rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Neighbour cutoff moved from autofocus.py to scan_planners.py

Browse source
This commit is contained in:
jaknapper 2025-06-23 14:13:08 +01:00
parent 2a0de9122b
commit 8ba40832e0
2 changed files with 8 additions and 8 deletions
Download patch file Download diff file Expand all files Collapse all files

12
src/openflexure_microscope_server/scan_planners.py
View file

@ -20,6 +20,11 @@ XYPosList: TypeAlias = list[XYPos]
XYZPosList: TypeAlias = list[XYZPos]
# how many times the minimum distance between images to include as a "nearby" image
# default 1.4 includes images offset in x or y, but not diagonally
NEIGHBOUR_CUTOFF = 1.4
def enforce_xy_tuple(value: XYPos) -> XYPos:
"""
Used for enforcing that an input is a tuple and is the correct length
@ -214,7 +219,7 @@ class ScanPlanner:
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 1.6 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 focussed locations are present
"""
@ -229,10 +234,9 @@ class ScanPlanner:
# Note linalg.norm always uses float64
dists = np.linalg.norm((path_pos - current_pos), axis=1)
# Get indices of all focused sites within 1.6x the minimum distance.
# 1.6x chosen as it includes offsets in x and y on the Picamera2 aspect ratio
# Get indices of all focused sites within NEIGHBOUR_CUTOFF the minimum distance.
# Note np.where always returns a tuple of arrays, hence the trailing [0]
indices = np.where(dists <= 1.6 * np.min(dists))[0]
indices = np.where(dists <= NEIGHBOUR_CUTOFF * np.min(dists))[0]
# Turning into an array allows slicing based on a list
focused_locations_array = np.array(self._focused_locations)

4
src/openflexure_microscope_server/things/autofocus.py
View file

@ -41,10 +41,6 @@ class StackParams(BaseModel):
# distance (in steps) to overshoot a move and then undo, to account for backlash
backlash_correction: int = 250
# how many times the minimum distance between images to include as a "nearby" image
# default 1.4 includes images offset in x or y, but not diagonally
neighbour_cutoff: float = 1.4
# how many images can be appended to the stack after the predicted peak to test for focus
# before assuming the focus was passed, and restarting the stack
stack_height_limit: int = 15