Module Gnumed.business.gmDICOM
GNUmed DICOM handling middleware
Expand source code
# -*- coding: utf-8 -*-
"""GNUmed DICOM handling middleware"""
#============================================================
__license__ = "GPL v2 or later"
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
# stdlib
import os
import sys
import re as regex
import logging
import http.client # exception names used by httplib2
import socket
import httplib2
import json
import shutil
import time
import datetime as pydt
from urllib.parse import urlencode
# 3rd party
from packaging import version
# GNUmed modules
if __name__ == '__main__':
sys.path.insert(0, '../../')
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmShellAPI
from Gnumed.pycommon import gmMimeLib
from Gnumed.pycommon import gmDateTime
_log = logging.getLogger('gm.dicom')
_map_gender_gm2dcm = {
'm': 'M',
'f': 'F',
'tm': 'M',
'tf': 'F',
'h': 'O'
}
#============================================================
class cOrthancServer:
"""Interface for the REST API of an Orthanc DICOM server.
"""
# REST API access to Orthanc DICOM servers
# def __init__(self):
# self.__server_identification = None
# self.__user = None
# self.__password = None
# self.__conn = None
# self.__server_url = None
#--------------------------------------------------------
def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None) -> bool:
try:
int(port)
except Exception:
_log.error('invalid port [%s]', port)
return False
if (host is None) or (host.strip() == ''):
host = 'localhost'
try:
self.__server_url = str('http://%s:%s' % (host, port))
except Exception:
_log.exception('cannot create server url from: host [%s] and port [%s]', host, port)
return False
self.__user = user
self.__password = password
_log.info('connecting as [%s] to Orthanc server at [%s]', self.__user, self.__server_url)
cache_dir = os.path.join(gmTools.gmPaths().user_tmp_dir, '.orthanc2gm-cache')
gmTools.mkdir(cache_dir, 0o700)
gmTools.create_directory_description_file(directory = cache_dir, readme = 'this directory caches Orthanc REST data, mainly DICOM files')
_log.debug('using cache directory: %s', cache_dir)
self.__conn = httplib2.Http(cache = cache_dir)
self.__conn.add_credentials(self.__user, self.__password)
_log.debug('connected to server: %s', self.server_identification)
self.connect_error = ''
if self.server_identification is False:
self.connect_error += 'retrieving server identification failed'
return False
if expected_minimal_version is not None:
if version.parse(self.server_identification['Version']) < version.parse(expected_minimal_version):
_log.error('server too old, needed [%s]', expected_minimal_version)
self.connect_error += 'server too old, needed version [%s]' % expected_minimal_version
return False
if expected_name is not None:
if self.server_identification['Name'] != expected_name:
_log.error('wrong server name, expected [%s]', expected_name)
self.connect_error += 'wrong server name, expected [%s]' % expected_name
return False
if expected_aet is not None:
if self.server_identification['DicomAet'] != expected_name:
_log.error('wrong server AET, expected [%s]', expected_aet)
self.connect_error += 'wrong server AET, expected [%s]' % expected_aet
return False
return True
#--------------------------------------------------------
def _get_server_identification(self):
try:
return self.__server_identification # pylint: disable=access-member-before-definition
except AttributeError:
pass
system_data = self.__run_GET(url = '%s/system' % self.__server_url)
if system_data is False:
_log.error('unable to get server identification')
return False
_log.debug('server: %s', system_data)
self.__server_identification = system_data
self.__initial_orthanc_encoding = self.__run_GET(url = '%s/tools/default-encoding' % self.__server_url)
_log.debug('initial Orthanc encoding: %s', self.__initial_orthanc_encoding)
# check time skew
tolerance = 60 # seconds
client_now_as_utc = pydt.datetime.utcnow()
start = time.time()
orthanc_now_str = self.__run_GET(url = '%s/tools/now' % self.__server_url) # 20180208T165832
end = time.time()
query_duration = end - start
orthanc_now_unknown_tz = pydt.datetime.strptime(orthanc_now_str, '%Y%m%dT%H%M%S')
_log.debug('GNUmed "now" (UTC): %s', client_now_as_utc)
_log.debug('Orthanc "now" (UTC): %s', orthanc_now_unknown_tz)
_log.debug('wire roundtrip (seconds): %s', query_duration)
_log.debug('maximum skew tolerance (seconds): %s', tolerance)
if query_duration > tolerance:
_log.info('useless to check GNUmed/Orthanc time skew, wire roundtrip (%s) > tolerance (%s)', query_duration, tolerance)
else:
if orthanc_now_unknown_tz > client_now_as_utc:
real_skew = orthanc_now_unknown_tz - client_now_as_utc
else:
real_skew = client_now_as_utc - orthanc_now_unknown_tz
_log.info('GNUmed/Orthanc time skew: %s', real_skew)
if real_skew > pydt.timedelta(seconds = tolerance):
_log.error('GNUmed/Orthanc time skew > tolerance (may be due to timezone differences on Orthanc < v1.3.2)')
return self.__server_identification
server_identification = property(_get_server_identification)
#--------------------------------------------------------
def _get_as_external_id_issuer(self):
# fixed type :: user level instance name :: DICOM AET
return 'Orthanc::%(Name)s::%(DicomAet)s' % self.__server_identification
as_external_id_issuer = property(_get_as_external_id_issuer)
#--------------------------------------------------------
def _get_url_browse_patients(self):
if self.__user is None:
return self.__server_url
return self.__server_url.replace('http://', 'http://%s@' % self.__user)
url_browse_patients = property(_get_url_browse_patients)
#--------------------------------------------------------
def get_url_browse_patient(self, patient_id):
# http://localhost:8042/#patient?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
return '%s/#patient?uuid=%s' % (self.url_browse_patients, patient_id)
#--------------------------------------------------------
def get_url_browse_study(self, study_id):
# http://localhost:8042/#study?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b
return '%s/#study?uuid=%s' % (self.url_browse_patients, study_id)
#--------------------------------------------------------
# download API
#--------------------------------------------------------
def get_matching_patients(self, person) -> list:
"""Fetch matching patients from an Orthanc DICOM server.
Matches are searched for via stored "external ID" and
via generically generated ID. The external IDs are
fetched from the patient store, must be of type
"PACS" and must be marked as issued by the
instantiated PACS <self.>
Args:
person: a gmPerson.cPerson instance
Returns:
A list of Orthanc patient UIDs.
"""
_log.info('searching for Orthanc patients matching %s', person)
pacs_ids = person.get_external_ids(id_type = 'PACS', issuer = self.as_external_id_issuer)
if len(pacs_ids) > 1:
_log.error('GNUmed patient has more than one ID for this PACS: %s', pacs_ids)
_log.error('the stored-in-GNUmed PACS ID is expected to be unique _per PACS_')
return []
pacs_ids2search_by = []
pacs_ids2search_by.extend([ pacs_id['value'] for pacs_id in pacs_ids ])
pacs_ids2search_by.extend(person.suggest_external_ids(target = 'PACS'))
matching_pats = []
for pacs_id in pacs_ids2search_by:
_log.debug('using PACS ID [%s]', pacs_id)
pats = self.get_patients_by_external_id(external_id = pacs_id, fuzzy = False)
if len(pats) > 1:
_log.warning('more than one Orthanc patient matches PACS ID: %s', pacs_id)
matching_pats.extend(pats)
if not matching_pats:
_log.debug('no matching patient found in PACS')
return matching_pats
#--------------------------------------------------------
def get_patients_by_external_id(self, external_id=None, fuzzy=False):
"""Search for instances by patient ID."""
_log.info('external ID >>>%s<<< fuzzy [%s]', external_id, fuzzy)
search_term = external_id.strip().strip('*').strip()
if fuzzy:
search_term = '*%s*' % search_term
search_data = {
'Level': 'Patient',
'CaseSensitive': False,
'Expand': True,
'Query': {'PatientID': search_term}
}
matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
# paranoia
for match in matches:
self.protect_patient(orthanc_id = match['ID'])
return matches
#--------------------------------------------------------
def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy:bool=False) -> list:
"""Search for patients by name.
Returns:
List of patients matching the search term(s).
"""
_log.info('name parts %s, gender [%s], dob [%s], fuzzy: [%s]', name_parts, gender, dob, fuzzy)
if len(name_parts) > 1:
return self.get_patients_by_name_parts(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)
search_term = name_parts[0].strip().strip('*').strip()
if search_term == '':
_log.debug('search term empty')
return []
if fuzzy:
search_term = '*%s*' % search_term
search_data:dict = {
'Level': 'Patient',
'CaseSensitive': False,
'Expand': True
}
search_data['Query'] = {'PatientName': search_term}
if gender:
gender = _map_gender_gm2dcm[gender.casefold()]
if gender:
search_data['Query']['PatientSex'] = gender
if dob:
search_data['Query']['PatientBirthDate'] = dob.strftime('%Y%m%d')
_log.info('server-side C-FIND SCU over REST search, mogrified search data: %s', search_data)
matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
return matches
#--------------------------------------------------------
def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False):
# fuzzy: allow partial/substring matches (but not across name part boundaries ',' or '^')
matching_patients = []
clean_parts = []
for part in name_parts:
if part.strip() == '':
continue
clean_parts.append(part.casefold().strip())
_log.info('client-side patient search, scrubbed search terms: %s', clean_parts)
pat_ids = self.__run_GET(url = '%s/patients' % self.__server_url)
if pat_ids is False:
_log.error('cannot retrieve patients')
return []
for pat_id in pat_ids:
orthanc_pat = self.__run_GET(url = '%s/patients/%s' % (self.__server_url, pat_id))
if orthanc_pat is False:
_log.error('cannot retrieve patient')
continue
orthanc_name = orthanc_pat['MainDicomTags']['PatientName'].casefold().strip()
if not fuzzy:
orthanc_name = orthanc_name.replace(' ', ',').replace('^', ',').split(',')
parts_in_orthanc_name = 0
for part in clean_parts:
if part in orthanc_name:
parts_in_orthanc_name += 1
if parts_in_orthanc_name == len(clean_parts):
_log.debug('name match: "%s" contains all of %s', orthanc_name, clean_parts)
if gender is not None:
gender = _map_gender_gm2dcm[gender.casefold()]
if gender is not None:
if orthanc_pat['MainDicomTags']['PatientSex'].casefold() != gender:
_log.debug('gender mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientSex'], gender)
continue
if dob is not None:
if orthanc_pat['MainDicomTags']['PatientBirthDate'] != dob.strftime('%Y%m%d'):
_log.debug('dob mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientBirthDate'], dob)
continue
matching_patients.append(orthanc_pat)
else:
_log.debug('name mismatch: "%s" does not contain all of %s', orthanc_name, clean_parts)
return matching_patients
#--------------------------------------------------------
def search_studies_by_patient_name(self, name:str) -> list:
"""Search for studies with the given patient name snippet.
A study (even at the Orthanc DB metadata level) will
contain the original patient name (unless manually
modified) in contrast to the (artificial Orthanc DB
metadata level) patient record. The latter contains
the first patient name that had been associated with
the given patient ID.
Args:
name: name snippet to search for
Returns:
The list of matching *studies* (not *patient*).
"""
_log.debug('search term [%s]', name)
search_term = name.strip().strip('*').strip()
if search_term == '':
_log.warning('search term empty')
return []
search_term = '*%s*' % search_term
search_data = {
'Level': 'Study',
'CaseSensitive': False,
'Expand': True,
'Query': {'PatientName': search_term}
}
matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
return matches
#--------------------------------------------------------
def search_studies_by_patient_id(self, patient_id:str) -> list:
"""Search for studies with the given patient ID snippet.
This relates to the external world patient ID as
stored in DICOM instances, not the Orthanc DB
metadata level patient UID.
Args:
patient_id: patient ID snippet to search for
Returns:
The list of matching *studies* (not *patient*).
"""
_log.debug('search term >>>%s<<<', patient_id)
search_term = patient_id.strip().strip('*').strip()
search_term = '*%s*' % search_term
search_data = {
'Level': 'Study',
'CaseSensitive': False,
'Expand': True,
'Query': {'PatientID': search_term}
}
matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data)
return matches
#--------------------------------------------------------
def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False):
return self.get_studies_list_by_orthanc_patient_list (
orthanc_patients = self.get_patients_by_name(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy)
)
#--------------------------------------------------------
def get_studies_list_by_external_id(self, external_id=None):
return self.get_studies_list_by_orthanc_patient_list (
orthanc_patients = self.get_patients_by_external_id(external_id = external_id)
)
#--------------------------------------------------------
def get_study_as_zip(self, study_id=None, filename=None):
if filename is None:
filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
_log.info('exporting study [%s] into [%s]', study_id, filename)
f = open(filename, 'wb')
f.write(self.__run_GET(url = '%s/studies/%s/archive' % (self.__server_url, str(study_id)), allow_cached = True))
f.close()
return filename
#--------------------------------------------------------
def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None):
if filename is None:
filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
_log.info('exporting study [%s] into [%s]', study_id, filename)
f = open(filename, 'wb')
f.write(self.__run_GET(url = '%s/studies/%s/media' % (self.__server_url, str(study_id)), allow_cached = True))
f.close()
return filename
#--------------------------------------------------------
def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None):
if filename is None:
filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip')
if study_ids is None:
_log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
f = open(filename, 'wb')
f.write(self.__run_GET(url = '%s/patients/%s/archive' % (self.__server_url, str(patient_id)), allow_cached = True))
f.close()
return filename
#--------------------------------------------------------
def _manual_get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):
if filename is None:
filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)
# all studies
if study_ids is None:
_log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
f = open(filename, 'wb')
url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
_log.debug(url)
f.write(self.__run_GET(url = url, allow_cached = True))
f.close()
if create_zip:
return filename
if target_dir is None:
target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
return False
return target_dir
# a selection of studies
dicomdir_cmd = 'gm-create_dicomdir' # args: 1) name of DICOMDIR to create 2) base directory where to start recursing for DICOM files
found, external_cmd = gmShellAPI.detect_external_binary(dicomdir_cmd)
if not found:
_log.error('[%s] not found', dicomdir_cmd)
return False
if create_zip:
sandbox_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
_log.info('exporting studies [%s] into [%s] (sandbox [%s])', study_ids, filename, sandbox_dir)
else:
sandbox_dir = target_dir
_log.info('exporting studies [%s] into [%s]', study_ids, sandbox_dir)
_log.debug('sandbox dir: %s', sandbox_dir)
idx = 0
for study_id in study_ids:
study_zip_name = gmTools.get_unique_filename(prefix = 'dcm-', suffix = '.zip')
# getting with DICOMDIR returns DICOMDIR compatible subdirs and filenames
study_zip_name = self.get_study_as_zip_with_dicomdir(study_id = study_id, filename = study_zip_name)
# non-beautiful per-study dir name required by subsequent DICOMDIR generation
idx += 1
study_unzip_dir = os.path.join(sandbox_dir, 'STUDY%s' % idx)
_log.debug('study [%s] -> %s -> %s', study_id, study_zip_name, study_unzip_dir)
# need to extract into per-study subdir because get-with-dicomdir
# returns identical-across-studies subdirs / filenames
if not gmTools.unzip_archive(study_zip_name, target_dir = study_unzip_dir, remove_archive = True):
return False
# create DICOMDIR across all studies,
# we simply ignore the already existing per-study DICOMDIR files
target_dicomdir_name = os.path.join(sandbox_dir, 'DICOMDIR')
gmTools.remove_file(target_dicomdir_name, log_error = False) # better safe than sorry
_log.debug('generating [%s]', target_dicomdir_name)
cmd = '%(cmd)s %(DICOMDIR)s %(startdir)s' % {
'cmd': external_cmd,
'DICOMDIR': target_dicomdir_name,
'startdir': sandbox_dir
}
success = gmShellAPI.run_command_in_shell (
command = cmd,
blocking = True
)
if not success:
_log.error('problem running [gm-create_dicomdir]')
return False
# paranoia
try:
open(target_dicomdir_name)
except Exception:
_log.error('[%s] not generated, aborting', target_dicomdir_name)
return False
# return path to extracted studies
if not create_zip:
return sandbox_dir
# else return ZIP of all studies
studies_zip = shutil.make_archive (
gmTools.fname_stem_with_path(filename),
'zip',
root_dir = gmTools.parent_dir(sandbox_dir),
base_dir = gmTools.dirname_stem(sandbox_dir),
logger = _log
)
_log.debug('archived all studies with one DICOMDIR into: %s', studies_zip)
# studies can be _large_ so attempt to get rid of intermediate files
gmTools.rmdir(sandbox_dir)
return studies_zip
#--------------------------------------------------------
def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False):
if filename is None:
filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir)
# all studies
if study_ids is None:
if patient_id is None:
raise ValueError('<patient_id> must be defined if <study_ids> is None')
_log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename)
f = open(filename, 'wb')
url = '%s/patients/%s/media' % (self.__server_url, str(patient_id))
_log.debug(url)
f.write(self.__run_GET(url = url, allow_cached = True))
f.close()
if create_zip:
return filename
if target_dir is None:
target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
return False
return target_dir
# selection of studies
_log.info('exporting %s studies into [%s]', len(study_ids), filename)
_log.debug('studies: %s', study_ids)
f = open(filename, 'wb')
# You have to make a POST request against URI "/tools/create-media", with a
# JSON body that contains the array of the resources of interest (as Orthanc
# identifiers). Here is a sample command-line:
# curl -X POST http://localhost:8042/tools/create-media -d '["8c4663df-c3e66066-9e20a8fc-dd14d1e5-251d3d84","2cd4848d-02f0005f-812ffef6-a210bbcf-3f01a00a","6eeded74-75005003-c3ae9738-d4a06a4f-6beedeb8","8a622020-c058291c-7693b63f-bc67aa2e-0a02e69c"]' -v > /tmp/a.zip
# (this will not create duplicates but will also not check for single-patient-ness)
url = '%s/tools/create-media-extended' % self.__server_url
_log.debug(url)
try:
downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
if not downloaded:
_log.error('this Orthanc version probably does not support "create-media-extended"')
except TypeError:
f.close()
_log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
return False
# retry with old URL
if not downloaded:
url = '%s/tools/create-media' % self.__server_url
_log.debug('retrying: %s', url)
try:
downloaded = self.__run_POST(url = url, data = study_ids, output_file = f)
if not downloaded:
return False
except TypeError:
_log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version')
return False
finally:
f.close()
if create_zip:
return filename
if target_dir is None:
target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-')
_log.debug('exporting studies into [%s]', target_dir)
if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True):
return False
return target_dir
#--------------------------------------------------------
def get_instance_dicom_tags(self, instance_id, simplified=True):
_log.debug('retrieving DICOM tags for instance [%s]', instance_id)
if simplified:
download_url = '%s/instances/%s/simplified-tags' % (self.__server_url, instance_id)
else:
download_url = '%s/instances/%s/tags' % (self.__server_url, instance_id)
return self.__run_GET(url = download_url, allow_cached = True)
#--------------------------------------------------------
def get_instance_preview(self, instance_id, filename=None):
if filename is None:
filename = gmTools.get_unique_filename(suffix = '.png')
_log.debug('exporting preview for instance [%s] into [%s]', instance_id, filename)
download_url = '%s/instances/%s/preview' % (self.__server_url, instance_id)
f = open(filename, 'wb')
try:
f.write(self.__run_GET(url = download_url, allow_cached = True))
except Exception:
_log.exception('cannot retrieve instance')
filename = None
finally:
f.close()
return filename
#--------------------------------------------------------
def get_instance(self, instance_id:str, filename:str=None, allow_cached:bool=True) -> str:
if filename is None:
filename = gmTools.get_unique_filename(suffix = '.dcm')
_log.debug('exporting instance [%s] into [%s]', instance_id, filename)
download_url = '%s/instances/%s/attachments/dicom/data' % (self.__server_url, instance_id)
f = open(filename, 'wb')
f.write(self.__run_GET(url = download_url, allow_cached = allow_cached))
f.close()
return filename
#--------------------------------------------------------
# server-side API
#--------------------------------------------------------
def get_patient(self, orthanc_id:str):
patient_data_url = '%s/patients/%s' % (self.__server_url, str(orthanc_id))
patient_data, status = self.__run_GET(patient_data_url, also_return_status = True)
if patient_data is False:
if status == 404:
_log.debug('no such patient: %s', orthanc_id)
return {}
_log.error('cannot retrieve patient data for [%s]', orthanc_id)
return False
return patient_data
#--------------------------------------------------------
def protect_patient(self, orthanc_id:str):
url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
if self.__run_GET(url) == 1:
_log.debug('patient already protected: %s', orthanc_id)
return True
_log.warning('patient [%s] not protected against recycling, enabling protection now', orthanc_id)
self.__run_PUT(url = url, data = '1')
if self.__run_GET(url) == 1:
return True
_log.error('cannot protect patient [%s] against recycling', orthanc_id)
return False
#--------------------------------------------------------
def unprotect_patient(self, orthanc_id):
url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
if self.__run_GET(url) == 0:
return True
_log.info('patient [%s] protected against recycling, disabling protection now', orthanc_id)
self.__run_PUT(url = url, data = '0')
if self.__run_GET(url) == 0:
return True
_log.error('cannot unprotect patient [%s] against recycling', orthanc_id)
return False
#--------------------------------------------------------
def patient_is_protected(self, orthanc_id):
url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id))
return (self.__run_GET(url) == 1)
#--------------------------------------------------------
def verify_patient_data(self, orthanc_id):
_log.info('verifying DICOM data of patient [%s]', orthanc_id)
bad_data = []
instances_url = '%s/patients/%s/instances' % (self.__server_url, orthanc_id)
instances = self.__run_GET(instances_url)
for instance in instances:
instance_id = instance['ID']
attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
attachments = self.__run_GET(attachments_url, allow_cached = True)
for attachment in attachments:
verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
# False, success = "{}"
#2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5
#2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'}
if self.__run_POST(verify_url) is not False:
continue
_log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment)
bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)})
return bad_data
#--------------------------------------------------------
def modify_patient_id(self, old_patient_id, new_patient_id):
"""Modify the patient ID stored in Orthanc.
