Merge branch 'smart_stack_as_mixin' into 'v3'
Move smart stacking into a mixin so it can be re-used in other workflows See merge request openflexure/openflexure-microscope-server!554
This commit is contained in:
Joe Knapper
commit
74476f18a0
2 changed files with 192 additions and 118 deletions
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@ -10,6 +10,7 @@ from typing import (
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Literal,
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Mapping,
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Optional,
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Protocol,
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TypeVar,
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)
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@ -305,6 +306,145 @@ class RectGridWorkflow(
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return not self._csm.calibration_required
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class SmartStackCompatibleSettings(Protocol):
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"""A protocol for the minimum settings needed for smart stack to work."""
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capture_params: CaptureParams
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autofocus_params: AutofocusParams
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smart_stack_params: SmartStackParams
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class SmartStackMixin:
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"""A mixin for scan workflows that use smart stacking."""
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stack_images_to_save: int = lt.setting(default=1, ge=1, le=9)
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"""The number of images to save in a stack.
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Defaults to 1 unless you need to see either side of focus
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"""
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stack_min_images_to_test: int = lt.setting(
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default=9, ge=MIN_TEST_IMAGE_COUNT, le=MAX_TEST_IMAGE_COUNT
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)
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"""The minimum number of images to capture in a stack.
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This many images are captured and tested for focus, if the focus is not central
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enough more images may be captured. After new images are captured, this value sets
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the number of images used for checking if focus is achieved.
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Defaults to 9 which balances reliability and speed.
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"""
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stack_dz: int = lt.setting(default=50, ge=10, le=400)
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"""Distance in steps between images in a z-stack.
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Suggested values:
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* 50 for 60-100x
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* 100 for 40x
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* 200 for 20x
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"""
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@property
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def as_workflow(self) -> ScanWorkflow:
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"""Return self as a ScanWorkflow.
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Ensures this mixin is only used with ScanWorkflow instances,
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raising TypeError otherwise.
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"""
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if not isinstance(self, ScanWorkflow):
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raise TypeError("SmartStackMixin must be mixed into a ScanWorkflow")
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return self
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def create_smart_stack_params(self, save_on_failure: bool) -> SmartStackParams:
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"""Set up the parameters used for all smart stacks in a scan.
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:returns: A StackSmartParams object with the required parameters.
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"""
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# Coerce min_images_to_test parameter
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min_images_to_test = self.stack_min_images_to_test
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if min_images_to_test % 2 == 0:
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min_images_to_test += 1
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self.as_workflow.logger.warning(
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"Minimum number of images to test should be odd, setting to "
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f"{min_images_to_test}."
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)
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# Set the Thing property to the coerced value
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self.stack_min_images_to_test = min_images_to_test
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# Coerce the images to save parameter to be odd, and less than
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# min_images_to_save
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images_to_save = self.stack_images_to_save
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if images_to_save > min_images_to_test:
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self.as_workflow.logger.warning(
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f"Cannot save {images_to_save} images as this above the minimum "
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f"number to test. Setting images to save to {MAX_TEST_IMAGE_COUNT}."
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)
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images_to_save = min_images_to_test
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elif images_to_save % 2 == 0:
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images_to_save += 1
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self.as_workflow.logger.warning(
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f"Images to save should be odd, setting to {images_to_save}."
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)
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# Set the Thing property to the coerced value
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self.stack_images_to_save = images_to_save
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return SmartStackParams(
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stack_dz=self.stack_dz,
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images_to_save=self.stack_images_to_save,
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min_images_to_test=self.stack_min_images_to_test,
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save_on_failure=save_on_failure,
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)
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def _perform_smart_stack(
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self, settings: SmartStackCompatibleSettings, xyz_pos: tuple[int, int, int]
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) -> tuple[bool, Optional[int]]:
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"""Perform acquisition a smart stack.
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:param settings: The settings for this scan as a HistoScanSettingsModel
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:param xyz_pos: The current position as a tuple or 3 ints.
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:return: A tuple of whether an image was taken, and the z-position for focus.
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If failed to find focus, returns for the focus z-position.
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"""
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focus_height: Optional[int]
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focused, focus_height = self.as_workflow._autofocus.run_smart_stack(
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stack_parameters=settings.smart_stack_params,
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capture_parameters=settings.capture_params,
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autofocus_parameters=settings.autofocus_params,
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)
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# An image was captured if we are focussed or we are not skipping background.
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imaged = focused or settings.smart_stack_params.save_on_failure
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if not imaged:
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msg = f"Stack failed at {xyz_pos}. Treating as background."
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self.as_workflow.logger.info(msg)
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# run_smart_stage always returns a focus height for the sharpest image even
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# if it failed to find a good focus. Set to None if not focussed.
