def update(self, dixel, **kwargs):
meta = dixel.meta.copy()
dixel.id = dixel.id.rstrip()
if dixel.level != DicomLevel.SERIES:
url = "{}/{}/{}/tags?simplify".format(self.url, str(dixel.level),
dixel.id)
else:
url = "{}/{}/{}/shared-tags?simplify".format(
self.url, str(dixel.level), dixel.id)
# r = self.session.get(url)
r = self.do_get(url)
if r.status_code != 200:
return dixel
tags = r.json()
tags = DixelTools.simplify_tags(tags)
meta.update(tags)
# Check anon status
url = "{}/{}/{}/metadata".format(self.url, str(dixel.level), dixel.id)
r = self.do_get(url)
# try:
# r = self.session.get(url)
# except requests.exceptions.ConnectionError:
# logging.warn(r.content)
if r.status_code != 200:
return Dixel(dixel.id, meta=meta, level=dixel.level)
return dixel
items = r.json()
if "AnonymizedFrom" in items:
meta['Anonymized'] = True
if dixel.level == "instance":
url = "{}/{}/{}/metadata/TransferSyntaxUID".format(
self.url, str(dixel.level), dixel.id)
# r = self.session.get(url)
r = self.do_get(url)
meta['TransferSyntaxUID'] = r.json()
url = "{}/{}/{}/metadata/SopClassUid".format(
self.url, str(dixel.level), dixel.id)
# r = self.session.get(url)
r = self.do_get(url)
meta['SOPClassUID'] = DixelTools.DICOM_SOPS.get(
r.json(), r.json()) # Text or return val
return Dixel(dixel.id, meta=meta, level=dixel.level)
def update(self, dixel, **kwargs):
meta = dixel.meta.copy()
if dixel.level != "series":
url = "{}/{}/{}/tags?simplify".format(self.url, str(dixel.level),
dixel.id)
else:
url = "{}/{}/{}/shared-tags?simplify".format(
self.url, str(dixel.level), dixel.id)
r = self.session.get(url)
tags = r.json()
tags = DixelTools.simplify_tags(tags)
meta.update(tags)
if dixel.level == "instance":
url = "{}/{}/{}/metadata/TransferSyntaxUID".format(
self.url, str(dixel.level), dixel.id)
r = self.session.get(url)
meta['TransferSyntaxUID'] = r.json()
url = "{}/{}/{}/metadata/SopClassUid".format(
self.url, str(dixel.level), dixel.id)
r = self.session.get(url)
meta['SOPClassUID'] = DixelTools.DICOM_SOPS.get(
r.json(), r.json()) # Text or return val
return Dixel(dixel.id, meta=meta, level=dixel.level)
def initialize_inventory(self):
res = set()
r = self.session.get("{0}/instances".format(self.url)).json()
for item in r:
res.add(Dixel(id=item, level=DicomLevel.INSTANCES))
# self.logger.debug(res)
return res
def anonymize(self, dixel, replacement_dict=None):
url = "{}/{}/{}/anonymize".format(self.url, str(dixel.level), dixel.id)
replacement_json = json.dumps(replacement_dict)
logging.debug(replacement_json)
headers = {'content-type': 'application/json'}
r = self.do_post(url, data=replacement_json, headers=headers)
# r = requests.post()
self.logger.debug(r.content)
if r.status_code == 200:
self.logger.debug('Anonymized {0} successfully!'.format(dixel))
e = Dixel(id=r.json()['ID'], level=dixel.level)
return e
else:
self.logger.warning('Could not anonymize {0}!'.format(dixel))
def load_csv(csv_file, secondary_id=None):
with open(csv_file, 'rU') as f:
items = csv.DictReader(f)
s = set()
for item in items:
# Need to create a unique identifier without having tags
# 1. Use OID if available
id = item.get('OID')
# 2. Use AN if available
if not id:
id = item.get('AccessionNumber')
# 3. If no AN, try PatientID + secondary_id (ie, Treatment Time)
if not id:
if not secondary_id:
raise ValueError("Needs AccessionNumber or MRN+Ref")
id = item.get('PatientID') + item.get(secondary_id)
d = Dixel(id, level=DicomLevel.STUDIES, meta=item)
s.add(d)
return s, items.fieldnames
def make_worklist(self, qdict):
# Return a set of predixel results
r = self.query(qdict)
logging.debug(pformat(r))
res = set()
for item in r:
meta = {
'AccessionNumber': item[0]["accession_number"],
'PatientID': item[0]["id"], # Montage ID