This changes all DICOM files of the patient,
identified via (DICOM level) old_patient_id, to
contain the new_patient_id. It will update the
associated Orthanc metadata DB entries accordingly.
"""
if old_patient_id == new_patient_id:
return True
modify_data = {
'Replace': {
'PatientID': new_patient_id
#,u'0010,0021': praxis.name / "GNUmed vX.X.X"
#,u'0010,1002': series of (old) patient IDs
}
, 'Force': True
# "Keep" doesn't seem to do what it suggests ATM
#, u'Keep': True
}
orth_pat_defs = self.get_patients_by_external_id(external_id = old_patient_id)
all_modified = True
for orth_pat_def in orth_pat_defs:
_log.info('modifying Orthanc patient [%s]: DICOM ID [%s] -> [%s]', orth_pat_def['ID'], old_patient_id, new_patient_id)
old_pat_data = self.get_patient(orth_pat_def['ID'])
_log.debug('to be modified: %s', old_pat_data)
if self.patient_is_protected(orth_pat_def['ID']):
_log.debug('patient protected: %s, unprotecting for modification', orth_pat_def['ID'])
if not self.unprotect_patient(orth_pat_def['ID']):
_log.error('cannot unlock patient [%s], skipping', orth_pat_def['ID'])
all_modified = False
continue
was_protected = True
else:
was_protected = False
pat_url = '%s/patients/%s' % (self.__server_url, orth_pat_def['ID'])
modify_url = '%s/modify' % pat_url
result = self.__run_POST(modify_url, data = modify_data)
_log.debug('modify result: %s', result)
if result is False:
_log.error('cannot modify patient [%s]', orth_pat_def['ID'])
all_modified = False
continue
newly_created_orthanc_patient_id = result['ID']
_log.info('newly created Orthanc patient ID: %s', newly_created_orthanc_patient_id)
mod_pat_data = self.get_patient(newly_created_orthanc_patient_id)
_log.debug('modified pat: %s', mod_pat_data)
_log.debug('deleting archived patient: %s', self.__run_DELETE(pat_url))
if was_protected:
if not self.protect_patient(newly_created_orthanc_patient_id):
_log.error('cannot re-lock (new) patient [%s]', newly_created_orthanc_patient_id)
return all_modified
#--------------------------------------------------------
# upload API
#--------------------------------------------------------
def upload_dicom_file(self, filename:str, check_mime_type:bool=False) -> bool:
"""Update a DICOM file.
Will silently ignore DICOMDIR files (which are application/dicom but
Orthanc does not process them).
Args:
filename: DICOM file to upload
check_mime_type: whether to check the file for being application/dicom, and to fail if not
Returns:
True/False
"""
_log.info('processing: %s', filename)
if gmTools.fname_stem(filename) == 'DICOMDIR':
_log.debug('ignoring, no use uploading DICOMDIR files to Orthanc')
return True
if check_mime_type:
mimetype = gmMimeLib.guess_mimetype(filename)
if mimetype != 'application/dicom':
_log.error('not considered a DICOM (application/dicom) file: %s, not uploading', mimetype)
return False
try:
f = open(filename, 'rb')
except Exception:
_log.exception('failed to open file')
return False
dcm_data = f.read()
f.close()
upload_url = '%s/instances' % self.__server_url
uploaded = self.__run_POST(upload_url, data = dcm_data, content_type = 'application/dicom')
if uploaded is False:
_log.error('upload failed')
return False
# typically a 404 following the upload of a DICOM file w/o identifiers
if uploaded == []:
_log.error('upload failed')
return False
_log.debug(uploaded)
# paranoia, as is our custom
verified = self.verify_instance (
instance_id = uploaded['ID'],
filename = filename,
attempt_download = True
)
return verified
#--------------------------------------------------------
def verify_instance(self, instance_id:str, filename:str=None, attempt_download:bool=False) -> bool:
_BINARY_ATTACHMENTS = ['dicom']
_log.debug('verifying instance [%s] against file [%s]', instance_id, filename)
is_valid = True
attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
attachments = self.__run_GET(attachments_url, allow_cached = False)
if not attachments:
_log.error('cannot retrieve instance attachment list')
return False
for attachment in attachments:
md5_orthanc = None
# 1) verify MD5 inside Orthanc, if available (checks Orthanc storage corruption)
available_fields_url = '%s/instances/%s/attachments/%s' % (self.__server_url, instance_id, attachment)
available_fields = self.__run_GET(available_fields_url, allow_cached = False)
if 'md5' in available_fields:
md5_url = '%s/md5' % available_fields_url
md5_orthanc = self.__run_GET(md5_url)
verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
if self.__run_POST(verify_url) is False:
_log.error('MD5 verification failed, instance [%s], attachment=%s, url [%s]', instance_id, attachment, verify_url)
_log.error('potentially Orthanc storage corruption')
is_valid = False
else:
_log.debug('MD5: Orthanc DB <-> Orthanc storage: match')
else:
_log.debug('MD5 of instance attachment not available in Orthanc, cannot verify backend storage status')
# 2) verify instance attachment can be downloaded
md5_downloaded = None
if attempt_download:
attachment_filename = gmTools.get_unique_filename()
download_url = '%s/instances/%s/attachments/%s/data' % (self.__server_url, instance_id, attachment)
attachment_data = self.__run_GET(url = download_url, allow_cached = False)
if isinstance(attachment_data, bytes):
attachment_file = open(attachment_filename, 'wb')
else:
attachment_file = open(attachment_filename, 'wt')
attachment_data = '%s' % attachment_data
attachment_file.write(attachment_data)
del attachment_data
attachment_file.close()
_log.debug('download: Orthanc -> localhost: success')
if attachment not in _BINARY_ATTACHMENTS:
_log.info('attachment of type [%s] not binary, cannot verify MD5 of download or local file against MD5 in Orthanc, skipping', attachment)
continue
md5_downloaded = gmTools.file2md5(attachment_filename)
else:
_log.debug('not downloading instance for verification')
# 3) verify MD5 of downloaded instance against Orthanc, if possible
if md5_downloaded and md5_orthanc:
if md5_downloaded == md5_orthanc:
_log.debug('MD5: Orthanc DB <-> localhost: match')
else:
_log.error('MD5 mismatch: Orthanc DB <-> localhost')
_log.error('download: %s', md5_downloaded)
_log.error('Orthanc : %s', md5_orthanc)
is_valid = False
if filename:
md5_local = gmTools.file2md5(filename)
else:
_log.debug('local file not available for verification')
md5_local = None
# 4) verify MD5 of download against local file
if md5_downloaded and md5_local:
if md5_downloaded == md5_local:
_log.debug('MD5: downloaded <-> pre-existing: match')
else:
_log.error('MD5 mismatch: downloaded <-> pre-existing')
_log.error('download: %s', md5_downloaded)
_log.error('locally : %s', md5_local)
is_valid = False
# 5) verify MD5 of local file against Orthanc
if md5_local and md5_orthanc:
if md5_local == md5_orthanc:
_log.debug('MD5: Orthanc DB <-> pre-existing: match')
else:
_log.error('MD5 mismatch: Orthanc DB <-> pre-existing')
_log.error('locally : %s', md5_local)
_log.error('Orthanc : %s', md5_orthanc)
is_valid = False
# 6) consider comparing the raw pixel data or comparing the output of exiftool etc
_log.debug('verified: %s', is_valid)
return is_valid
#--------------------------------------------------------
def upload_dicom_files(self, files=None, check_mime_type=False):
uploaded = []
not_uploaded = []
for filename in files:
success = self.upload_dicom_file(filename, check_mime_type = check_mime_type)
if success:
uploaded.append(filename)
continue
not_uploaded.append(filename)
if len(not_uploaded) > 0:
_log.error('not all files uploaded')
return (uploaded, not_uploaded)
#--------------------------------------------------------
def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True):
#--------------------
def _on_error(exc):
_log.error('DICOM (?) file not accessible: %s', exc.filename)
_log.error(exc)
#--------------------
_log.debug('uploading DICOM files from [%s]', directory)
if not recursive:
files2try = os.listdir(directory)
_log.debug('found %s files', len(files2try))
if ignore_other_files:
files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
_log.debug('DICOM files therein: %s', len(files2try))
return self.upload_dicom_files(files = files2try, check_mime_type = check_mime_type)
_log.debug('recursing for DICOM files')
uploaded = []
not_uploaded = []
for curr_root, curr_root_subdirs, curr_root_files in os.walk(directory, onerror = _on_error):
_log.debug('recursing into [%s]', curr_root)
files2try = [ os.path.join(curr_root, f) for f in curr_root_files ]
_log.debug('found %s files', len(files2try))
if ignore_other_files:
files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ]
_log.debug('DICOM files therein: %s', len(files2try))
up, not_up = self.upload_dicom_files (
files = files2try,
check_mime_type = check_mime_type
)
uploaded.extend(up)
not_uploaded.extend(not_up)
return (uploaded, not_uploaded)
#--------------------------------------------------------
def upload_by_DICOMDIR(self, DICOMDIR=None):
pass
#--------------------------------------------------------
# helper functions
#--------------------------------------------------------
def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None):
study_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentPatient', 'Series']
series_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentStudy', 'Instances']
studies_by_patient = []
# loop over patients
for pat in orthanc_patients:
pat_dict = {
'orthanc_id': pat['ID'],
'name': None,
'external_id': None,
'date_of_birth': None,
'gender': None,
'studies': []
}
try:
pat_dict['name'] = pat['MainDicomTags']['PatientName'].strip()
except KeyError:
pass
try:
pat_dict['external_id'] = pat['MainDicomTags']['PatientID'].strip()
except KeyError:
pass
try:
pat_dict['date_of_birth'] = pat['MainDicomTags']['PatientBirthDate'].strip()
except KeyError:
pass
try:
pat_dict['gender'] = pat['MainDicomTags']['PatientSex'].strip()
except KeyError:
pass
for key in pat_dict:
if pat_dict[key] in ['unknown', '(null)', '']:
pat_dict[key] = None
pat_dict[key] = cleanup_dicom_string(pat_dict[key])
studies_by_patient.append(pat_dict)
# loop over studies of patient
orth_studies = self.__run_GET(url = '%s/patients/%s/studies' % (self.__server_url, pat['ID']))
if orth_studies is False:
_log.error('cannot retrieve studies')
return []
for orth_study in orth_studies:
study_dict = {
'orthanc_id': orth_study['ID'],
'date': None,
'time': None,
'description': None,
'referring_doc': None,
'requesting_doc': None,
'requesting_org': None,
'performing_doc': None,
'operator_name': None,
'radiographer_code': None,
'radiology_org': None,
'radiology_dept': None,
'radiology_org_addr': None,
'station_name': None,
'series': []
}
try:
study_dict['date'] = orth_study['MainDicomTags']['StudyDate'].strip()
except KeyError:
pass
try:
study_dict['time'] = orth_study['MainDicomTags']['StudyTime'].strip()
except KeyError:
pass
try:
study_dict['description'] = orth_study['MainDicomTags']['StudyDescription'].strip()
except KeyError:
pass
try:
study_dict['referring_doc'] = orth_study['MainDicomTags']['ReferringPhysicianName'].strip()
except KeyError:
pass
try:
study_dict['requesting_doc'] = orth_study['MainDicomTags']['RequestingPhysician'].strip()
except KeyError:
pass
try:
study_dict['requesting_org'] = orth_study['MainDicomTags']['RequestingService'].strip()
except KeyError:
pass
try:
study_dict['radiology_org_addr'] = orth_study['MainDicomTags']['InstitutionAddress'].strip()
except KeyError:
pass
try:
study_dict['radiology_org'] = orth_study['MainDicomTags']['InstitutionName'].strip()
if study_dict['radiology_org_addr'] is not None:
if study_dict['radiology_org'] in study_dict['radiology_org_addr']:
study_dict['radiology_org'] = None
except KeyError:
pass
try:
study_dict['radiology_dept'] = orth_study['MainDicomTags']['InstitutionalDepartmentName'].strip()
if study_dict['radiology_org'] is not None:
if study_dict['radiology_dept'] in study_dict['radiology_org']:
study_dict['radiology_dept'] = None
if study_dict['radiology_org_addr'] is not None:
if study_dict['radiology_dept'] in study_dict['radiology_org_addr']:
study_dict['radiology_dept'] = None
except KeyError:
pass
try:
study_dict['station_name'] = orth_study['MainDicomTags']['StationName'].strip()
if study_dict['radiology_org'] is not None:
if study_dict['station_name'] in study_dict['radiology_org']:
study_dict['station_name'] = None
if study_dict['radiology_org_addr'] is not None:
if study_dict['station_name'] in study_dict['radiology_org_addr']:
study_dict['station_name'] = None
if study_dict['radiology_dept'] is not None:
if study_dict['station_name'] in study_dict['radiology_dept']:
study_dict['station_name'] = None
except KeyError:
pass
for key in study_dict:
if study_dict[key] in ['unknown', '(null)', '']:
study_dict[key] = None
study_dict[key] = cleanup_dicom_string(study_dict[key])
study_dict['all_tags'] = {}
try:
orth_study['PatientMainDicomTags']
except KeyError:
orth_study['PatientMainDicomTags'] = pat['MainDicomTags']
for key in orth_study:
if key == 'MainDicomTags':
for mkey in orth_study['MainDicomTags']:
study_dict['all_tags'][mkey] = orth_study['MainDicomTags'][mkey].strip()
continue
if key == 'PatientMainDicomTags':
for pkey in orth_study['PatientMainDicomTags']:
study_dict['all_tags'][pkey] = orth_study['PatientMainDicomTags'][pkey].strip()
continue
study_dict['all_tags'][key] = orth_study[key]
_log.debug('study: %s', list(study_dict['all_tags']))
for key in study_keys2hide:
try: del study_dict['all_tags'][key]
except KeyError: pass
pat_dict['studies'].append(study_dict)
# loop over series in study
for orth_series_id in orth_study['Series']:
orth_series = self.__run_GET(url = '%s/series/%s' % (self.__server_url, orth_series_id))
ordered_slices = self.__run_GET(url = '%s/series/%s/ordered-slices' % (self.__server_url, orth_series_id))
if ordered_slices is False:
slices = orth_series['Instances']
else:
slices = [ s[0] for s in ordered_slices['SlicesShort'] ]
if orth_series is False:
_log.error('cannot retrieve series')
return []
series_dict = {
'orthanc_id': orth_series['ID'],
'instances': slices,
'modality': None,
'date': None,
'time': None,
'description': None,
'body_part': None,
'protocol': None,
'performed_procedure_step_description': None,
'acquisition_device_processing_description': None,
'operator_name': None,
'radiographer_code': None,
'performing_doc': None
}
try:
series_dict['modality'] = orth_series['MainDicomTags']['Modality'].strip()
except KeyError:
pass
try:
series_dict['date'] = orth_series['MainDicomTags']['SeriesDate'].strip()
except KeyError:
pass
try:
series_dict['description'] = orth_series['MainDicomTags']['SeriesDescription'].strip()
except KeyError:
pass
try:
series_dict['time'] = orth_series['MainDicomTags']['SeriesTime'].strip()
except KeyError:
pass
try:
series_dict['body_part'] = orth_series['MainDicomTags']['BodyPartExamined'].strip()
except KeyError:
pass
try:
series_dict['protocol'] = orth_series['MainDicomTags']['ProtocolName'].strip()
except KeyError:
pass
try:
series_dict['performed_procedure_step_description'] = orth_series['MainDicomTags']['PerformedProcedureStepDescription'].strip()
except KeyError:
pass
try:
series_dict['acquisition_device_processing_description'] = orth_series['MainDicomTags']['AcquisitionDeviceProcessingDescription'].strip()
except KeyError:
pass
try:
series_dict['operator_name'] = orth_series['MainDicomTags']['OperatorsName'].strip()
except KeyError:
pass
try:
series_dict['radiographer_code'] = orth_series['MainDicomTags']['RadiographersCode'].strip()
except KeyError:
pass
try:
series_dict['performing_doc'] = orth_series['MainDicomTags']['PerformingPhysicianName'].strip()
except KeyError:
pass
for key in series_dict:
if series_dict[key] in ['unknown', '(null)', '']:
series_dict[key] = None
if series_dict['description'] == series_dict['protocol']:
_log.debug('<series description> matches <series protocol>, ignoring protocol')
series_dict['protocol'] = None
if series_dict['performed_procedure_step_description'] in [series_dict['description'], series_dict['protocol']]:
series_dict['performed_procedure_step_description'] = None
if series_dict['performed_procedure_step_description'] is not None:
# weed out "numeric" only
if regex.match ('[.,/\|\-\s\d]+', series_dict['performed_procedure_step_description'], flags = regex.UNICODE):
series_dict['performed_procedure_step_description'] = None
if series_dict['acquisition_device_processing_description'] in [series_dict['description'], series_dict['protocol']]:
series_dict['acquisition_device_processing_description'] = None
if series_dict['acquisition_device_processing_description'] is not None:
# weed out "numeric" only
if regex.match ('[.,/\|\-\s\d]+', series_dict['acquisition_device_processing_description'], flags = regex.UNICODE):
series_dict['acquisition_device_processing_description'] = None
if series_dict['date'] == study_dict['date']:
_log.debug('<series date> matches <study date>, ignoring date')
series_dict['date'] = None
if series_dict['time'] == study_dict['time']:
_log.debug('<series time> matches <study time>, ignoring time')
series_dict['time'] = None
for key in series_dict:
series_dict[key] = cleanup_dicom_string(series_dict[key])
series_dict['all_tags'] = {}
for key in orth_series:
if key == 'MainDicomTags':
for mkey in orth_series['MainDicomTags']:
series_dict['all_tags'][mkey] = orth_series['MainDicomTags'][mkey].strip()
continue
series_dict['all_tags'][key] = orth_series[key]
_log.debug('series: %s', list(series_dict['all_tags']))
for key in series_keys2hide:
try: del series_dict['all_tags'][key]
except KeyError: pass
study_dict['operator_name'] = series_dict['operator_name'] # will collapse all operators into that of the last series
study_dict['radiographer_code'] = series_dict['radiographer_code'] # will collapse all into that of the last series
study_dict['performing_doc'] = series_dict['performing_doc'] # will collapse all into that of the last series
study_dict['series'].append(series_dict)
return studies_by_patient
#--------------------------------------------------------
# generic REST helpers
#--------------------------------------------------------
def run_GET(self, url=None, data=None, allow_cached=False):
url = '%s/%s' % (self.__server_url, url)
return self.__run_GET(url = url, data = data, allow_cached = allow_cached)
#--------------------------------------------------------
def __run_GET(self, url=None, data=None, allow_cached=False, also_return_status=False):
if data is None:
data = {}
headers = {}
if not allow_cached:
headers['cache-control'] = 'no-cache'
params = ''
if data:
params = '?' + urlencode(data)
url_with_params = url + params
#_log.debug('URL with parameters: >>>%s<<<', url_with_params)
try:
response, content = self.__conn.request(url_with_params, 'GET', headers = headers)
except (OverflowError, socket.error, http.client.ResponseNotReady, http.client.InvalidURL, http.client.RemoteDisconnected, httplib2.ServerNotFoundError):
# http.client.RemoteDisconnected: observed during GET while Orthanc was shutting down for backup
_log.exception('exception in GET')
_log.debug(' url: %s', url_with_params)
_log.debug(' headers: %s', headers)
if also_return_status:
return (False, -1)
return False
if response.status not in [ 200 ]:
_log.error('GET returned non-OK status: %s', response.status)
_log.debug(' url: %s', url_with_params)
_log.debug(' headers: %s', headers)
_log.error(' response: %s', response)
_log.debug(' content: %s', content)
if also_return_status:
return (False, response.status)
return False
#_log.debug('response: %s', response)
#_log.debug('type(content): %s', type(content))
content_type = response['content-type'].strip()
if content_type.startswith('text/plain'):
