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Factor out moving to the next scan point into a method

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This commit is contained in:
Richard Bowman 2024-02-01 16:49:18 +00:00
parent f60e6f2a0b
commit 6e4e79f2d2
1 changed files with 34 additions and 21 deletions
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55
src/openflexure_microscope_server/things/smart_scan.py
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@ -372,6 +372,34 @@ class SmartScanThing(Thing):
return folder_path
raise FileExistsError("Could not create a new scan folder: all names in use!")
def move_to_next_point(
self,
stage: StageDep,
logger: InvocationLogger,
path: list[list[int]],
focused_path: list[list[int]],
) -> list[int]:
"""Remove the first point from the path, and move there.
This will move to the next XY position in `path`, taking the `z` value
either from the current z value of the stage, or from `focused_path`.
Returns the point we have moved to.
"""
loc = [path[0][0], path[0][1]]
path.remove(path[0])
if len(focused_path) > 1:
z_index = closest(loc, focused_path)
z = int(focused_path[z_index][2])
else:
z = stage.position["z"]
logger.info(f"Moving to {loc}")
stage.move_absolute(
x=int(loc[0]), y=int(loc[1]), z = z - self.autofocus_dz / 2
)
return loc + [z]
@thing_action
def sample_scan(
self,
@ -485,29 +513,14 @@ class SmartScanThing(Thing):
with open(os.path.join(images_folder, 'scan_inputs.json'), 'w', encoding='utf-8') as f:
json.dump(data, f, ensure_ascii=False, indent=4)
# move to each x-y position. in z, move to the height of the closest x-y position that successfully focused
# Make the initial move (which probably does nothing)
# NB we will move to the next scan point at the **end** of the loop, so that it can
# happen concurrently with saving the images.
loc = self.move_to_next_point(stage, logger, path=path, focused_path=focused_path)
while len(path) > 0:
ensure_free_disk_space(scan_folder)
loc = [path[0][0], path[0][1], stage.position["z"]]
path.remove(path[0])
# TODO: combine this with the move below for speed (I think this could just be "else")
logger.info(f"Moving to {loc}")
if len(focused_path) > 1:
z_index = closest(loc, focused_path)
z=int(focused_path[z_index][2])
else:
z = loc[2]
# print('Moving to {0}'.format([coords[0], coords[1], focused_path[z_index][2]]))
# print(focused_path)
stage.move_absolute(
x=int(loc[0]), y=int(loc[1]), z = z - self.autofocus_dz / 2
)
# Check if the image is background
if self.skip_background:
image_is_sample = background_detect.image_is_sample()
@ -566,7 +579,7 @@ class SmartScanThing(Thing):
logger.info(
"The focus has shifted further than we expect: retrying."
)
stage.move_absolute(z=int(focused_path[z_index][2]))
stage.move_absolute(z=int(loc[2]))
attempts += 1