def _insert_entity_resources(ovEntity, xnatEntity):
xnat = xnatEntity._intf
for rsrc in iterate_entity_collection(xnatEntity.resources):
label = xnat_api(rsrc.label)
if not label:
label = "<empty>"
for f in iterate_entity_collection(rsrc.files):
url, uti = file_info(xnat, f)
ovEntity.addURLResource(uti, xnat_api(f.label) + ' (' + label + ')', url)
def import_project(dsc, xnatProject, timezone='UTC'):
"""
Import a single XNAT project.
"""
projectID = xnat_api(xnatProject.id)
name = xnat_api(xnatProject.attrs.get, 'xnat:projectData/name')
purpose = xnat_api(xnatProject.attrs.get, 'xnat:projectData/description')
# Find the earliest session date in the project
xnat = xnatProject._intf
sessionTypes = xnat.inspect.experiment_types()
if len(sessionTypes) == 0:
sessionTypes = ('xnat:mrSessionData', 'xnat:ctSessionData')
#raise XnatImportError("No session types defined in database")
minSessionDate = None
for sessionType in sessionTypes:
columns = (sessionType + '/DATE', sessionType + '/PROJECT')
xnat_api_pause()
query = xnat.select(sessionType, columns=columns).where([
(sessionType + '/Project', '=', projectID), 'AND'
])
sessionDates = [
datetime.fromtimestamp(mktime(strptime(row['date'], DATE_FORMAT)))
for row in query if len(row['date']) > 0
]
if len(sessionDates) > 0:
for sd in sessionDates:
if minSessionDate is not None:
if sd < minSessionDate:
minSessionDate = sd
else:
minSessionDate = sd
if minSessionDate is not None:
startTime = to_joda_datetime(minSessionDate, timezone)
else:
startTime = api.datetime()
ctx = dsc.getContext()
project = ctx.insertProject(name, purpose, startTime)
_import_entity_common(project, xnatProject)
for s in iterate_entity_collection(xnatProject.subjects):
src = import_source(dsc, s)
for session in iterate_entity_collection(s.sessions):
import_session(dsc, src, project, session)
return project
def _insert_entity_resources(ovEntity, xnatEntity):
xnat = xnatEntity._intf
for rsrc in iterate_entity_collection(xnatEntity.resources):
label = xnat_api(rsrc.label)
if not label:
label = "<empty>"
for f in iterate_entity_collection(rsrc.files):
url, uti = file_info(xnat, f)
ovEntity.addURLResource(uti,
xnat_api(f.label) + ' (' + label + ')',
url)
def import_project(dsc, xnatProject, timezone="UTC"):
"""
Import a single XNAT project.
"""
projectID = xnat_api(xnatProject.id)
name = xnat_api(xnatProject.attrs.get, "xnat:projectData/name")
purpose = xnat_api(xnatProject.attrs.get, "xnat:projectData/description")
# Find the earliest session date in the project
xnat = xnatProject._intf
sessionTypes = xnat.inspect.experiment_types()
if len(sessionTypes) == 0:
sessionTypes = ("xnat:mrSessionData", "xnat:ctSessionData")
# raise XnatImportError("No session types defined in database")
minSessionDate = None
for sessionType in sessionTypes:
columns = (sessionType + "/DATE", sessionType + "/PROJECT")
xnat_api_pause()
query = xnat.select(sessionType, columns=columns).where([(sessionType + "/Project", "=", projectID), "AND"])
sessionDates = [
datetime.fromtimestamp(mktime(strptime(row["date"], DATE_FORMAT))) for row in query if len(row["date"]) > 0
]
if len(sessionDates) > 0:
for sd in sessionDates:
if minSessionDate is not None:
if sd < minSessionDate:
minSessionDate = sd
else:
minSessionDate = sd
if minSessionDate is not None:
startTime = to_joda_datetime(minSessionDate, timezone)
else:
startTime = api.datetime()
ctx = dsc.getContext()
