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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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31
src/openflexure_microscope_server/scan_planners.py
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@ -155,8 +155,7 @@ class ScanPlanner:
return tuple(position) in self._remaining_locations
def get_next_location_and_z_estimate(self) -> tuple[XYPos, Optional[int]]:
"""Return the next location to scan, and the estimated z-position
for this location.
"""Return the next location to scan and its estimated z-position.
Note z-position may be None! This indicates that the current z, position
should be used.
@ -176,9 +175,12 @@ class ScanPlanner:
return next_location, z
def closest_focus_site(self, xy_pos: XYPos) -> Optional[XYZPos]:
"""Return the xyz position of the closest site where focus was achieved
to the input xy_position, with the most recently taken image returned in
the case of a tie
"""Return the xyz position of the closest site where focus was achieved.
The most recently taken image is returned in the case of a tie.
:param xy_pos: The xy_position which the returned position should be closest
to.
Returns None if there if no focussed locations are present
"""
@ -338,9 +340,10 @@ class SmartSpiral(ScanPlanner):
self._remaining_locations.sort(key=sort_key)
def get_next_location_and_z_estimate(self) -> tuple[XYPos, Optional[int]]:
"""Return the next location to scan, and the estimated z-position
for this location. This overrides the default behaviour of ScanPlanner
to take the lowest value of nearest neighbours as this works best for smart stack
"""Return the next location to scan and its estimated z-position.
This overrides the default behaviour of ScanPlanner to take the lowest value of
nearest neighbours as this works best for smart stack.
Note z-position may be None! This indicates that the current z position
should be used.
@ -361,9 +364,11 @@ class SmartSpiral(ScanPlanner):
def select_nearby_focus_site(self, xy_pos: XYPos) -> Optional[XYZPos]:
"""Return the xyz position of the nearby site with the lowest z position.
Lowest position is best, as starting too high causes smart stacking to
autofocus and restart. Starting too low just requires extra movements in +z.
Nearby is defined as within NEIGHBOUR_CUTOFF times the distance to the closest neighbour.
Nearby is defined as within NEIGHBOUR_CUTOFF times the distance to the closest
neighbour.
Returns None if there if no focused locations are present
"""
@ -397,12 +402,10 @@ class SmartSpiral(ScanPlanner):
starting_pos: XYPos | np.ndarray,
ending_pos: XYPos | np.ndarray,
) -> float:
"""Return the number of moves between two xy positions in the x or y direction
whichever is largest
"""Return the larger of x moves or y moves between two xy positions.
Args:
starting_pos: the position to measure from
ending_pos: the position to measure to
:param starting_pos: the position to measure from
:param ending_pos: the position to measure to
"""
move_size = np.array([self._dx, self._dy])