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