Apply suggestions from code review of branch fast-stack
Co-authored-by: Beth Probert <beth_probert@outlook.com>
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5 changed files with 16 additions and 14 deletions
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@ -357,7 +357,7 @@ class SmartSpiral(ScanPlanner):
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for this location. This overrides the default behaviour of ScanPlanner
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to take the lowest value of nearest neighbours as this works best for smart stack
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Note z-position may be None! This indicates that the current z, position
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Note z-position may be None! This indicates that the current z position
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should be used.
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"""
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if self.scan_complete:
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@ -365,7 +365,7 @@ class SmartSpiral(ScanPlanner):
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next_location = self._remaining_locations[0]
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# If focussed locations exist, return the neighbour with the lowest z position
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# If focused locations exist, return the neighbour with the lowest z position
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closest_pos = self.select_nearby_focus_site(next_location)
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if closest_pos is None:
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z = None
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@ -381,7 +381,7 @@ class SmartSpiral(ScanPlanner):
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autofocus and restart. Starting too low just requires extra movements in +z.
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Nearby is defined as within NEIGHBOUR_CUTOFF times the distance to the closest neighbour.
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Returns None if there if no focussed locations are present
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Returns None if there if no focused locations are present
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"""
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if not self._focused_locations:
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return None
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@ -390,7 +390,7 @@ class SmartSpiral(ScanPlanner):
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current_pos = np.array(xy_pos, dtype="float64")
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path_pos = np.array(self._focused_locations, dtype="float64")[:, :2]
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# Use linalg.norm to calculate the direct distance bweween the points
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# Use linalg.norm to calculate the direct distance between the points
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# Note linalg.norm always uses float64
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dists = np.linalg.norm((path_pos - current_pos), axis=1)
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@ -37,7 +37,7 @@ class StackParams:
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:param min_images_to_test: The minimum number of images in the stack before, the
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stack is evaluated for focus. As more images are captured evaluation of the focus
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is always evaluated with the same number of images. i.e. if min_images_to_test=9,
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then 9 images are captured, if the stack is not well focussed, a 10th image is
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then 9 images are captured, if the stack is not well focused, a 10th image is
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captured and images 2 to 10 are evaluated for focus
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:param autofocus_dz: The number of steps in a full autofocus (when required)
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:param images_dir: The directory to save images to disk
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@ -582,7 +582,7 @@ class AutofocusThing(Thing):
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# If the sharpest image isn't found within the maximum number of images
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# end the loop and return "restart"
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while len(captures) <= stack_parameters.max_images_to_test:
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while len(captures) < stack_parameters.max_images_to_test:
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time.sleep(stack_parameters.settling_time)
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# Append a new image to the stack
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@ -69,7 +69,7 @@ class CameraMemoryBuffer:
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def add_image(
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self, image: Any, metadata: Optional[dict] = None, buffer_max: int = 1
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) -> None:
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) -> int:
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"""
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Add an image to the Memory buffer
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