# utf8 ?
# urldecode ?
# latin1 = Orthanc default = tools/default-encoding ?
# ascii ?
content = content.decode('utf8')
elif content_type.startswith('application/json'):
try:
content = json.loads(content)
except Exception:
_log.exception('failed to json.loads(content) despite application/json indicated, returning content and hoping for the best')
mime_type, charset_def = content_type.split(';')
charset = charset_def.strip().split('=')[1]
#content = content.decode('utf8')
content = content.decode(charset)
#_log.debug(content)
else:
_log.error('content: <%s>, not <text/plain> or <application/json> -- returning raw content', content_type)
if also_return_status:
return (content, response.status)
return content
#--------------------------------------------------------
def __run_POST(self, url=None, data=None, content_type=None, output_file=None):
body = data
headers = {'content-type' : content_type}
if isinstance(data, str):
if content_type is None:
headers['content-type'] = 'text/plain'
elif isinstance(data, bytes):
if content_type is None:
headers['content-type'] = 'application/octet-stream'
else:
body = json.dumps(data)
headers['content-type'] = 'application/json'
try:
try:
response, content = self.__conn.request(url, 'POST', body = body, headers = headers)
except BrokenPipeError:
_log.debug('retrying after BrokenPipeError')
response, content = self.__conn.request(url, 'POST', body = body, headers = headers)
except (socket.error, http.client.ResponseNotReady, OverflowError):
_log.exception('exception in POST')
_log.debug(' url: %s', url)
_log.debug(' headers: %s', headers)
_log.debug(' body: %s', body[:16])
return False
if response.status == 404:
_log.debug('no data, response: %s', response)
if output_file is None:
return []
return False
if response.status not in [ 200, 302 ]:
_log.error('POST returned non-OK (not 200,302) status: %s', response.status)
_log.debug(' url: %s', url)
_log.debug(' headers: %s', headers)
_log.debug(' body: %s', body[:16])
_log.error(' response: %s', response)
_log.debug(' content: %s', content)
return False
try:
content = json.loads(content)
except Exception:
pass
if output_file is None:
return content
output_file.write(content)
return True
#--------------------------------------------------------
def __run_PUT(self, url=None, data=None, content_type=None):
body = data
headers = {'content-type' : content_type}
if isinstance(data, str):
if content_type is None:
headers['content-type'] = 'text/plain'
elif isinstance(data, bytes):
if content_type is None:
headers['content-type'] = 'application/octet-stream'
else:
body = json.dumps(data)
headers['content-type'] = 'application/json'
try:
try:
response, content = self.__conn.request(url, 'PUT', body = body, headers = headers)
except BrokenPipeError:
response, content = self.__conn.request(url, 'PUT', body = body, headers = headers)
except (socket.error, http.client.ResponseNotReady, OverflowError):
_log.exception('exception in PUT')
_log.debug(' url: %s', url)
_log.debug(' headers: %s', headers)
_log.debug(' body: %s', body[:16])
return False
if response.status == 404:
_log.debug('no data, response: %s', response)
return []
if response.status not in [ 200, 302 ]:
_log.error('PUT returned non-OK status: %s', response.status)
_log.debug(' url: %s', url)
_log.debug(' headers: %s', headers)
_log.debug(' body: %s', body[:16])
_log.error(' response: %s', response)
_log.debug(' content: %s', content)
return False
if response['content-type'].startswith('text/plain'):
# utf8 ?
# urldecode ?
# latin1 = Orthanc default = tools/default-encoding ?
# ascii ?
return content.decode('utf8')
if response['content-type'].startswith('application/json'):
try:
return json.loads(content)
except Exception:
return content
return content
#--------------------------------------------------------
def __run_DELETE(self, url=None):
try:
response, content = self.__conn.request(url, 'DELETE')
except (http.client.ResponseNotReady, socket.error, OverflowError):
_log.exception('exception in DELETE')
_log.debug(' url: %s', url)
return False
if response.status not in [ 200 ]:
_log.error('DELETE returned non-OK status: %s', response.status)
_log.debug(' url: %s', url)
_log.error(' response: %s', response)
_log.debug(' content: %s', content)
return False
if response['content-type'].startswith('text/plain'):
# utf8 ?
# urldecode ?
# latin1 = Orthanc default = tools/default-encoding ?
# ascii ?
return content.decode('utf8')
if response['content-type'].startswith('application/json'):
try:
return json.loads(content)
except Exception:
return content
return content
#--------------------------------------------------------
def _get_server_url(self):
return self.__server_url
server_url = property(_get_server_url)
#------------------------------------------------------------
def cleanup_dicom_string(dicom_str:str) -> str:
if not isinstance(dicom_str, str):
return dicom_str
dicom_str = regex.sub('\^+', ' ', dicom_str.strip('^'))
#dicom_str = dicom_str.replace('\r\n', ' [CR] ')
return dicom_str
#---------------------------------------------------------------------------
def dicomize_file(filename:str=None, title:str=None, person=None, dcm_name:str=None, verbose:bool=False, dcm_template_file:str=None, dcm_transfer_series:bool=True, content_date=None) -> str:
"""Encapsulate a file inside a DCM file.
Dates and times of the instance are set to 'now'.
Works for PDF documents and images which are/can be converted to JPG.
Args:
filename: the file to encapsulate
title: document title, defaults to filename
person: a GNUmed person instance from which to derive demographics, None -> derive from *dcm_template_file*
dcm_name: filename for the resulting DICOM file, None -> auto-create name
verbose: passed to external converter
dcm_template_file: DICOM file from which to derive patient demographics and study ID, None -> *person* must be defined
dcm_transfer_series: only applies if *dcm_template_file* given
True = derive series from *dcm_template_file*,
False = only derive study from *dcm_template_file* and create a new series
content_date: date/time to use for study/series/instance, as needed; None -> use now()
Returns:
DICOM file name or None on failure.
"""
assert (filename is not None), '<filename> must not be None'
assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None'
# already DCM ?
if gmMimeLib.guess_mimetype(filename) == 'application/dicom':
_log.error('already a DICOM file: %s', filename)
if dcm_name is None:
return filename
return shutil.copy2(filename, dcm_name)
dcm_fname = dicomize_pdf (
pdf_name = filename,
title = title,
person = person,
dcm_name = dcm_name,
verbose = verbose,
dcm_template_file = dcm_template_file,
dcm_transfer_series = dcm_transfer_series,
content_date = content_date
)
if dcm_fname is not None:
return dcm_fname
_log.debug('does not seem to be a PDF: %s', filename)
converted_fname = gmMimeLib.convert_file(filename = filename, target_mime = 'image/jpeg')
if converted_fname is None:
_log.error('cannot convert to JPG: %s', filename)
return None
dcm_name = dicomize_jpg (
jpg_name = converted_fname,
title = title,
person = person,
dcm_name = dcm_name,
verbose = verbose,
dcm_template_file = dcm_template_file,
dcm_transfer_series = dcm_transfer_series,
content_date = content_date
)
return dcm_name
#---------------------------------------------------------------------------
def dicomize_pdf(pdf_name:str=None, title:str=None, person=None, dcm_name:str=None, verbose:bool=False, dcm_template_file:str=None, dcm_transfer_series:bool=True, content_date=None) -> str:
"""Encapsulate a PDF file inside a DCM file.
Dates and times of the instance are set to 'now'.
Args:
pdf_name: the PDF file to encapsulate
title: document title, None -> *pdf_name*, also used as study/series description
person: see *dicomize_file()*
dcm_name: see *dicomize_file()*
verbose: see *dicomize_file()*
dcm_template_file: see *dicomize_file()*
dcm_transfer_series: see *dicomize_file()*
content_date: see *dicomize_file()*
Returns:
DICOM file name or None on failure.
"""
assert (pdf_name is not None), '<pdf_name> must not be None'
assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None'
if dcm_name is None:
dcm_name = gmTools.get_unique_filename(suffix = '.dcm')
_log.debug('%s -> %s', pdf_name, dcm_name)
if title is None:
title = gmTools.fname_stem(pdf_name)
if content_date is None:
content_date = gmDateTime.pydt_now_here()
cmd_line = [
'pdf2dcm',
'--title', title,
'--key', '0008,1030=%s' % title, # StudyDescription
'--key', '0008,103E=%s' % title, # SeriesDescription
'--key', '0008,0021=%s' % content_date.strftime('%Y%m%d'), # SeriesDate
'--key', '0008,0023=%s' % content_date.strftime('%Y%m%d'), # ContentDate
'--key', '0008,0031=%s' % content_date.strftime('%H%M%s.0'),# SeriesTime
'--key', '0008,0033=%s' % content_date.strftime('%H%M%s.0') # ContentTime
]
if dcm_template_file is None:
# StudyDate
cmd_line.append('--key')
cmd_line.append('0008,0020=%s' % content_date.strftime('%Y%m%d'))
# StudyTime
cmd_line.append('--key')
cmd_line.append('0008,0030=%s' % content_date.strftime('%H%M%s.0'))
# PatientName
name = person.active_name
cmd_line.append('--patient-id')
cmd_line.append(person.suggest_external_id(target = 'PACS'))
cmd_line.append('--patient-name')
cmd_line.append(('%s^%s' % (name['lastnames'], name['firstnames'])).replace(' ', '^'))
if person['dob']:
cmd_line.append('--patient-birthdate')
cmd_line.append(person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False))
if person['gender']:
cmd_line.append('--patient-sex')
cmd_line.append(_map_gender_gm2dcm[person['gender']])
else:
_log.debug('DCM template file: %s', dcm_template_file)
if dcm_transfer_series:
cmd_line.append('--series-from')
cmd_line.append(dcm_template_file)
else:
cmd_line.append('--study-from')
cmd_line.append(dcm_template_file)
if verbose:
cmd_line.append('--log-level')
cmd_line.append('trace')
cmd_line.append(pdf_name)
cmd_line.append(dcm_name)
success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose)
if success:
return dcm_name
return None
#---------------------------------------------------------------------------
def dicomize_jpg(jpg_name:str=None, title:str=None, person=None, dcm_name:str=None, verbose:bool=False, dcm_template_file:str=None, dcm_transfer_series:bool=True, content_date=None) -> str:
"""Encapsulate a JPG file inside a DCM file.
Dates and times of the instance are set to 'now'.
Args:
jpg_name: the JPG file to encapsulate
title: document title, None -> *jpg_name*, used as study/series description
person: see *dicomize_file()*
dcm_name: see *dicomize_file()*
verbose: see *dicomize_file()*
dcm_template_file: see *dicomize_file()*
dcm_transfer_series: see *dicomize_file()*
content_date: see *dicomize_file()*
Returns:
DICOM file name or None on failure.
"""
assert (jpg_name is not None), '<jpg_name> must not be None'
assert (not ((person is None) and (dcm_template_file is None))), 'both <person> and <dcm_template_file> are None, but one is needed'
if dcm_name is None:
dcm_name = gmTools.get_unique_filename(suffix = '.dcm')
_log.debug('%s -> %s', jpg_name, dcm_name)
if title is None:
title = gmTools.fname_stem(jpg_name)
if content_date is None:
content_date = gmDateTime.pydt_now_here()
cmd_line = [
'img2dcm',
'--keep-appn', # carry over EXIF data
'--insist-on-jfif', # process valid JFIF only
'--key', '0008,1030=%s' % title, # StudyDescription
'--key', '0008,103E=%s' % title, # SeriesDescription
'--key', '0008,0021=%s' % content_date.strftime('%Y%m%d'), # SeriesDate
'--key', '0008,0031=%s' % content_date.strftime('%H%M%s.0'), # SeriesTime
'--key', '0008,0023=%s' % content_date.strftime('%Y%m%d'), # ContentDate
'--key', '0008,0033=%s' % content_date.strftime('%H%M%s.0') # ContentTime
]
if dcm_template_file is None:
# StudyDate
cmd_line.append('--key')
cmd_line.append('0008,0020=%s' % content_date.strftime('%Y%m%d'))
# StudyTime
cmd_line.append('--key')
cmd_line.append('0008,0030=%s' % content_date.strftime('%H%M%s.0'))
# PatientName
name = person.active_name
cmd_line.append('--key')
cmd_line.append('0010,0010=%s' % ('%s^%s' % (
name['lastnames'],
name['firstnames'])
).replace(' ', '^'))
# PatientID
cmd_line.append('--key')
cmd_line.append('0010,0020=%s' % person.suggest_external_id(target = 'PACS'))
# DOB
cmd_line.append('--key')
cmd_line.append('0010,0030=%s' % person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False))
# gender
if person['gender']:
cmd_line.append('--key')
cmd_line.append('0010,0040=%s' % _map_gender_gm2dcm[person['gender']])
else:
_log.debug('DCM template file: %s', dcm_template_file)
if dcm_transfer_series:
cmd_line.append('--series-from')
cmd_line.append(dcm_template_file)
else:
cmd_line.append('--study-from')
cmd_line.append(dcm_template_file)
if verbose:
cmd_line.append('--log-level')
cmd_line.append('trace')
cmd_line.append(jpg_name)
cmd_line.append(dcm_name)
success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose)
if success:
return dcm_name
return None
#---------------------------------------------------------------------------
def run_file2dicom_tool(fname:str=None, dcm_template:str=None) -> str:
"""Convert a file into DICOM format.
This offers a primitive text user interface.
Args:
fname: the file to convert, must be image or PDF
dcm_template: a DCM file to use as template for study/series data, optional
Returns:
name of the new DICOM file, or None
"""
if dcm_template is None:
from Gnumed.pycommon import gmPG2
gmPG2.request_login_params(setup_pool = True)
from Gnumed.business import gmPersonSearch
pat = gmPersonSearch.ask_for_patient()
if pat is None:
return None
else:
pat = None
dt = None
while dt is None:
iso = input('enter date (ISO - YYYY-MM-DD): ')
try:
dt = pydt.datetime.fromisoformat(iso)
except ValueError:
if iso.strip() == '':
return None
dt = None
desc = input('enter description (ASCII): ')
if desc.strip() == '':
desc = None
print('patient:', pat)
print('DCM template:', dcm_template)
print()
print('file to convert:', fname)
print('series date:', dt)
print('description:', desc)
input('hit <ENTER> to convert')
dcm = dicomize_file (
filename = fname,
person = pat,
dcm_name = fname + '.dcm',
verbose = True,
content_date = dt,
title = desc,
dcm_template_file = dcm_template
)
print('DCM file:', dcm)
#============================================================
# main
#------------------------------------------------------------
if __name__ == "__main__":
if len(sys.argv) == 1:
sys.exit()
if sys.argv[1] != 'test':
fname = sys.argv[1]
try: dcm_template = sys.argv[2]
except IndexError: dcm_template = None
run_file2dicom_tool(fname, dcm_template)
sys.exit()
#--------------------------------------------------------
def orthanc_console(host, port):
print('Please enter patient name parts, separated by SPACE.')
while True:
entered_name = gmTools.prompted_input(prompt = "\nEnter person search term or leave blank to exit")
if entered_name in ['exit', 'quit', 'bye', None]:
print("user cancelled patient search")
break
pats = orthanc.get_patients_by_external_id(external_id = entered_name)
if len(pats) > 0:
print('Patients found:')
for pat in pats:
print(' -> ', pat)
continue
pats = orthanc.get_patients_by_name(name_parts = entered_name.split(), fuzzy = True)
print('Patients found:')
for pat in pats:
print(' -> ', pat)
print(' verifying ...')
bad_data = orthanc.verify_patient_data(pat['ID'])
print(' bad data:')
for bad in bad_data:
print(' -> ', bad)
continue
continue
pats = orthanc.get_studies_list_by_patient_name(name_parts = entered_name.split(), fuzzy = True)
print('Patients found from studies list:')
for pat in pats:
print(' -> ', pat['name'])
for study in pat['studies']:
print(' ', gmTools.format_dict_like(study, relevant_keys = ['orthanc_id', 'date', 'time'], template = 'study [%%(orthanc_id)s] at %%(date)s %%(time)s contains %s series' % len(study['series'])))
# for series in study['series']:
# print (
# u' ',
# gmTools.format_dict_like (
# series,
# relevant_keys = ['orthanc_id', 'date', 'time', 'modality', 'instances', 'body_part', 'protocol', 'description', 'station'],
# template = u'series [%(orthanc_id)s] at %(date)s %(time)s: "%(description)s" %(modality)s@%(station)s (%(protocol)s) of body part "%(body_part)s" holds images:\n%(instances)s'
# )
# )
# print(orthanc.get_studies_with_dicomdir(study_ids = [study['orthanc_id']], filename = 'study_%s.zip' % study['orthanc_id'], create_zip = True))
#print(orthanc.get_study_as_zip(study_id = study['orthanc_id'], filename = 'study_%s.zip' % study['orthanc_id']))
#print(orthanc.get_studies_as_zip_with_dicomdir(study_ids = [ s['orthanc_id'] for s in pat['studies'] ], filename = 'studies_of_%s.zip' % pat['orthanc_id']))
print('--------')
#--------------------------------------------------------
def run_console():
orthanc_console(host, port)
#--------------------------------------------------------
def test_modify_patient_id():
print('Please enter patient name parts, separated by SPACE.')
