def main(args, parser):
"""inspect currently serves to inspect the header fields of a set
of dicom files against a standard, and flag images that don't
pass the different levels of criteria
"""
# If a deid is given, check against format
deid = args.deid
if deid is not None:
params = load_deid(deid)
if params["format"] != args.format:
bot.error(
"Format in deid (%s) doesn't match choice here (%s) exiting."
% (params["format"], args.format)
)
# Get list of dicom files
base = args.folder
if base is None:
bot.info("No input folder specified, will use demo dicom-cookies.")
base = get_dataset("dicom-cookies")
dicom_files = list(
get_files(base, pattern=args.pattern)
) # todo : consider using generator functionality
result = has_burned_pixels(dicom_files, deid=deid)
print("\nSUMMARY ================================\n")
if result["clean"]:
bot.custom(
prefix="CLEAN", message="%s files" % len(result["clean"]), color="CYAN"
)
if result["flagged"]:
for group, files in result["flagged"].items():
bot.flag("%s %s files" % (group, len(files)))
if args.save:
folders = "-".join([os.path.basename(folder) for folder in base])
outfile = "pixel-flag-results-%s-%s.tsv" % (
folders,
datetime.datetime.now().strftime("%y-%m-%d"),
)
with open(outfile, "w") as filey:
filey.writelines("dicom_file\tpixels_flagged\tflag_list\treason\n")
for clean in result["clean"]:
filey.writelines("%s\tCLEAN\t\t\n" % clean)
for flagged, details in result["flagged"].items():
if details["flagged"] is True:
for result in details["results"]:
group = result["group"]
reason = result["reason"]
filey.writelines(
"%s\tFLAGGED\t%s\t%s\n" % (flagged, group, reason)
)
print("Result written to %s" % outfile)
def main(args, parser):
'''inspect currently serves to inspect the header fields of a set
of dicom files against a standard, and flag images that don't
pass the different levels of criteria
'''
# Global output folder
#output_folder = args.outfolder
#if output_folder is None:
# output_folder = tempfile.mkdtemp()
# If a deid is given, check against format
deid = args.deid
if deid is not None:
params = load_deid(deid)
if params['format'] != args.format:
bot.error(
"Format in deid (%s) doesn't match choice here (%s) exiting." %
(params['format'], args.format))
# Get list of dicom files
base = args.folder
if base is None:
bot.info("No input folder specified, will use demo dicom-cookies.")
base = get_dataset('dicom-cookies')
dicom_files = list(get_files(
base,
pattern=args.pattern)) # todo : consider using generator functionality
result = has_burned_pixels(dicom_files, deid=deid)
print('\nSUMMARY ================================\n')
if len(result['clean']) > 0:
bot.custom(prefix='CLEAN',
message="%s files" % len(result['clean']),
color="CYAN")
if len(result['flagged']) > 0:
for group, files in result['flagged'].items():
bot.flag("%s %s files" % (group, len(files)))
if args.save is True:
folders = '-'.join([os.path.basename(folder) for folder in base])
outfile = "pixel-flag-results-%s-%s.tsv" % (
folders, datetime.datetime.now().strftime('%y-%m-%d'))
with open(outfile, 'w') as filey:
filey.writelines('dicom_file\tpixels_flagged\tflag_list\treason\n')
for clean in result['clean']:
filey.writelines('%s\tCLEAN\t\t\n' % clean)
for flagged, details in result['flagged'].items():
if details['flagged'] is True:
for result in details['results']:
group = result['group']
reason = result['reason']
filey.writelines('%s\tFLAGGED\t%s\t%s\n' %
(flagged, group, reason))
print('Result written to %s' % outfile)
#!/usr/bin/env python3
# This is a complete example of inspecting pixels for PHI
# based on a deid.dicom specification
# https://pydicom.github.io/deid
# This will get a set of example cookie dicoms
from deid.dicom import get_files, has_burned_pixels
from pydicom import read_file
from deid.data import get_dataset
from deid.logger import bot
import os
bot.level = 3
base = get_dataset("dicom-cookies")
dicom_files = list(
get_files(base)) # todo : consider using generator functionality
results = has_burned_pixels(dicom_files=dicom_files, deid="examples/deid")
# The dictionary has a "clean" list, and a "flagged" list,
# Eg:
# {'clean': [],
# 'flagged': {'/home/vanessa/Documents/Dropbox/Code/dicom/deid/deid/data/dicom-cookies/image1.dcm': {'flagged': True,
# 'results': [{'coordinates': [],
# 'group': 'blacklist',
# 'reason': ' ImageType missing or ImageType empty '}]},
def import_dicomdir(dicom_dir, run_get_identifiers=True):
'''import dicom directory manages importing a valid dicom set into
the application, and is a celery job triggered by the watcher.
