def xnat_pull(projectid, subjectid, experimentid, storagepath):
""" Pull the complete set of files from a XNAT project, subject and experiment id """
absstoragepath = op.abspath(storagepath)
# we define the unique experimental id based on the user input
# see push for more comments
# subj_id = '%s_%s' % (projectid, subjectid)
# exp_id = '%s_%s' % (subj_id, experimentid)
subj_id = '%s' % subjectid
exp_id = '%s_%s' % (projectid, experimentid)
experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (
projectid, subj_id, exp_id)
metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
# download meta.cml
metacmlpath = op.join(absstoragepath, 'meta.cml')
meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
xnat_interface.select(meta_uri).get(metacmlpath)
# parse meta.cml
f = open(metacmlpath, 'rb')
remote_connectome = cf.parseString(f.read())
f.close()
if DEBUG_msg:
print "Remote connectome", remote_connectome.to_xml()
# loop over objects and download them to pyxnat cache / or path
for ele in remote_connectome.get_all():
if DEBUG_msg:
print("Downloading connectome object")
ele.print_summary()
cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
experiment_uri, '%s_%s' % (exp_id, ele.__class__.__name__),
quote_for_xnat(ele.name) + ele.get_file_ending())
# download file
# does file folder exist?
eleobjfolderfname = op.join(absstoragepath, ele.get_unique_relpath())
if not op.exists(op.split(eleobjfolderfname)[0]):
os.makedirs(op.split(eleobjfolderfname)[0])
xnat_interface.select(cobj_uri).get(eleobjfolderfname)
# update current connectome container
print("=============")
print("You can load the pulled connectome file with:")
print("import cfflib as cf; mycon = cf.load('%s')" %
op.join(absstoragepath, 'meta.cml'))
print("=============")
return True
def xnat_pull( projectid, subjectid, experimentid, storagepath):
""" Pull the complete set of files from a XNAT project, subject and experiment id """
absstoragepath = op.abspath(storagepath)
# we define the unique experimental id based on the user input
# see push for more comments
# subj_id = '%s_%s' % (projectid, subjectid)
# exp_id = '%s_%s' % (subj_id, experimentid)
subj_id = '%s' % subjectid
exp_id = '%s_%s' % (projectid, experimentid)
experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (projectid, subj_id, exp_id)
metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
# download meta.cml
metacmlpath = op.join(absstoragepath, 'meta.cml')
meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
xnat_interface.select(meta_uri).get(metacmlpath)
# parse meta.cml
f = open(metacmlpath, 'rb')
remote_connectome = cf.parseString(f.read())
f.close()
if DEBUG_msg:
print "Remote connectome", remote_connectome.to_xml()
# loop over objects and download them to pyxnat cache / or path
for ele in remote_connectome.get_all():
if DEBUG_msg:
print("Downloading connectome object")
ele.print_summary()
cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
experiment_uri,
'%s_%s' % (exp_id, ele.__class__.__name__),
quote_for_xnat(ele.name) + ele.get_file_ending()
)
# download file
# does file folder exist?
eleobjfolderfname = op.join(absstoragepath, ele.get_unique_relpath())
if not op.exists(op.split(eleobjfolderfname)[0]):
os.makedirs( op.split(eleobjfolderfname)[0] )
xnat_interface.select(cobj_uri).get(eleobjfolderfname)
# update current connectome container
print("=============")
print("You can load the pulled connectome file with:")
print("import cfflib as cf; mycon = cf.load('%s')" % op.join(absstoragepath, 'meta.cml'))
print("=============")
return True
def _load_from_meta_cml(filename):
""" Load connectome file from a meta.cml file. """
with open(filename, 'r') as metacml:
metastr = metacml.read()
connectome = cf.parseString(metastr)
# update references
connectome._update_parent_reference()
connectome.iszip = False
connectome.fname = op.abspath(filename)
# check if names are unique!
connectome.check_names_unique()
return connectome
def _load_from_cff(filename, *args, **kwargs):
""" Load connectome file given filename
Returns
-------
connectome : ``Connectome``
Connectome Instance
"""
# XXX: take care to have allowZip64 = True (but not supported by unix zip/unzip, same for ubuntu?) ?
_zipfile = ZipFile(filename, 'a', ZIP_DEFLATED)
try:
metadata_string = _zipfile.read('meta.cml')
except: # XXX: what is the correct exception for read error?
raise RuntimeError('Can not extract meta.cml from connectome file.')