entered_name = gmTools.prompted_input(prompt = "\nEnter person search term or leave blank to exit")
if entered_name in ['exit', 'quit', 'bye', None]:
print("user cancelled patient search")
return
pats = orthanc.get_patients_by_name(name_parts = entered_name.split(), fuzzy = True)
if len(pats) == 0:
print('no patient found')
return
pat = pats[0]
print('test patient:')
print(pat)
old_id = pat['MainDicomTags']['PatientID']
new_id = old_id + '-1'
print('setting [%s] to [%s]:' % (old_id, new_id), orthanc.modify_patient_id(old_id, new_id))
#--------------------------------------------------------
def test_upload_file():
orthanc.upload_dicom_file(filename = sys.argv[4], check_mime_type = True)
#--------------------------------------------------------
def test_upload_files():
#orthanc.upload_dicom_file(sys.argv[2])
orthanc.upload_from_directory(directory = sys.argv[4], recursive = True, check_mime_type = False, ignore_other_files = True)
#--------------------------------------------------------
def test_get_instance_preview():
print(orthanc.get_instance_preview('f4f07d22-0d8265ef-112ea4e9-dc140e13-350c06d1'))
print(orthanc.get_instance('f4f07d22-0d8265ef-112ea4e9-dc140e13-350c06d1'))
#--------------------------------------------------------
def test_get_instance_tags():
instance_id = 'f4f07d22-0d8265ef-112ea4e9-dc140e13-350c06d1'
for key, value in orthanc.get_instance_dicom_tags(instance_id, simplified = False).items():
print(key, ':', value)
print()
#print(orthanc.get_instance_dicom_tags(instance_id, simplified = True))
#--------------------------------------------------------
def test_pdf2dcm():
#print(pdf2dcm(filename = filename, patient_id = 'ID::abcABC', dob = '19900101'))
#from Gnumed.business import gmPerson
#pers = gmPerson.cPerson(12)
from Gnumed.business import gmPersonSearch
pers = gmPersonSearch.ask_for_patient()
if pers is None:
return
print(pers)
try:
print(dicomize_pdf(pdf_name = sys.argv[2], person = pers, dcm_name = None, verbose = True, dcm_template_file = sys.argv[3]))#, title = 'test'))
except IndexError:
print(dicomize_pdf(pdf_name = sys.argv[2], person = pers, dcm_name = None, verbose = True))#, title = 'test'))
#--------------------------------------------------------
def test_img2dcm():
from Gnumed.pycommon import gmPG2
gmPG2.request_login_params(setup_pool = True)
#print(pdf2dcm(filename = filename, patient_id = 'ID::abcABC', dob = '19900101'))
#from Gnumed.business import gmPerson
#pers = gmPerson.cPerson(12)
from Gnumed.business import gmPersonSearch
pers = gmPersonSearch.ask_for_patient()
if pers is None:
return
dt = None
while dt is None:
iso = input('enter date: ')
try:
dt = pydt.datetime.fromisoformat(iso)
except ValueError:
if iso.strip() == '':
return
print(pers)
print(iso)
input('enter to continue')
try:
print(dicomize_jpg(jpg_name = sys.argv[2], person = pers, dcm_name = sys.argv[2]+'.dcm', verbose = True, dcm_template_file = sys.argv[3]))#, title = 'test'))
except IndexError:
print(dicomize_jpg (
jpg_name = sys.argv[2],
person = pers,
dcm_name = sys.argv[2]+'.dcm',
verbose = True,
content_date = dt
))#, title = 'test'))
#--------------------------------------------------------
def test_file2dcm():
from Gnumed.business import gmPersonSearch
person = gmPersonSearch.ask_for_patient()
if person is None:
return
print(person)
try:
print(dicomize_file(filename = sys.argv[2], person = person, dcm_name = sys.argv[2]+'.dcm', verbose = True, dcm_template_file = sys.argv[3], title = sys.argv[4]))
except IndexError:
pass
try:
print(dicomize_file(filename = sys.argv[2], person = person, dcm_name = sys.argv[2]+'.dcm', verbose = True, title = sys.argv[3]))
except IndexError:
print(dicomize_file(filename = sys.argv[2], person = person, dcm_name = sys.argv[2]+'.dcm', verbose = True))
#--------------------------------------------------------
def test_patient():
print(orthanc.get_patient('89729867-a08815a6-37c59f5a-f1f6ea57-6c1e17cb'))
input()
print(orthanc.get_patient('1cff9d34-96047a5a-afb97dd0-33a84dc7-a710ef8f'))
return
#'/patients/89729867-a08815a6-37c59f5a-f1f6ea57-6c1e17cb'
orthanc_id = '89729867-a08815a6-37c59f5a-f1f6ea57-6c1e17cb'
instances_url = 'patients/%s/instances' % orthanc_id
print(instances_url)
#new_patient_id = 'xxx'
instances = orthanc.run_GET(instances_url)
for instance in instances:
instance_id = instance['ID']
tags = orthanc.get_instance_dicom_tags(instance_id, simplified = False)
if tags['0010,0030']['Value'] != '19810416':
continue
#orthanc.modify_patient_id_of_instance(instance_id, new_patient_id)
#print(tags['0010,0030']['PatientID'])
#print(tags['0010,0030']['PatientName'])
#continue
for key, value in tags.items():
print(key, ':', value)
# instance_id = instance['ID']
# attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id)
# attachments = self.__run_GET(attachments_url, allow_cached = True)
# for attachment in attachments:
# verify_url = '%s/%s/verify-md5' % (attachments_url, attachment)
# # False, success = "{}"
# #2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5
# #2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'}
# if self.__run_POST(verify_url) is not False:
# continue
# _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment)
# bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)})
#--------------------------------------------------------
def test_verify_instance():
# u'Path': u'/instances/1440110e-9cd02a98-0b1c0452-087d35db-3fd5eb05'
#instance_id = '1440110e-9cd02a98-0b1c0452-087d35db-3fd5eb05'
#instance_id = '5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6'
instance_id = '7e99fa76-3699ab68-7fd9d2de-c621b331-b4fe7394'
print('verifying [%s]' % instance_id)
result = orthanc.verify_instance (
instance_id = instance_id
# , filename = None
, attempt_download = True
)
print(result)
#--------------------------------------------------------
def _connect():
global host
try:
host = sys.argv[2]
except IndexError:
host = None
global port
try:
port = sys.argv[3]
except IndexError:
port = '8042'
global orthanc
orthanc = cOrthancServer()
if not orthanc.connect(host, port, user = None, password = None, expected_minimal_version = '1'): #, expected_aet = 'another AET'
print('error connecting to server:', orthanc.connect_error)
sys.exit(-1)
print('Connected to Orthanc server "%s" (AET [%s] - version [%s] - DB [%s])' % (
orthanc.server_identification['Name'],
orthanc.server_identification['DicomAet'],
orthanc.server_identification['Version'],
orthanc.server_identification['DatabaseVersion']
))
print('')
#--------------------------------------------------------
#test_pdf2dcm()
#test_img2dcm()
#test_file2dcm()
#sys.exit
#_connect()
#run_console()
#test_verify_instance()
#test_modify_patient_id()
#test_upload_files()
#test_upload_file()
#test_get_instance_preview()
#test_get_instance_tags()
#test_patient()Functions
def cleanup_dicom_string(dicom_str: str) ‑> str-
Expand source code
def cleanup_dicom_string(dicom_str:str) -> str: if not isinstance(dicom_str, str): return dicom_str dicom_str = regex.sub('\^+', ' ', dicom_str.strip('^')) #dicom_str = dicom_str.replace('\r\n', ' [CR] ') return dicom_str def dicomize_file(filename: str = None, title: str = None, person=None, dcm_name: str = None, verbose: bool = False, dcm_template_file: str = None, dcm_transfer_series: bool = True, content_date=None) ‑> str-
Encapsulate a file inside a DCM file.
Dates and times of the instance are set to 'now'.
Works for PDF documents and images which are/can be converted to JPG.
Args
filename- the file to encapsulate
title- document title, defaults to filename
person- a GNUmed person instance from which to derive demographics, None -> derive from dcm_template_file
dcm_name- filename for the resulting DICOM file, None -> auto-create name
verbose- passed to external converter
dcm_template_file- DICOM file from which to derive patient demographics and study ID, None -> person must be defined
dcm_transfer_series- only applies if dcm_template_file given True = derive series from dcm_template_file, False = only derive study from dcm_template_file and create a new series
content_date- date/time to use for study/series/instance, as needed; None -> use now()
Returns
DICOM file name or None on failure.
Expand source code
def dicomize_file(filename:str=None, title:str=None, person=None, dcm_name:str=None, verbose:bool=False, dcm_template_file:str=None, dcm_transfer_series:bool=True, content_date=None) -> str: """Encapsulate a file inside a DCM file. Dates and times of the instance are set to 'now'. Works for PDF documents and images which are/can be converted to JPG. Args: filename: the file to encapsulate title: document title, defaults to filename person: a GNUmed person instance from which to derive demographics, None -> derive from *dcm_template_file* dcm_name: filename for the resulting DICOM file, None -> auto-create name verbose: passed to external converter dcm_template_file: DICOM file from which to derive patient demographics and study ID, None -> *person* must be defined dcm_transfer_series: only applies if *dcm_template_file* given True = derive series from *dcm_template_file*, False = only derive study from *dcm_template_file* and create a new series content_date: date/time to use for study/series/instance, as needed; None -> use now() Returns: DICOM file name or None on failure. """ assert (filename is not None), '<filename> must not be None' assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None' # already DCM ? if gmMimeLib.guess_mimetype(filename) == 'application/dicom': _log.error('already a DICOM file: %s', filename) if dcm_name is None: return filename return shutil.copy2(filename, dcm_name) dcm_fname = dicomize_pdf ( pdf_name = filename, title = title, person = person, dcm_name = dcm_name, verbose = verbose, dcm_template_file = dcm_template_file, dcm_transfer_series = dcm_transfer_series, content_date = content_date ) if dcm_fname is not None: return dcm_fname _log.debug('does not seem to be a PDF: %s', filename) converted_fname = gmMimeLib.convert_file(filename = filename, target_mime = 'image/jpeg') if converted_fname is None: _log.error('cannot convert to JPG: %s', filename) return None dcm_name = dicomize_jpg ( jpg_name = converted_fname, title = title, person = person, dcm_name = dcm_name, verbose = verbose, dcm_template_file = dcm_template_file, dcm_transfer_series = dcm_transfer_series, content_date = content_date ) return dcm_name def dicomize_jpg(jpg_name: str = None, title: str = None, person=None, dcm_name: str = None, verbose: bool = False, dcm_template_file: str = None, dcm_transfer_series: bool = True, content_date=None) ‑> str-
Encapsulate a JPG file inside a DCM file.
Dates and times of the instance are set to 'now'.
Args
jpg_name- the JPG file to encapsulate
title- document title, None -> jpg_name, used as study/series description
person- see dicomize_file()
dcm_name- see dicomize_file()
verbose- see dicomize_file()
dcm_template_file- see dicomize_file()
dcm_transfer_series- see dicomize_file()
content_date- see dicomize_file()
Returns
DICOM file name or None on failure.
Expand source code
def dicomize_jpg(jpg_name:str=None, title:str=None, person=None, dcm_name:str=None, verbose:bool=False, dcm_template_file:str=None, dcm_transfer_series:bool=True, content_date=None) -> str: """Encapsulate a JPG file inside a DCM file. Dates and times of the instance are set to 'now'. Args: jpg_name: the JPG file to encapsulate title: document title, None -> *jpg_name*, used as study/series description person: see *dicomize_file()* dcm_name: see *dicomize_file()* verbose: see *dicomize_file()* dcm_template_file: see *dicomize_file()* dcm_transfer_series: see *dicomize_file()* content_date: see *dicomize_file()* Returns: DICOM file name or None on failure. """ assert (jpg_name is not None), '<jpg_name> must not be None' assert (not ((person is None) and (dcm_template_file is None))), 'both <person> and <dcm_template_file> are None, but one is needed' if dcm_name is None: dcm_name = gmTools.get_unique_filename(suffix = '.dcm') _log.debug('%s -> %s', jpg_name, dcm_name) if title is None: title = gmTools.fname_stem(jpg_name) if content_date is None: content_date = gmDateTime.pydt_now_here() cmd_line = [ 'img2dcm', '--keep-appn', # carry over EXIF data '--insist-on-jfif', # process valid JFIF only '--key', '0008,1030=%s' % title, # StudyDescription '--key', '0008,103E=%s' % title, # SeriesDescription '--key', '0008,0021=%s' % content_date.strftime('%Y%m%d'), # SeriesDate '--key', '0008,0031=%s' % content_date.strftime('%H%M%s.0'), # SeriesTime '--key', '0008,0023=%s' % content_date.strftime('%Y%m%d'), # ContentDate '--key', '0008,0033=%s' % content_date.strftime('%H%M%s.0') # ContentTime ] if dcm_template_file is None: # StudyDate cmd_line.append('--key') cmd_line.append('0008,0020=%s' % content_date.strftime('%Y%m%d')) # StudyTime cmd_line.append('--key') cmd_line.append('0008,0030=%s' % content_date.strftime('%H%M%s.0')) # PatientName name = person.active_name cmd_line.append('--key') cmd_line.append('0010,0010=%s' % ('%s^%s' % ( name['lastnames'], name['firstnames']) ).replace(' ', '^')) # PatientID cmd_line.append('--key') cmd_line.append('0010,0020=%s' % person.suggest_external_id(target = 'PACS')) # DOB cmd_line.append('--key') cmd_line.append('0010,0030=%s' % person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False)) # gender if person['gender']: cmd_line.append('--key') cmd_line.append('0010,0040=%s' % _map_gender_gm2dcm[person['gender']]) else: _log.debug('DCM template file: %s', dcm_template_file) if dcm_transfer_series: cmd_line.append('--series-from') cmd_line.append(dcm_template_file) else: cmd_line.append('--study-from') cmd_line.append(dcm_template_file) if verbose: cmd_line.append('--log-level') cmd_line.append('trace') cmd_line.append(jpg_name) cmd_line.append(dcm_name) success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose) if success: return dcm_name return None def dicomize_pdf(pdf_name: str = None, title: str = None, person=None, dcm_name: str = None, verbose: bool = False, dcm_template_file: str = None, dcm_transfer_series: bool = True, content_date=None) ‑> str-
Encapsulate a PDF file inside a DCM file.
Dates and times of the instance are set to 'now'.
Args
pdf_name- the PDF file to encapsulate
title- document title, None -> pdf_name, also used as study/series description
person- see dicomize_file()
dcm_name- see dicomize_file()
verbose- see dicomize_file()
dcm_template_file- see dicomize_file()
dcm_transfer_series- see dicomize_file()
content_date- see dicomize_file()
Returns
DICOM file name or None on failure.
Expand source code
def dicomize_pdf(pdf_name:str=None, title:str=None, person=None, dcm_name:str=None, verbose:bool=False, dcm_template_file:str=None, dcm_transfer_series:bool=True, content_date=None) -> str: """Encapsulate a PDF file inside a DCM file. Dates and times of the instance are set to 'now'. Args: pdf_name: the PDF file to encapsulate title: document title, None -> *pdf_name*, also used as study/series description person: see *dicomize_file()* dcm_name: see *dicomize_file()* verbose: see *dicomize_file()* dcm_template_file: see *dicomize_file()* dcm_transfer_series: see *dicomize_file()* content_date: see *dicomize_file()* Returns: DICOM file name or None on failure. """ assert (pdf_name is not None), '<pdf_name> must not be None' assert (not ((person is None) and (dcm_template_file is None))), '<person> or <dcm_template_file> must not be None' if dcm_name is None: dcm_name = gmTools.get_unique_filename(suffix = '.dcm') _log.debug('%s -> %s', pdf_name, dcm_name) if title is None: title = gmTools.fname_stem(pdf_name) if content_date is None: content_date = gmDateTime.pydt_now_here() cmd_line = [ 'pdf2dcm', '--title', title, '--key', '0008,1030=%s' % title, # StudyDescription '--key', '0008,103E=%s' % title, # SeriesDescription '--key', '0008,0021=%s' % content_date.strftime('%Y%m%d'), # SeriesDate '--key', '0008,0023=%s' % content_date.strftime('%Y%m%d'), # ContentDate '--key', '0008,0031=%s' % content_date.strftime('%H%M%s.0'),# SeriesTime '--key', '0008,0033=%s' % content_date.strftime('%H%M%s.0') # ContentTime ] if dcm_template_file is None: # StudyDate cmd_line.append('--key') cmd_line.append('0008,0020=%s' % content_date.strftime('%Y%m%d')) # StudyTime cmd_line.append('--key') cmd_line.append('0008,0030=%s' % content_date.strftime('%H%M%s.0')) # PatientName name = person.active_name cmd_line.append('--patient-id') cmd_line.append(person.suggest_external_id(target = 'PACS')) cmd_line.append('--patient-name') cmd_line.append(('%s^%s' % (name['lastnames'], name['firstnames'])).replace(' ', '^')) if person['dob']: cmd_line.append('--patient-birthdate') cmd_line.append(person.get_formatted_dob(format = '%Y%m%d', honor_estimation = False)) if person['gender']: cmd_line.append('--patient-sex') cmd_line.append(_map_gender_gm2dcm[person['gender']]) else: _log.debug('DCM template file: %s', dcm_template_file) if dcm_transfer_series: cmd_line.append('--series-from') cmd_line.append(dcm_template_file) else: cmd_line.append('--study-from') cmd_line.append(dcm_template_file) if verbose: cmd_line.append('--log-level') cmd_line.append('trace') cmd_line.append(pdf_name) cmd_line.append(dcm_name) success, exit_code, stdout = gmShellAPI.run_process(cmd_line = cmd_line, encoding = 'utf8', verbose = verbose) if success: return dcm_name return None def run_file2dicom_tool(fname: str = None, dcm_template: str = None) ‑> str-
Convert a file into DICOM format.
This offers a primitive text user interface.
Args
fname- the file to convert, must be image or PDF
dcm_template- a DCM file to use as template for study/series data, optional
Returns
name of the new DICOM file, or None
Expand source code
def run_file2dicom_tool(fname:str=None, dcm_template:str=None) -> str: """Convert a file into DICOM format. This offers a primitive text user interface. Args: fname: the file to convert, must be image or PDF dcm_template: a DCM file to use as template for study/series data, optional Returns: name of the new DICOM file, or None """ if dcm_template is None: from Gnumed.pycommon import gmPG2 gmPG2.request_login_params(setup_pool = True) from Gnumed.business import gmPersonSearch pat = gmPersonSearch.ask_for_patient() if pat is None: return None else: pat = None dt = None while dt is None: iso = input('enter date (ISO - YYYY-MM-DD): ') try: dt = pydt.datetime.fromisoformat(iso) except ValueError: if iso.strip() == '': return None dt = None desc = input('enter description (ASCII): ') if desc.strip() == '': desc = None print('patient:', pat) print('DCM template:', dcm_template) print() print('file to convert:', fname) print('series date:', dt) print('description:', desc) input('hit <ENTER> to convert') dcm = dicomize_file ( filename = fname, person = pat, dcm_name = fname + '.dcm', verbose = True, content_date = dt, title = desc, dcm_template_file = dcm_template ) print('DCM file:', dcm)
Classes
class cOrthancServer-
Interface for the REST API of an Orthanc DICOM server.