Here we also flag (and disclude) images that have a header value
that indicates pixel identifiers.
'''
start_time = time.time()
if os.path.exists(dicom_dir):
try:
dicom_files = ls_fullpath(dicom_dir)
except NotADirectoryError:
bot.error('%s is not a directory, skipping.' % dicom_dir)
return
bot.debug("Importing %s, found %s .dcm files" %
(dicom_dir, len(dicom_files)))
# The batch --> the folder with a set of dicoms tied to one request
dcm_folder = os.path.basename(dicom_dir)
batch, created = Batch.objects.get_or_create(uid=dcm_folder)
batch.logs['STARTING_IMAGE_COUNT'] = len(dicom_files)
# Data quality check: keep a record of study dates
study_dates = dict()
size_bytes = sum(os.path.getsize(f) for f in dicom_files)
messages = [] # print all unique messages / warnings at end
# Add in each dicom file to the series
for dcm_file in dicom_files:
try:
# The dicom folder will be named based on the accession#
dcm = read_file(dcm_file, force=True)
dicom_uid = os.path.basename(dcm_file)
# Keep track of studyDate
study_date = dcm.get('StudyDate')
if study_date not in study_dates:
study_dates[study_date] = 0
study_dates[study_date] += 1
flag, flag_group, reason = has_burned_pixels(
dicom_file=dcm_file, quiet=True, deid=STUDY_DEID)
# If the image is flagged, we don't include and move on
continue_processing = True
if flag is True:
if flag_group not in ["whitelist"]:
continue_processing = False
message = "%s is flagged in %s: %s, skipping" % (
dicom_uid, flag_group, reason)
batch = add_batch_warning(message, batch, quiet=True)
message = "BurnedInAnnotation found for batch %s" % batch.uid
if message not in messages:
messages.append(message)
if continue_processing is True:
# Create the Image object in the database
# A dicom instance number must be unique for its batch
dicom = Image.objects.create(batch=batch, uid=dicom_uid)
# Save the dicom file to storage
# basename = "%s/%s" %(batch.id,os.path.basename(dcm_file))
dicom = save_image_dicom(dicom=dicom,
dicom_file=dcm_file) # Also saves
# Generate image name based on [SUID] added later
# accessionnumberSUID.seriesnumber.imagenumber,
name = "%s_%s.dcm" % (dcm.get('SeriesNumber'),
dcm.get('InstanceNumber'))
dicom.name = name
dicom.save()
# Only remove files successfully imported
#os.remove(dcm_file)
# Note that on error we don't remove files
except InvalidDicomError:
message = "InvalidDicomError: %s skipping." % (dcm_file)
batch = add_batch_error(message, batch)
except KeyError:
message = "KeyError: %s is possibly invalid, skipping." % (
dcm_file)
batch = add_batch_error(message, batch)
except Exception as e:
message = "Exception: %s, for %s, skipping." % (e, dcm_file)
# Print summary messages all at once
for message in messages:
bot.warning(message)
if len(study_dates) > 1:
message = "% study dates found for %s" % (len(study_dates),
dcm_file)
batch = add_batch_error(message, batch)
# Save batch thus far
batch.qa['StudyDate'] = study_dates
batch.qa['StartTime'] = start_time
batch.qa['SizeBytes'] = size_bytes
batch.save()
# If there were no errors on import, we should remove the directory
#if not batch.has_error:
# Should only be called given no error, and should trigger error if not empty
#os.rmdir(dicom_dir)
# At the end, submit the dicoms to be anonymized as a batch
count = batch.image_set.count()
if count > 0:
if ANONYMIZE_PIXELS is True:
bot.warning(
"Anonimization of pixels is not yet implemented. Images were skipped."
)
# When this is implemented, the function will be modified to add these images
# to the batch, which will then be first sent through a function to
# scrub pixels before header data is looked at.
# scrub_pixels(bid=batch.id)
#else:
if run_get_identifiers is True:
bot.debug("get_identifiers submit batch %s with %s dicoms." %
(batch.uid, count))
return get_identifiers(bid=batch.id)
else:
bot.debug("Finished batch %s with %s dicoms" %
(batch.uid, count))
return batch
else:
# No images for further processing
batch.status = "EMPTY"
batch.qa['FinishTime'] = time.time()
message = "%s is flagged EMPTY, no images pass filter" % (batch.id)
batch = add_batch_warning(message, batch)
batch.save()
return
else:
bot.warning('Cannot find %s' % dicom_dir)