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if not focused:
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focus_height = None
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return imaged, focus_height
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def smart_stack_property_controls(self) -> list[PropertyControl]:
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"""Return smart stack property controls for the UI."""
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return [
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property_control_for(
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self.as_workflow,
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"stack_images_to_save",
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label="Images in Stack to Save",
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),
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property_control_for(
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self.as_workflow,
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"stack_min_images_to_test",
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label="Minimum number of images to test for focus",
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),
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property_control_for(
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self.as_workflow, "stack_dz", label="Stack dz (steps)", step=5
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),
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]
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class HistoScanSettingsModel(RectGridSettingsModel):
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"""The settings for a scan with the HistoScanWorkflow.
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@ -317,7 +457,7 @@ class HistoScanSettingsModel(RectGridSettingsModel):
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smart_stack_params: SmartStackParams
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class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel], SmartStackMixin):
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"""A workflow optimised for scanning Histopathology samples.
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This workflow automatically plans its own path around a sample spiralling out from
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@ -350,36 +490,6 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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max_range: int = lt.setting(default=45000, ge=0)
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"""The maximum distance in steps from the centre of the scan."""
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# Stacking settings
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stack_images_to_save: int = lt.setting(default=1, ge=1, le=9)
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"""The number of images to save in a stack.
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Defaults to 1 unless you need to see either side of focus
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"""
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stack_min_images_to_test: int = lt.setting(
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default=9, ge=MIN_TEST_IMAGE_COUNT, le=MAX_TEST_IMAGE_COUNT
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)
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"""The minimum number of images to capture in a stack.
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This many images are captures and tested for focus, if the focus is not central
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enough more images may be captured. After new images are captured, this value sets
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the number of images used for checking if focus is achieved.
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Defaults to 9 which balances reliability and speed.
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"""
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stack_dz: int = lt.setting(default=50, ge=10, le=400)
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"""Distance in steps between images in a z-stack.
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Suggested values:
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* 50 for 60-100x
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* 100 for 40x
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* 200 for 20x
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"""
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equal_distances: bool = lt.setting(default=False)
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"""Make the distances in x and y equal in motor steps, rather than in overlap.
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@ -443,49 +553,9 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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**base_kwargs,
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max_dist=self.max_range,
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skip_background=self.skip_background,
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smart_stack_params=self.create_smart_stack_params(),
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)
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def create_smart_stack_params(
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self,
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) -> SmartStackParams:
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"""Set up the parameters used for all smart stacks in a scan.
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:returns: A StackSmartParams object with the required parameters.
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"""
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# Coerce min_images_to_test parameter
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min_images_to_test = self.stack_min_images_to_test
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if min_images_to_test % 2 == 0:
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min_images_to_test += 1
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self.logger.warning(
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"Minimum number of images to test should be odd, setting to "
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f"{min_images_to_test}."
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)
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# Set the Thing property to the coerced value
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self.stack_min_images_to_test = min_images_to_test
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# Coerce the images to save parameter to be odd, and less than
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# min_images_to_save
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images_to_save = self.stack_images_to_save
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if images_to_save > min_images_to_test:
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self.logger.warning(
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f"Cannot save {images_to_save} images as this above the minimum "
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f"number to test. Setting images to save to {MAX_TEST_IMAGE_COUNT}."
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)
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images_to_save = min_images_to_test
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elif images_to_save % 2 == 0:
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images_to_save += 1
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self.logger.warning(
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f"Images to save should be odd, setting to {images_to_save}."
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)
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# Set the Thing property to the coerced value
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self.stack_images_to_save = images_to_save
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return SmartStackParams(
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stack_dz=self.stack_dz,
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images_to_save=self.stack_images_to_save,
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min_images_to_test=self.stack_min_images_to_test,
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save_on_failure=not self.skip_background,
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smart_stack_params=self.create_smart_stack_params(
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save_on_failure=not self.skip_background
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),
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)
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def pre_scan_routine(self, settings: HistoScanSettingsModel) -> None:
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@ -544,25 +614,7 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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self.logger.info(msg)
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return False, None
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focus_height: Optional[int]
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focused, focus_height = self._autofocus.run_smart_stack(
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stack_parameters=settings.smart_stack_params,
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capture_parameters=settings.capture_params,
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autofocus_parameters=settings.autofocus_params,
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)
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# An image was captured if we are focussed or we are not skipping background.
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imaged = focused or settings.smart_stack_params.save_on_failure
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if not imaged:
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msg = f"Stack failed at {xyz_pos}. Treating as background."
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self.logger.info(msg)
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# run_smart_stage always returns a focus height for the sharpest image even
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# if it failed to find a good focus. Set to None if not focussed.
