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