Expand source code
class cOrthancServer: """Interface for the REST API of an Orthanc DICOM server. """ # REST API access to Orthanc DICOM servers # def __init__(self): # self.__server_identification = None # self.__user = None # self.__password = None # self.__conn = None # self.__server_url = None #-------------------------------------------------------- def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None) -> bool: try: int(port) except Exception: _log.error('invalid port [%s]', port) return False if (host is None) or (host.strip() == ''): host = 'localhost' try: self.__server_url = str('http://%s:%s' % (host, port)) except Exception: _log.exception('cannot create server url from: host [%s] and port [%s]', host, port) return False self.__user = user self.__password = password _log.info('connecting as [%s] to Orthanc server at [%s]', self.__user, self.__server_url) cache_dir = os.path.join(gmTools.gmPaths().user_tmp_dir, '.orthanc2gm-cache') gmTools.mkdir(cache_dir, 0o700) gmTools.create_directory_description_file(directory = cache_dir, readme = 'this directory caches Orthanc REST data, mainly DICOM files') _log.debug('using cache directory: %s', cache_dir) self.__conn = httplib2.Http(cache = cache_dir) self.__conn.add_credentials(self.__user, self.__password) _log.debug('connected to server: %s', self.server_identification) self.connect_error = '' if self.server_identification is False: self.connect_error += 'retrieving server identification failed' return False if expected_minimal_version is not None: if version.parse(self.server_identification['Version']) < version.parse(expected_minimal_version): _log.error('server too old, needed [%s]', expected_minimal_version) self.connect_error += 'server too old, needed version [%s]' % expected_minimal_version return False if expected_name is not None: if self.server_identification['Name'] != expected_name: _log.error('wrong server name, expected [%s]', expected_name) self.connect_error += 'wrong server name, expected [%s]' % expected_name return False if expected_aet is not None: if self.server_identification['DicomAet'] != expected_name: _log.error('wrong server AET, expected [%s]', expected_aet) self.connect_error += 'wrong server AET, expected [%s]' % expected_aet return False return True #-------------------------------------------------------- def _get_server_identification(self): try: return self.__server_identification # pylint: disable=access-member-before-definition except AttributeError: pass system_data = self.__run_GET(url = '%s/system' % self.__server_url) if system_data is False: _log.error('unable to get server identification') return False _log.debug('server: %s', system_data) self.__server_identification = system_data self.__initial_orthanc_encoding = self.__run_GET(url = '%s/tools/default-encoding' % self.__server_url) _log.debug('initial Orthanc encoding: %s', self.__initial_orthanc_encoding) # check time skew tolerance = 60 # seconds client_now_as_utc = pydt.datetime.utcnow() start = time.time() orthanc_now_str = self.__run_GET(url = '%s/tools/now' % self.__server_url) # 20180208T165832 end = time.time() query_duration = end - start orthanc_now_unknown_tz = pydt.datetime.strptime(orthanc_now_str, '%Y%m%dT%H%M%S') _log.debug('GNUmed "now" (UTC): %s', client_now_as_utc) _log.debug('Orthanc "now" (UTC): %s', orthanc_now_unknown_tz) _log.debug('wire roundtrip (seconds): %s', query_duration) _log.debug('maximum skew tolerance (seconds): %s', tolerance) if query_duration > tolerance: _log.info('useless to check GNUmed/Orthanc time skew, wire roundtrip (%s) > tolerance (%s)', query_duration, tolerance) else: if orthanc_now_unknown_tz > client_now_as_utc: real_skew = orthanc_now_unknown_tz - client_now_as_utc else: real_skew = client_now_as_utc - orthanc_now_unknown_tz _log.info('GNUmed/Orthanc time skew: %s', real_skew) if real_skew > pydt.timedelta(seconds = tolerance): _log.error('GNUmed/Orthanc time skew > tolerance (may be due to timezone differences on Orthanc < v1.3.2)') return self.__server_identification server_identification = property(_get_server_identification) #-------------------------------------------------------- def _get_as_external_id_issuer(self): # fixed type :: user level instance name :: DICOM AET return 'Orthanc::%(Name)s::%(DicomAet)s' % self.__server_identification as_external_id_issuer = property(_get_as_external_id_issuer) #-------------------------------------------------------- def _get_url_browse_patients(self): if self.__user is None: return self.__server_url return self.__server_url.replace('http://', 'http://%s@' % self.__user) url_browse_patients = property(_get_url_browse_patients) #-------------------------------------------------------- def get_url_browse_patient(self, patient_id): # http://localhost:8042/#patient?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b return '%s/#patient?uuid=%s' % (self.url_browse_patients, patient_id) #-------------------------------------------------------- def get_url_browse_study(self, study_id): # http://localhost:8042/#study?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b return '%s/#study?uuid=%s' % (self.url_browse_patients, study_id) #-------------------------------------------------------- # download API #-------------------------------------------------------- def get_matching_patients(self, person) -> list: """Fetch matching patients from an Orthanc DICOM server. Matches are searched for via stored "external ID" and via generically generated ID. The external IDs are fetched from the patient store, must be of type "PACS" and must be marked as issued by the instantiated PACS <self.> Args: person: a gmPerson.cPerson instance Returns: A list of Orthanc patient UIDs. """ _log.info('searching for Orthanc patients matching %s', person) pacs_ids = person.get_external_ids(id_type = 'PACS', issuer = self.as_external_id_issuer) if len(pacs_ids) > 1: _log.error('GNUmed patient has more than one ID for this PACS: %s', pacs_ids) _log.error('the stored-in-GNUmed PACS ID is expected to be unique _per PACS_') return [] pacs_ids2search_by = [] pacs_ids2search_by.extend([ pacs_id['value'] for pacs_id in pacs_ids ]) pacs_ids2search_by.extend(person.suggest_external_ids(target = 'PACS')) matching_pats = [] for pacs_id in pacs_ids2search_by: _log.debug('using PACS ID [%s]', pacs_id) pats = self.get_patients_by_external_id(external_id = pacs_id, fuzzy = False) if len(pats) > 1: _log.warning('more than one Orthanc patient matches PACS ID: %s', pacs_id) matching_pats.extend(pats) if not matching_pats: _log.debug('no matching patient found in PACS') return matching_pats #-------------------------------------------------------- def get_patients_by_external_id(self, external_id=None, fuzzy=False): """Search for instances by patient ID.""" _log.info('external ID >>>%s<<< fuzzy [%s]', external_id, fuzzy) search_term = external_id.strip().strip('*').strip() if fuzzy: search_term = '*%s*' % search_term search_data = { 'Level': 'Patient', 'CaseSensitive': False, 'Expand': True, 'Query': {'PatientID': search_term} } matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) # paranoia for match in matches: self.protect_patient(orthanc_id = match['ID']) return matches #-------------------------------------------------------- def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy:bool=False) -> list: """Search for patients by name. Returns: List of patients matching the search term(s). """ _log.info('name parts %s, gender [%s], dob [%s], fuzzy: [%s]', name_parts, gender, dob, fuzzy) if len(name_parts) > 1: return self.get_patients_by_name_parts(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy) search_term = name_parts[0].strip().strip('*').strip() if search_term == '': _log.debug('search term empty') return [] if fuzzy: search_term = '*%s*' % search_term search_data:dict = { 'Level': 'Patient', 'CaseSensitive': False, 'Expand': True } search_data['Query'] = {'PatientName': search_term} if gender: gender = _map_gender_gm2dcm[gender.casefold()] if gender: search_data['Query']['PatientSex'] = gender if dob: search_data['Query']['PatientBirthDate'] = dob.strftime('%Y%m%d') _log.info('server-side C-FIND SCU over REST search, mogrified search data: %s', search_data) matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) return matches #-------------------------------------------------------- def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False): # fuzzy: allow partial/substring matches (but not across name part boundaries ',' or '^') matching_patients = [] clean_parts = [] for part in name_parts: if part.strip() == '': continue clean_parts.append(part.casefold().strip()) _log.info('client-side patient search, scrubbed search terms: %s', clean_parts) pat_ids = self.__run_GET(url = '%s/patients' % self.__server_url) if pat_ids is False: _log.error('cannot retrieve patients') return [] for pat_id in pat_ids: orthanc_pat = self.__run_GET(url = '%s/patients/%s' % (self.__server_url, pat_id)) if orthanc_pat is False: _log.error('cannot retrieve patient') continue orthanc_name = orthanc_pat['MainDicomTags']['PatientName'].casefold().strip() if not fuzzy: orthanc_name = orthanc_name.replace(' ', ',').replace('^', ',').split(',') parts_in_orthanc_name = 0 for part in clean_parts: if part in orthanc_name: parts_in_orthanc_name += 1 if parts_in_orthanc_name == len(clean_parts): _log.debug('name match: "%s" contains all of %s', orthanc_name, clean_parts) if gender is not None: gender = _map_gender_gm2dcm[gender.casefold()] if gender is not None: if orthanc_pat['MainDicomTags']['PatientSex'].casefold() != gender: _log.debug('gender mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientSex'], gender) continue if dob is not None: if orthanc_pat['MainDicomTags']['PatientBirthDate'] != dob.strftime('%Y%m%d'): _log.debug('dob mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientBirthDate'], dob) continue matching_patients.append(orthanc_pat) else: _log.debug('name mismatch: "%s" does not contain all of %s', orthanc_name, clean_parts) return matching_patients #-------------------------------------------------------- def search_studies_by_patient_name(self, name:str) -> list: """Search for studies with the given patient name snippet. A study (even at the Orthanc DB metadata level) will contain the original patient name (unless manually modified) in contrast to the (artificial Orthanc DB metadata level) patient record. The latter contains the first patient name that had been associated with the given patient ID. Args: name: name snippet to search for Returns: The list of matching *studies* (not *patient*). """ _log.debug('search term [%s]', name) search_term = name.strip().strip('*').strip() if search_term == '': _log.warning('search term empty') return [] search_term = '*%s*' % search_term search_data = { 'Level': 'Study', 'CaseSensitive': False, 'Expand': True, 'Query': {'PatientName': search_term} } matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) return matches #-------------------------------------------------------- def search_studies_by_patient_id(self, patient_id:str) -> list: """Search for studies with the given patient ID snippet. This relates to the external world patient ID as stored in DICOM instances, not the Orthanc DB metadata level patient UID. Args: patient_id: patient ID snippet to search for Returns: The list of matching *studies* (not *patient*). """ _log.debug('search term >>>%s<<<', patient_id) search_term = patient_id.strip().strip('*').strip() search_term = '*%s*' % search_term search_data = { 'Level': 'Study', 'CaseSensitive': False, 'Expand': True, 'Query': {'PatientID': search_term} } matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) return matches #-------------------------------------------------------- def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False): return self.get_studies_list_by_orthanc_patient_list ( orthanc_patients = self.get_patients_by_name(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy) ) #-------------------------------------------------------- def get_studies_list_by_external_id(self, external_id=None): return self.get_studies_list_by_orthanc_patient_list ( orthanc_patients = self.get_patients_by_external_id(external_id = external_id) ) #-------------------------------------------------------- def get_study_as_zip(self, study_id=None, filename=None): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip') _log.info('exporting study [%s] into [%s]', study_id, filename) f = open(filename, 'wb') f.write(self.__run_GET(url = '%s/studies/%s/archive' % (self.__server_url, str(study_id)), allow_cached = True)) f.close() return filename #-------------------------------------------------------- def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip') _log.info('exporting study [%s] into [%s]', study_id, filename) f = open(filename, 'wb') f.write(self.__run_GET(url = '%s/studies/%s/media' % (self.__server_url, str(study_id)), allow_cached = True)) f.close() return filename #-------------------------------------------------------- def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip') if study_ids is None: _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename) f = open(filename, 'wb') f.write(self.__run_GET(url = '%s/patients/%s/archive' % (self.__server_url, str(patient_id)), allow_cached = True)) f.close() return filename #-------------------------------------------------------- def _manual_get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir) # all studies if study_ids is None: _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename) f = open(filename, 'wb') url = '%s/patients/%s/media' % (self.__server_url, str(patient_id)) _log.debug(url) f.write(self.__run_GET(url = url, allow_cached = True)) f.close() if create_zip: return filename if target_dir is None: target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-') if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True): return False return target_dir # a selection of studies dicomdir_cmd = 'gm-create_dicomdir' # args: 1) name of DICOMDIR to create 2) base directory where to start recursing for DICOM files found, external_cmd = gmShellAPI.detect_external_binary(dicomdir_cmd) if not found: _log.error('[%s] not found', dicomdir_cmd) return False if create_zip: sandbox_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-') _log.info('exporting studies [%s] into [%s] (sandbox [%s])', study_ids, filename, sandbox_dir) else: sandbox_dir = target_dir _log.info('exporting studies [%s] into [%s]', study_ids, sandbox_dir) _log.debug('sandbox dir: %s', sandbox_dir) idx = 0 for study_id in study_ids: study_zip_name = gmTools.get_unique_filename(prefix = 'dcm-', suffix = '.zip') # getting with DICOMDIR returns DICOMDIR compatible subdirs and filenames study_zip_name = self.get_study_as_zip_with_dicomdir(study_id = study_id, filename = study_zip_name) # non-beautiful per-study dir name required by subsequent DICOMDIR generation idx += 1 study_unzip_dir = os.path.join(sandbox_dir, 'STUDY%s' % idx) _log.debug('study [%s] -> %s -> %s', study_id, study_zip_name, study_unzip_dir) # need to extract into per-study subdir because get-with-dicomdir # returns identical-across-studies subdirs / filenames if not gmTools.unzip_archive(study_zip_name, target_dir = study_unzip_dir, remove_archive = True): return False # create DICOMDIR across all studies, # we simply ignore the already existing per-study DICOMDIR files target_dicomdir_name = os.path.join(sandbox_dir, 'DICOMDIR') gmTools.remove_file(target_dicomdir_name, log_error = False) # better safe than sorry _log.debug('generating [%s]', target_dicomdir_name) cmd = '%(cmd)s %(DICOMDIR)s %(startdir)s' % { 'cmd': external_cmd, 'DICOMDIR': target_dicomdir_name, 'startdir': sandbox_dir } success = gmShellAPI.run_command_in_shell ( command = cmd, blocking = True ) if not success: _log.error('problem running [gm-create_dicomdir]') return False # paranoia try: open(target_dicomdir_name) except Exception: _log.error('[%s] not generated, aborting', target_dicomdir_name) return False # return path to extracted studies if not create_zip: return sandbox_dir # else return ZIP of all studies studies_zip = shutil.make_archive ( gmTools.fname_stem_with_path(filename), 'zip', root_dir = gmTools.parent_dir(sandbox_dir), base_dir = gmTools.dirname_stem(sandbox_dir), logger = _log ) _log.debug('archived all studies with one DICOMDIR into: %s', studies_zip) # studies can be _large_ so attempt to get rid of intermediate files gmTools.rmdir(sandbox_dir) return studies_zip #-------------------------------------------------------- def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir) # all studies if study_ids is None: if patient_id is None: raise ValueError('<patient_id> must be defined if <study_ids> is None') _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename) f = open(filename, 'wb') url = '%s/patients/%s/media' % (self.__server_url, str(patient_id)) _log.debug(url) f.write(self.__run_GET(url = url, allow_cached = True)) f.close() if create_zip: return filename if target_dir is None: target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-') if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True): return False return target_dir # selection of studies _log.info('exporting %s studies into [%s]', len(study_ids), filename) _log.debug('studies: %s', study_ids) f = open(filename, 'wb') # You have to make a POST request against URI "/tools/create-media", with a # JSON body that contains the array of the resources of interest (as Orthanc # identifiers). Here is a sample command-line: # curl -X POST http://localhost:8042/tools/create-media -d '["8c4663df-c3e66066-9e20a8fc-dd14d1e5-251d3d84","2cd4848d-02f0005f-812ffef6-a210bbcf-3f01a00a","6eeded74-75005003-c3ae9738-d4a06a4f-6beedeb8","8a622020-c058291c-7693b63f-bc67aa2e-0a02e69c"]' -v > /tmp/a.zip # (this will not create duplicates but will also not check for single-patient-ness) url = '%s/tools/create-media-extended' % self.__server_url _log.debug(url) try: downloaded = self.__run_POST(url = url, data = study_ids, output_file = f) if not downloaded: _log.error('this Orthanc version probably does not support "create-media-extended"') except TypeError: f.close() _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version') return False # retry with old URL if not downloaded: url = '%s/tools/create-media' % self.__server_url _log.debug('retrying: %s', url) try: downloaded = self.__run_POST(url = url, data = study_ids, output_file = f) if not downloaded: return False except TypeError: _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version') return False finally: f.close() if create_zip: return filename if target_dir is None: target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-') _log.debug('exporting studies into [%s]', target_dir) if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True): return False return target_dir #-------------------------------------------------------- def get_instance_dicom_tags(self, instance_id, simplified=True): _log.debug('retrieving DICOM tags for instance [%s]', instance_id) if simplified: download_url = '%s/instances/%s/simplified-tags' % (self.__server_url, instance_id) else: download_url = '%s/instances/%s/tags' % (self.__server_url, instance_id) return self.__run_GET(url = download_url, allow_cached = True) #-------------------------------------------------------- def get_instance_preview(self, instance_id, filename=None): if filename is None: filename = gmTools.get_unique_filename(suffix = '.png') _log.debug('exporting preview for instance [%s] into [%s]', instance_id, filename) download_url = '%s/instances/%s/preview' % (self.__server_url, instance_id) f = open(filename, 'wb') try: f.write(self.__run_GET(url = download_url, allow_cached = True)) except Exception: _log.exception('cannot retrieve instance') filename = None finally: f.close() return filename #-------------------------------------------------------- def get_instance(self, instance_id:str, filename:str=None, allow_cached:bool=True) -> str: if filename is None: filename = gmTools.get_unique_filename(suffix = '.dcm') _log.debug('exporting instance [%s] into [%s]', instance_id, filename) download_url = '%s/instances/%s/attachments/dicom/data' % (self.__server_url, instance_id) f = open(filename, 'wb') f.write(self.__run_GET(url = download_url, allow_cached = allow_cached)) f.close() return filename #-------------------------------------------------------- # server-side API #-------------------------------------------------------- def get_patient(self, orthanc_id:str): patient_data_url = '%s/patients/%s' % (self.__server_url, str(orthanc_id)) patient_data, status = self.__run_GET(patient_data_url, also_return_status = True) if patient_data is False: if status == 404: _log.debug('no such patient: %s', orthanc_id) return {} _log.error('cannot retrieve patient data for [%s]', orthanc_id) return False return patient_data #-------------------------------------------------------- def protect_patient(self, orthanc_id:str): url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id)) if self.__run_GET(url) == 1: _log.debug('patient already protected: %s', orthanc_id) return True _log.warning('patient [%s] not protected against recycling, enabling protection now', orthanc_id) self.__run_PUT(url = url, data = '1') if self.__run_GET(url) == 1: return True _log.error('cannot protect patient [%s] against recycling', orthanc_id) return False #-------------------------------------------------------- def unprotect_patient(self, orthanc_id): url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id)) if self.__run_GET(url) == 0: return True _log.info('patient [%s] protected against recycling, disabling protection now', orthanc_id) self.__run_PUT(url = url, data = '0') if self.__run_GET(url) == 0: return True _log.error('cannot unprotect patient [%s] against recycling', orthanc_id) return False #-------------------------------------------------------- def patient_is_protected(self, orthanc_id): url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id)) return (self.__run_GET(url) == 1) #-------------------------------------------------------- def verify_patient_data(self, orthanc_id): _log.info('verifying DICOM data of patient [%s]', orthanc_id) bad_data = [] instances_url = '%s/patients/%s/instances' % (self.