def lookup_accessions(cache, report_db, lazy=True):
# Use a proxy and a condition (time) to identify study_level accession nums/stuids
for key in cache.keys():
d = Dixel(key=key, cache=cache)
if d.dlvl != DLVL.STUDIES:
logging.debug("Can only lookup AccessionNumber for study level dixels, skipping MRN {}".format(d.data['PatientID']))
continue
if lazy and d.data.get('AccessionNumber'):
logging.debug("Already have AccessionNumber info for {}, skipping.".format(d.data['AccessionNumber']))
continue
report_db.find(d, time_delta="-1d")
d.persist()
def index_dcm_dir(dcm_dir):
global R, Q
file_cache = R
accession_cache = Q
# worklist = set()
n = 0
for root, dirs, files in os.walk(dcm_dir):
for name in files:
# Ignore junk files
if name.startswith("."):
continue
n = n + 1
fp = os.path.join(root, name)
# logging.debug(fp)
#ETAFF
try:
# Create an instance dixel with a fp key
d = Dixel(fp,
cache=file_cache,
init_fn=Dixel.read_dcm,
dlvl=DLVL.INSTANCES)
accession_num = d.data['AccessionNumber']
accession_cache.sadd(accession_num, fp)
# worklist.add(d)
except Exception, e:
# logging.debug(e.message)
pass
def upload_dcm_file(fp):
global orthanc, R, compress, instance_manifest
try:
# Create a ro dixel (skips persisting calls)
d = Dixel(key=fp, cache=R, ro=True)
except ValueError:
# Couldn't create dixel from cache for some reason, fall back to reindex it
logging.warning('Trying to index rogue fp {}'.format(fp))
d = Dixel(key=fp, cache=R, init_fn=Dixel.read_dcm, dlvl=DLVL.INSTANCES)
accession_num = d.data['AccessionNumber']
Q.sadd(accession_num, fp)
# logging.debug(instance_manifest)
if not instance_manifest or d.oid() not in instance_manifest:
logging.debug("Putting: {}".format(fp))
orthanc.add(d, compress=compress,
lazy=False) # Implemented MT lazy here
else:
logging.debug("Ignoring: {}".format(fp))
def set_anon_ids(cache=None, mint=None, lazy=True, dixel=None):
def set_anon_id(d):
if lazy and not \
(d.data.get('AnonID') and
d.data.get('AnonName') and
d.data.get('AnonDoB') ):
name = d.data.get('PatientName')
gender = d.data.get('PatientSex', 'U')
dob = d.data.get('PatientBirthDate')
if not name or not dob:
logging.debug('Inadequate data to anonymize {}'.format(
d.data.get('PatientID')))
raise KeyError
dob = "-".join([dob[:4], dob[4:6], dob[6:]])
anon = mint.pseudo_identity(name=name, gender=gender, dob=dob)
d.data['AnonID'] = anon[0]
d.data['AnonName'] = anon[1]
d.data['AnonDoB'] = anon[2]
d.persist()
if not mint:
mint = PseudoMint()
if dixel:
set_anon_id(dixel)
return
if cache:
for key in cache.keys():
d = Dixel(key=key, cache=cache)
try:
set_anon_id(d)
except KeyError, e:
logging.error(e)
def lookup_child_uids(cache, c_cache, child_qs, proxy, remote_aet):
# Use a proxy to lookup child StudyUID, SeriesUID, and SOPInstanceUID data
for key in cache.keys():
