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Sarc dev fixing crawl function #90

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Sarc dev fixing crawl function #90

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a72bc50
Add .Dcm handling to crawl_one
strixy16 Jun 16, 2023
a0fe3a3
Fix crawl overwriting patient key in database_dict
strixy16 Jun 16, 2023
94e521c
Updated dictionary merge to work for Python 3.5 or greater
strixy16 Jun 16, 2023
d443791
Fixed main call
strixy16 Jun 16, 2023
4721be3
Handling RTSTRUCT containing ROIs for mulitple CTs
strixy16 Jul 26, 2023
7d2b919
Dropped the file name from folder for RTSTRUCT output
strixy16 Aug 2, 2023
2976574
Added working function to get missing reference ct values
strixy16 Aug 2, 2023
d9c5621
Remove second df conversion
strixy16 Aug 3, 2023
56b0939
added file name back to RTSTRUCT folder listing
strixy16 Aug 3, 2023
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11 changes: 8 additions & 3 deletions imgtools/utils/crawl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ def crawl_one(folder):
database = {}
for path, _, _ in os.walk(folder):
# find dicoms
dicoms = glob.glob(pathlib.Path(path, "**", "*.dcm").as_posix(), recursive=True)
dicoms = glob.glob(pathlib.Path(path, "**", "*.[Dd]cm").as_posix(), recursive=True)
# print('\n', folder, dicoms)
# instance (slice) information
for dcm in dicoms:
Expand Down Expand Up @@ -182,13 +182,18 @@ def crawl(top,
database_list = []
folders = glob.glob(pathlib.Path(top, "*").as_posix())

# This is a list of dictionaries, each dictionary is a directory containing image dirs
database_list = Parallel(n_jobs=n_jobs)(delayed(crawl_one)(pathlib.Path(top, folder).as_posix()) for folder in tqdm(folders))

# convert list to dictionary
# convert list of dictionaries to single dictionary with each key being a patient ID
database_dict = {}
for db in database_list:
for key in db:
database_dict[key] = db[key]
# If multiple directories have same patient ID, merge their information together
if key in database_dict:
database_dict[key] = database_dict[key] | db[key]
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else:
database_dict[key] = db[key]

# save one level above imaging folders
parent, dataset = os.path.split(top)
Expand Down