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Merge branch 'rename-rom-thing' into 'v3'

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Change RangeofMotionThing to StageMeasureThing

See merge request openflexure/openflexure-microscope-server!626
This commit is contained in:
Joe Knapper 2026-06-29 14:45:28 +00:00
commit 8f40f4d4e4
3 changed files with 208 additions and 164 deletions
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63
src/openflexure_microscope_server/things/stage_measure.py
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@ -1,16 +1,9 @@
"""File contains all the functions used to measure the range of motion.
"""File contains functions used to measure the stage against the camera.
The range of motion is measured by first taking 5 'medium' sized steps which gives
enough positions to predict future z positions. Next, one 'big' step is taken followed
by 3 'small' steps to test that the stage is still moving as expected and has not
reached the edge. Once the edge has been found and to account for the possibility that
the edge was reached during a "big" step, the stage is moved in a sequence of steps
in the opposite direction until motion is detected. This is position is taken as the
true final position.
This includes:
Throughout the test, parasitic motion (motion in the axis not being measured)
is tracked and an error is raised if it exceeds a minimum amount. Currently
this is 10% of the expected motion is the measured axis.
* Finding the centre of motion
* Measuring the range of motion
"""
import json
@ -43,8 +36,8 @@ PARASITIC_MOTION_TOL = 0.1
DETECT_MOTION_TOL = 0.65
class RomDataTracker:
"""Class for tracking range of motion data.
class CamStageTracker:
"""Class for tracking camera and stage movement together.
The attributes storing data are:
@ -119,7 +112,7 @@ class ParasiticMotionError(lt.exceptions.InvocationError):
"""
class RangeofMotionThing(OFMThing):
class StageMeasurementThing(OFMThing):
"""A class used to measure the range of motion of the stage in X and Y."""
_class_settings = {"validate_properties_on_set": True}
@ -138,12 +131,24 @@ class RangeofMotionThing(OFMThing):
super().__init__(thing_server_interface)
self._lock = Lock()
self._stream_resolution: Optional[tuple[int, int]] = None
self._rom_data = RomDataTracker()
self._cam_stage_data = CamStageTracker()
@lt.action
def perform_rom_test(self) -> Mapping[str, Any]:
"""Measures the range of motion of the stage across the x and y axes.
The range of motion is measured by first taking 5 'medium' sized steps which
gives enough positions to predict future z positions. Next, one 'big' step is
taken followed by 3 'small' steps to test that the stage is still moving as
expected and has not reached the edge. Once the edge has been found and to
account for the possibility that the edge was reached during a "big" step, the
stage is moved in a sequence of steps in the opposite direction until motion is
detected. This position is taken as the final position.
Throughout the test, parasitic motion (motion in the axis not being measured)
is tracked and an error is raised if it exceeds a minimum amount. Currently
this is 10% of the expected motion in the measured axis.
:return: Results dictionary separated into keys of each axis and direction.
"""
got_lock = self._lock.acquire(blocking=False)
@ -175,13 +180,15 @@ class RangeofMotionThing(OFMThing):
axis_limits = []
for axis_dir in directions:
# Create a new tracker at start of measurement.
self._rom_data = RomDataTracker()
self._cam_stage_data = CamStageTracker()
self._move_until_edge(axis=axis, direction=axis_dir)
# Append final position from tracker
axis_limits.append(self._rom_data.final_position[axis])
axis_limits.append(self._cam_stage_data.final_position[axis])
axis_string = "positive" if axis_dir == 1 else "negative"
stage_dic[f"{axis}_{axis_string}"] = self._rom_data.stage_coords
cor_dic[f"{axis}_{axis_string}"] = self._rom_data.offsets
stage_dic[f"{axis}_{axis_string}"] = (
self._cam_stage_data.stage_coords
)