project = ctx.insertProject(name, purpose, startTime)
_import_entity_common(project, xnatProject)
for s in iterate_entity_collection(xnatProject.subjects):
src = import_source(dsc, s)
for session in iterate_entity_collection(s.sessions):
import_session(dsc, src, project, session)
return project
def should_set_subject_datatype_property(self):
xnatProject = self._import_first_project()[0]
ctx = self.dsc.getContext()
for s in iterate_entity_collection(xnatProject.subjects):
subjectID = xnat_api(s.id)
sources = ctx.getSources(subjectID)
eq_(1, len(sources))
eq_(sources[0].getOwnerProperty(DATATYPE_PROPERTY), xnat_api(s.datatype))
def should_import_all_subjects_for_project(self):
xnatProject = self._import_first_project()[0]
ctx = self.dsc.getContext()
for s in iterate_entity_collection(xnatProject.subjects):
subjectID = xnat_api(s.id)
sources = ctx.getSources(subjectID)
eq_(1, len(sources))
eq_(sources[0].getOwnerProperty('xnat:subjectURI'), s._uri)
def should_import_all_subjects_for_project(self):
xnatProject = self._import_first_project()[0]
ctx = self.dsc.getContext()
for s in iterate_entity_collection(xnatProject.subjects):
subjectID = xnat_api(s.id)
sources = ctx.getSources(subjectID)
eq_(1, len(sources))
eq_(sources[0].getOwnerProperty('xnat:subjectURI'), s._uri)
def should_set_subject_datatype_property(self):
xnatProject = self._import_first_project()[0]
ctx = self.dsc.getContext()
for s in iterate_entity_collection(xnatProject.subjects):
subjectID = xnat_api(s.id)
sources = ctx.getSources(subjectID)
eq_(1, len(sources))
eq_(sources[0].getOwnerProperty(DATATYPE_PROPERTY),
xnat_api(s.datatype))
except (DatabaseError, StopIteration):
_log.error("Unable to retrieve parameter " + k)
except DatabaseError, e:
_log.error("Unable to set parameters")
parametersDict = {}
parameters = dict2map(parametersDict)
scannerParameters = parameters
ovation = api.ovation_package()
BYTE_DATATYPE = ovation.NumericDataType(
ovation.NumericDataFormat.SignedFixedPointDataType, 1,
ovation.NumericByteOrder.ByteOrderNeutral)
for r in iterate_entity_collection(xnatScan.resources):
_log.info(" Resource " + xnat_api(r.label))
# Insert one epoch group per resource group
resourceGroup = g.insertEpochGroup(xnat_api(r.label), g.getStartTime())
for f in iterate_entity_collection(r.files):
# Import one epoch per resource file
e = resourceGroup.insertEpoch(
g.getStartTime(),
g.getEndTime(), #TODO
scanType,
parameters)
url, uti = file_info(xnatScan._intf, f)
_log.info(" File " + xnat_api(r.label))
if k.startswith(dtype + '/parameters/'):
parametersDict[k] = xnat_api(xnatScan.attrs.get, k)
except (DatabaseError,StopIteration):
_log.error("Unable to retrieve parameter " + k)
except DatabaseError, e:
_log.error("Unable to set parameters")
parametersDict = {}
parameters = dict2map(parametersDict)
scannerParameters = parameters
ovation = api.ovation_package()
BYTE_DATATYPE = ovation.NumericDataType(ovation.NumericDataFormat.SignedFixedPointDataType, 1, ovation.NumericByteOrder.ByteOrderNeutral)
for r in iterate_entity_collection(xnatScan.resources):
_log.info(" Resource " + xnat_api(r.label))
# Insert one epoch group per resource group
resourceGroup = g.insertEpochGroup(xnat_api(r.label),
g.getStartTime())
for f in iterate_entity_collection(r.files):
# Import one epoch per resource file
e = resourceGroup.insertEpoch(
g.getStartTime(),
g.getEndTime(), #TODO
scanType,
parameters
)
url,uti = file_info(xnatScan._intf, f)