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Optional autofocus and other minor tweaks

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Chish36 2025-07-23 14:47:29 +01:00 • committed by Julian Stirling
parent 0bf3b4210a
commit 154870142d
1 changed files with 10 additions and 8 deletions
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18
src/openflexure_microscope_server/things/stage_measure.py
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@ -69,13 +69,13 @@ def predict_z(pixel_per_step: float, positions: list, axis: str, direction: int,
lateral_positions = [i[axis] for i in positions] lateral_positions = [i[axis] for i in positions]
z_positions = [i['z'] for i in positions] z_positions = [i['z'] for i in positions]
parameters, covariance = curve_fit(quadratic, lateral_positions, z_positions) parameters, covariance = curve_fit(quadratic, lateral_positions, z_positions)
relative_move = direction * 2 * res_dic[axis]/(2*pixel_per_step) # This is the number of steps to cover 200% of the FOV. relative_move = (direction * res_dic[axis])/pixel_per_step # This is the number of steps to cover 200% of the FOV.
z_dest = quadratic(stage.position[axis] + relative_move, *parameters) z_dest = quadratic(stage.position[axis] + relative_move, *parameters)
z_diff = z_dest - stage.position['z'] z_diff = z_dest - stage.position['z']
return z_diff return z_diff
def move_and_measure(step_size: dict, axis: str, delta: dict, image1, csm: CSMDep, autofocus: AutofocusDep, cam:CamDep): def move_and_measure(step_size: dict, axis: str, delta: dict, image1, autofocus_proc: bool, focus_data: list, csm: CSMDep, autofocus: AutofocusDep, cam:CamDep):
""" """
Moves the stage and measures the offset between the two positions. Moves the stage and measures the offset between the two positions.
""" """
@ -85,7 +85,8 @@ def move_and_measure(step_size: dict, axis: str, delta: dict, image1, csm: CSMDe
else: else:
csm.move_in_image_coordinates(x = 0, y = step_size['y']) csm.move_in_image_coordinates(x = 0, y = step_size['y'])
wrong_axis = 'x' wrong_axis = 'x'
focus_data = autofocus.looping_autofocus(dz = 800) if autofocus_proc == True:
focus_data = 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]) delta['x'] = int(offset[1])
@ -144,13 +145,14 @@ class RangeofMotionThing(Thing):
parasitic_motion = False parasitic_motion = False
stage_coords.append(stage.position) stage_coords.append(stage.position)
focused_positions.append(stage.position)
logger.info("Moving the stage in 4 medium sized steps.") logger.info("Moving the stage in 5 medium sized steps.")
# Medium sized steps # Medium sized steps
for loop in range(4): for loop in range(5):
image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1) image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
delta, offset, focus_data, wrong_axis = move_and_measure(step_size = z_steps, axis = axis, delta = delta, image1 = image1, csm = csm, autofocus = autofocus, cam = cam) delta, offset, focus_data, wrong_axis = move_and_measure(step_size = z_steps, axis = axis, delta = delta, image1 = image1, autofocus_proc = True, focus_data = focus_data, csm = csm, autofocus = autofocus, cam = cam)
logger.info(f"Offset measured as {delta[axis]}") logger.info(f"Offset measured as {delta[axis]}")
stage_coords.append(stage.position) stage_coords.append(stage.position)
cor_lat_steps.append(offset) cor_lat_steps.append(offset)
@ -186,7 +188,7 @@ class RangeofMotionThing(Thing):
for loop in range(3): for loop in range(3):
image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1) image1 = cv2.resize(np.array(Image.open(cam.grab_jpeg().open())), dsize=(0,0), fx= 1, fy= 1)
delta, offset, focus_data, wrong_axis = move_and_measure(step_size = step_sizes_small, axis = axis, delta = delta, image1 = image1, csm = csm, autofocus = autofocus, cam = cam) delta, offset, focus_data, wrong_axis = move_and_measure(step_size = step_sizes_small, axis = axis, delta = delta, image1 = image1, autofocus_proc = False, focus_data = focus_data, csm = csm, autofocus = autofocus, cam = cam)
logger.info(f"Offset measured as {delta[axis]}") logger.info(f"Offset measured as {delta[axis]}")
while np.abs(delta[axis]) < minimum_offset_small[axis] and failure_count < 3: while np.abs(delta[axis]) < minimum_offset_small[axis] and failure_count < 3:
@ -198,7 +200,7 @@ class RangeofMotionThing(Thing):
image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels image_0 = image1, image_1 = image2, sigma=10, fractional_threshold=0.1, pad=True)] # Units is pixels
delta['x'] = int(offset[1]) delta['x'] = int(offset[1])
delta['y'] = int(offset[0]) delta['y'] = int(offset[0])
logger.info(f"Displacement found was {np.abs(delta[axis])}. Minimum offset is {minimum_offset_small[axis]}") logger.info(f"Displacement found was {delta[axis]}. Minimum offset is {minimum_offset_small[axis]}")
stage_coords.append(stage.position) stage_coords.append(stage.position)
cor_lat_steps.append(offset) cor_lat_steps.append(offset)