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Made changes to docstrings and a few minor code changes.

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Chish36 2025-08-06 11:44:20 +01:00 • committed by Julian Stirling
parent 875bf1a6de
commit 8dad346320
1 changed files with 34 additions and 41 deletions
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75
src/openflexure_microscope_server/things/stage_measure.py
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@ -45,10 +45,15 @@ def _generate_move_dicts(
) -> dict[str, float]:
"""Create a single dictionary of x and y moves for moving in image coordinates.
This can either be used to create move sizes or minimum move sizes. For example,
the stage must move a minimum distance for a move to be considered successful.
We define the minimum with this function. This is also used to define the maximally
allowed motion in the wrong axis.
:param fov_perc: The percentage of field of view the stage should move by.
:param stream_resolution: The resolution of the stream from the camera.
:param direction: The direction the stage moves.
:param factor: Multiplicative factor which changes the final result.
:param factor: Reduction factor which allows for minimum move sizes to be created.
:return: A dictionary with keys 'x' and 'y' with a pixel distance move the stage can make.
"""
return {
@ -66,11 +71,11 @@ def _predict_z(
) -> float:
"""Predict the next z position for a move using previous positions.
:params positions: The list of positions used for predicting z.
This will usually be a list of all previous positions.
:params axis: The axis in which the stage is moving. This must be 'x' or 'y'.
:params relative_move: The move which the function is trying to predict z for.
Here, this is inputted with units of pixels.
:param positions: The list of positions used for predicting z.
This will be a list of all previous positions.
:param axis: The axis in which the stage is moving. This must be 'x' or 'y'.
:param relative_move: The move which the function is trying to predict z for.
Here, this is inputted with units of pixels.
:param stage: A direct_thing_client dependency for the the microscope stage.
:param csm: A direct_thing_client dependency for camera stage mapping.
:return: A number of pixels the stage needs to move in z.
@ -89,7 +94,6 @@ def _predict_z(
return z_dest - stage.position["z"]
def _move_and_measure(
step_size: dict[str, float],
axis: Literal["x", "y"],
@ -102,14 +106,14 @@ def _move_and_measure(
) -> tuple[npt.ArrayLike, str]:
"""Move the stage and measure the offset between the two positions.
:params step_size: A dictionary with keys 'x' and 'y' with pixel distances.
:params axis: The axis in which the stage is moving. This must be 'x' or 'y'.
:params data: The object used to track stage coordinates, correlation and delta.
: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.
:param step_size: A dictionary with keys 'x' and 'y' with pixel distances.
:param axis: The axis in which the stage is moving. This must be 'x' or 'y'.
:param data: The object used to track stage coordinates, correlation and delta.
:param image1: An image taken before moving to be correlated with image2.
:param autofocus_proc: If true, looping.autofocus will be used after the stage moves.
:param csm: A direct_thing_client dependency for camera stage mapping.
:param autofocus: A direct_thing_client dependency for autofocus.
:param camera: A raw_thing_client depeendency for the camera.
:param cam: A raw_thing_client depeendency for the camera.
: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'.
"""
@ -124,12 +128,9 @@ def _move_and_measure(
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(
offset = fft_image_tracking.displacement_between_images(
image_0=image1, image_1=image2, sigma=10, fractional_threshold=0.1, pad=True
)
] # Units is pixels
) # Units is pixels
data.delta["x"] = int(offset[1])
data.delta["y"] = int(offset[0])
@ -202,13 +203,19 @@ def _check_stage_operation(
) -> None:
"""Carries out 3 small moves in a given direction and axis.
Each position after the first is correlated with the previous position
to check the stage has moved as far as it should. If the correlation is
less than expected, 3 attempts are made to refocus the image to ensure that
image quality is not causing the correlation to be unsuccessful. If the correlation
is still too low then the edge is found.
:params small_step: The integer value used to generate the small step sizes.
:params stream_resolution: The resolution of the stream from the camera.
:param direction: The direction the stage moves.
:params axis: The axis which is being measured. This must be 'x' or 'y'.
:params data: The object used to track stage coordinates, correlation and delta.
:params minimum_offset_small: A dictionary containing the minimum values for
a successful correlation.
a successful correlation.
:param csm: A direct_thing_client dependency for camera stage mapping.
:param camera: A raw_thing_client depeendency for the camera.
:param stage: A raw_thing_client depeendency for the microscope stage.
@ -247,16 +254,14 @@ def _check_stage_operation(
np.array(Image.open(cam.grab_jpeg().open())), dsize=(0, 0), fx=1, fy=1
)
failure_count += 1
offset = [
x * 1
for x in fft_image_tracking.displacement_between_images(
offset = fft_image_tracking.displacement_between_images(
image_0=image1,
image_1=image2,
sigma=10,
fractional_threshold=0.1,
pad=True,
)
] # Units is pixels
# Units is pixels
data.delta["x"] = int(offset[1])
data.delta["y"] = int(offset[0])
logger.info(
@ -296,18 +301,9 @@ def _motion_detection(
:param camera: A raw_thing_client depeendency for the camera.
:return: The stage coordinates where motion was detected.
"""
displacements = [
1,
2,
4,
8,
16,
32,
64,
128,
256,
512,
] # Array of increasing pixel sizes
# Array of increasing pixel sizes (powers of 2 from 1 to 512)
displacements = [2**i for i in range(10)]
motion_minimum = 20 # minimum number of pixels for motion to be detected
this_motion_step = {"x": 0, "y": 0}
@ -324,16 +320,13 @@ def _motion_detection(
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(
offset = fft_image_tracking.displacement_between_images(
image_0=image1,
image_1=image2,
sigma=10,
fractional_threshold=0.1,
pad=True,
)
]
delta["x"] = int(offset[1])
delta["y"] = int(offset[0])
logger.info(f"Offset measured as {np.abs(delta[axis])}")
@ -388,8 +381,8 @@ class RangeofMotionThing(lt.Thing):
:param cam: A raw_thing_client depeendency for the camera.
:param csm: A raw_thing_client depeendency for camera stage mapping.
:param logger: A raw_thing_client depeendency for the logger.
:params axis: The axis which is being measured. This must be 'x' or 'y'.
:params direction: The direction which is being measured. This must be 1 or -1.
:param axis: The axis which is being measured. This must be 'x' or 'y'.
:param direction: The direction which is being measured. This must be 1 or -1.
:return: Results dictionary containing stage positions,
correlations and the final position.
"""