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Looping autofocus on failed smart stack

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This commit is contained in:
jaknapper 2025-06-10 18:24:12 +01:00
parent 3e164102f6
commit 712f524414
1 changed files with 10 additions and 19 deletions
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29
src/openflexure_microscope_server/things/autofocus.py
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@ -12,8 +12,6 @@ import logging
import time import time
from typing import Annotated, Mapping, Optional, Sequence from typing import Annotated, Mapping, Optional, Sequence
import os import os
import shutil
import glob
from fastapi import Depends from fastapi import Depends
import numpy as np import numpy as np
@ -297,6 +295,7 @@ class AutofocusThing(Thing):
metadata_getter: GetThingStates, metadata_getter: GetThingStates,
capture: CaptureDep, capture: CaptureDep,
images_dir: str, images_dir: str,
sharpness_monitor: SharpnessMonitorDep,
) -> None: ) -> None:
"""Run a z stack, saving all images to stack_dir and copying the """Run a z stack, saving all images to stack_dir and copying the
central image to stack_dir""" central image to stack_dir"""
@ -355,9 +354,16 @@ class AutofocusThing(Thing):
sharpnesses = [] sharpnesses = []
heights = [] heights = []
capture_count = 0 capture_count = 0
stage.move_absolute( stage.move_absolute(z=starting_height - stack_z_range)
z=starting_height - stack_dz * (images_to_test - 1) self.looping_autofocus(
stage=stage,
sharpness_monitor=sharpness_monitor,
dz=2000,
) )
stage.move_relative(
z=-(overshoot + backlash_correction + stack_z_range / 2)
)
stage.move_relative(z=backlash_correction)
stage.move_relative(z=stack_dz) stage.move_relative(z=stack_dz)
sharpest_index = np.argmax(sharpnesses[-images_to_test:]) sharpest_index = np.argmax(sharpnesses[-images_to_test:])
@ -370,21 +376,6 @@ class AutofocusThing(Thing):
return heights[-images_to_test:][sharpest_index] return heights[-images_to_test:][sharpest_index]
def copy_central_image_from_stack(
self,
images_dir: str,
stack_dir: str,
):
"""Gets a list of images in a folder (stack_dir), sorts them, and copies the central image
to images dir."""
image_list = glob.glob(os.path.join(stack_dir, "*"))
image_list.sort()
central_index = (len(image_list) - 1) // 2
central_image = image_list[central_index]
xy_location = os.path.basename(stack_dir)
shutil.copy(central_image, os.path.join(images_dir, f"{xy_location}.jpeg"))
def test_stack(self, sharpnesses: list): def test_stack(self, sharpnesses: list):
"""Test a list of sharpnesses, to decide whether the focal plane is within them""" """Test a list of sharpnesses, to decide whether the focal plane is within them"""
sharpest_index = np.argmax(sharpnesses) sharpest_index = np.argmax(sharpnesses)