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Apply suggestions from code review of branch recentre-with-rom-methods

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Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
This commit is contained in:
Julian Stirling 2025-11-11 12:37:09 +00:00
parent f7d03d8c00
commit b8742b449c
2 changed files with 14 additions and 12 deletions
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10
src/openflexure_microscope_server/things/camera_stage_mapping.py
View file

@ -309,18 +309,18 @@ def csm_img_to_stage(
) -> Mapping[str, int]: ) -> Mapping[str, int]:
"""Apply any CSM matrix to image coordinates. """Apply any CSM matrix to image coordinates.
This is designed x and y must be kwargs and extra kwargs are ignored allowing: x and y must be kwargs and extra kwargs are ignored, allowing:
``csm_img_to_stage(matrix, **position)`` to run for a mapping position. ``csm_img_to_stage(matrix, **position)`` to run for a mapping position.
Note that x and y are the actual (x, y) of the image, not the (m, n) indices used Note that x and y are the actual (x, y) of the image, not the (m, n) indices used
numpy by numpy
:param matrix: The matrix to use in the calculation :param matrix: The matrix to use in the calculation
:param x: the x image coordinate (keyword only) :param x: the x image coordinate (keyword only)
:param y: the y image coordinate (keyword only) :param y: the y image coordinate (keyword only)
:return: The resulting stage coordinates as a mapping. :return: The resulting stage coordinates as a mapping.
""" """
# Note this is (y,x) not x,y to put it in numpy image indices # Note this is (y,x) not (x,y) to put it in numpy image indices
relative_move: np.ndarray = np.dot(np.array([y, x]), np.array(matrix)) relative_move: np.ndarray = np.dot(np.array([y, x]), np.array(matrix))
return {"x": round(relative_move[0]), "y": round(relative_move[1])} return {"x": round(relative_move[0]), "y": round(relative_move[1])}
@ -334,7 +334,7 @@ def csm_stage_to_img(
) -> Mapping[str, float]: ) -> Mapping[str, float]:
"""Apply any CSM matrix to stage coordinates to get image coordinates. """Apply any CSM matrix to stage coordinates to get image coordinates.
This is designed x and y must be kwargs and extra kwargs are ignored allowing: x and y must be kwargs and extra kwargs are ignored, allowing:
``csm_img_to_stage(matrix, **position)`` to run for a mapping position. ``csm_img_to_stage(matrix, **position)`` to run for a mapping position.
Note that x and y are the actual (x, y) of the image, not the (m, n) indices used Note that x and y are the actual (x, y) of the image, not the (m, n) indices used
@ -347,5 +347,5 @@ def csm_stage_to_img(
""" """
inverse_matrix = np.linalg.inv(np.array(matrix)) inverse_matrix = np.linalg.inv(np.array(matrix))
relative_move = np.dot(np.array([x, y]), inverse_matrix) relative_move = np.dot(np.array([x, y]), inverse_matrix)
# Note that the relative move (y, x) as it is from numpy and is in matrix coords. # Note that the relative move is (y, x) as it is from numpy and is in matrix coords.
return {"x": float(relative_move[1]), "y": float(relative_move[0])} return {"x": float(relative_move[1]), "y": float(relative_move[0])}

16
src/openflexure_microscope_server/things/stage_measure.py
View file

@ -100,7 +100,7 @@ class RomDataTracker:
turning_loc = fit_func.deriv().roots[0] turning_loc = fit_func.deriv().roots[0]
turning_z = fit_func(turning_loc) turning_z = fit_func(turning_loc)
# As we only move in 1 direction pull the other axis from the coords. # As we only move in 1 direction, pull the other axis from the coords.
other_axis = "x" if axis == "y" else "y" other_axis = "x" if axis == "y" else "y"
other_coord = self.stage_coords[-1][other_axis] other_coord = self.stage_coords[-1][other_axis]
return {axis: int(turning_loc), other_axis: other_coord, "z": int(turning_z)} return {axis: int(turning_loc), other_axis: other_coord, "z": int(turning_z)}
@ -426,7 +426,7 @@ class RangeofMotionThing(lt.Thing):
def _img_dir_from_stage_coords( def _img_dir_from_stage_coords(
self, target: dict[str, int], axis: Literal["x", "y"], rom_deps: RomDeps self, target: dict[str, int], axis: Literal["x", "y"], rom_deps: RomDeps
) -> Literal[1, -1]: ) -> Literal[1, -1]:
"""For a target location in stage coords return the direction in image coordinates. """For a target location in stage coords, return the direction in image coordinates.
:param target: The target poisiton in stage coordinates :param target: The target poisiton in stage coordinates
:param axis: The axis which is being measured. This must be 'x' or 'y'. :param axis: The axis which is being measured. This must be 'x' or 'y'.
@ -434,9 +434,11 @@ class RangeofMotionThing(lt.Thing):
:return: Direction to move in image coordinates. :return: Direction to move in image coordinates.
""" """
target_im_coords = rom_deps.csm.convert_stage_to_image_coordinates(**target) target_im_coords = rom_deps.csm.convert_stage_to_image_coordinates(**target)
here = rom_deps.stage.position current_loc = rom_deps.stage.position
here_im_coords = rom_deps.csm.convert_stage_to_image_coordinates(**here) current_loc_im_coords = rom_deps.csm.convert_stage_to_image_coordinates(
return -1 if target_im_coords[axis] < here_im_coords[axis] else 1 **current_loc
)
return -1 if target_im_coords[axis] < current_loc_im_coords[axis] else 1
def _distance_in_img_percentage( def _distance_in_img_percentage(
self, target: dict[str, int], axis: Literal["x", "y"], rom_deps: RomDeps self, target: dict[str, int], axis: Literal["x", "y"], rom_deps: RomDeps
@ -453,8 +455,8 @@ class RangeofMotionThing(lt.Thing):
"Stream resolution must be set before converting coords to percentage" "Stream resolution must be set before converting coords to percentage"
) )
here = rom_deps.stage.position current_loc = rom_deps.stage.position
move_stage = {key: target[key] - here[key] for key in target} move_stage = {key: target[key] - current_loc[key] for key in target}
move_img = rom_deps.csm.convert_stage_to_image_coordinates(**move_stage) move_img = rom_deps.csm.convert_stage_to_image_coordinates(**move_stage)
img_index = 0 if axis == "x" else 1 img_index = 0 if axis == "x" else 1