# create connectome instance
connectome = cf.parseString(metadata_string)
# update references
connectome._update_parent_reference()
# add additional attributes
connectome.src = filename
# it is from the zip file
connectome.iszip = True
# if it is a zip file, we can assume that the src paths are given relatively
connectome._zipfile = _zipfile
# check if all referenced container elements exist in the archive
connectome.check_file_in_cff()
# check if names are unique!
connectome.check_names_unique()
return connectome
def xnat_push(connectome_obj,
projectid,
subjectid,
experimentid,
overwrite=False):
""" Push all the connectome objects to the remote XNAT server.
Parameters
----------
connectome_obj : connectome object
The connectome object you want to push
projectid : string
The id of the project, has to be unique across an XNAT server
subjectid : string
The id of the subject
experimentid : string
The id of the experiment
overwrite : boolean
Overwrite remote version of the connectome object with
the connectome object contained in the local connectome container
"""
def _push_metacml(experiment_uri):
_, fname = tempfile.mkstemp()
f = open(fname, 'wb')
f.write(connectome_obj.to_xml())
f.close()
# finally update remote meta.cml
meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
xnat_interface.select(meta_uri).insert(fname, experiments = 'xnat:imageSessionData', \
use_label=True)
if xnat_interface is None:
raise Exception(
'You need to setup the XNAT connection first with set_xnat_connection'
)
# we define the unique experimental id based on the user input
# user do not expect this composed identifiers, so we directly use
# the given parameters to construct the path
# originally, we thought that this is required because there have to be
# unique subject identifiers across the whole XNAT instance
# we seems not to be required anymore
# subj_id = '%s_%s' % (projectid, subjectid)
# exp_id = '%s_%s' % (subj_id, experimentid)
subj_id = '%s' % subjectid
exp_id = '%s_%s' % (projectid, experimentid)
experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (
projectid, subj_id, exp_id)
metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
# does the experiment exists
if xnat_interface.select(metacml_uri).exists():
# it exists
# compare it to the local object
remote_metacml = open(xnat_interface.select(metacml_uri).get(), 'rb')
remote_connectome = cf.parseString(remote_metacml.read())
# loop over local connectome objects and check if the exists remotely
all_local_cobj = connectome_obj.get_all()
# connectome objects we need to add to the remote metacml
push_objects = []
for ele in all_local_cobj:
if DEBUG_msg:
print "Working on element %s" % ele.name
if (ele in remote_connectome.get_all() and overwrite) or \
not ele in remote_connectome.get_all():
if DEBUG_msg:
print "We push element %s" % ele.name
print "Element in remote? " + str(
ele in remote_connectome.get_all())
# push connectome object to remote
cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
experiment_uri, '%s_%s' % (exp_id, ele.__class__.__name__),
quote_for_xnat(ele.name) + ele.get_file_ending())
if DEBUG_msg:
print "uri", cobj_uri
# insert data file to xnat
xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
assessors = 'xnat:imageAssessorData', use_label=True)
# add element for updating metacml later on the remote
push_objects.append(ele)
else:
# we do not push
if DEBUG_msg:
print "We do nothing with element %s (already on remote and no overwrite)" % ele.name
# synchronize meta_cml
# we need to retrieve the remote connectome objects and add it to the
# local if they no not yet exists
for el in remote_connectome.get_all():
if not el in connectome_obj.get_all():
connectome_obj.add_connectome_object(el)
#for el in push_objects:
# add all push_objects to remote meta_cml
# remote_connectome.add_connectome_object(el)
# update cmetadata (overwriting remote with local)
remote_connectome.connectome_meta = connectome_obj.connectome_meta
_push_metacml(experiment_uri)
if DEBUG_msg:
print "Current local connectome container", connectome_obj.to_xml()
print "Current remote connectome container", remote_connectome.to_xml(
)
print "Current push objects", push_objects
else:
# create meta.cml
# loop over local connectome objects and check if the exists remotely
all_local_cobj = connectome_obj.get_all()
for ele in all_local_cobj:
print "We push element %s" % ele.name
# push connectome object to remote
cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
experiment_uri, '%s_%s' %
(exp_id, ele.__class__.__name__), quote_for_xnat(ele.name))
# insert data file to xnat
xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
assessors = 'xnat:imageAssessorData', use_label=True)
# push the current connectome object to remote
_push_metacml(experiment_uri)
def xnat_push(connectome_obj, projectid, subjectid, experimentid, overwrite = False):
""" Push all the connectome objects to the remote XNAT server.
