def __init__(self, **kwargs):
super(Interface, self).__init__()
self.address = kwargs.get('address')
self.aetitle = kwargs.get('aetitle')
self.auth = (kwargs.get('user'), kwargs.get('pword'))
self.name = kwargs.get('name', 'None')
self.name = self.name.split('+')[0]
self.api_key = kwargs.get('api_key')
self.proxy = kwargs.get('proxy')
self.j_proxy = kwargs.get('j_proxy')
# Create a session/juniper session
if self.j_proxy is None:
self.session = SessionWrapper(**kwargs)
else:
self.session = JuniperSessionWrapper(**kwargs)
# Should be "available studies" plus a registry of all studies somewhere else
self.series = {}
self.studies = {}
self.subjects = {}
self.logger = logging.getLogger(self.__class__.__name__)
self.logger.info('Created interface')
def __init__(self, **kwargs):
super(Interface, self).__init__()
self.address = kwargs.get('address')
self.aetitle = kwargs.get('aetitle')
self.auth = (kwargs.get('user'), kwargs.get('pword'))
self.name = kwargs.get('name', 'None')
self.name = self.name.split('+')[0]
self.api_key = kwargs.get('api_key')
self.proxy = kwargs.get('proxy')
self.j_proxy = kwargs.get('j_proxy')
# Create a session/juniper session
if self.j_proxy is None:
self.session = SessionWrapper(**kwargs)
else:
self.session = JuniperSessionWrapper(**kwargs)
# Should be "available studies" plus a registry of all studies somewhere else
self.series = {}
self.studies = {}
self.subjects = {}
self.logger = logging.getLogger(self.__class__.__name__)
self.logger.info('Created interface')
class Interface(object):
# -----------------------------
# Available DicomData across all interfaces
# -----------------------------
available_series = {}
available_studies = {}
available_subjects = {}
# -----------------------------
# Public factory
# -----------------------------
@classmethod
def factory(cls, name, _config):
from OrthancInterface import OrthancInterface
from XNATInterface import XNATInterface
from DICOMInterface import DICOMInterface
from MontageInterface import MontageInterface
from TCIAInterface import TCIAInterface
# Accepts a config dict and returns an interface
config = _config[name]
name = name.split('+')[0]
if config['type'] == 'xnat':
return XNATInterface(name=name, **config)
elif config['type'] == 'orthanc':
return OrthancInterface(name=name, **config)
elif config['type'] == 'dicom':
proxy = Interface.factory(config['proxy'], _config)
return DICOMInterface(name=name, proxy=proxy, **_config)
elif config['type'] == 'montage':
return MontageInterface(name=name, **config)
elif config['type'] == 'tcia':
return TCIAInterface(name=name, **config)
else:
logger = logging.getLogger(Interface.factory.__name__)
logger.warn("Unknown repo type '%s' in config", name)
pass
# -----------------------------
# Baseclass __init__
# -----------------------------
def __init__(self, **kwargs):
super(Interface, self).__init__()
self.address = kwargs.get('address')
self.aetitle = kwargs.get('aetitle')
self.auth = (kwargs.get('user'), kwargs.get('pword'))
self.name = kwargs.get('name', 'None')
self.name = self.name.split('+')[0]
self.api_key = kwargs.get('api_key')
self.proxy = kwargs.get('proxy')
self.j_proxy = kwargs.get('j_proxy')
# Create a session/juniper session
if self.j_proxy is None:
self.session = SessionWrapper(**kwargs)
else:
self.session = JuniperSessionWrapper(**kwargs)
# Should be "available studies" plus a registry of all studies somewhere else
self.series = {}
self.studies = {}
self.subjects = {}
self.logger = logging.getLogger(self.__class__.__name__)
self.logger.info('Created interface')
# -----------------------------
# Abstract Public API:
# - find
# - send
# - receive
# - delete
# -----------------------------
def find(self, level, question, source=None):
# Level is a HDN type: subject, studies, or series
# Question is a dictionary of property names and values
# by default, the source is _this_ interface,
# returns a WORKLIST, a list of session, study, or subject items
raise NotImplementedError
def retrieve(self, item, source):
raise NotImplementedError
def send(self, item, target):
raise NotImplementedError
def delete(self, worklist):
raise NotImplementedError
# -----------------------------
# Abstract Private/Hidden API:
# - upload_data
# - download_data
# - subject_from_id
# - study_from_id
# - series_from_id
# - all_studies (optional)
# -----------------------------
# Each interface needs to implement methods for moving data around
def upload_data(self, item):
raise NotImplementedError
def download_data(self, item):
raise NotImplementedError