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if not focused:
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focus_height = None
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return imaged, focus_height
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return self._perform_smart_stack(settings, xyz_pos)
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@lt.action
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def check_background(self) -> str:
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@ -594,17 +646,7 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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property_control_for(
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self, "overlap", label="Image Overlap (0.1-0.7)", step=0.05
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),
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property_control_for(
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self, "stack_images_to_save", label="Images in Stack to Save"
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),
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property_control_for(
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self,
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"stack_min_images_to_test",
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label="Minimum number of images to test for focus",
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),
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property_control_for(
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self, "stack_dz", label="Stack dz (steps)", step=5
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),
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*self.smart_stack_property_controls(),
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property_control_for(
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self, "autofocus_dz", label="Autofocus Range (steps)", step=200
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),
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@ -665,6 +707,7 @@ class RegularGridSettingsModel(RectGridSettingsModel):
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x_count: int
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y_count: int
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smart_stack_params: SmartStackParams
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style: Literal["snake", "raster"]
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@ -674,7 +717,9 @@ RegGridSettingModelType = TypeVar(
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class RegularGridWorkflow(
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RectGridWorkflow[RegGridSettingModelType], Generic[RegGridSettingModelType]
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RectGridWorkflow[RegGridSettingModelType],
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SmartStackMixin,
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Generic[RegGridSettingModelType],
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):
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"""A base workflow for any workflow that uses a regular rectangular grid."""
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@ -694,6 +739,7 @@ class RegularGridWorkflow(
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x_count=self.x_count,
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y_count=self.y_count,
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style=self._grid_style,
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smart_stack_params=self.create_smart_stack_params(save_on_failure=True),
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)
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def pre_scan_routine(self, settings: RegGridSettingModelType) -> None:
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@ -737,12 +783,7 @@ class RegularGridWorkflow(
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:return: A tuple of whether an image was taken, and the z-position for focus.
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If failed to find focus, returns for the focus z-position.
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"""
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return self._autofocus_and_capture(
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xyz_pos=xyz_pos,
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dz=settings.autofocus_params.dz,
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images_dir=settings.capture_params.images_dir,
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save_resolution=settings.capture_params.save_resolution,
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)
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return self._perform_smart_stack(settings, xyz_pos)
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@lt.endpoint("get", "settings_ui", responses=UI_ELEMENT_RESPONSE)
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def settings_ui(self) -> UIElementList:
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@ -754,6 +795,7 @@ class RegularGridWorkflow(
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),
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property_control_for(self, "x_count", label="Number of columns"),
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property_control_for(self, "y_count", label="Number of rows"),
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*self.smart_stack_property_controls(),
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property_control_for(
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self, "autofocus_dz", label="Autofocus Range (steps)"
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),
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@ -810,17 +852,20 @@ class RasterWorkflow(RegularGridWorkflow[RegularGridSettingsModel]):
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_grid_style = "raster"
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class CChipScanSettingsModel(RegularGridSettingsModel):
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class CChipScanSettingsModel(RectGridSettingsModel):
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"""The settings for a scan with the CChipWorkflow.
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This includes settings calculated when starting. This will be held by smart scan
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during a scan and serialised to disk.
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"""
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x_count: int
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y_count: int
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stack_params: StackParams
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style: Literal["snake", "raster"]
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class CChipWorkflow(RegularGridWorkflow[CChipScanSettingsModel]):
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class CChipWorkflow(RectGridWorkflow[CChipScanSettingsModel]):
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"""A workflow optimised for scanning the well of a CChip.
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This workflow generates a list of coordinates in a rectangle, and snakes
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@ -836,7 +881,8 @@ class CChipWorkflow(RegularGridWorkflow[CChipScanSettingsModel]):
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),
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readonly=True,
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)
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_grid_style = "snake"
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_grid_style: Literal["snake"] = "snake"
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_planner_cls = RegularGridPlanner
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_settings_model = CChipScanSettingsModel
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overlap: float = lt.setting(default=0.1, ge=0.1, le=0.7)
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@ -880,6 +926,26 @@ class CChipWorkflow(RegularGridWorkflow[CChipScanSettingsModel]):
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stack_params=stack_params,
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)
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def new_scan_planner(
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self, settings: CChipScanSettingsModel, position: Mapping[str, int]
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) -> ScanPlanner:
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"""Return a new scan planner object.
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:param settings: The settings for this scan as the relevant SettingsModel type.
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:param position: The starting position as a mapping of axes names to int.
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"""
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planner_settings = {
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"dx": settings.dx,
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"dy": settings.dy,
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"x_count": settings.x_count,
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"y_count": settings.y_count,
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"style": settings.style,
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}
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return self._planner_cls(
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initial_position=(position["x"], position["y"]),
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planner_settings=planner_settings,
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)
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def pre_scan_routine(self, settings: CChipScanSettingsModel) -> None:
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"""No autofocus, a looping autofocus on a CChip could corrupt the entire scan."""
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pass
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|
|
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