Parameters
----------
connectome_obj : connectome object
The connectome object you want to push
projectid : string
The id of the project, has to be unique across an XNAT server
subjectid : string
The id of the subject
experimentid : string
The id of the experiment
overwrite : boolean
Overwrite remote version of the connectome object with
the connectome object contained in the local connectome container
"""
def _push_metacml(experiment_uri):
_, fname = tempfile.mkstemp()
f=open(fname, 'wb')
f.write(connectome_obj.to_xml())
f.close()
# finally update remote meta.cml
meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
xnat_interface.select(meta_uri).insert(fname, experiments = 'xnat:imageSessionData', \
use_label=True)
if xnat_interface is None:
raise Exception('You need to setup the XNAT connection first with set_xnat_connection')
# we define the unique experimental id based on the user input
# user do not expect this composed identifiers, so we directly use
# the given parameters to construct the path
# originally, we thought that this is required because there have to be
# unique subject identifiers across the whole XNAT instance
# we seems not to be required anymore
# subj_id = '%s_%s' % (projectid, subjectid)
# exp_id = '%s_%s' % (subj_id, experimentid)
subj_id = '%s' % subjectid
exp_id = '%s_%s' % (projectid, experimentid)
experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (projectid, subj_id, exp_id)
metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
# does the experiment exists
if xnat_interface.select(metacml_uri).exists():
# it exists
# compare it to the local object
remote_metacml = open(xnat_interface.select(metacml_uri).get(), 'rb')
remote_connectome = cf.parseString(remote_metacml.read())
# loop over local connectome objects and check if the exists remotely
all_local_cobj = connectome_obj.get_all()
# connectome objects we need to add to the remote metacml
push_objects = []
for ele in all_local_cobj:
if DEBUG_msg:
print "Working on element %s" % ele.name
if (ele in remote_connectome.get_all() and overwrite) or \
not ele in remote_connectome.get_all():
if DEBUG_msg:
print "We push element %s" % ele.name
print "Element in remote? " + str(ele in remote_connectome.get_all())
# push connectome object to remote
cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
experiment_uri,
'%s_%s' % (exp_id, ele.__class__.__name__),
quote_for_xnat(ele.name) + ele.get_file_ending()
)
if DEBUG_msg:
print "uri", cobj_uri
# insert data file to xnat
xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
assessors = 'xnat:imageAssessorData', use_label=True)
# add element for updating metacml later on the remote
push_objects.append(ele)
else:
# we do not push
if DEBUG_msg:
print "We do nothing with element %s (already on remote and no overwrite)" % ele.name
# synchronize meta_cml
# we need to retrieve the remote connectome objects and add it to the
# local if they no not yet exists
for el in remote_connectome.get_all():
if not el in connectome_obj.get_all():
connectome_obj.add_connectome_object(el)
#for el in push_objects:
# add all push_objects to remote meta_cml
# remote_connectome.add_connectome_object(el)
# update cmetadata (overwriting remote with local)
remote_connectome.connectome_meta = connectome_obj.connectome_meta
_push_metacml(experiment_uri)
if DEBUG_msg:
print "Current local connectome container", connectome_obj.to_xml()
print "Current remote connectome container", remote_connectome.to_xml()
print "Current push objects", push_objects
else:
# create meta.cml
# loop over local connectome objects and check if the exists remotely
all_local_cobj = connectome_obj.get_all()
for ele in all_local_cobj:
print "We push element %s" % ele.name
# push connectome object to remote
cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
experiment_uri,
'%s_%s' % (exp_id, ele.__class__.__name__),
quote_for_xnat(ele.name)
)
# insert data file to xnat
xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
assessors = 'xnat:imageAssessorData', use_label=True)
# push the current connectome object to remote
_push_metacml(experiment_uri)