d = Dixel(key=key, cache=cache)
if d.dlvl == DLVL.SERIES:
logging.info("Already found a series for this dixel, skipping")
continue
for q in child_qs:
qkey = "{}-{}".format(key, str(hash(pformat(q)))[-4:])
data = dict(d.data)
data.update(q)
# logging.debug(pformat(data))
e = Dixel(key=qkey, data=data, cache=c_cache)
# Can't put this in init() for some reason
e.dlvl = d.dlvl.child()
ret = proxy.find(e, remote_aet)
if ret:
# logging.debug(pformat(ret[0]))
e.data['StudyInstanceUID'] = ret[0].get("StudyInstanceUID")
e.data['PatientName'] = ret[0].get("PatientName")
e.data['PatientBirthDate'] = ret[0].get("PatientBirthDate")
e.data['PatientSex'] = ret[0].get("PatientSex")
if e.dlvl == DLVL.SERIES or e.dlvl == DLVL.INSTANCES:
e.data['SeriesInstanceUID'] = ret[0].get(
"SeriesInstanceUID")
if e.dlvl == DLVL.SERIES:
e.data['SeriesDescription'] = ret[0].get(
"SeriesDescription")
e.data['SeriesNumber'] = ret[0].get("SeriesNumber")
e.data['SeriesNumInstances'] = ret[0].get(
'NumberOfSeriesRelatedInstances')
if e.dlvl == DLVL.INSTANCES:
e.data['SOPInstanceUID'] = ret[0].get("SOPInstanceUID")
e.persist()
def copy_from_pacs(proxy,
remote_aet,
cache,
save_dir,
anon_map=None,
lazy=True,
clean_proxy=True,
depth=0,
dry_run=False,
anon=True):
def dixel_save_dir(fn, save_dir, depth):
fd = save_dir
if depth:
for de in range(depth):
fd = os.path.join(fd, fn[de])
return fd
for key in cache.keys():
d = Dixel(key=key, cache=cache)
# An AnonID isn't usually going to be assigned until
# there has been a DICOM UID lookup, so this is a
# reasonable check for "record complete"
if anon and not d.data.get('AnonID'):
logging.warn("No anon ID for MRN {}".format(d.data['PatientID']))
d.data['status'] = "missing_info"
continue
# if d.data.get('status', 'ready') != "ready":
# continue
if anon:
d.data['fn_base'] = d.data['AnonAccessionNum']
else:
d.data['fn_base'] = d.data['AccessionNumber']
fn = '{}.zip'.format(d.data['fn_base'])
dsd = dixel_save_dir(fn, save_dir, depth)
fp = os.path.join(dsd, fn)
# Check if file already exists for lazy!
if lazy and os.path.exists(fp):
logging.debug('Skipping {}: already exists'.format(fn[0:7]))
d.data['status'] = "done"
continue
# loc = d.data.get('RetrieveAETitle').lower()
# if not proxy.remote_names.get(loc):
# logging.warn("Skipping {}: No retrieve loc provided".format(fn))
# continue
if dry_run:
logging.debug("Skipping {}: Dry-run, no retreive attempted".format(
fn[0:7]))
continue
if not d in proxy:
proxy.find(d, remote_aet, retrieve=True)
if not d in proxy:
logging.warn("Failed {}: Unsuccessful retrieval!".format(fn[0:7]))
d.data['status'] = "unretrievable"
d.persist()
continue
if anon:
r = proxy.anonymize(d, replacement_map=anon_map)
# logging.debug(r)
d.data['AnonOID'] = r['ID']
d.persist()
