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Delta is tracked with class now

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Chish36 2025-07-30 12:04:29 +01:00 • committed by Julian Stirling
parent 63bd34f548
commit 4106d0348c
1 changed files with 25 additions and 34 deletions
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59
src/openflexure_microscope_server/things/stage_measure.py
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@ -68,7 +68,7 @@ def predict_z(positions: list, axis: str, relative_move: float, stage: StageDep,
def move_and_measure( def move_and_measure(
step_size: dict[str, float], step_size: dict[str, float],
axis: str, delta: dict[str, int], axis: str, data,
image1, autofocus_proc: bool, image1, autofocus_proc: bool,
csm: CSMDep, csm: CSMDep,
autofocus: AutofocusDep, autofocus: AutofocusDep,
@ -92,23 +92,22 @@ def move_and_measure(
autofocus.looping_autofocus(dz = 800) autofocus.looping_autofocus(dz = 800)
image2 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1) image2 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
offset = [x * 1 for x in fft_image_tracking.displacement_between_images(image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels offset = [x * 1 for x in fft_image_tracking.displacement_between_images(image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels
delta['x'] = int(offset[1]) data.delta['x'] = int(offset[1])
delta['y'] = int(offset[0]) data.delta['y'] = int(offset[0])
return delta, offset, wrong_axis return offset, wrong_axis
def acquie_z_predict_points( def acquie_z_predict_points(
stream_resolution: list[int], stream_resolution: list[int],
direction: int, direction: int,
axis: str, axis: str,
delta: dict[str, int],
data, data,
csm: CSMDep, csm: CSMDep,
cam: CamDep, cam: CamDep,
stage: StageDep, stage: StageDep,
autofocus: AutofocusDep, autofocus: AutofocusDep,
logger: lt.deps.InvocationLogger, logger: lt.deps.InvocationLogger,
) -> dict[str, int]: ) -> None:
"""Carries out the medium sized steps section of the range of motion test to get 5 points to make z position predictions with. """Carries out the medium sized steps section of the range of motion test to get 5 points to make z position predictions with.
:params stream_resolution: The resolution of the stream from the camera. :params stream_resolution: The resolution of the stream from the camera.
@ -127,29 +126,27 @@ def acquie_z_predict_points(
image1 = cv2.resize( image1 = cv2.resize(
np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1 np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1
) )
delta, offset, wrong_axis = move_and_measure( offset, wrong_axis = move_and_measure(
step_size=generate_move_dicts(medium_step, stream_resolution, direction), step_size=generate_move_dicts(medium_step, stream_resolution, direction),
axis=axis, axis=axis,
delta=delta, data=data,
image1=image1, image1=image1,
autofocus_proc=True, autofocus_proc=True,
csm=csm, csm=csm,
autofocus=autofocus, autofocus=autofocus,
cam=cam, cam=cam,
) )
logger.info(f"Offset measured as {delta[axis]}") logger.info(f"Offset measured as {data.delta[axis]}")
data.measure(stage.position, offset) data.measure(stage.position, offset)
assert(np.abs(delta[wrong_axis]) < np.abs(wrong_axis_max_medium[wrong_axis])) assert(np.abs(data.delta[wrong_axis]) < np.abs(wrong_axis_max_medium[wrong_axis]))
return delta
def check_stage_operation( def check_stage_operation(
small_step: int, small_step: int,
stream_resolution: list[int], stream_resolution: list[int],
direction: int, direction: int,
axis: str, axis: str,
delta: dict[str, int],
data, data,
minimum_offset_small: dict[str, float], minimum_offset_small: dict[str, float],
csm: CSMDep, csm: CSMDep,
@ -157,7 +154,7 @@ def check_stage_operation(
stage: StageDep, stage: StageDep,
autofocus: AutofocusDep, autofocus: AutofocusDep,
logger: lt.deps.InvocationLogger, logger: lt.deps.InvocationLogger,
) -> dict[str, int]: ) -> None:
"""Carries out 3 small moves in a given direction and axis. """Carries out 3 small moves in a given direction and axis.
:params small_step: The integer value used to generate the small step sizes. :params small_step: The integer value used to generate the small step sizes.
