rahix/openflexure-microscope-server
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Zip a stitched image with the scan name in the filename

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jaknapper 2024-03-05 13:38:24 +00:00
parent 61d94e205d
commit f08840f0e8
1 changed files with 8 additions and 3 deletions
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11
src/openflexure_microscope_server/things/smart_scan.py
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@ -385,8 +385,8 @@ class SmartScanThing(Thing):
os.makedirs(self.scans_folder_path) os.makedirs(self.scans_folder_path)
if not scan_name: if not scan_name:
scan_name = "scan" scan_name = "scan"
for j in range(999999): for j in range(9999):
folder_path = os.path.join(self.scans_folder_path, f"{scan_name}_{j:06}") folder_path = os.path.join(self.scans_folder_path, f"{scan_name}_{j:04}")
if not os.path.exists(folder_path): if not os.path.exists(folder_path):
os.makedirs(folder_path) os.makedirs(folder_path)
self._latest_scan_name = os.path.basename(folder_path) self._latest_scan_name = os.path.basename(folder_path)
@ -1095,9 +1095,14 @@ class SmartScanThing(Thing):
# and should only be zipped at the end of the scan - otherwise they'll # and should only be zipped at the end of the scan - otherwise they'll
# be appended on every loop as we can't overwrite files in the zip # be appended on every loop as we can't overwrite files in the zip
files_to_delay = ['TileConfiguration', 'tiling_cache', 'stitched.jp', 'stitched_from', 'stitched.om'] files_to_delay = ['TileConfiguration', 'tiling_cache', 'stitched.jp', 'stitched_from', 'stitched.om']
tiff_name = ""
with zipfile.ZipFile(zip_fname, mode="a") as zip: with zipfile.ZipFile(zip_fname, mode="a") as zip:
for file in files: for file in files:
if 'stitched.jp' in file:
stitch_name = os.path.split(file)[1]
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): 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 pass
@ -1118,7 +1123,7 @@ class SmartScanThing(Thing):
# TODO: if you download multiple times, you get duplicate files - is this a problem? # TODO: if you download multiple times, you get duplicate files - is this a problem?
if download_zip: if download_zip:
with zipfile.ZipFile(zip_fname, mode="a") as zip: with zipfile.ZipFile(zip_fname, mode="a") as zip:
for fname in ["stitched_from_stage.jpg", "stitched.jpg"]: for fname in ["stitched_from_stage.jpg", stitch_name, tiff_name]:
fpath = os.path.join(images_folder, fname) fpath = os.path.join(images_folder, fname)
if os.path.exists(fpath): if os.path.exists(fpath):
logger.info(f'copying {fpath} to upper level') logger.info(f'copying {fpath} to upper level')