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Typehint added and import removed.

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Chish36 2025-08-06 16:51:20 +01:00 • committed by Julian Stirling
parent 1afaa53413
commit ab9a324122
1 changed files with 22 additions and 21 deletions
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43
src/openflexure_microscope_server/things/stage_measure.py
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@ -14,7 +14,6 @@ this is 10% of the expected motion is the measured axis.
""" """
import numpy as np import numpy as np
import cv2
from typing import Literal from typing import Literal
from PIL import Image from PIL import Image
import time import time
@ -94,6 +93,7 @@ def _predict_z(
return z_dest - stage.position["z"] return z_dest - stage.position["z"]
def _move_and_measure( def _move_and_measure(
step_size: dict[str, float], step_size: dict[str, float],
axis: Literal["x", "y"], axis: Literal["x", "y"],
@ -127,8 +127,8 @@ def _move_and_measure(
autofocus.looping_autofocus(dz=800) autofocus.looping_autofocus(dz=800)
image2 = np.array(Image.open(cam.grab_jpeg().open())) image2 = np.array(Image.open(cam.grab_jpeg().open()))
offset = fft_image_tracking.displacement_between_images( offset = fft_image_tracking.displacement_between_images(
image_0=image1, image_1=image2, sigma=10, fractional_threshold=0.1, pad=True image_0=image1, image_1=image2, sigma=10, fractional_threshold=0.1, pad=True
) # Units is pixels ) # Units is pixels
data.delta["x"] = int(offset[1]) data.delta["x"] = int(offset[1])
data.delta["y"] = int(offset[0]) data.delta["y"] = int(offset[0])
@ -164,7 +164,7 @@ def _acquire_z_predict_points(
medium_step, stream_resolution, direction, factor=0.1 medium_step, stream_resolution, direction, factor=0.1
) )
for _loop in range(5): for _loop in range(5):
image1 = np.array(Image.open(cam.grab_jpeg().open())) image1 = np.array(Image.open(cam.grab_jpeg().open()))
offset, wrong_axis = _move_and_measure( offset, wrong_axis = _move_and_measure(
step_size=_generate_move_dicts(medium_step, stream_resolution, direction), step_size=_generate_move_dicts(medium_step, stream_resolution, direction),
axis=axis, axis=axis,
@ -175,6 +175,7 @@ def _acquire_z_predict_points(
autofocus=autofocus, autofocus=autofocus,
cam=cam, cam=cam,
) )
logger.info(f"Offset measured as {data.delta[axis]}") logger.info(f"Offset measured as {data.delta[axis]}")
data.measure(stage.position, offset) data.measure(stage.position, offset)
@ -247,13 +248,13 @@ def _check_stage_operation(
image2 = np.array(Image.open(cam.grab_jpeg().open())) image2 = np.array(Image.open(cam.grab_jpeg().open()))
failure_count += 1 failure_count += 1
offset = fft_image_tracking.displacement_between_images( offset = fft_image_tracking.displacement_between_images(
image_0=image1, image_0=image1,
image_1=image2, image_1=image2,
sigma=10, sigma=10,
fractional_threshold=0.1, fractional_threshold=0.1,
pad=True, pad=True,
) )
# Units is pixels # Units is pixels
data.delta["x"] = int(offset[1]) data.delta["x"] = int(offset[1])
data.delta["y"] = int(offset[0]) data.delta["y"] = int(offset[0])
logger.info( logger.info(
@ -282,7 +283,7 @@ def _motion_detection(
stage: StageDep, stage: StageDep,
cam: CamDep, cam: CamDep,
logger: lt.deps.InvocationLogger, logger: lt.deps.InvocationLogger,
) -> dict: ) -> dict[str, int]:
"""Move the stage until motion is detected along a specified axis and direction. """Move the stage until motion is detected along a specified axis and direction.
:params axis: The axis in which the stage is moving. This must be 'x' or 'y'. :params axis: The axis in which the stage is moving. This must be 'x' or 'y'.
@ -309,12 +310,12 @@ def _motion_detection(
csm.move_in_image_coordinates(x=this_motion_step["x"], y=this_motion_step["y"]) csm.move_in_image_coordinates(x=this_motion_step["x"], y=this_motion_step["y"])
image2 = np.array(Image.open(cam.grab_jpeg().open())) image2 = np.array(Image.open(cam.grab_jpeg().open()))
offset = fft_image_tracking.displacement_between_images( offset = fft_image_tracking.displacement_between_images(
image_0=image1, image_0=image1,
image_1=image2, image_1=image2,
sigma=10, sigma=10,
fractional_threshold=0.1, fractional_threshold=0.1,
pad=True, pad=True,
) )
delta["x"] = int(offset[1]) delta["x"] = int(offset[1])
delta["y"] = int(offset[0]) delta["y"] = int(offset[0])
logger.info(f"Offset measured as {np.abs(delta[axis])}") logger.info(f"Offset measured as {np.abs(delta[axis])}")
@ -523,9 +524,9 @@ class RangeofMotionThing(lt.Thing):
direction=axis_dir[1], direction=axis_dir[1],
) )
# Save results from single axis and direction # Save results from single axis and direction
rom_results[f"{'positive' if axis_dir[1] == 1 else 'negative'} {axis_dir[0]}"] = ( rom_results[
axis_dir_results f"{'positive' if axis_dir[1] == 1 else 'negative'} {axis_dir[0]}"
) ] = axis_dir_results
end_time = time.time() end_time = time.time()
total_time = (end_time - start_time) / 60 total_time = (end_time - start_time) / 60