# Factories for HDN types
def subject_from_id(self, subject_id):
raise NotImplementedError
def study_from_id(self, study_id):
raise NotImplementedError
def series_from_id(self, series_id):
raise NotImplementedError
# Optional but frequently useful shortcut
def all_studies(self):
raise NotImplementedError
# -----------------------------
# Baseclass Public API:
# - copy
# - move
# - upload_archive
# - download_archive
# -----------------------------
def copy(self, worklist, source, target, anonymize=False):
# Sends data for items in WORKLIST from the source to the target
# if the source is self and the target is a string/file, it downloads
# if the source is a string/file and the target is self, it uploads
# if the source is a DICOM node and the target is self, it retrieves
# TODO: Create anonymized study if necessary and delete it when done
if not isinstance(worklist, list):
worklist = [worklist]
for item in worklist:
# Figure out case
if isinstance(source, basestring) and (target is None or target is self):
# It's probably a file being uploaded
self.upload_archive(item, source)
elif source is self and isinstance(target, basestring):
# It's probably a file being downloaded
self.download_archive(item, target)
elif source is self:
# Sending to DICOM modality or Orthanc peer
self.send(item, target)
elif target is self:
self.retrieve(item, source)
def move(self, worklist, source, target, anonymize=False):
self.copy(worklist, source, target, anonymize)
self.delete(worklist)
def upload_archive(self, item, fn):
if os.path.isdir(fn):
self.logger.info('Uploading image folder %s', fn)
item.data = self.zipdir(fn)
elif os.path.isfile(fn):
self.logger.info('Uploading image archive %s', fn)
f = open(fn, 'rb')
item.data = f.read()
f.close()
self.upload_data(item)
def download_archive(self, item, fn):
self.logger.info('Downloading image archive %s', fn)
self.download_data(item)
if fn is not None:
f = open(fn + '.zip', 'wb')
f.write(item.data)
f.close()
# -----------------------------
# Private/Hidden Helpers
# - do_get
# - do_post
# - do_put
# - do_delete
# - do_return
# - zipdir
# -----------------------------
def do_return(self, r):
return self.session.do_return(r)
def do_delete(self, *url, **kwargs):
return self.session.do_delete(*url, **kwargs)
def do_get(self, *url, **kwargs):
return self.session.do_get(*url, **kwargs)
def do_put(self, *url, **kwargs):
return self.session.do_put(*url, **kwargs)
def do_post(self, *url, **kwargs):
return self.session.do_post(*url, **kwargs)
def zipdir(self, top, fno=None):
file_like_object = io.BytesIO()
if fno is None:
self.logger.info('Creating in-memory zip')
zipf = zipfile.ZipFile(file_like_object, 'w', zipfile.ZIP_DEFLATED)
else:
self.logger.info('Creating zip file')
zipf = zipfile.ZipFile(fno, 'w', zipfile.ZIP_DEFLATED)
for dirpath, dirnames, filenames in os.walk(top):
for f in filenames:
fn = os.path.join(dirpath, f)
# self.logger.debug(fn)
zipf.write(fn, os.path.relpath(fn, top))
zipf.close()
if fno is None:
return file_like_object.getvalue()
class Interface(object):
# -----------------------------
# Available DicomData across all interfaces
# -----------------------------
available_series = {}
available_studies = {}
available_subjects = {}
# -----------------------------
# Public factory
# -----------------------------
@classmethod
def factory(cls, name, _config):
from OrthancInterface import OrthancInterface
from XNATInterface import XNATInterface
from DICOMInterface import DICOMInterface
from MontageInterface import MontageInterface
from TCIAInterface import TCIAInterface
# Accepts a config dict and returns an interface
config = _config[name]
name = name.split('+')[0]
if config['type'] == 'xnat':
return XNATInterface(name=name, **config)
elif config['type'] == 'orthanc':
return OrthancInterface(name=name, **config)
elif config['type'] == 'dicom':
proxy = Interface.factory(config['proxy'], _config)
return DICOMInterface(name=name, proxy=proxy, **_config)
elif config['type'] == 'montage':
return MontageInterface(name=name, **config)
elif config['type'] == 'tcia':
return TCIAInterface(name=name, **config)
else:
logger = logging.getLogger(Interface.factory.__name__)
logger.warn("Unknown repo type '%s' in config", name)
pass
# -----------------------------
# Baseclass __init__
# -----------------------------
def __init__(self, **kwargs):
super(Interface, self).__init__()
self.address = kwargs.get('address')
self.aetitle = kwargs.get('aetitle')
self.auth = (kwargs.get('user'), kwargs.get('pword'))
self.name = kwargs.get('name', 'None')