__server_url, orthanc_id) instances = self.__run_GET(instances_url) for instance in instances: instance_id = instance['ID'] attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id) attachments = self.__run_GET(attachments_url, allow_cached = True) for attachment in attachments: verify_url = '%s/%s/verify-md5' % (attachments_url, attachment) # False, success = "{}" #2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5 #2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'} if self.__run_POST(verify_url) is not False: continue _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment) bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)}) return bad_data #-------------------------------------------------------- def modify_patient_id(self, old_patient_id, new_patient_id): """Modify the patient ID stored in Orthanc. This changes all DICOM files of the patient, identified via (DICOM level) old_patient_id, to contain the new_patient_id. It will update the associated Orthanc metadata DB entries accordingly. """ if old_patient_id == new_patient_id: return True modify_data = { 'Replace': { 'PatientID': new_patient_id #,u'0010,0021': praxis.name / "GNUmed vX.X.X" #,u'0010,1002': series of (old) patient IDs } , 'Force': True # "Keep" doesn't seem to do what it suggests ATM #, u'Keep': True } orth_pat_defs = self.get_patients_by_external_id(external_id = old_patient_id) all_modified = True for orth_pat_def in orth_pat_defs: _log.info('modifying Orthanc patient [%s]: DICOM ID [%s] -> [%s]', orth_pat_def['ID'], old_patient_id, new_patient_id) old_pat_data = self.get_patient(orth_pat_def['ID']) _log.debug('to be modified: %s', old_pat_data) if self.patient_is_protected(orth_pat_def['ID']): _log.debug('patient protected: %s, unprotecting for modification', orth_pat_def['ID']) if not self.unprotect_patient(orth_pat_def['ID']): _log.error('cannot unlock patient [%s], skipping', orth_pat_def['ID']) all_modified = False continue was_protected = True else: was_protected = False pat_url = '%s/patients/%s' % (self.__server_url, orth_pat_def['ID']) modify_url = '%s/modify' % pat_url result = self.__run_POST(modify_url, data = modify_data) _log.debug('modify result: %s', result) if result is False: _log.error('cannot modify patient [%s]', orth_pat_def['ID']) all_modified = False continue newly_created_orthanc_patient_id = result['ID'] _log.info('newly created Orthanc patient ID: %s', newly_created_orthanc_patient_id) mod_pat_data = self.get_patient(newly_created_orthanc_patient_id) _log.debug('modified pat: %s', mod_pat_data) _log.debug('deleting archived patient: %s', self.__run_DELETE(pat_url)) if was_protected: if not self.protect_patient(newly_created_orthanc_patient_id): _log.error('cannot re-lock (new) patient [%s]', newly_created_orthanc_patient_id) return all_modified #-------------------------------------------------------- # upload API #-------------------------------------------------------- def upload_dicom_file(self, filename:str, check_mime_type:bool=False) -> bool: """Update a DICOM file. Will silently ignore DICOMDIR files (which are application/dicom but Orthanc does not process them). Args: filename: DICOM file to upload check_mime_type: whether to check the file for being application/dicom, and to fail if not Returns: True/False """ _log.info('processing: %s', filename) if gmTools.fname_stem(filename) == 'DICOMDIR': _log.debug('ignoring, no use uploading DICOMDIR files to Orthanc') return True if check_mime_type: mimetype = gmMimeLib.guess_mimetype(filename) if mimetype != 'application/dicom': _log.error('not considered a DICOM (application/dicom) file: %s, not uploading', mimetype) return False try: f = open(filename, 'rb') except Exception: _log.exception('failed to open file') return False dcm_data = f.read() f.close() upload_url = '%s/instances' % self.__server_url uploaded = self.__run_POST(upload_url, data = dcm_data, content_type = 'application/dicom') if uploaded is False: _log.error('upload failed') return False # typically a 404 following the upload of a DICOM file w/o identifiers if uploaded == []: _log.error('upload failed') return False _log.debug(uploaded) # paranoia, as is our custom verified = self.verify_instance ( instance_id = uploaded['ID'], filename = filename, attempt_download = True ) return verified #-------------------------------------------------------- def verify_instance(self, instance_id:str, filename:str=None, attempt_download:bool=False) -> bool: _BINARY_ATTACHMENTS = ['dicom'] _log.debug('verifying instance [%s] against file [%s]', instance_id, filename) is_valid = True attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id) attachments = self.__run_GET(attachments_url, allow_cached = False) if not attachments: _log.error('cannot retrieve instance attachment list') return False for attachment in attachments: md5_orthanc = None # 1) verify MD5 inside Orthanc, if available (checks Orthanc storage corruption) available_fields_url = '%s/instances/%s/attachments/%s' % (self.__server_url, instance_id, attachment) available_fields = self.__run_GET(available_fields_url, allow_cached = False) if 'md5' in available_fields: md5_url = '%s/md5' % available_fields_url md5_orthanc = self.__run_GET(md5_url) verify_url = '%s/%s/verify-md5' % (attachments_url, attachment) if self.__run_POST(verify_url) is False: _log.error('MD5 verification failed, instance [%s], attachment=%s, url [%s]', instance_id, attachment, verify_url) _log.error('potentially Orthanc storage corruption') is_valid = False else: _log.debug('MD5: Orthanc DB <-> Orthanc storage: match') else: _log.debug('MD5 of instance attachment not available in Orthanc, cannot verify backend storage status') # 2) verify instance attachment can be downloaded md5_downloaded = None if attempt_download: attachment_filename = gmTools.get_unique_filename() download_url = '%s/instances/%s/attachments/%s/data' % (self.__server_url, instance_id, attachment) attachment_data = self.__run_GET(url = download_url, allow_cached = False) if isinstance(attachment_data, bytes): attachment_file = open(attachment_filename, 'wb') else: attachment_file = open(attachment_filename, 'wt') attachment_data = '%s' % attachment_data attachment_file.write(attachment_data) del attachment_data attachment_file.close() _log.debug('download: Orthanc -> localhost: success') if attachment not in _BINARY_ATTACHMENTS: _log.info('attachment of type [%s] not binary, cannot verify MD5 of download or local file against MD5 in Orthanc, skipping', attachment) continue md5_downloaded = gmTools.file2md5(attachment_filename) else: _log.debug('not downloading instance for verification') # 3) verify MD5 of downloaded instance against Orthanc, if possible if md5_downloaded and md5_orthanc: if md5_downloaded == md5_orthanc: _log.debug('MD5: Orthanc DB <-> localhost: match') else: _log.error('MD5 mismatch: Orthanc DB <-> localhost') _log.error('download: %s', md5_downloaded) _log.error('Orthanc : %s', md5_orthanc) is_valid = False if filename: md5_local = gmTools.file2md5(filename) else: _log.debug('local file not available for verification') md5_local = None # 4) verify MD5 of download against local file if md5_downloaded and md5_local: if md5_downloaded == md5_local: _log.debug('MD5: downloaded <-> pre-existing: match') else: _log.error('MD5 mismatch: downloaded <-> pre-existing') _log.error('download: %s', md5_downloaded) _log.error('locally : %s', md5_local) is_valid = False # 5) verify MD5 of local file against Orthanc if md5_local and md5_orthanc: if md5_local == md5_orthanc: _log.debug('MD5: Orthanc DB <-> pre-existing: match') else: _log.error('MD5 mismatch: Orthanc DB <-> pre-existing') _log.error('locally : %s', md5_local) _log.error('Orthanc : %s', md5_orthanc) is_valid = False # 6) consider comparing the raw pixel data or comparing the output of exiftool etc _log.debug('verified: %s', is_valid) return is_valid #-------------------------------------------------------- def upload_dicom_files(self, files=None, check_mime_type=False): uploaded = [] not_uploaded = [] for filename in files: success = self.upload_dicom_file(filename, check_mime_type = check_mime_type) if success: uploaded.append(filename) continue not_uploaded.append(filename) if len(not_uploaded) > 0: _log.error('not all files uploaded') return (uploaded, not_uploaded) #-------------------------------------------------------- def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True): #-------------------- def _on_error(exc): _log.error('DICOM (?) file not accessible: %s', exc.filename) _log.error(exc) #-------------------- _log.debug('uploading DICOM files from [%s]', directory) if not recursive: files2try = os.listdir(directory) _log.debug('found %s files', len(files2try)) if ignore_other_files: files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ] _log.debug('DICOM files therein: %s', len(files2try)) return self.upload_dicom_files(files = files2try, check_mime_type = check_mime_type) _log.debug('recursing for DICOM files') uploaded = [] not_uploaded = [] for curr_root, curr_root_subdirs, curr_root_files in os.walk(directory, onerror = _on_error): _log.debug('recursing into [%s]', curr_root) files2try = [ os.path.join(curr_root, f) for f in curr_root_files ] _log.debug('found %s files', len(files2try)) if ignore_other_files: files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ] _log.debug('DICOM files therein: %s', len(files2try)) up, not_up = self.upload_dicom_files ( files = files2try, check_mime_type = check_mime_type ) uploaded.extend(up) not_uploaded.extend(not_up) return (uploaded, not_uploaded) #-------------------------------------------------------- def upload_by_DICOMDIR(self, DICOMDIR=None): pass #-------------------------------------------------------- # helper functions #-------------------------------------------------------- def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None): study_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentPatient', 'Series'] series_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentStudy', 'Instances'] studies_by_patient = [] # loop over patients for pat in orthanc_patients: pat_dict = { 'orthanc_id': pat['ID'], 'name': None, 'external_id': None, 'date_of_birth': None, 'gender': None, 'studies': [] } try: pat_dict['name'] = pat['MainDicomTags']['PatientName'].strip() except KeyError: pass try: pat_dict['external_id'] = pat['MainDicomTags']['PatientID'].strip() except KeyError: pass try: pat_dict['date_of_birth'] = pat['MainDicomTags']['PatientBirthDate'].strip() except KeyError: pass try: pat_dict['gender'] = pat['MainDicomTags']['PatientSex'].strip() except KeyError: pass for key in pat_dict: if pat_dict[key] in ['unknown', '(null)', '']: pat_dict[key] = None pat_dict[key] = cleanup_dicom_string(pat_dict[key]) studies_by_patient.append(pat_dict) # loop over studies of patient orth_studies = self.__run_GET(url = '%s/patients/%s/studies' % (self.__server_url, pat['ID'])) if orth_studies is False: _log.error('cannot retrieve studies') return [] for orth_study in orth_studies: study_dict = { 'orthanc_id': orth_study['ID'], 'date': None, 'time': None, 'description': None, 'referring_doc': None, 'requesting_doc': None, 'requesting_org': None, 'performing_doc': None, 'operator_name': None, 'radiographer_code': None, 'radiology_org': None, 'radiology_dept': None, 'radiology_org_addr': None, 'station_name': None, 'series': [] } try: study_dict['date'] = orth_study['MainDicomTags']['StudyDate'].strip() except KeyError: pass try: study_dict['time'] = orth_study['MainDicomTags']['StudyTime'].strip() except KeyError: pass try: study_dict['description'] = orth_study['MainDicomTags']['StudyDescription'].strip() except KeyError: pass try: study_dict['referring_doc'] = orth_study['MainDicomTags']['ReferringPhysicianName'].strip() except KeyError: pass try: study_dict['requesting_doc'] = orth_study['MainDicomTags']['RequestingPhysician'].strip() except KeyError: pass try: study_dict['requesting_org'] = orth_study['MainDicomTags']['RequestingService'].strip() except KeyError: pass try: study_dict['radiology_org_addr'] = orth_study['MainDicomTags']['InstitutionAddress'].strip() except KeyError: pass try: study_dict['radiology_org'] = orth_study['MainDicomTags']['InstitutionName'].strip() if study_dict['radiology_org_addr'] is not None: if study_dict['radiology_org'] in study_dict['radiology_org_addr']: study_dict['radiology_org'] = None except KeyError: pass try: study_dict['radiology_dept'] = orth_study['MainDicomTags']['InstitutionalDepartmentName'].strip() if study_dict['radiology_org'] is not None: if study_dict['radiology_dept'] in study_dict['radiology_org']: study_dict['radiology_dept'] = None if study_dict['radiology_org_addr'] is not None: if study_dict['radiology_dept'] in study_dict['radiology_org_addr']: study_dict['radiology_dept'] = None except KeyError: pass try: study_dict['station_name'] = orth_study['MainDicomTags']['StationName'].strip() if study_dict['radiology_org'] is not None: if study_dict['station_name'] in study_dict['radiology_org']: study_dict['station_name'] = None if study_dict['radiology_org_addr'] is not None: if study_dict['station_name'] in study_dict['radiology_org_addr']: study_dict['station_name'] = None if study_dict['radiology_dept'] is not None: if study_dict['station_name'] in study_dict['radiology_dept']: study_dict['station_name'] = None except KeyError: pass for key in study_dict: if study_dict[key] in ['unknown', '(null)', '']: study_dict[key] = None study_dict[key] = cleanup_dicom_string(study_dict[key]) study_dict['all_tags'] = {} try: orth_study['PatientMainDicomTags'] except KeyError: orth_study['PatientMainDicomTags'] = pat['MainDicomTags'] for key in orth_study: if key == 'MainDicomTags': for mkey in orth_study['MainDicomTags']: study_dict['all_tags'][mkey] = orth_study['MainDicomTags'][mkey].strip() continue if key == 'PatientMainDicomTags': for pkey in orth_study['PatientMainDicomTags']: study_dict['all_tags'][pkey] = orth_study['PatientMainDicomTags'][pkey].strip() continue study_dict['all_tags'][key] = orth_study[key] _log.debug('study: %s', list(study_dict['all_tags'])) for key in study_keys2hide: try: del study_dict['all_tags'][key] except KeyError: pass pat_dict['studies'].append(study_dict) # loop over series in study for orth_series_id in orth_study['Series']: orth_series = self.__run_GET(url = '%s/series/%s' % (self.__server_url, orth_series_id)) ordered_slices = self.__run_GET(url = '%s/series/%s/ordered-slices' % (self.__server_url, orth_series_id)) if ordered_slices is False: slices = orth_series['Instances'] else: slices = [ s[0] for s in ordered_slices['SlicesShort'] ] if orth_series is False: _log.error('cannot retrieve series') return [] series_dict = { 'orthanc_id': orth_series['ID'], 'instances': slices, 'modality': None, 'date': None, 'time': None, 'description': None, 'body_part': None, 'protocol': None, 'performed_procedure_step_description': None, 'acquisition_device_processing_description': None, 'operator_name': None, 'radiographer_code': None, 'performing_doc': None } try: series_dict['modality'] = orth_series['MainDicomTags']['Modality'].strip() except KeyError: pass try: series_dict['date'] = orth_series['MainDicomTags']['SeriesDate'].strip() except KeyError: pass try: series_dict['description'] = orth_series['MainDicomTags']['SeriesDescription'].strip() except KeyError: pass try: series_dict['time'] = orth_series['MainDicomTags']['SeriesTime'].strip() except KeyError: pass try: series_dict['body_part'] = orth_series['MainDicomTags']['BodyPartExamined'].strip() except KeyError: pass try: series_dict['protocol'] = orth_series['MainDicomTags']['ProtocolName'].strip() except KeyError: pass try: series_dict['performed_procedure_step_description'] = orth_series['MainDicomTags']['PerformedProcedureStepDescription'].strip() except KeyError: pass try: series_dict['acquisition_device_processing_description'] = orth_series['MainDicomTags']['AcquisitionDeviceProcessingDescription'].strip() except KeyError: pass try: series_dict['operator_name'] = orth_series['MainDicomTags']['OperatorsName'].strip() except KeyError: pass try: series_dict['radiographer_code'] = orth_series['MainDicomTags']['RadiographersCode'].strip() except KeyError: pass try: series_dict['performing_doc'] = orth_series['MainDicomTags']['PerformingPhysicianName'].strip() except KeyError: pass for key in series_dict: if series_dict[key] in ['unknown', '(null)', '']: series_dict[key] = None if series_dict['description'] == series_dict['protocol']: _log.debug('<series description> matches <series protocol>, ignoring protocol') series_dict['protocol'] = None if series_dict['performed_procedure_step_description'] in [series_dict['description'], series_dict['protocol']]: series_dict['performed_procedure_step_description'] = None if series_dict['performed_procedure_step_description'] is not None: # weed out "numeric" only if regex.match ('[.,/\|\-\s\d]+', series_dict['performed_procedure_step_description'], flags = regex.UNICODE): series_dict['performed_procedure_step_description'] = None if series_dict['acquisition_device_processing_description'] in [series_dict['description'], series_dict['protocol']]: series_dict['acquisition_device_processing_description'] = None if series_dict['acquisition_device_processing_description'] is not None: # weed out "numeric" only if regex.match ('[.,/\|\-\s\d]+', series_dict['acquisition_device_processing_description'], flags = regex.UNICODE): series_dict['acquisition_device_processing_description'] = None if series_dict['date'] == study_dict['date']: _log.debug('<series date> matches <study date>, ignoring date') series_dict['date'] = None if series_dict['time'] == study_dict['time']: _log.debug('<series time> matches <study time>, ignoring time') series_dict['time'] = None for key in series_dict: series_dict[key] = cleanup_dicom_string(series_dict[key]) series_dict['all_tags'] = {} for key in orth_series: if key == 'MainDicomTags': for mkey in orth_series['MainDicomTags']: series_dict['all_tags'][mkey] = orth_series['MainDicomTags'][mkey].strip() continue series_dict['all_tags'][key] = orth_series[key] _log.debug('series: %s', list(series_dict['all_tags'])) for key in series_keys2hide: try: del series_dict['all_tags'][key] except KeyError: pass study_dict['operator_name'] = series_dict['operator_name'] # will collapse all operators into that of the last series study_dict['radiographer_code'] = series_dict['radiographer_code'] # will collapse all into that of the last series study_dict['performing_doc'] = series_dict['performing_doc'] # will collapse all into that of the last series study_dict['series'].append(series_dict) return studies_by_patient #-------------------------------------------------------- # generic REST helpers #-------------------------------------------------------- def run_GET(self, url=None, data=None, allow_cached=False): url = '%s/%s' % (self.__server_url, url) return self.__run_GET(url = url, data = data, allow_cached = allow_cached) #-------------------------------------------------------- def __run_GET(self, url=None, data=None, allow_cached=False, also_return_status=False): if data is None: data = {} headers = {} if not allow_cached: headers['cache-control'] = 'no-cache' params = '' if data: params = '?' + urlencode(data) url_with_params = url + params #_log.debug('URL with parameters: >>>%s<<<', url_with_params) try: response, content = self.__conn.request(url_with_params, 'GET', headers = headers) except (OverflowError, socket.error, http.client.ResponseNotReady, http.client.InvalidURL, http.client.RemoteDisconnected, httplib2.ServerNotFoundError): # http.client.RemoteDisconnected: observed during GET while Orthanc was shutting down for backup _log.exception('exception in GET') _log.debug(' url: %s', url_with_params) _log.debug(' headers: %s', headers) if also_return_status: return (False, -1) return False if response.status not in [ 200 ]: _log.error('GET returned non-OK status: %s', response.status) _log.debug(' url: %s', url_with_params) _log.debug(' headers: %s', headers) _log.error(' response: %s', response) _log.debug(' content: %s', content) if also_return_status: return (False, response.status) return False #_log.debug('response: %s', response) #_log.debug('type(content): %s', type(content)) content_type = response['content-type'].strip() if content_type.startswith('text/plain'): # utf8 ? # urldecode ? # latin1 = Orthanc default = tools/default-encoding ? # ascii ? content = content.decode('utf8') elif content_type.startswith('application/json'): try: content = json.loads(content) except Exception: _log.exception('failed to json.loads(content) despite application/json indicated, returning content and hoping for the best') mime_type, charset_def = content_type.split(';') charset = charset_def.strip().split('=')[1] #content = content.decode('utf8') content = content.decode(charset) #_log.debug(content) else: _log.error('content: <%s>, not <text/plain> or <application/json> -- returning raw content', content_type) if also_return_status: return (content, response.status) return content #-------------------------------------------------------- def __run_POST(self, url=None, data=None, content_type=None, output_file=None): body = data headers = {'content-type' : content_type} if isinstance(data, str): if content_type is None: headers['content-type'] = 'text/plain' elif isinstance(data, bytes): if content_type is None: headers['content-type'] = 'application/octet-stream' else: body = json.dumps(data) headers['content-type'] = 'application/json' try: try: response, content = self.__conn.request(url, 'POST', body = body, headers = headers) except BrokenPipeError: _log.debug('retrying after BrokenPipeError') response, content = self.__conn.request(url, 'POST', body = body, headers = headers) except (socket.error, http.client.ResponseNotReady, OverflowError): _log.exception('exception in POST') _log.debug(' url: %s', url) _log.debug(' headers: %s', headers) _log.debug(' body: %s', body[:16]) return False if response.status == 404: _log.debug('no data, response: %s', response) if output_file is None: return [] return False if response.status not in [ 200, 302 ]: _log.error('POST returned non-OK (not 200,302) status: %s', response.status) _log.debug(' url: %s', url) _log.debug(' headers: %s', headers) _log.debug(' body: %s', body[:16]) _log.error(' response: %s', response) _log.debug(' content: %s', content) return False try: content = json.loads(content) except Exception: pass if output_file is None: return content output_file.write(content) return True #-------------------------------------------------------- def __run_PUT(self, url=None, data=None, content_type=None): body = data headers = {'content-type' : content_type} if isinstance(data, str): if content_type is None: headers['content-type'] = 'text/plain' elif isinstance(data, bytes): if content_type is None: headers['content-type'] = 'application/octet-stream' else: body = json.dumps(data) headers['content-type'] = 'application/json' try: try: response, content = self.__conn.request(url, 'PUT', body = body, headers = headers) except BrokenPipeError: response, content = self.__conn.request(url, 'PUT', body = body, headers = headers) except (socket.error, http.client.ResponseNotReady, OverflowError): _log.exception('exception in PUT') _log.debug(' url: %s', url) _log.debug(' headers: %s', headers) _log.debug(' body: %s', body[:16]) return False if response.status == 404: _log.debug('no data, response: %s', response) return [] if response.status not in [ 200, 302 ]: _log.error('PUT returned non-OK status: %s', response.status) _log.debug(' url: %s', url) _log.debug(' headers: %s', headers) _log.debug(' body: %s', body[:16]) _log.error(' response: %s', response) _log.debug(' content: %s', content) return False if response['content-type'].startswith('text/plain'): # utf8 ? # urldecode ? # latin1 = Orthanc default = tools/default-encoding ? # ascii ? return content.decode('utf8') if response['content-type'].startswith('application/json'): try: return json.loads(content) except Exception: return content return content #-------------------------------------------------------- def __run_DELETE(self, url=None): try: response, content = self.__conn.request(url, 'DELETE') except (http.client.ResponseNotReady, socket.error, OverflowError): _log.exception('exception in DELETE') _log.debug(' url: %s', url) return False if response.status not in [ 200 ]: _log.error('DELETE returned non-OK status: %s', response.status) _log.debug(' url: %s', url) _log.error(' response: %s', response) _log.debug(' content: %s', content) return False if response['content-type'].startswith('text/plain'): # utf8 ? # urldecode ? # latin1 = Orthanc default = tools/default-encoding ? # ascii ? return content.decode('utf8') if response['content-type'].startswith('application/json'): try: return json.loads(content) except Exception: return content return content #-------------------------------------------------------- def _get_server_url(self): return self.__server_url server_url = property(_get_server_url)Instance variables
