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Removed commented out code

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jaknapper 2025-04-09 12:07:03 +01:00
parent e28a160b22
commit a5d1f1e965
1 changed files with 1 additions and 39 deletions
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40
src/openflexure_microscope_server/things/smart_scan.py
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@ -102,48 +102,17 @@ def limit_focus_change(prev_pos, prev_z, new_pos, new_z, limit):
else:
movement_ratio = np.divide(focus_change, dist, dtype="float64")
# print('Movement ratio is {0} in z per lateral step. The limit is {1}'.format(round(movement_ratio, 4), round(limit,4)))
# print(f'This is the distance between {prev_pos}, {prev_z} and {new_pos}, {new_z}')
if movement_ratio > limit:
return "reject"
else:
return "accept"
# def distance_to_site(current, next):
# current = np.array(current, dtype="float64")
# next = np.array(next, dtype="float64")
# if (next[1] - current[1]) ** 2 + (next[0] - current[0]) ** 2 < 0:
# print(f"Negative distance between {next} and {current}")
# return np.sqrt(
# (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.abs(np.divide(np.subtract(current_loc, starting_loc), step_size)))
# def set_template(microscope, pos):
# microscope.move(pos)
# background = microscope.grab_image_array()
# background_LUV = cv2.cvtColor(background, cv2.COLOR_RGB2LUV)
# ch1 = (background_LUV.T[0]).flatten()
# ch2 = (background_LUV.T[1]).flatten()
# ch3 = (background_LUV.T[2]).flatten()
# points = np.array([np.asarray(ch1),np.asarray(ch2),np.asarray(ch3)]).T
# # we get the mean and standard deviation of values in each channel
# mu, std = np.apply_along_axis(norm.fit, 0, points)
# stats_list = np.vstack([mu, std])
# return stats_list
def distance_to_site(current, next):
next = np.array(next, dtype="float64")
current = np.array(current, dtype="float64")
@ -170,6 +139,7 @@ def generate_config(
mean_loc = np.mean(positions, axis=0)
# TODO: positions from recent scans need to be 2x bigger - change to CSM res?
# TODO: fully test this with whether it works in Fiji as expected
camera_to_sample_matrix = scale_csm(
camera_to_sample_matrix, csm_calibration_width, img_width
@ -529,7 +499,6 @@ class SmartScanThing(Thing):
# TODO: generalise to have 2D displacements for x and y (as the
# camera and stage may not be aligned).
CSM = csm.image_to_stage_displacement_matrix
# csm_calibration_width = csm.last_calibration["image_resolution"][1]
overlap = self.overlap
@ -698,9 +667,6 @@ class SmartScanThing(Thing):
# add the current position to the list of all positions visited
true_path.append(loc)
# if len(names) > 1:
# generate_config(images_folder, positions, names, CSM, csm_calibration_width, img_width, logger)
temp_path = []
for i in path:
@ -1179,7 +1145,6 @@ class SmartScanThing(Thing):
raise FileNotFoundError(
f"Tried to make a zip archive of {images_folder} but it does not exist."
)
# logger.info("Creating zip archive of images (may take some time)...")
zip_fname = f"{os.path.join(scan_folder, 'images')}.zip"
@ -1217,13 +1182,10 @@ class SmartScanThing(Thing):
if ".ome.tiff" in file:
tiff_name = os.path.split(file)[1]
if any(banned_name in file for banned_name in files_to_delay):
# logger.info(f'we only add {file} into zip at the end of the scan')
pass
elif file in current_zip:
# logger.info(f'{file} is already in zip')
pass
elif ".zip" in file or "raw" in file:
# logger.info('Not adding the .zip to itself')
pass
else:
logger.info(f"appending {file} to zip")