cor_dic[f"{axis}_{axis_string}"] = self._cam_stage_data.offsets
# Calculate step range.
step_range.append(abs(axis_limits[0] - axis_limits[1]))
@ -261,7 +268,7 @@ class RangeofMotionThing(OFMThing):
# Start by performing an autofocus and recording starting position
self._autofocus.looping_autofocus(dz=1000)
starting_position = self._stage.position
self._rom_data.stage_coords.append(starting_position)
self._cam_stage_data.stage_coords.append(starting_position)
try:
dir_str = "positive" if direction == 1 else "negative"
@ -278,7 +285,7 @@ class RangeofMotionThing(OFMThing):
self._big_z_corrected_movement(axis=axis, direction=direction)
# Autofocus and record position
self._autofocus.looping_autofocus(dz=800)
self._rom_data.stage_coords.append(self._stage.position)
self._cam_stage_data.stage_coords.append(self._stage.position)
# Perform small moves to check stage is still moving.
still_moving = self._stage_still_moves(axis=axis, direction=direction)
@ -289,7 +296,7 @@ class RangeofMotionThing(OFMThing):
self._move_back_until_motion_detected(axis=axis, direction=direction)
# Replace final position.
self._rom_data.stage_coords[-1] = self._stage.position
self._cam_stage_data.stage_coords[-1] = self._stage.position
finally:
self._stage.move_absolute(
@ -303,7 +310,7 @@ class RangeofMotionThing(OFMThing):
"""
self.logger.info(f"Finding centre in {axis}.")
# A new tracker for this axis.
self._rom_data = RomDataTracker()
self._cam_stage_data = CamStageTracker()
# Direction is in image coords, initial assumption is that centre is at (0,0).
direction = self._img_dir_from_stage_coords({"x": 0, "y": 0, "z": 0}, axis)
@ -313,7 +320,7 @@ class RangeofMotionThing(OFMThing):
# Find z then make a number of moves (autofocussing and logging position)
# 5 moves initially (2 subsequently).
self._autofocus.looping_autofocus(dz=1000)
self._rom_data.stage_coords.append(self._stage.position)
self._cam_stage_data.stage_coords.append(self._stage.position)
self._moves_for_z_prediction(
axis=axis,
direction=direction,
@ -348,7 +355,7 @@ class RangeofMotionThing(OFMThing):
False for "the stage is not centred". The second value is the direction to
move in, this only has meaning if the first value is False.
"""
estimate = self._rom_data.find_turning_point(axis=axis)
estimate = self._cam_stage_data.find_turning_point(axis=axis)
img_perc = self._distance_in_img_percentage(estimate, axis)
# if the distance is less than 1 big step away then move to it and exit
@ -462,7 +469,7 @@ class RangeofMotionThing(OFMThing):
for _loop in range(n_moves):
offset = self._move_and_measure(movement=movement)
self._rom_data.record_movement(self._stage.position, offset)
self._cam_stage_data.record_movement(self._stage.position, offset)
if _parasitic_motion_detected(movement, offset):
raise ParasiticMotionError(
"Parasitic motion detected during images to calculate z-curvature. "
@ -486,7 +493,7 @@ class RangeofMotionThing(OFMThing):
# Convert to stage coordinates
stage_movement = self._csm.convert_image_to_stage_coordinates(**movement)
z_disp = self._rom_data.predict_z_displacement(
z_disp = self._cam_stage_data.predict_z_displacement(
axis=axis,
stage_movement=stage_movement,
stage_position=self._stage.position,
@ -527,7 +534,7 @@ class RangeofMotionThing(OFMThing):
)
parasitic_motion = _parasitic_motion_detected(movement, offset)
self.logger.info(f"Offset measured as {int(offset[axis])}")
self._rom_data.record_movement(self._stage.position, offset)
self._cam_stage_data.record_movement(self._stage.position, offset)
if abs(offset[axis]) < abs_min_offset or parasitic_motion:
# If the offset is below the abs min offset, or significant