var as_external_id_issuer-
Expand source code
def _get_as_external_id_issuer(self): # fixed type :: user level instance name :: DICOM AET return 'Orthanc::%(Name)s::%(DicomAet)s' % self.__server_identification var server_identification-
Expand source code
def _get_server_identification(self): try: return self.__server_identification # pylint: disable=access-member-before-definition except AttributeError: pass system_data = self.__run_GET(url = '%s/system' % self.__server_url) if system_data is False: _log.error('unable to get server identification') return False _log.debug('server: %s', system_data) self.__server_identification = system_data self.__initial_orthanc_encoding = self.__run_GET(url = '%s/tools/default-encoding' % self.__server_url) _log.debug('initial Orthanc encoding: %s', self.__initial_orthanc_encoding) # check time skew tolerance = 60 # seconds client_now_as_utc = pydt.datetime.utcnow() start = time.time() orthanc_now_str = self.__run_GET(url = '%s/tools/now' % self.__server_url) # 20180208T165832 end = time.time() query_duration = end - start orthanc_now_unknown_tz = pydt.datetime.strptime(orthanc_now_str, '%Y%m%dT%H%M%S') _log.debug('GNUmed "now" (UTC): %s', client_now_as_utc) _log.debug('Orthanc "now" (UTC): %s', orthanc_now_unknown_tz) _log.debug('wire roundtrip (seconds): %s', query_duration) _log.debug('maximum skew tolerance (seconds): %s', tolerance) if query_duration > tolerance: _log.info('useless to check GNUmed/Orthanc time skew, wire roundtrip (%s) > tolerance (%s)', query_duration, tolerance) else: if orthanc_now_unknown_tz > client_now_as_utc: real_skew = orthanc_now_unknown_tz - client_now_as_utc else: real_skew = client_now_as_utc - orthanc_now_unknown_tz _log.info('GNUmed/Orthanc time skew: %s', real_skew) if real_skew > pydt.timedelta(seconds = tolerance): _log.error('GNUmed/Orthanc time skew > tolerance (may be due to timezone differences on Orthanc < v1.3.2)') return self.__server_identification var server_url-
Expand source code
def _get_server_url(self): return self.__server_url var url_browse_patients-
Expand source code
def _get_url_browse_patients(self): if self.__user is None: return self.__server_url return self.__server_url.replace('http://', 'http://%s@' % self.__user)
Methods
def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None) ‑> bool-
Expand source code
def connect(self, host, port, user, password, expected_minimal_version=None, expected_name=None, expected_aet=None) -> bool: try: int(port) except Exception: _log.error('invalid port [%s]', port) return False if (host is None) or (host.strip() == ''): host = 'localhost' try: self.__server_url = str('http://%s:%s' % (host, port)) except Exception: _log.exception('cannot create server url from: host [%s] and port [%s]', host, port) return False self.__user = user self.__password = password _log.info('connecting as [%s] to Orthanc server at [%s]', self.__user, self.__server_url) cache_dir = os.path.join(gmTools.gmPaths().user_tmp_dir, '.orthanc2gm-cache') gmTools.mkdir(cache_dir, 0o700) gmTools.create_directory_description_file(directory = cache_dir, readme = 'this directory caches Orthanc REST data, mainly DICOM files') _log.debug('using cache directory: %s', cache_dir) self.__conn = httplib2.Http(cache = cache_dir) self.__conn.add_credentials(self.__user, self.__password) _log.debug('connected to server: %s', self.server_identification) self.connect_error = '' if self.server_identification is False: self.connect_error += 'retrieving server identification failed' return False if expected_minimal_version is not None: if version.parse(self.server_identification['Version']) < version.parse(expected_minimal_version): _log.error('server too old, needed [%s]', expected_minimal_version) self.connect_error += 'server too old, needed version [%s]' % expected_minimal_version return False if expected_name is not None: if self.server_identification['Name'] != expected_name: _log.error('wrong server name, expected [%s]', expected_name) self.connect_error += 'wrong server name, expected [%s]' % expected_name return False if expected_aet is not None: if self.server_identification['DicomAet'] != expected_name: _log.error('wrong server AET, expected [%s]', expected_aet) self.connect_error += 'wrong server AET, expected [%s]' % expected_aet return False return True def get_instance(self, instance_id: str, filename: str = None, allow_cached: bool = True) ‑> str-
Expand source code
def get_instance(self, instance_id:str, filename:str=None, allow_cached:bool=True) -> str: if filename is None: filename = gmTools.get_unique_filename(suffix = '.dcm') _log.debug('exporting instance [%s] into [%s]', instance_id, filename) download_url = '%s/instances/%s/attachments/dicom/data' % (self.__server_url, instance_id) f = open(filename, 'wb') f.write(self.__run_GET(url = download_url, allow_cached = allow_cached)) f.close() return filename -
Expand source code
def get_instance_dicom_tags(self, instance_id, simplified=True): _log.debug('retrieving DICOM tags for instance [%s]', instance_id) if simplified: download_url = '%s/instances/%s/simplified-tags' % (self.__server_url, instance_id) else: download_url = '%s/instances/%s/tags' % (self.__server_url, instance_id) return self.__run_GET(url = download_url, allow_cached = True) def get_instance_preview(self, instance_id, filename=None)-
Expand source code
def get_instance_preview(self, instance_id, filename=None): if filename is None: filename = gmTools.get_unique_filename(suffix = '.png') _log.debug('exporting preview for instance [%s] into [%s]', instance_id, filename) download_url = '%s/instances/%s/preview' % (self.__server_url, instance_id) f = open(filename, 'wb') try: f.write(self.__run_GET(url = download_url, allow_cached = True)) except Exception: _log.exception('cannot retrieve instance') filename = None finally: f.close() return filename def get_matching_patients(self, person) ‑> list-
Fetch matching patients from an Orthanc DICOM server.
Matches are searched for via stored "external ID" and via generically generated ID. The external IDs are fetched from the patient store, must be of type "PACS" and must be marked as issued by the instantiated PACS
Args
person- a gmPerson.cPerson instance
Returns
A list of Orthanc patient UIDs.
Expand source code
def get_matching_patients(self, person) -> list: """Fetch matching patients from an Orthanc DICOM server. Matches are searched for via stored "external ID" and via generically generated ID. The external IDs are fetched from the patient store, must be of type "PACS" and must be marked as issued by the instantiated PACS <self.> Args: person: a gmPerson.cPerson instance Returns: A list of Orthanc patient UIDs. """ _log.info('searching for Orthanc patients matching %s', person) pacs_ids = person.get_external_ids(id_type = 'PACS', issuer = self.as_external_id_issuer) if len(pacs_ids) > 1: _log.error('GNUmed patient has more than one ID for this PACS: %s', pacs_ids) _log.error('the stored-in-GNUmed PACS ID is expected to be unique _per PACS_') return [] pacs_ids2search_by = [] pacs_ids2search_by.extend([ pacs_id['value'] for pacs_id in pacs_ids ]) pacs_ids2search_by.extend(person.suggest_external_ids(target = 'PACS')) matching_pats = [] for pacs_id in pacs_ids2search_by: _log.debug('using PACS ID [%s]', pacs_id) pats = self.get_patients_by_external_id(external_id = pacs_id, fuzzy = False) if len(pats) > 1: _log.warning('more than one Orthanc patient matches PACS ID: %s', pacs_id) matching_pats.extend(pats) if not matching_pats: _log.debug('no matching patient found in PACS') return matching_pats def get_patient(self, orthanc_id: str)-
Expand source code
def get_patient(self, orthanc_id:str): patient_data_url = '%s/patients/%s' % (self.__server_url, str(orthanc_id)) patient_data, status = self.__run_GET(patient_data_url, also_return_status = True) if patient_data is False: if status == 404: _log.debug('no such patient: %s', orthanc_id) return {} _log.error('cannot retrieve patient data for [%s]', orthanc_id) return False return patient_data def get_patients_by_external_id(self, external_id=None, fuzzy=False)-
Search for instances by patient ID.
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def get_patients_by_external_id(self, external_id=None, fuzzy=False): """Search for instances by patient ID.""" _log.info('external ID >>>%s<<< fuzzy [%s]', external_id, fuzzy) search_term = external_id.strip().strip('*').strip() if fuzzy: search_term = '*%s*' % search_term search_data = { 'Level': 'Patient', 'CaseSensitive': False, 'Expand': True, 'Query': {'PatientID': search_term} } matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) # paranoia for match in matches: self.protect_patient(orthanc_id = match['ID']) return matches def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy: bool = False) ‑> list-
Search for patients by name.
Returns
List of patients matching the search term(s).
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def get_patients_by_name(self, name_parts=None, gender=None, dob=None, fuzzy:bool=False) -> list: """Search for patients by name. Returns: List of patients matching the search term(s). """ _log.info('name parts %s, gender [%s], dob [%s], fuzzy: [%s]', name_parts, gender, dob, fuzzy) if len(name_parts) > 1: return self.get_patients_by_name_parts(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy) search_term = name_parts[0].strip().strip('*').strip() if search_term == '': _log.debug('search term empty') return [] if fuzzy: search_term = '*%s*' % search_term search_data:dict = { 'Level': 'Patient', 'CaseSensitive': False, 'Expand': True } search_data['Query'] = {'PatientName': search_term} if gender: gender = _map_gender_gm2dcm[gender.casefold()] if gender: search_data['Query']['PatientSex'] = gender if dob: search_data['Query']['PatientBirthDate'] = dob.strftime('%Y%m%d') _log.info('server-side C-FIND SCU over REST search, mogrified search data: %s', search_data) matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) return matches def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False)-
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def get_patients_by_name_parts(self, name_parts=None, gender=None, dob=None, fuzzy=False): # fuzzy: allow partial/substring matches (but not across name part boundaries ',' or '^') matching_patients = [] clean_parts = [] for part in name_parts: if part.strip() == '': continue clean_parts.append(part.casefold().strip()) _log.info('client-side patient search, scrubbed search terms: %s', clean_parts) pat_ids = self.__run_GET(url = '%s/patients' % self.__server_url) if pat_ids is False: _log.error('cannot retrieve patients') return [] for pat_id in pat_ids: orthanc_pat = self.__run_GET(url = '%s/patients/%s' % (self.__server_url, pat_id)) if orthanc_pat is False: _log.error('cannot retrieve patient') continue orthanc_name = orthanc_pat['MainDicomTags']['PatientName'].casefold().strip() if not fuzzy: orthanc_name = orthanc_name.replace(' ', ',').replace('^', ',').split(',') parts_in_orthanc_name = 0 for part in clean_parts: if part in orthanc_name: parts_in_orthanc_name += 1 if parts_in_orthanc_name == len(clean_parts): _log.debug('name match: "%s" contains all of %s', orthanc_name, clean_parts) if gender is not None: gender = _map_gender_gm2dcm[gender.casefold()] if gender is not None: if orthanc_pat['MainDicomTags']['PatientSex'].casefold() != gender: _log.debug('gender mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientSex'], gender) continue if dob is not None: if orthanc_pat['MainDicomTags']['PatientBirthDate'] != dob.strftime('%Y%m%d'): _log.debug('dob mismatch: dicom=[%s] gnumed=[%s], skipping', orthanc_pat['MainDicomTags']['PatientBirthDate'], dob) continue matching_patients.append(orthanc_pat) else: _log.debug('name mismatch: "%s" does not contain all of %s', orthanc_name, clean_parts) return matching_patients def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None)-
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def get_studies_as_zip(self, study_ids=None, patient_id=None, filename=None): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip') if study_ids is None: _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename) f = open(filename, 'wb') f.write(self.__run_GET(url = '%s/patients/%s/archive' % (self.__server_url, str(patient_id)), allow_cached = True)) f.close() return filename def get_studies_list_by_external_id(self, external_id=None)-
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def get_studies_list_by_external_id(self, external_id=None): return self.get_studies_list_by_orthanc_patient_list ( orthanc_patients = self.get_patients_by_external_id(external_id = external_id) ) def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None)-
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def get_studies_list_by_orthanc_patient_list(self, orthanc_patients=None): study_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentPatient', 'Series'] series_keys2hide = ['ModifiedFrom', 'Type', 'ID', 'ParentStudy', 'Instances'] studies_by_patient = [] # loop over patients for pat in orthanc_patients: pat_dict = { 'orthanc_id': pat['ID'], 'name': None, 'external_id': None, 'date_of_birth': None, 'gender': None, 'studies': [] } try: pat_dict['name'] = pat['MainDicomTags']['PatientName'].strip() except KeyError: pass try: pat_dict['external_id'] = pat['MainDicomTags']['PatientID'].strip() except KeyError: pass try: pat_dict['date_of_birth'] = pat['MainDicomTags']['PatientBirthDate'].strip() except KeyError: pass try: pat_dict['gender'] = pat['MainDicomTags']['PatientSex'].strip() except KeyError: pass for key in pat_dict: if pat_dict[key] in ['unknown', '(null)', '']: pat_dict[key] = None pat_dict[key] = cleanup_dicom_string(pat_dict[key]) studies_by_patient.append(pat_dict) # loop over studies of patient orth_studies = self.__run_GET(url = '%s/patients/%s/studies' % (self.__server_url, pat['ID'])) if orth_studies is False: _log.error('cannot retrieve studies') return [] for orth_study in orth_studies: study_dict = { 'orthanc_id': orth_study['ID'], 'date': None, 'time': None, 'description': None, 'referring_doc': None, 'requesting_doc': None, 'requesting_org': None, 'performing_doc': None, 'operator_name': None, 'radiographer_code': None, 'radiology_org': None, 'radiology_dept': None, 'radiology_org_addr': None, 'station_name': None, 'series': [] } try: study_dict['date'] = orth_study['MainDicomTags']['StudyDate'].strip() except KeyError: pass try: study_dict['time'] = orth_study['MainDicomTags']['StudyTime'].strip() except KeyError: pass try: study_dict['description'] = orth_study['MainDicomTags']['StudyDescription'].strip() except KeyError: pass try: study_dict['referring_doc'] = orth_study['MainDicomTags']['ReferringPhysicianName'].strip() except KeyError: pass try: study_dict['requesting_doc'] = orth_study['MainDicomTags']['RequestingPhysician'].strip() except KeyError: pass try: study_dict['requesting_org'] = orth_study['MainDicomTags']['RequestingService'].strip() except KeyError: pass try: study_dict['radiology_org_addr'] = orth_study['MainDicomTags']['InstitutionAddress'].strip() except KeyError: pass try: study_dict['radiology_org'] = orth_study['MainDicomTags']['InstitutionName'].strip() if study_dict['radiology_org_addr'] is not None: if study_dict['radiology_org'] in study_dict['radiology_org_addr']: study_dict['radiology_org'] = None except KeyError: pass try: study_dict['radiology_dept'] = orth_study['MainDicomTags']['InstitutionalDepartmentName'].strip() if study_dict['radiology_org'] is not None: if study_dict['radiology_dept'] in study_dict['radiology_org']: study_dict['radiology_dept'] = None if study_dict['radiology_org_addr'] is not None: if study_dict['radiology_dept'] in study_dict['radiology_org_addr']: study_dict['radiology_dept'] = None except KeyError: pass try: study_dict['station_name'] = orth_study['MainDicomTags']['StationName'].strip() if study_dict['radiology_org'] is not None: if study_dict['station_name'] in study_dict['radiology_org']: study_dict['station_name'] = None if study_dict['radiology_org_addr'] is not None: if study_dict['station_name'] in study_dict['radiology_org_addr']: study_dict['station_name'] = None if study_dict['radiology_dept'] is not None: if study_dict['station_name'] in study_dict['radiology_dept']: study_dict['station_name'] = None except KeyError: pass for key in study_dict: if study_dict[key] in ['unknown', '(null)', '']: study_dict[key] = None study_dict[key] = cleanup_dicom_string(study_dict[key]) study_dict['all_tags'] = {} try: orth_study['PatientMainDicomTags'] except KeyError: orth_study['PatientMainDicomTags'] = pat['MainDicomTags'] for key in orth_study: if key == 'MainDicomTags': for mkey in orth_study['MainDicomTags']: study_dict['all_tags'][mkey] = orth_study['MainDicomTags'][mkey].strip() continue if key == 'PatientMainDicomTags': for pkey in orth_study['PatientMainDicomTags']: study_dict['all_tags'][pkey] = orth_study['PatientMainDicomTags'][pkey].strip() continue study_dict['all_tags'][key] = orth_study[key] _log.debug('study: %s', list(study_dict['all_tags'])) for key in study_keys2hide: try: del study_dict['all_tags'][key] except KeyError: pass pat_dict['studies'].append(study_dict) # loop over series in study for orth_series_id in orth_study['Series']: orth_series = self.__run_GET(url = '%s/series/%s' % (self.__server_url, orth_series_id)) ordered_slices = self.__run_GET(url = '%s/series/%s/ordered-slices' % (self.__server_url, orth_series_id)) if ordered_slices is False: slices = orth_series['Instances'] else: slices = [ s[0] for s in ordered_slices['SlicesShort'] ] if orth_series is False: _log.error('cannot retrieve series') return [] series_dict = { 'orthanc_id': orth_series['ID'], 'instances': slices, 'modality': None, 'date': None, 'time': None, 'description': None, 'body_part': None, 'protocol': None, 'performed_procedure_step_description': None, 'acquisition_device_processing_description': None, 'operator_name': None, 'radiographer_code': None, 'performing_doc': None } try: series_dict['modality'] = orth_series['MainDicomTags']['Modality'].strip() except KeyError: pass try: series_dict['date'] = orth_series['MainDicomTags']['SeriesDate'].strip() except KeyError: pass try: series_dict['description'] = orth_series['MainDicomTags']['SeriesDescription'].strip() except KeyError: pass try: series_dict['time'] = orth_series['MainDicomTags']['SeriesTime'].strip() except KeyError: pass try: series_dict['body_part'] = orth_series['MainDicomTags']['BodyPartExamined'].strip() except KeyError: pass try: series_dict['protocol'] = orth_series['MainDicomTags']['ProtocolName'].strip() except KeyError: pass try: series_dict['performed_procedure_step_description'] = orth_series['MainDicomTags']['PerformedProcedureStepDescription'].strip() except KeyError: pass try: series_dict['acquisition_device_processing_description'] = orth_series['MainDicomTags']['AcquisitionDeviceProcessingDescription'].strip() except KeyError: pass try: series_dict['operator_name'] = orth_series['MainDicomTags']['OperatorsName'].strip() except KeyError: pass try: series_dict['radiographer_code'] = orth_series['MainDicomTags']['RadiographersCode'].strip() except KeyError: pass try: series_dict['performing_doc'] = orth_series['MainDicomTags']['PerformingPhysicianName'].strip() except KeyError: pass for key in series_dict: if series_dict[key] in ['unknown', '(null)', '']: series_dict[key] = None if series_dict['description'] == series_dict['protocol']: _log.debug('<series description> matches <series protocol>, ignoring protocol') series_dict['protocol'] = None if series_dict['performed_procedure_step_description'] in [series_dict['description'], series_dict['protocol']]: series_dict['performed_procedure_step_description'] = None if series_dict['performed_procedure_step_description'] is not None: # weed out "numeric" only if regex.match ('[.,/\|\-\s\d]+', series_dict['performed_procedure_step_description'], flags = regex.UNICODE): series_dict['performed_procedure_step_description'] = None if series_dict['acquisition_device_processing_description'] in [series_dict['description'], series_dict['protocol']]: series_dict['acquisition_device_processing_description'] = None if series_dict['acquisition_device_processing_description'] is not None: # weed out "numeric" only if regex.match ('[.,/\|\-\s\d]+', series_dict['acquisition_device_processing_description'], flags = regex.UNICODE): series_dict['acquisition_device_processing_description'] = None if series_dict['date'] == study_dict['date']: _log.debug('<series date> matches <study date>, ignoring date') series_dict['date'] = None if series_dict['time'] == study_dict['time']: _log.debug('<series time> matches <study time>, ignoring time') series_dict['time'] = None for key in series_dict: series_dict[key] = cleanup_dicom_string(series_dict[key]) series_dict['all_tags'] = {} for key in orth_series: if key == 'MainDicomTags': for mkey in orth_series['MainDicomTags']: series_dict['all_tags'][mkey] = orth_series['MainDicomTags'][mkey].strip() continue series_dict['all_tags'][key] = orth_series[key] _log.debug('series: %s', list(series_dict['all_tags'])) for key in series_keys2hide: try: del series_dict['all_tags'][key] except KeyError: pass study_dict['operator_name'] = series_dict['operator_name'] # will collapse all operators into that of the last series study_dict['radiographer_code'] = series_dict['radiographer_code'] # will collapse all into that of the last series study_dict['performing_doc'] = series_dict['performing_doc'] # will collapse all into that of the last series study_dict['series'].append(series_dict) return studies_by_patient def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False)-
