # The explicit cast is necessary for MyPy
### Capturing
@ -200,7 +199,7 @@ class ScanExtension(BaseExtension):
metadata: Optional[dict] = None,
annotations: Optional[Dict[str, str]] = None,
tags: Optional[List[str]] = None,
detect_empty_fields_and_skip_autofocus: bool = False
detect_empty_fields_and_skip_autofocus: bool = False,
):
metadata = metadata or {}
annotations = annotations or {}
@ -213,7 +212,7 @@ class ScanExtension(BaseExtension):
# Construct an x-y grid (worry about z later)
x_y_grid = construct_grid(
initial_position[:2], stride_size[:2], grid[:2], style=style
) # This is a list of lists.
) # This is a list of lists.
# Keep task progress
# NB the number of points is found from the number of elements in
@ -225,7 +224,6 @@ class ScanExtension(BaseExtension):
if not basename:
basename = generate_basename()
# Add dataset metadata
dataset_d = {
"id": uuid.uuid4(),
@ -252,11 +250,17 @@ class ScanExtension(BaseExtension):
if detect_empty_fields_and_skip_autofocus:
# Check for the background detect extension if we need it, 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.")
raise RuntimeError(
"Detecting background fields requires the background detect extension and it was not found."
)
focused_positions: List[XyzCoordinate] = [] # Positions where we found sharp images
focused_positions: List[
XyzCoordinate
] = [] # Positions where we found sharp images
# Now step through each point in the x-y coordinate array
for line in x_y_grid:
@ -267,7 +271,11 @@ class ScanExtension(BaseExtension):
# point, except when we're at the start of a row when it will be the first
# point of the preceding row.
closest_focused_point = closest_point_in_xy(x_y, focused_positions)
next_z = closest_focused_point[2] if closest_focused_point else initial_position[2]
next_z = (
closest_focused_point[2]
if closest_focused_point
else initial_position[2]
)
# Move to new grid position
logging.debug("Moving to step %s", ([x_y[0], x_y[1], next_z]))
microscope.stage.move_abs((x_y[0], x_y[1], next_z))
@ -279,7 +287,9 @@ class ScanExtension(BaseExtension):
logging.debug(f"Background detection verdict: {verdict}")
if verdict["classification"] == "background":
skip_autofocus = True
logging.info(f"Detected an empty field at {x_y}, skipping autofocus.")
logging.info(
f"Detected an empty field at {x_y}, skipping autofocus."
)
if autofocus_enabled and not skip_autofocus:
if fast_autofocus:
@ -297,11 +307,19 @@ class ScanExtension(BaseExtension):
here = microscope.stage.position
# Check if we've moved worryingly far in Z
if closest_focused_point:
lateral_move = np.sqrt(np.sum((np.array(here)[:2] - np.array(closest_focused_point)[:2])**2))
lateral_move = np.sqrt(
np.sum(
(
np.array(here)[:2]
- np.array(closest_focused_point)[:2]
)
** 2
)
)
axial_move = np.abs(here[2] - closest_focused_point[2])
if axial_move > lateral_move * 0.4:
autofocus_accepted = False
logging.warn(
logging.warning(
f"During a scan, there was a large axial jump from {closest_focused_point}"
f" to {here}. This may mean autofocus has failed."
)
@ -473,5 +491,7 @@ class TileScanAPI(ActionView):
fast_autofocus=args.get("fast_autofocus"),
annotations=args.get("annotations"),
tags=args.get("tags"),
detect_empty_fields_and_skip_autofocus=args.get("detect_empty_fields_and_skip_autofocus"),
detect_empty_fields_and_skip_autofocus=args.get(
"detect_empty_fields_and_skip_autofocus"
),
)