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Merge branch 'spiral_path' into 'v3'

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Pseudo spiral scan path and fixed dx-dy inversion

See merge request openflexure/openflexure-microscope-server!166
This commit is contained in:
Joe Knapper 2024-01-08 16:10:17 +00:00
commit 125bae9c6d
1 changed files with 9 additions and 5 deletions
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14
src/openflexure_microscope_server/things/smart_scan.py
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@ -108,6 +108,9 @@ def distance_to_site(current, next):
(next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2, dtype="float64"
)
def steps_from_centre(current_loc, starting_loc, dx, dy):
step_size = np.array([dx,dy])
return np.max(np.divide(np.abs(np.subtract(current_loc, starting_loc)), step_size))
# def set_template(microscope, pos):
# microscope.move(pos)
@ -364,8 +367,9 @@ class SmartScanThing(Thing):
# TODO: this downsampling by two is to deal with a camera issue
img_width = int(arr.shape[1] / 2)
dx = int(np.dot(np.array([0, arr.shape[0] * (1 - overlap)]), CSM)[0])
dy = int(np.dot(np.array([arr.shape[1] * (1 - overlap), 0]), CSM)[1])
dx = int(np.dot(np.array([0, arr.shape[1] * (1 - overlap)]), CSM)[0])
dy = int(np.dot(np.array([arr.shape[0] * (1 - overlap), 0]), CSM)[1])
logger.info(f"Based on an overlap of {overlap}, we will make steps of {dx}, {dy}")
dz = 3000 # This is used for autofocus - make configurable?
@ -379,7 +383,6 @@ class SmartScanThing(Thing):
ids = []
start_time = time.strftime("%H_%M_%S-%d_%m_%Y")
scan_path = self.new_scan_folder()
images_folder = os.path.join(scan_path, "images")
os.mkdir(images_folder)
@ -391,9 +394,10 @@ class SmartScanThing(Thing):
recentre.looping_autofocus()
# move to each x-y position. in z, move to the height of the closest x-y position that successfully focused
while len(path) > 0:
loc = [path[0][0], path[0][1], stage.position["z"]]
path.remove(loc[:2])
path.remove(path[0])
# TODO: combine this with the move below for speed (I think this could just be "else")
stage.move_absolute(x=int(loc[0]), y=int(loc[1]), z=int(loc[2]))
@ -492,7 +496,7 @@ class SmartScanThing(Thing):
if len(names) > 1:
generate_config(images_folder, positions, names, CSM, csm_calibration_width, img_width, logger)
path = sorted(path, key=lambda x: distance_to_site(loc[:2], x))
path = sorted(path, key=lambda x: (steps_from_centre(x, true_path[0][:2], dx, dy), distance_to_site(loc[:2], x)))
if len(true_path) > 750:
break