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Merge branch 'jpeg-capture-in-stacking' into 'v3'

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2MP from 8MP capturing

Closes #364, #413, #298, #303, #288, #358, and #433

See merge request openflexure/openflexure-microscope-server!251
This commit is contained in:
Joe Knapper 2025-06-25 17:57:51 +00:00
commit 378998d230
15 changed files with 2085 additions and 315 deletions
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62
src/openflexure_microscope_server/things/autofocus.py
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@ -23,16 +23,14 @@ from labthings_fastapi.dependencies.blocking_portal import BlockingPortal
from labthings_fastapi.decorators import thing_action, thing_property
from labthings_fastapi.dependencies.metadata import GetThingStates
from labthings_fastapi.types.numpy import NDArray
from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
from labthings_fastapi.dependencies.invocation import InvocationLogger
from .camera import RawCameraDependency as Camera
from .camera import CameraDependency as WrappedCamera
from .stage import StageDependency as Stage
from .capture import CaptureThing
CaptureDep = direct_thing_client_dependency(CaptureThing, "/capture/")
STACK_OVERSHOOT = 200
SETTLING_TIME = 0.3
@ -282,9 +280,9 @@ class AutofocusThing(Thing):
stage: Stage,
logger: InvocationLogger,
metadata_getter: GetThingStates,
capture: CaptureDep,
images_dir: str,
stack_dir: str,
capture_resolution: tuple[int, int],
) -> None:
"""Run a z stack, saving all images to stack_dir and copying the
central image to stack_dir"""
@ -292,27 +290,41 @@ class AutofocusThing(Thing):
images_to_capture = self.stack_images_to_capture
stack_z_range = stack_dz * (images_to_capture - 1)
stage.move_relative(z=-stack_z_range / 2)
if stack_z_range > 0:
# Perform backlash corrected move. See issue #420
stage.move_relative(z=-(STACK_OVERSHOOT + stack_z_range / 2))
stage.move_relative(z=STACK_OVERSHOOT)
time.sleep(0.3)
for capture_count in range(images_to_capture):
time.sleep(SETTLING_TIME)
jpeg_path = os.path.join(
stack_dir,
f"{capture_count}.jpeg",
)
capture._capture_and_save(
jpeg_path=jpeg_path,
cam=cam,
logger=logger,
metadata_getter=metadata_getter,
)
jpeg_path = os.path.join(stack_dir, f"{capture_count}.jpeg")
start_time = time.time()
cam.capture_to_memory(logger=logger, metadata_getter=metadata_getter)
captured_time = time.time()
# If the stack isn't complete yet, move
if capture_count + 1 < images_to_capture:
stage.move_relative(z=stack_dz)
moved_time = time.time()
self.copy_central_image_from_stack(images_dir, stack_dir)
cam.save_from_memory(
jpeg_path=jpeg_path,
logger=logger,
save_resolution=capture_resolution,
)
saved_time = time.time()
time_remaining = SETTLING_TIME - (saved_time - start_time)
if time_remaining > 0:
time.sleep(time_remaining)
logger.info(f"Settled for an extra {round(time_remaining, 3)} seconds")
logger.debug(f"Capturing took {round(captured_time - start_time, 2)} s")
logger.debug(f"Saving took {round(saved_time - moved_time, 2)} s")
logger.debug(
f"Effective settling time was {round(time.time() - moved_time, 2)} s"
)
self.copy_sharpest_image_from_stack(images_dir, stack_dir, logger)
def copy_central_image_from_stack(
self,
@ -328,3 +340,19 @@ class AutofocusThing(Thing):
xy_location = os.path.basename(stack_dir)
shutil.copy(central_image, os.path.join(images_dir, f"{xy_location}.jpeg"))
def copy_sharpest_image_from_stack(
self,
images_dir: str,
stack_dir: str,
logger: InvocationLogger,
) -> None:
"""Gets a list of images in a folder (stack_dir), sorts them by filesize, and copies the sharpest
image to images dir."""
image_list = glob.glob(os.path.join(stack_dir, "*"))
image_list = sorted(image_list, key=os.path.getsize)
sharpest_image = image_list[-1]
xy_location = os.path.basename(stack_dir)
logger.info(sharpest_image)
shutil.copy(sharpest_image, os.path.join(images_dir, f"{xy_location}.jpeg"))