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Julian Stirling 2025-07-10 01:58:14 +01:00
parent 35d47fe3ed
commit 4dc41bb008
20 changed files with 153 additions and 115 deletions
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37
src/openflexure_microscope_server/things/autofocus.py
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@ -159,8 +159,7 @@ def _get_capture_by_id(captures: list[CaptureInfo], buffer_id: int) -> CaptureIn
def _get_capture_index_by_id(captures: list[CaptureInfo], buffer_id: int) -> int:
"""Return the index of the capture with the matching id from a list of CaptureInfo
objects
"""Return the index of the capture with the matching id.
:param captures: A list of capture objects
:param buffer_id: The buffer id of the image to return
@ -432,10 +431,13 @@ class AutofocusThing(lt.Thing):
autofocus_dz: int,
save_resolution: tuple[int, int],
) -> tuple[bool, int]:
"""Run a smart stack, which captures images offset in z, testing
whether the sharpest image is towards the centre of the stack.
The sharpest image, and optionally images around the sharpest,
will be saved using their coordinates to images_dir
"""Run a smart stack.
A smart stack captures images offset in z, testing whether the sharpest image
is towards the centre of the stack.
The sharpest image, and optionally images around the sharpest, will be saved
to the images_dir with their coordinates in the filename.
:param cam: Camera Dependency supplied by LabThings dependency injection
@ -506,15 +508,13 @@ class AutofocusThing(lt.Thing):
stage: Stage,
sharpness_monitor: SharpnessMonitorDep,
) -> None:
"""Return to the initial height of the current stack, and run
a looping autofocus.
"""Return to the initial z position and run a looping autofocus.
:param initial_z_pos: The initial z positions of previous captures
:param autofocus_dz: the range in steps to autofocus
``stage`` and ``sharpness_monitor`` are Thing dependencies passed through
from the calling action
from the calling action.
"""
stage.move_absolute(z=initial_z_pos)
self.looping_autofocus(
@ -530,8 +530,10 @@ class AutofocusThing(lt.Thing):
stack_parameters: StackParams,
cam: WrappedCamera,
) -> int:
"""Save the required captures to disk. Will save the sharpest image,
and any images either side of focus.
"""Save the required captures to disk.
This will save the sharpest image, and optionally extra images either
side of focus (see ``stack_parameters.images_to_save``).
:param sharpest_id: the buffer id index of the sharpest image
:param captures: a list of captures, including file name, image data and
@ -559,8 +561,12 @@ class AutofocusThing(lt.Thing):
cam: WrappedCamera,
stage: Stage,
) -> tuple[bool, list[CaptureInfo], Optional[int]]:
"""Capture a series of images offset by stack_parameters.stack_dz, and test whether
the sharpest image is towards the centre of the stack.
"""Capture a series of images checking that sharpest image central
The images are seperated in z offset by stack_parameters.stack_dz, as they
are captured the last stack_parameters.min_images_to_test images are checked
to see if the sharpest image is central enough in the stack. If it is the stack
completes.
:param stack_parameters: a StackParams object holding stack parameters
:param cam: Camera Dependency to be passed through from the calling action
@ -644,8 +650,7 @@ class AutofocusThing(lt.Thing):
def check_stack_result(
self, captures: list[CaptureInfo]
) -> tuple[Literal["success", "continue", "restart"], int]:
"""Test a list of captures, to decide whether the sharpest image from a
stack is centrally enough in the stack
"""Check if the sharpest image in a list of captures is central enough.
:param captures: a list of the capture objects to for testing if the
sharpness has converged in the centre