# Need an oid and an anon name to save...
e = Dixel(key=d.data['AnonOID'],
data={
'OID': d.data['AnonOID'],
'fn_base': d.data['fn_base']
},
dlvl=d.dlvl)
file_data = proxy.get(e, get_type='file')
e.write_file(file_data, save_dir=dsd)
if clean_proxy:
proxy.remove(e)
else:
file_data = proxy.get(d, get_type='file')
d.write_file(file_data, save_dir=dsd)
if clean_proxy:
proxy.remove(d)
d.data['status'] = "done"
logging.info("Grabbed {}".format(fn[0:7]))
def lookup_uids(cache, proxy, remote_aet, retrieve=False, lazy=True):
# Use a proxy to lookup StudyUID, SeriesUID, and SOPInstanceUID data
for key in cache.keys():
d = Dixel(key=key, cache=cache)
if lazy and not retrieve and \
(d.dlvl == DLVL.STUDIES and d.data.get('StudyInstanceUID')) or \
(d.dlvl == DLVL.SERIES and d.data.get('StudyInstanceUID') and
d.data.get('SeriesInstanceUID')) or \
(d.dlvl == DLVL.INSTANCES and d.data.get('StudyInstanceUID') and
d.data.get('SeriesInstanceUID') and
d.data.get('SOPInstanceUID')):
logging.debug("Already have UID info for {}, skipping.".format(
d.data['AccessionNumber']))
continue
# retrieve = True
# logging.debug(d.data['PatientLastName'])
d.data['PatientID'] = ""
ret = proxy.find(d, remote_aet, retrieve=retrieve)
if ret:
# Take the first entry in ret and update the STUID/SERUID/INSTUID so we can retrieve
if not d.data.get("AccessionNumber"):
d.data['AccessionNumber'] = ret[0].get("AccessionNumber")
d.data['StudyInstanceUID'] = ret[0].get("StudyInstanceUID")
d.data['PatientID'] = ret[0].get("PatientID")
d.data['PatientName'] = ret[0].get("PatientName")
d.data['PatientBirthDate'] = ret[0].get("PatientBirthDate")
d.data['PatientSex'] = ret[0].get("PatientSex")
if d.dlvl == DLVL.SERIES or d.dlvl == DLVL.INSTANCES:
d.data['SeriesInstanceUID'] = ret[0].get("SeriesInstanceUID")
if d.dlvl == DLVL.SERIES:
d.data['SeriesDescription'] = ret[0].get("SeriesDescription")
d.data['SeriesNumber'] = ret[0].get("SeriesNumber")
d.data['SeriesNumInstances'] = ret[0].get(
'NumberOfSeriesRelatedInstances')
if d.dlvl == DLVL.INSTANCES:
d.data['SOPInstanceUID'] = ret[0].get("SOPInstanceUID")
d.persist()
else:
logging.warning("No answers for {}".format(
d.data["AccessionNumber"]))
def copy_from_pacs(proxy, remote_aet, cache, save_dir, anon_map=None, lazy=True, clean_proxy=True, depth=0, dry_run=False):
def dixel_save_dir(d, save_dir, depth):
fd = save_dir
if depth:
for de in range(depth):
fd = os.path.join(fd, d.data['AnonID'][de])
return fd
for key in cache.keys():
d = Dixel(key=key, cache=cache)
# An AnonID isn't usually going to be assigned until
# there has been a DICOM UID lookup, so this is a
# reasonable check for "record complete"
if not d.data.get('AnonID'):
logging.warn("No anon ID for MRN {}".format(d.data['PatientID']))
continue
dsd = dixel_save_dir(d, save_dir, depth)
fp = os.path.join(dsd, d.data['AnonID'] + '.zip')
# Check if file already exists for lazy!
if lazy and os.path.exists(fp):
logging.debug('{} already exists -- skipping'.format(d.data['AnonID'] + '.zip'))
continue
loc = d.data.get('RetrieveAETitle').lower()
if not proxy.remote_names.get(loc):
logging.warn("No retrieve loc for {}.zip".format(d.data['AnonID']))
continue
if dry_run:
logging.debug("Dry-run, so not trying to retreive {}.zip".format(d.data['AnonID']))
continue
if not d in proxy:
proxy.find(d, remote_aet, retrieve=True)
if not d in proxy:
logging.warn("{} was not retrieved successfully!".format(d.data["AccessionNumber"]))
d.data['status'] = "unretrievable"
d.persist()
continue
r = proxy.anonymize(d, replacement_map=anon_map)
logging.debug(r)
d.data['AnonOID'] = r['ID']
d.persist()
# Need an oid and an anon name to save...
e = Dixel(key=d.data['AnonOID'],
data={'OID': d.data['AnonOID'],
'PatientID': d.data['AnonID']},
dlvl=d.dlvl)
file_data = proxy.get(e, get_type='file')
e.write_file(file_data, save_dir=dsd)
if clean_proxy:
proxy.remove(d)
proxy.remove(e)