Ensure smart stack exits and saves on failure only if check background is false
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Julian Stirling
parent
d3bd921db2
commit
dabb195b08
2 changed files with 40 additions and 34 deletions
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@ -421,37 +421,35 @@ class AutofocusThing(lt.Thing):
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is close to focus, but not quite within ``dz/2``. It will attempt to autofocus
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up to 10 times.
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"""
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repeat = True
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attempts = 0
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backlash = 200
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with sharpness_monitor.run():
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while repeat and attempts < 10:
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while attempts < 10:
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if start == "centre":
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stage.move_relative(x=0, y=0, z=-(backlash + dz / 2))
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stage.move_relative(x=0, y=0, z=backlash)
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# Always start centrally for future runs
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start = "centre"
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focus_data_index, _ = sharpness_monitor.focus_rel(
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dz, block_cancellation=True
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)
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_times, heights, sizes = sharpness_monitor.move_data(focus_data_index)
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peak_height = heights[np.argmax(sizes)]
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height_min = np.min(heights)
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height_max = np.max(heights)
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target_min = np.min(heights) + dz / 5
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target_max = np.max(heights) - dz / 5
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# move to the peak
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stage.move_absolute(z=peak_height - backlash)
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stage.move_absolute(z=peak_height)
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if target_min < peak_height < target_max:
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# If it is within the target range then break.
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break
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if (
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peak_height - height_min < dz / 5
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or height_max - peak_height < dz / 5
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):
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attempts += 1
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start = "centre"
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stage.move_absolute(z=peak_height - backlash)
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stage.move_absolute(z=peak_height)
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else:
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repeat = False
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stage.move_relative(x=0, y=0, z=-(dz + backlash))
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stage.move_absolute(z=peak_height)
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return heights.tolist(), sizes.tolist()
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stack_images_to_save = lt.ThingSetting(
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@ -566,7 +564,8 @@ class AutofocusThing(lt.Thing):
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stage: Stage,
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sharpness_monitor: SharpnessMonitorDep,
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stack_parameters: StackParams,
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) -> tuple[bool, int]:
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save_on_failure: bool = False,
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) -> tuple[bool, Optional[int]]:
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"""Run a smart stack.
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A smart stack captures images offset in z, testing whether the sharpest image
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@ -582,15 +581,16 @@ class AutofocusThing(lt.Thing):
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supplied by LabThings dependency injection
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:param stack_parameters: A StackParams object containing the required
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parameters to run a stack.
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:param save_on_failure: Whether to save an image even if the capture failed
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:returns: A tuple containing:
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* A boolean, True if stack was successfully
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* The z position of the sharpest image
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"""
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tries = 0
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# Loop until a stack is successful
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while tries < stack_parameters.max_attempts:
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attempt = 0
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while True:
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attempt += 1
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success, captures, sharpest_id = self.z_stack(
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stack_parameters=stack_parameters,
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cam=cam,
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@ -600,6 +600,9 @@ class AutofocusThing(lt.Thing):
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if success:
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break
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if attempt >= stack_parameters.max_attempts:
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break
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# The z position of the first images in the previous attempt.
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initial_z_pos = captures[0].position["z"]
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# If a stack is not successful, move to the start and autofocus
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@ -613,15 +616,14 @@ class AutofocusThing(lt.Thing):
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# Save stack_parameters.image_to_save images centred on the sharpest capture.
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# If the smart_stack failed the exact number of images saved may not be
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# stack_parameters.image_to_save
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self.save_stack(
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sharpest_id=sharpest_id,
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captures=captures,
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stack_parameters=stack_parameters,
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cam=cam,
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)
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if success or save_on_failure:
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self.save_stack(
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sharpest_id=sharpest_id,
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captures=captures,
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stack_parameters=stack_parameters,
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cam=cam,
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)
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# Return whether or not the smart stack was successful, and the z position of
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# the sharpest image, for path planning and tracking
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return success, _get_capture_by_id(captures, sharpest_id).position["z"]
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def reset_stack(
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@ -683,7 +685,7 @@ class AutofocusThing(lt.Thing):
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stack_parameters: StackParams,
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cam: CameraClient,
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stage: Stage,
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) -> tuple[bool, list[CaptureInfo], Optional[int]]:
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) -> tuple[bool, list[CaptureInfo], int]:
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"""Capture a series of images checking that sharpest image central.
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The images are separated in z offset by stack_parameters.stack_dz, as they
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@ -699,7 +701,7 @@ class AutofocusThing(lt.Thing):
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* the stack result (True for successful stack, False for failed stack),
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* a list of CaptureInfo objects,
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* the buffer_id of the sharpest image (or None if the stack failed).
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* the buffer_id of the sharpest image
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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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@ -739,10 +741,10 @@ class AutofocusThing(lt.Thing):
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return True, captures, capture_id
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if result == "restart":
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return False, captures, None
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return False, captures, capture_id
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# If reached here the result was "continue"
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stage.move_relative(z=stack_parameters.stack_dz)
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return False, captures, None
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return False, captures, capture_id
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def capture_stack_image(
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self,
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