@ -177,20 +174,20 @@ def check_stage_operation(
image1 = cv2.resize( image1 = cv2.resize(
np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1 np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1
) )
delta, offset, wrong_axis = move_and_measure( offset, wrong_axis = move_and_measure(
step_size=generate_move_dicts(small_step, stream_resolution, direction), step_size=generate_move_dicts(small_step, stream_resolution, direction),
axis=axis, axis=axis,
delta=delta, data=data,
image1=image1, image1=image1,
autofocus_proc=False, autofocus_proc=False,
csm=csm, csm=csm,
autofocus=autofocus, autofocus=autofocus,
cam=cam, cam=cam,
) )
logger.info(f"Offset measured as {delta[axis]}") logger.info(f"Offset measured as {data.delta[axis]}")
while ( while (
np.abs(delta[axis]) < np.abs(minimum_offset_small[axis]) np.abs(data.delta[axis]) < np.abs(minimum_offset_small[axis])
and failure_count < 3 and failure_count < 3
): ):
logger.info( logger.info(
@ -211,20 +208,19 @@ def check_stage_operation(
pad=True, pad=True,
) )
] # Units is pixels ] # Units is pixels
delta["x"] = int(offset[1]) data.delta["x"] = int(offset[1])
delta["y"] = int(offset[0]) data.delta["y"] = int(offset[0])
logger.info( logger.info(
f"Displacement found was {delta[axis]}. Minimum offset is {minimum_offset_small[axis]}" f"Displacement found was {data.delta[axis]}. Minimum offset is {minimum_offset_small[axis]}"
) )
data.measure(stage.position, offset) data.measure(stage.position, offset)
assert np.abs(delta[wrong_axis]) < np.abs(wrong_axis_max_small[wrong_axis]) assert np.abs(data.delta[wrong_axis]) < np.abs(wrong_axis_max_small[wrong_axis])
if np.abs(delta[axis]) < np.abs(minimum_offset_small[axis]): # this means the edge has been found if np.abs(data.delta[axis]) < np.abs(minimum_offset_small[axis]): # this means the edge has been found
logger.info("Edge has been found.") logger.info("Edge has been found.")
break break
return delta
def motion_detection( def motion_detection(
axis: str, axis: str,
@ -273,10 +269,11 @@ def motion_detection(
class RomDataTracker(): class RomDataTracker():
"""Class for tracking range of motion data.""" """Class for tracking range of motion data."""
def __init__(self, stage_coords, cor_lat_steps): def __init__(self, stage_coords, cor_lat_steps, delta):
"""Define useful data tracked througout test.""" """Define useful data tracked througout test."""
self.stage_coords = stage_coords self.stage_coords = stage_coords
self.cor_lat_steps = cor_lat_steps self.cor_lat_steps = cor_lat_steps
self.delta = delta
def measure(self, current_pos, cor): def measure(self, current_pos, cor):
"""Store useful data.""" """Store useful data."""
@ -306,7 +303,7 @@ class RangeofMotionThing(lt.Thing):
starting_position = list(stage.position.values()) starting_position = list(stage.position.values())
rom_data = RomDataTracker([], []) rom_data = RomDataTracker([], [], {'x':0, 'y':0})
axis_results = {} axis_results = {}
try: try:
@ -324,20 +321,15 @@ class RangeofMotionThing(lt.Thing):
small_step = 20 small_step = 20
step_sizes_big = generate_move_dicts(big_step, stream_resolution, direction) step_sizes_big = generate_move_dicts(big_step, stream_resolution, direction)
delta = {
'x':0,
'y':0
}
rom_data.stage_coords.append(stage.position) rom_data.stage_coords.append(stage.position)
logger.info("Moving the stage in 5 medium sized steps.") logger.info("Moving the stage in 5 medium sized steps.")
delta = acquie_z_predict_points( acquie_z_predict_points(
stream_resolution=stream_resolution, stream_resolution=stream_resolution,
direction=direction, direction=direction,
axis=axis, axis=axis,
delta=delta,
data=rom_data, data=rom_data,
csm=csm, csm=csm,
cam=cam, cam=cam,
@ -352,7 +344,7 @@ class RangeofMotionThing(lt.Thing):
small_step, stream_resolution, direction, factor=0.65 small_step, stream_resolution, direction, factor=0.65
) )
while np.abs(delta[axis]) > np.abs(minimum_offset_small[axis]): while np.abs(rom_data.delta[axis]) > np.abs(minimum_offset_small[axis]):
z_diff = predict_z(positions = rom_data.stage_coords, axis = axis, relative_move = step_sizes_big[axis], stage = stage, csm = csm) z_diff = predict_z(positions = rom_data.stage_coords, axis = axis, relative_move = step_sizes_big[axis], stage = stage, csm = csm)
logger.info("Z calibration complete.") logger.info("Z calibration complete.")
@ -370,12 +362,11 @@ class RangeofMotionThing(lt.Thing):
rom_data.stage_coords.append(stage.position) rom_data.stage_coords.append(stage.position)
delta = check_stage_operation( check_stage_operation(
small_step=small_step, small_step=small_step,
stream_resolution=stream_resolution, stream_resolution=stream_resolution,
direction=direction, direction=direction,
axis=axis, axis=axis,
delta=delta,
data = rom_data, data = rom_data,
minimum_offset_small=minimum_offset_small, minimum_offset_small=minimum_offset_small,
csm=csm, csm=csm,