'ReportText': item[0]['text'],
'ExamType': item[0]['exam_type']['code'] # IMG code
}
res.add(
Dixel(id=meta['AccessionNumber'],
meta=meta,
level=DicomLevel.STUDIES))
return res
def initialize_preinventory(self):
self.logger.debug('Walking file tree')
all_paths = []
all_files = []
for paths, _, files in os.walk(self.loc):
all_paths = all_paths + list(
itertools.repeat(paths, times=len(files)))
all_files = all_files + files
preinventory = set()
for path, fn in zip(all_paths, all_files):
full_path = os.path.join(path, fn)
id = full_path
meta = {'fn': fn, 'path': path, 'full_path': full_path}
preinventory.add(Dixel(id, meta=meta))
# self.logger.debug(preinventory)
return preinventory
def update(self, dixel):
magic_type = magic.from_file(dixel.meta['full_path'], mime=True)
if magic_type == 'application/dicom':
tags = pydicom.read_file(dixel.meta['full_path'])
# self.logger.debug(tags)
meta = {
'PatientID': tags[0x0010, 0x0020].value,
'StudyInstanceUID': tags[0x0020, 0x000d].value,
'SeriesInstanceUID': tags[0x0020, 0x000e].value,
'SOPInstanceUID': tags[0x0008, 0x0018].value,
'TransferSyntaxUID': tags.file_meta.TransferSyntaxUID,
'MediaStorage': tags.file_meta.MediaStorageSOPClassUID,
'AccessionNumber': tags[0x0008, 0x0050].value,
'HasPixels': 'PixelData' in tags
}
try:
meta['Dimensions'] = [
tags[0x0028, 0x0010].value, tags[0x0028, 0x0011].value
]
except KeyError:
pass
meta['id'] = DixelTools.orthanc_id(meta['PatientID'],
meta['StudyInstanceUID'],
meta['SeriesInstanceUID'],
meta['SOPInstanceUID'])
# Keep other meta data, such as file path
meta.update(dixel.meta)
self.logger.debug('{0} ({1}) id: {2}'.format(
dixel.meta['fn'], magic_type, meta['id']))
return Dixel(meta['id'], meta=meta, level=DicomLevel.INSTANCES)
def update(self, dixel, time_delta=0, **kwargs):
# if dixel.meta['mid']:
# # Already looked this exam up
# return dixel
qdict = kwargs.get('qdict', {})
PatientID = dixel.meta['PatientID']
earliest, latest = DixelTools.daterange(dixel.meta['ReferenceTime'],
time_delta)
AccessionNumber = None
q = PatientID
if dixel.meta.get("AccessionNumber"):
AccessionNumber = dixel.meta["AccessionNumber"]
q = q + "+" + AccessionNumber
qdict["q"] = q
qdict["start_date"] = earliest
qdict["end_date"] = latest
r = self.query(qdict)
# Got some hits
if r:
self.logger.debug(pformat(r))
data = None
if AccessionNumber:
# Check and see if there is a match in r
found = False
for r_item in r:
if r_item["accession_number"] == AccessionNumber:
# Use this data
data = r_item
found = True
break
if found == False:
self.logger.warning(
"Can't find Accession {0} in results!".format(
AccessionNumber))
return dixel
else:
# If there is no AN, just use the first study returned
data = r[0]
# TODO: Should really take extractions as an argument
# dmap = kwargs.get('dmap', {})
#
# for k, v in dmap:
# dixel.meta[k]
suffix = kwargs.get('suffix', '')
dixel.meta["Age"] = data["patient_age"]
dixel.meta["First Name"] = data["patient_first_name"].capitalize()
dixel.meta["Last Name"] = data["patient_last_name"].capitalize()
dixel.meta["AccessionNumber" + suffix] = data["accession_number"]
dixel.meta["MID" + suffix] = data["id"] # Montage ID
dixel.meta["Report" + suffix] = data['text'] # Report text
dixel.meta["ExamCode" +
suffix] = data['exam_type']['code'] # IMG code
# Try to find exam completed time
for event in data['events']:
if event['event_type'] == 5:
dixel.meta["ExamCompleted" + suffix] = event['date']
return Dixel(id=dixel.meta["AccessionNumber" + suffix],
meta=dixel.meta,
level=DicomLevel.STUDIES)
# No results
else:
return dixel
def initialize_studies(self):
res = set()
r = self.do_get("{0}/studies".format(self.url)).json()
for item in r:
res.add(Dixel(id=item, level=DicomLevel.SERIES))
return res