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def get_studies_list_by_patient_name(self, name_parts=None, gender=None, dob=None, fuzzy=False): return self.get_studies_list_by_orthanc_patient_list ( orthanc_patients = self.get_patients_by_name(name_parts = name_parts, gender = gender, dob = dob, fuzzy = fuzzy) ) def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False)-
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def get_studies_with_dicomdir(self, study_ids=None, patient_id=None, target_dir=None, filename=None, create_zip=False): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip', tmp_dir = target_dir) # all studies if study_ids is None: if patient_id is None: raise ValueError('<patient_id> must be defined if <study_ids> is None') _log.info('exporting all studies of patient [%s] into [%s]', patient_id, filename) f = open(filename, 'wb') url = '%s/patients/%s/media' % (self.__server_url, str(patient_id)) _log.debug(url) f.write(self.__run_GET(url = url, allow_cached = True)) f.close() if create_zip: return filename if target_dir is None: target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-') if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True): return False return target_dir # selection of studies _log.info('exporting %s studies into [%s]', len(study_ids), filename) _log.debug('studies: %s', study_ids) f = open(filename, 'wb') # You have to make a POST request against URI "/tools/create-media", with a # JSON body that contains the array of the resources of interest (as Orthanc # identifiers). Here is a sample command-line: # curl -X POST http://localhost:8042/tools/create-media -d '["8c4663df-c3e66066-9e20a8fc-dd14d1e5-251d3d84","2cd4848d-02f0005f-812ffef6-a210bbcf-3f01a00a","6eeded74-75005003-c3ae9738-d4a06a4f-6beedeb8","8a622020-c058291c-7693b63f-bc67aa2e-0a02e69c"]' -v > /tmp/a.zip # (this will not create duplicates but will also not check for single-patient-ness) url = '%s/tools/create-media-extended' % self.__server_url _log.debug(url) try: downloaded = self.__run_POST(url = url, data = study_ids, output_file = f) if not downloaded: _log.error('this Orthanc version probably does not support "create-media-extended"') except TypeError: f.close() _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version') return False # retry with old URL if not downloaded: url = '%s/tools/create-media' % self.__server_url _log.debug('retrying: %s', url) try: downloaded = self.__run_POST(url = url, data = study_ids, output_file = f) if not downloaded: return False except TypeError: _log.exception('cannot retrieve multiple studies as one archive with DICOMDIR, probably not supported by this Orthanc version') return False finally: f.close() if create_zip: return filename if target_dir is None: target_dir = gmTools.mk_sandbox_dir(prefix = 'dcm-') _log.debug('exporting studies into [%s]', target_dir) if not gmTools.unzip_archive(filename, target_dir = target_dir, remove_archive = True): return False return target_dir def get_study_as_zip(self, study_id=None, filename=None)-
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def get_study_as_zip(self, study_id=None, filename=None): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip') _log.info('exporting study [%s] into [%s]', study_id, filename) f = open(filename, 'wb') f.write(self.__run_GET(url = '%s/studies/%s/archive' % (self.__server_url, str(study_id)), allow_cached = True)) f.close() return filename def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None)-
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def get_study_as_zip_with_dicomdir(self, study_id=None, filename=None): if filename is None: filename = gmTools.get_unique_filename(prefix = r'DCM-', suffix = r'.zip') _log.info('exporting study [%s] into [%s]', study_id, filename) f = open(filename, 'wb') f.write(self.__run_GET(url = '%s/studies/%s/media' % (self.__server_url, str(study_id)), allow_cached = True)) f.close() return filename def get_url_browse_patient(self, patient_id)-
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def get_url_browse_patient(self, patient_id): # http://localhost:8042/#patient?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b return '%s/#patient?uuid=%s' % (self.url_browse_patients, patient_id) def get_url_browse_study(self, study_id)-
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def get_url_browse_study(self, study_id): # http://localhost:8042/#study?uuid=0da01e38-cf792452-65c1e6af-b77faf5a-b637a05b return '%s/#study?uuid=%s' % (self.url_browse_patients, study_id) def modify_patient_id(self, old_patient_id, new_patient_id)-
Modify the patient ID stored in Orthanc.
This changes all DICOM files of the patient, identified via (DICOM level) old_patient_id, to contain the new_patient_id. It will update the associated Orthanc metadata DB entries accordingly.
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def modify_patient_id(self, old_patient_id, new_patient_id): """Modify the patient ID stored in Orthanc. This changes all DICOM files of the patient, identified via (DICOM level) old_patient_id, to contain the new_patient_id. It will update the associated Orthanc metadata DB entries accordingly. """ if old_patient_id == new_patient_id: return True modify_data = { 'Replace': { 'PatientID': new_patient_id #,u'0010,0021': praxis.name / "GNUmed vX.X.X" #,u'0010,1002': series of (old) patient IDs } , 'Force': True # "Keep" doesn't seem to do what it suggests ATM #, u'Keep': True } orth_pat_defs = self.get_patients_by_external_id(external_id = old_patient_id) all_modified = True for orth_pat_def in orth_pat_defs: _log.info('modifying Orthanc patient [%s]: DICOM ID [%s] -> [%s]', orth_pat_def['ID'], old_patient_id, new_patient_id) old_pat_data = self.get_patient(orth_pat_def['ID']) _log.debug('to be modified: %s', old_pat_data) if self.patient_is_protected(orth_pat_def['ID']): _log.debug('patient protected: %s, unprotecting for modification', orth_pat_def['ID']) if not self.unprotect_patient(orth_pat_def['ID']): _log.error('cannot unlock patient [%s], skipping', orth_pat_def['ID']) all_modified = False continue was_protected = True else: was_protected = False pat_url = '%s/patients/%s' % (self.__server_url, orth_pat_def['ID']) modify_url = '%s/modify' % pat_url result = self.__run_POST(modify_url, data = modify_data) _log.debug('modify result: %s', result) if result is False: _log.error('cannot modify patient [%s]', orth_pat_def['ID']) all_modified = False continue newly_created_orthanc_patient_id = result['ID'] _log.info('newly created Orthanc patient ID: %s', newly_created_orthanc_patient_id) mod_pat_data = self.get_patient(newly_created_orthanc_patient_id) _log.debug('modified pat: %s', mod_pat_data) _log.debug('deleting archived patient: %s', self.__run_DELETE(pat_url)) if was_protected: if not self.protect_patient(newly_created_orthanc_patient_id): _log.error('cannot re-lock (new) patient [%s]', newly_created_orthanc_patient_id) return all_modified def patient_is_protected(self, orthanc_id)-
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def patient_is_protected(self, orthanc_id): url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id)) return (self.__run_GET(url) == 1) def protect_patient(self, orthanc_id: str)-
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def protect_patient(self, orthanc_id:str): url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id)) if self.__run_GET(url) == 1: _log.debug('patient already protected: %s', orthanc_id) return True _log.warning('patient [%s] not protected against recycling, enabling protection now', orthanc_id) self.__run_PUT(url = url, data = '1') if self.__run_GET(url) == 1: return True _log.error('cannot protect patient [%s] against recycling', orthanc_id) return False def run_GET(self, url=None, data=None, allow_cached=False)-
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def run_GET(self, url=None, data=None, allow_cached=False): url = '%s/%s' % (self.__server_url, url) return self.__run_GET(url = url, data = data, allow_cached = allow_cached) def search_studies_by_patient_id(self, patient_id: str) ‑> list-
Search for studies with the given patient ID snippet.
This relates to the external world patient ID as stored in DICOM instances, not the Orthanc DB metadata level patient UID.
Args
patient_id- patient ID snippet to search for
Returns
The list of matching studies (not patient).
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def search_studies_by_patient_id(self, patient_id:str) -> list: """Search for studies with the given patient ID snippet. This relates to the external world patient ID as stored in DICOM instances, not the Orthanc DB metadata level patient UID. Args: patient_id: patient ID snippet to search for Returns: The list of matching *studies* (not *patient*). """ _log.debug('search term >>>%s<<<', patient_id) search_term = patient_id.strip().strip('*').strip() search_term = '*%s*' % search_term search_data = { 'Level': 'Study', 'CaseSensitive': False, 'Expand': True, 'Query': {'PatientID': search_term} } matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) return matches def search_studies_by_patient_name(self, name: str) ‑> list-
Search for studies with the given patient name snippet.
A study (even at the Orthanc DB metadata level) will contain the original patient name (unless manually modified) in contrast to the (artificial Orthanc DB metadata level) patient record. The latter contains the first patient name that had been associated with the given patient ID.
Args
name- name snippet to search for
Returns
The list of matching studies (not patient).
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def search_studies_by_patient_name(self, name:str) -> list: """Search for studies with the given patient name snippet. A study (even at the Orthanc DB metadata level) will contain the original patient name (unless manually modified) in contrast to the (artificial Orthanc DB metadata level) patient record. The latter contains the first patient name that had been associated with the given patient ID. Args: name: name snippet to search for Returns: The list of matching *studies* (not *patient*). """ _log.debug('search term [%s]', name) search_term = name.strip().strip('*').strip() if search_term == '': _log.warning('search term empty') return [] search_term = '*%s*' % search_term search_data = { 'Level': 'Study', 'CaseSensitive': False, 'Expand': True, 'Query': {'PatientName': search_term} } matches = self.__run_POST(url = '%s/tools/find' % self.__server_url, data = search_data) return matches def unprotect_patient(self, orthanc_id)-
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def unprotect_patient(self, orthanc_id): url = '%s/patients/%s/protected' % (self.__server_url, str(orthanc_id)) if self.__run_GET(url) == 0: return True _log.info('patient [%s] protected against recycling, disabling protection now', orthanc_id) self.__run_PUT(url = url, data = '0') if self.__run_GET(url) == 0: return True _log.error('cannot unprotect patient [%s] against recycling', orthanc_id) return False def upload_by_DICOMDIR(self, DICOMDIR=None)-
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def upload_by_DICOMDIR(self, DICOMDIR=None): pass def upload_dicom_file(self, filename: str, check_mime_type: bool = False) ‑> bool-
Update a DICOM file.
Will silently ignore DICOMDIR files (which are application/dicom but Orthanc does not process them).
Args
filename- DICOM file to upload
check_mime_type- whether to check the file for being application/dicom, and to fail if not
Returns
True/False
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def upload_dicom_file(self, filename:str, check_mime_type:bool=False) -> bool: """Update a DICOM file. Will silently ignore DICOMDIR files (which are application/dicom but Orthanc does not process them). Args: filename: DICOM file to upload check_mime_type: whether to check the file for being application/dicom, and to fail if not Returns: True/False """ _log.info('processing: %s', filename) if gmTools.fname_stem(filename) == 'DICOMDIR': _log.debug('ignoring, no use uploading DICOMDIR files to Orthanc') return True if check_mime_type: mimetype = gmMimeLib.guess_mimetype(filename) if mimetype != 'application/dicom': _log.error('not considered a DICOM (application/dicom) file: %s, not uploading', mimetype) return False try: f = open(filename, 'rb') except Exception: _log.exception('failed to open file') return False dcm_data = f.read() f.close() upload_url = '%s/instances' % self.__server_url uploaded = self.__run_POST(upload_url, data = dcm_data, content_type = 'application/dicom') if uploaded is False: _log.error('upload failed') return False # typically a 404 following the upload of a DICOM file w/o identifiers if uploaded == []: _log.error('upload failed') return False _log.debug(uploaded) # paranoia, as is our custom verified = self.verify_instance ( instance_id = uploaded['ID'], filename = filename, attempt_download = True ) return verified def upload_dicom_files(self, files=None, check_mime_type=False)-
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def upload_dicom_files(self, files=None, check_mime_type=False): uploaded = [] not_uploaded = [] for filename in files: success = self.upload_dicom_file(filename, check_mime_type = check_mime_type) if success: uploaded.append(filename) continue not_uploaded.append(filename) if len(not_uploaded) > 0: _log.error('not all files uploaded') return (uploaded, not_uploaded) def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True)-
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def upload_from_directory(self, directory=None, recursive=False, check_mime_type=False, ignore_other_files=True): #-------------------- def _on_error(exc): _log.error('DICOM (?) file not accessible: %s', exc.filename) _log.error(exc) #-------------------- _log.debug('uploading DICOM files from [%s]', directory) if not recursive: files2try = os.listdir(directory) _log.debug('found %s files', len(files2try)) if ignore_other_files: files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ] _log.debug('DICOM files therein: %s', len(files2try)) return self.upload_dicom_files(files = files2try, check_mime_type = check_mime_type) _log.debug('recursing for DICOM files') uploaded = [] not_uploaded = [] for curr_root, curr_root_subdirs, curr_root_files in os.walk(directory, onerror = _on_error): _log.debug('recursing into [%s]', curr_root) files2try = [ os.path.join(curr_root, f) for f in curr_root_files ] _log.debug('found %s files', len(files2try)) if ignore_other_files: files2try = [ f for f in files2try if gmMimeLib.guess_mimetype(f) == 'application/dicom' ] _log.debug('DICOM files therein: %s', len(files2try)) up, not_up = self.upload_dicom_files ( files = files2try, check_mime_type = check_mime_type ) uploaded.extend(up) not_uploaded.extend(not_up) return (uploaded, not_uploaded) def verify_instance(self, instance_id: str, filename: str = None, attempt_download: bool = False) ‑> bool-
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def verify_instance(self, instance_id:str, filename:str=None, attempt_download:bool=False) -> bool: _BINARY_ATTACHMENTS = ['dicom'] _log.debug('verifying instance [%s] against file [%s]', instance_id, filename) is_valid = True attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id) attachments = self.__run_GET(attachments_url, allow_cached = False) if not attachments: _log.error('cannot retrieve instance attachment list') return False for attachment in attachments: md5_orthanc = None # 1) verify MD5 inside Orthanc, if available (checks Orthanc storage corruption) available_fields_url = '%s/instances/%s/attachments/%s' % (self.__server_url, instance_id, attachment) available_fields = self.__run_GET(available_fields_url, allow_cached = False) if 'md5' in available_fields: md5_url = '%s/md5' % available_fields_url md5_orthanc = self.__run_GET(md5_url) verify_url = '%s/%s/verify-md5' % (attachments_url, attachment) if self.__run_POST(verify_url) is False: _log.error('MD5 verification failed, instance [%s], attachment=%s, url [%s]', instance_id, attachment, verify_url) _log.error('potentially Orthanc storage corruption') is_valid = False else: _log.debug('MD5: Orthanc DB <-> Orthanc storage: match') else: _log.debug('MD5 of instance attachment not available in Orthanc, cannot verify backend storage status') # 2) verify instance attachment can be downloaded md5_downloaded = None if attempt_download: attachment_filename = gmTools.get_unique_filename() download_url = '%s/instances/%s/attachments/%s/data' % (self.__server_url, instance_id, attachment) attachment_data = self.__run_GET(url = download_url, allow_cached = False) if isinstance(attachment_data, bytes): attachment_file = open(attachment_filename, 'wb') else: attachment_file = open(attachment_filename, 'wt') attachment_data = '%s' % attachment_data attachment_file.write(attachment_data) del attachment_data attachment_file.close() _log.debug('download: Orthanc -> localhost: success') if attachment not in _BINARY_ATTACHMENTS: _log.info('attachment of type [%s] not binary, cannot verify MD5 of download or local file against MD5 in Orthanc, skipping', attachment) continue md5_downloaded = gmTools.file2md5(attachment_filename) else: _log.debug('not downloading instance for verification') # 3) verify MD5 of downloaded instance against Orthanc, if possible if md5_downloaded and md5_orthanc: if md5_downloaded == md5_orthanc: _log.debug('MD5: Orthanc DB <-> localhost: match') else: _log.error('MD5 mismatch: Orthanc DB <-> localhost') _log.error('download: %s', md5_downloaded) _log.error('Orthanc : %s', md5_orthanc) is_valid = False if filename: md5_local = gmTools.file2md5(filename) else: _log.debug('local file not available for verification') md5_local = None # 4) verify MD5 of download against local file if md5_downloaded and md5_local: if md5_downloaded == md5_local: _log.debug('MD5: downloaded <-> pre-existing: match') else: _log.error('MD5 mismatch: downloaded <-> pre-existing') _log.error('download: %s', md5_downloaded) _log.error('locally : %s', md5_local) is_valid = False # 5) verify MD5 of local file against Orthanc if md5_local and md5_orthanc: if md5_local == md5_orthanc: _log.debug('MD5: Orthanc DB <-> pre-existing: match') else: _log.error('MD5 mismatch: Orthanc DB <-> pre-existing') _log.error('locally : %s', md5_local) _log.error('Orthanc : %s', md5_orthanc) is_valid = False # 6) consider comparing the raw pixel data or comparing the output of exiftool etc _log.debug('verified: %s', is_valid) return is_valid def verify_patient_data(self, orthanc_id)-
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def verify_patient_data(self, orthanc_id): _log.info('verifying DICOM data of patient [%s]', orthanc_id) bad_data = [] instances_url = '%s/patients/%s/instances' % (self.__server_url, orthanc_id) instances = self.__run_GET(instances_url) for instance in instances: instance_id = instance['ID'] attachments_url = '%s/instances/%s/attachments' % (self.__server_url, instance_id) attachments = self.__run_GET(attachments_url, allow_cached = True) for attachment in attachments: verify_url = '%s/%s/verify-md5' % (attachments_url, attachment) # False, success = "{}" #2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #986): cannot POST: http://localhost:8042/instances/5a8206f4-24619e76-6650d9cd-792cdf25-039e96e6/attachments/dicom-as-json/verify-md5 #2018-02-08 19:11:27 ERROR gm.dicom [-1211701504 MainThread] (gmDICOM.py::__run_POST() #987): response: {'status': '400', 'content-length': '0'} if self.__run_POST(verify_url) is not False: continue _log.error('bad MD5 of DICOM file at url [%s]: patient=%s, attachment_type=%s', verify_url, orthanc_id, attachment) bad_data.append({'patient': orthanc_id, 'instance': instance_id, 'type': attachment, 'orthanc': '%s [%s]' % (self.server_identification, self.__server_url)}) return bad_data