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Rename to StackParams, move undershoots into Params

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jaknapper 2025-06-23 13:45:26 +01:00
parent 7cff0f8f44
commit ee128ad91f
1 changed files with 45 additions and 36 deletions
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81
src/openflexure_microscope_server/things/autofocus.py
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@ -29,8 +29,9 @@ from .camera import CameraDependency as WrappedCamera
from .stage import StageDependency as Stage from .stage import StageDependency as Stage
from .capture import RawCaptureDependency as CaptureDep from .capture import RawCaptureDependency as CaptureDep
class StackInfo(BaseModel):
"""Dataclass with default scan parameters""" class StackParams(BaseModel):
"""Pydantic model for scan parameters"""
# These are generic settings that seem to apply well to a standard scan # These are generic settings that seem to apply well to a standard scan
# and are not altered by default when running a scan # and are not altered by default when running a scan
@ -51,7 +52,7 @@ class StackInfo(BaseModel):
# how far below (in factors of stack_dz) the estimated optimal starting position to # how far below (in factors of stack_dz) the estimated optimal starting position to
# begin the stack. Better to start slightly too low and require many images, rather than # begin the stack. Better to start slightly too low and require many images, rather than
# too high and needing to autofocus and restart the stack # too high and needing to autofocus and restart the stack
undershoot: int = 5 img_undershoot: int = 5
# These we expect to be overwritten by AutofocusThing properties # These we expect to be overwritten by AutofocusThing properties
stack_dz: int = 50 stack_dz: int = 50
@ -59,6 +60,14 @@ class StackInfo(BaseModel):
images_to_test: int = 5 images_to_test: int = 5
autofocus_dz: int = 2000 autofocus_dz: int = 2000
stack_z_range: int = stack_dz * (images_to_test - 1)
# Starting too low by "steps_undershoot" makes smart stacking faster.
# Starting a stack too high requires it to move to the start,
# autofocus and then re-stack. Starting slightly too low only
# requires extra +z movements and captures.
steps_undershoot: int = stack_dz * img_undershoot
class JPEGSharpnessMonitor: class JPEGSharpnessMonitor:
__globals__ = globals() # Required for FastAPI dependency __globals__ = globals() # Required for FastAPI dependency
@ -334,20 +343,13 @@ class AutofocusThing(Thing):
""" """
# Set the variables to prevent changes from the GUI or other windows # Set the variables to prevent changes from the GUI or other windows
stack_parameters = StackInfo( stack_parameters = StackParams(
stack_dz = self.stack_dz, stack_dz=self.stack_dz,
images_to_capture = self.stack_images_to_capture, images_to_capture=self.stack_images_to_capture,
images_to_test = self.stack_images_to_test, images_to_test=self.stack_images_to_test,
autofocus_dz = autofocus_dz autofocus_dz=autofocus_dz,
) )
stack_z_range = stack_parameters.stack_dz * (stack_parameters.images_to_test - 1)
# Starting too low by "undershoot" makes smart stacking faster.
# Starting a stack too high requires it to move to the start,
# autofocus and then re-stack. Starting slightly too low only
# requires extra +z movements and captures.
undershoot = stack_parameters.stack_dz * stack_parameters.undershoot
# Ensure the stack settings are appropriate # Ensure the stack settings are appropriate
self.validate_stack_inputs(stack_parameters) self.validate_stack_inputs(stack_parameters)
@ -356,8 +358,6 @@ class AutofocusThing(Thing):
while not success: while not success:
result, heights, captures, sharpest_index = self.z_stack( result, heights, captures, sharpest_index = self.z_stack(
images_dir, images_dir,
stack_z_range,
undershoot,
stack_parameters, stack_parameters,
stage, stage,
cam, cam,
@ -387,7 +387,7 @@ class AutofocusThing(Thing):
) )
# Return the z position of the sharpest image, for path planning and tracking # Return the z position of the sharpest image, for path planning and tracking
return heights[-stack_parameters.images_to_test:][sharpest_index] return heights[-stack_parameters.images_to_test :][sharpest_index]
def reset_stack( def reset_stack(
self, self,
@ -415,7 +415,7 @@ class AutofocusThing(Thing):
self, self,
sharpest_index: int, sharpest_index: int,
captures: list[list], captures: list[list],
stack_parameters: StackInfo, stack_parameters: StackParams,
logger: InvocationLogger, logger: InvocationLogger,
capture: CaptureDep, capture: CaptureDep,
) -> int: ) -> int:
@ -425,7 +425,7 @@ class AutofocusThing(Thing):
Arguments: Arguments:
sharpest_index: the index of the sharpest image, within the "images_to_test" slice sharpest_index: the index of the sharpest image, within the "images_to_test" slice
