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

Removed focus_data

Browse source
This commit is contained in:
Chish36 2025-07-30 11:16:35 +01:00 • committed by Julian Stirling
parent db0dc11274
commit 63bd34f548
1 changed files with 8 additions and 18 deletions
Download patch file Download diff file Expand all files Collapse all files

26
src/openflexure_microscope_server/things/stage_measure.py
View file

@ -70,7 +70,6 @@ def move_and_measure(
step_size: dict[str, float], step_size: dict[str, float],
axis: str, delta: dict[str, int], axis: str, delta: dict[str, int],
image1, autofocus_proc: bool, image1, autofocus_proc: bool,
focus_data: list[float],
csm: CSMDep, csm: CSMDep,
autofocus: AutofocusDep, autofocus: AutofocusDep,
cam:CamDep) -> tuple: cam:CamDep) -> tuple:
@ -81,8 +80,7 @@ def move_and_measure(
:params delta: A dictionary of 'x' and 'y' offsets. :params delta: A dictionary of 'x' and 'y' offsets.
:params image1: An image taken before moving to be correlated with image2. :params image1: An image taken before moving to be correlated with image2.
:params autofocus_proc: If true, looping.autofocus will be used after the stage moves. :params autofocus_proc: If true, looping.autofocus will be used after the stage moves.
:params focus_data: A list of focus data returned by the autofocus procedure. :return: All required data for the next move. This includes the updated delta value and offset. Also returns what wrong_axis is i.e. if the direction is 'x', wrong_axis = 'y'.
:return: All required data for the next move. This includes the updated delta value, offset and focus_data. Also returns what wrong_axis is i.e. if the direction is 'x', wrong_axis = 'y'.
""" """
if axis == 'x': if axis == 'x':
csm.move_in_image_coordinates(x = step_size['x'], y = 0) csm.move_in_image_coordinates(x = step_size['x'], y = 0)
@ -91,20 +89,19 @@ def move_and_measure(
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'
if autofocus_proc: if autofocus_proc:
focus_data = 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]) delta['x'] = int(offset[1])
delta['y'] = int(offset[0]) delta['y'] = int(offset[0])
return delta, offset, focus_data, wrong_axis return delta, 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], delta: dict[str, int],
focus_data: list[float],
data, data,
csm: CSMDep, csm: CSMDep,
cam: CamDep, cam: CamDep,
@ -118,7 +115,6 @@ def acquie_z_predict_points(
:param direction: The direction the stage moves. :param direction: The direction the stage moves.
:params axis: The axis which is being measured. This must be 'x' or 'y'. :params axis: The axis which is being measured. This must be 'x' or 'y'.
:params delta: A dictionary of 'x' and 'y' offsets. :params delta: A dictionary of 'x' and 'y' offsets.
:params focus_data: A list of focus data returned by the autofocus procedure.
:params stage_coords: A list of all previous positions the stage has been. :params stage_coords: A list of all previous positions the stage has been.
:params cor_lat_steps: A list of all correlation values. :params cor_lat_steps: A list of all correlation values.
:return: Stage_coords and cor_lat_steps are lists of data tracked throughout the test. Delta is updated and tracked after each move. :return: Stage_coords and cor_lat_steps are lists of data tracked throughout the test. Delta is updated and tracked after each move.
@ -131,13 +127,12 @@ 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, focus_data, wrong_axis = move_and_measure( delta, 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, delta=delta,
image1=image1, image1=image1,
autofocus_proc=True, autofocus_proc=True,
focus_data=focus_data,
csm=csm, csm=csm,
autofocus=autofocus, autofocus=autofocus,
cam=cam, cam=cam,
@ -155,7 +150,6 @@ def check_stage_operation(
direction: int, direction: int,
axis: str, axis: str,
delta: dict[str, int], delta: dict[str, int],
focus_data: list[float],
data, data,
minimum_offset_small: dict[str, float], minimum_offset_small: dict[str, float],
csm: CSMDep, csm: CSMDep,
@ -171,7 +165,6 @@ def check_stage_operation(
:param direction: The direction the stage moves. :param direction: The direction the stage moves.
:params axis: The axis which is being measured. This must be 'x' or 'y'. :params axis: The axis which is being measured. This must be 'x' or 'y'.
:params delta: A dictionary of 'x' and 'y' offsets. :params delta: A dictionary of 'x' and 'y' offsets.
:params focus_data: A list of focus data returned by the autofocus procedure.
:params stage_coords: A list of all previous positions the stage has been. :params stage_coords: A list of all previous positions the stage has been.
:params cor_lat_steps: A list of all correlation values. :params cor_lat_steps: A list of all correlation values.
:params minimum_offset_small: A dictionary containing the minimum values for a successful correlation. :params minimum_offset_small: A dictionary containing the minimum values for a successful correlation.
@ -184,13 +177,12 @@ 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, focus_data, wrong_axis = move_and_measure( delta, 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, delta=delta,
image1=image1, image1=image1,
autofocus_proc=False, autofocus_proc=False,
focus_data=focus_data,
csm=csm, csm=csm,
autofocus=autofocus, autofocus=autofocus,
cam=cam, cam=cam,
@ -204,7 +196,7 @@ def check_stage_operation(
logger.info( logger.info(
f"Correlation failed. Refocusing to check. Attempt {failure_count + 1}/3" f"Correlation failed. Refocusing to check. Attempt {failure_count + 1}/3"
) )
focus_data = autofocus.looping_autofocus(dz=1000) autofocus.looping_autofocus(dz=1000)
image2 = cv2.resize( image2 = 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
) )
@ -310,7 +302,7 @@ class RangeofMotionThing(lt.Thing):
:params direction: The direction which is being measured. This must be 1 or -1. :params direction: The direction which is being measured. This must be 1 or -1.
:return: Results dictionary containing stage positions, correlations and the final position. :return: Results dictionary containing stage positions, correlations and the final position.
""" """
focus_data = autofocus.looping_autofocus(dz = 1000) autofocus.looping_autofocus(dz = 1000)
starting_position = list(stage.position.values()) starting_position = list(stage.position.values())
@ -346,7 +338,6 @@ class RangeofMotionThing(lt.Thing):
direction=direction, direction=direction,
axis=axis, axis=axis,
delta=delta, delta=delta,
focus_data=focus_data,
data=rom_data, data=rom_data,
csm=csm, csm=csm,
cam=cam, cam=cam,
@ -375,7 +366,7 @@ class RangeofMotionThing(lt.Thing):
else: else:
csm.move_in_image_coordinates(x = 0, y = step_sizes_big['y']) csm.move_in_image_coordinates(x = 0, y = step_sizes_big['y'])
focus_data = autofocus.looping_autofocus(dz = 800) autofocus.looping_autofocus(dz = 800)
rom_data.stage_coords.append(stage.position) rom_data.stage_coords.append(stage.position)
@ -385,7 +376,6 @@ class RangeofMotionThing(lt.Thing):
direction=direction, direction=direction,
axis=axis, axis=axis,
delta=delta, delta=delta,
focus_data=focus_data,
data = rom_data, data = rom_data,
minimum_offset_small=minimum_offset_small, minimum_offset_small=minimum_offset_small,
csm=csm, csm=csm,