self.name = self.name.split('+')[0]
self.api_key = kwargs.get('api_key')
self.proxy = kwargs.get('proxy')
self.j_proxy = kwargs.get('j_proxy')
# Create a session/juniper session
if self.j_proxy is None:
self.session = SessionWrapper(**kwargs)
else:
self.session = JuniperSessionWrapper(**kwargs)
# Should be "available studies" plus a registry of all studies somewhere else
self.series = {}
self.studies = {}
self.subjects = {}
self.logger = logging.getLogger(self.__class__.__name__)
self.logger.info('Created interface')
# -----------------------------
# Abstract Public API:
# - find
# - send
# - receive
# - delete
# -----------------------------
def find(self, level, question, source=None):
# Level is a HDN type: subject, studies, or series
# Question is a dictionary of property names and values
# by default, the source is _this_ interface,
# returns a WORKLIST, a list of session, study, or subject items
raise NotImplementedError
def retrieve(self, item, source):
raise NotImplementedError
def send(self, item, target):
raise NotImplementedError
def delete(self, worklist):
raise NotImplementedError
# -----------------------------
# Abstract Private/Hidden API:
# - upload_data
# - download_data
# - subject_from_id
# - study_from_id
# - series_from_id
# - all_studies (optional)
# -----------------------------
# Each interface needs to implement methods for moving data around
def upload_data(self, item):
raise NotImplementedError
def download_data(self, item):
raise NotImplementedError
# Factories for HDN types
def subject_from_id(self, subject_id):
raise NotImplementedError
def study_from_id(self, study_id):
raise NotImplementedError
def series_from_id(self, series_id):
raise NotImplementedError
# Optional but frequently useful shortcut
def all_studies(self):
raise NotImplementedError
# -----------------------------
# Baseclass Public API:
# - copy
# - move
# - upload_archive
# - download_archive
# -----------------------------
def copy(self, worklist, source, target, anonymize=False):
# Sends data for items in WORKLIST from the source to the target
# if the source is self and the target is a string/file, it downloads
# if the source is a string/file and the target is self, it uploads
# if the source is a DICOM node and the target is self, it retrieves
# TODO: Create anonymized study if necessary and delete it when done
if not isinstance(worklist, list):
worklist = [worklist]
for item in worklist:
# Figure out case
if isinstance(source, basestring) and (target is None
or target is self):
# It's probably a file being uploaded
self.upload_archive(item, source)
elif source is self and isinstance(target, basestring):
# It's probably a file being downloaded
self.download_archive(item, target)
elif source is self:
# Sending to DICOM modality or Orthanc peer
self.send(item, target)
elif target is self:
self.retrieve(item, source)
def move(self, worklist, source, target, anonymize=False):
self.copy(worklist, source, target, anonymize)
self.delete(worklist)
def upload_archive(self, item, fn):
if os.path.isdir(fn):
self.logger.info('Uploading image folder %s', fn)
item.data = self.zipdir(fn)
elif os.path.isfile(fn):
self.logger.info('Uploading image archive %s', fn)
f = open(fn, 'rb')
item.data = f.read()
f.close()
self.upload_data(item)
def download_archive(self, item, fn):
self.logger.info('Downloading image archive %s', fn)
self.download_data(item)
if fn is not None:
f = open(fn + '.zip', 'wb')
f.write(item.data)
f.close()
# -----------------------------
# Private/Hidden Helpers
# - do_get
# - do_post
# - do_put
# - do_delete
# - do_return
# - zipdir
# -----------------------------
def do_return(self, r):
return self.session.do_return(r)
def do_delete(self, *url, **kwargs):
return self.session.do_delete(*url, **kwargs)
def do_get(self, *url, **kwargs):
return self.session.do_get(*url, **kwargs)
def do_put(self, *url, **kwargs):
return self.session.do_put(*url, **kwargs)
def do_post(self, *url, **kwargs):
return self.session.do_post(*url, **kwargs)
def zipdir(self, top, fno=None):
file_like_object = io.BytesIO()
if fno is None:
self.logger.info('Creating in-memory zip')
zipf = zipfile.ZipFile(file_like_object, 'w', zipfile.ZIP_DEFLATED)
else:
self.logger.info('Creating zip file')
zipf = zipfile.ZipFile(fno, 'w', zipfile.ZIP_DEFLATED)
for dirpath, dirnames, filenames in os.walk(top):
for f in filenames:
fn = os.path.join(dirpath, f)
# self.logger.debug(fn)
zipf.write(fn, os.path.relpath(fn, top))
zipf.close()
if fno is None:
return file_like_object.getvalue()