captures: a list of captures, including file name, image data and metadata captures: a list of captures, including file name, image data and metadata
stack_parameters: a StackInfo dataclass with stack settings stack_parameters: a StackParams Pydantic model with stack settings
variables logger and capture are Thing dependencies passed through from the calling action variables logger and capture are Thing dependencies passed through from the calling action
""" """
# Find the range of images from the stack to capture # Find the range of images from the stack to capture
@ -437,9 +437,11 @@ class AutofocusThing(Thing):
# Loop through the range, saving each capture to disk # Loop through the range, saving each capture to disk
for capture_index in stack_range: for capture_index in stack_range:
capture._save_capture( capture._save_capture(
jpeg_path=captures[-stack_parameters.images_to_test:][capture_index][0], jpeg_path=captures[-stack_parameters.images_to_test :][capture_index][
image=captures[-stack_parameters.images_to_test:][capture_index][1], 0
metadata=captures[-stack_parameters.images_to_test:][capture_index][2], ],
image=captures[-stack_parameters.images_to_test :][capture_index][1],
metadata=captures[-stack_parameters.images_to_test :][capture_index][2],
logger=logger, logger=logger,
) )
return sharpest_index return sharpest_index
@ -447,9 +449,7 @@ class AutofocusThing(Thing):
def z_stack( def z_stack(
self, self,
images_dir: str, images_dir: str,
stack_z_range: int, stack_parameters: StackParams,
overshoot: int,
stack_parameters: StackInfo,
stage: Stage, stage: Stage,
cam: WrappedCamera, cam: WrappedCamera,
capture: CaptureDep, capture: CaptureDep,
@ -463,14 +463,18 @@ class AutofocusThing(Thing):
Arguments: Arguments:
images_dir: a string of the path to write all images images_dir: a string of the path to write all images
stack_z_range: the height in steps of the stack to test stack_parameters: a StackParams Pydantic model with stack settings
overshoot: how far below the estimated optimal starting position to begin stacking
stack_parameters: a StackInfo dataclass with stack settings
variables stage to metadata_getter are Thing dependencies passed through from the calling action variables stage to metadata_getter are Thing dependencies passed through from the calling action
""" """
# Move down by the height of the z stack, plus an overshoot # Move down by the height of the z stack, plus an overshoot
# Better to start too low and take too many images than too high and need to refocus # Better to start too low and take too many images than too high and need to refocus
stage.move_relative(z=-(overshoot + stack_parameters.backlash_correction + stack_z_range / 2)) stage.move_relative(
z=-(
stack_parameters.steps_undershoot
+ stack_parameters.backlash_correction
+ stack_parameters.stack_z_range / 2
)
)
stage.move_relative(z=stack_parameters.backlash_correction) stage.move_relative(z=stack_parameters.backlash_correction)
captures = [] captures = []
@ -496,10 +500,14 @@ class AutofocusThing(Thing):
# If the number of images is enough to test, test them # If the number of images is enough to test, test them
if len(captures) >= stack_parameters.images_to_test: if len(captures) >= stack_parameters.images_to_test:
stack_result = self.check_stack_result(sharpnesses[-stack_parameters.images_to_test:]) stack_result = self.check_stack_result(
sharpnesses[-stack_parameters.images_to_test :]
)
if stack_result == "success": if stack_result == "success":
sharpest_index = np.argmax(sharpnesses[-stack_parameters.images_to_test:]) sharpest_index = np.argmax(
sharpnesses[-stack_parameters.images_to_test :]
)
return "success", heights, captures, sharpest_index return "success", heights, captures, sharpest_index
if stack_result == "restart": if stack_result == "restart":
@ -545,9 +553,7 @@ class AutofocusThing(Thing):
return captures, heights, sharpnesses return captures, heights, sharpnesses
def validate_stack_inputs( def validate_stack_inputs(self, stack_parameters) -> None:
self, stack_parameters
) -> None:
"""Check the stack settings are appropriate, and raise an error if not """Check the stack settings are appropriate, and raise an error if not
Arguments: Arguments:
@ -560,7 +566,10 @@ class AutofocusThing(Thing):
) )
if stack_parameters.images_to_test % 2 == 0: if stack_parameters.images_to_test % 2 == 0:
raise RuntimeError("Images to test should be odd") raise RuntimeError("Images to test should be odd")
if stack_parameters.images_to_test <= 0 or stack_parameters.images_to_capture <= 0: if (
stack_parameters.images_to_test <= 0
or stack_parameters.images_to_capture <= 0
):
raise RuntimeError("Stack parameters need to be at least 1") raise RuntimeError("Stack parameters need to be at least 1")
def check_stack_result(self, sharpnesses: list[int]) -> str: def check_stack_result(self, sharpnesses: list[int]) -> str: