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Autofocus verify based on sharpness range, removed repetitive logging

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jaknapper 2024-02-15 11:02:44 +00:00
parent f1c315783c
commit aed5a22983
2 changed files with 22 additions and 15 deletions
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27
src/openflexure_microscope_server/things/smart_scan.py
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@ -642,7 +642,7 @@ class SmartScanThing(Thing):
while True:
jpeg_zs, jpeg_sizes = autofocus.looping_autofocus(dz=self.autofocus_dz, start = 'base')
current_height = stage.position["z"]
autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, leniency = 1)
autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, threshold = 0.92)
logger.info(f"We just tested the focus! Result was {autofocus_success}")
if autofocus_success:
@ -655,7 +655,7 @@ class SmartScanThing(Thing):
nearest_focused_site[-1],
loc[0:2],
current_height,
0.3,
0.5,
)
# if there haven't been any previous autofocuses, we have to assume this one worked
@ -721,6 +721,7 @@ class SmartScanThing(Thing):
logger.info(f'Rejected moving to {i} as it is out of range')
path = temp_path.copy()
path = sorted(path, key=lambda x: (steps_from_centre(x, true_path[0][:2], dx, dy), distance_to_site(loc[:2], x)))
self.create_zip_of_scan(logger = logger, scan_name = scan_folder.split('scans/')[1], download_zip = False)
except InvocationCancelledError:
logger.error("Stopping scan because it was cancelled.")
@ -1036,7 +1037,12 @@ class SmartScanThing(Thing):
)
if not os.path.isdir(images_folder):
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)...")
# logger.info("Creating zip archive of images (may take some time)...")
from pathlib import Path
root_directory = Path(images_folder)
print(sum(f.stat().st_size for f in root_directory.glob('**/*') if f.is_file()))
zip_fname = f'{os.path.join(scan_folder, "images")}.zip'
@ -1050,8 +1056,6 @@ class SmartScanThing(Thing):
# get a list of files in the existing zip
current_zip = self.get_files_in_zip(zip_fname)
logger.info(current_zip)
# get a list of files in the folder we're zipping
folder_path = self.scan_folder_path(scan_name)
files = glob.glob(folder_path + '/**/*', recursive=True)
@ -1065,11 +1069,14 @@ class SmartScanThing(Thing):
with zipfile.ZipFile(zip_fname, mode="a") as zip:
for file in files:
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')
# 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')
elif ".zip" in file:
logger.info('Not adding the .zip to itself')
# 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')
zip.write(os.path.join(folder_path, file), arcname=file)
@ -1090,7 +1097,7 @@ class SmartScanThing(Thing):
if any(banned_name in file for banned_name in files_to_delay):
logger.info(f'we are finally adding {file} into zip')
zip.write(os.path.join(folder_path, file), arcname=file)
logger.info('about to download zip')
return ZipBlob.from_file(zip_fname)
@thing_action