def from_mrfile(cls, mrfile, nims_path, archived=True):
series_uid = nimsutil.pack_dicom_uid(mrfile.series_uid)
dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.filetype == mrfile.filetype)
.first())
if not dataset:
alt_dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.kind == u'primary')
.first())
if not alt_dataset:
kind = u'primary'
elif alt_dataset.priority < mrfile.priority:
kind = u'primary'
alt_dataset.kind = u'secondary'
else:
kind = u'secondary'
epoch = Epoch.from_mrfile(mrfile)
dataset = cls(
container=epoch,
priority = mrfile.priority,
filetype=mrfile.filetype,
compressed=mrfile.compressed,
kind=kind,
label=cls.default_labels[mrfile.filetype],
archived=archived,
)
transaction.commit()
DBSession.add(dataset)
nimsutil.make_joined_path(nims_path, dataset.relpath)
return dataset
def from_mrfile(cls, mrfile):
uid = nimsutil.pack_dicom_uid(mrfile.exam_uid)
session = cls.query.filter_by(uid=uid).first()
if not session:
subject = Subject.from_mrfile(mrfile)
# If we trusted the scan operator to carefully enter their uid in the
# 'operator' field, then we could make create=True. Or we could add some
# fancy code to fuzzily infer their intent, perhaps even ldap-ing the uid
# central authority and/or querying the schedule database. But for now,
# just let the operator be None if the user isn't already in the system.
operator = User.by_uid(unicode(mrfile.operator), create=False)
session = Session(uid=uid, exam=int(mrfile.exam_no) if isinstance(mrfile.exam_no, (unicode, int)) else 0, subject=subject, operator=operator)
return session
def get_metadata(filename):
try:
pf = nimsutil.pfile.PFile(filename)
except nimsutil.pfile.PFileError:
md = None
else:
md = Metadata()
md.datatype = u"GE PFile"
md.exam_no = pf.exam_no
md.series_no = pf.series_no
md.acq_no = pf.acq_no
md.exam_uid = nimsutil.pack_dicom_uid(pf.exam_uid)
md.series_uid = nimsutil.pack_dicom_uid(pf.series_uid)
md.psd_name = unicode(pf.psd_name)
md.physio_flag = pf.physio_flag
md.series_desc = nimsutil.clean_string(pf.series_desc)
md.timestamp = pf.timestamp
md.duration = pf.duration
all_groups = [rg.id for rg in ResearchGroup.query.all()]
md.subj_code, md.subj_fn, md.subj_ln, md.subj_dob = nimsutil.parse_subject(pf.patient_name, pf.patient_dob)
md.group_name, md.exp_name = nimsutil.parse_patient_id(pf.patient_id, ResearchGroup.get_all_ids())
return md
def get_metadata(filename):
try:
dcm = nimsutil.dicomutil.DicomFile(filename)
except nimsutil.dicomutil.DicomError:
md = None
else:
md = Metadata()
md.datatype = u"Dicom Files"
md.exam_no = dcm.exam_no
md.series_no = dcm.series_no
md.acq_no = dcm.acq_no
md.exam_uid = nimsutil.pack_dicom_uid(dcm.exam_uid)
md.series_uid = nimsutil.pack_dicom_uid(dcm.series_uid)
md.psd_name = unicode(dcm.psd_name)
md.physio_flag = dcm.physio_flag
md.series_desc = nimsutil.clean_string(dcm.series_desc)
md.timestamp = dcm.timestamp
md.duration = dcm.duration
md.subj_code, md.subj_fn, md.subj_ln, md.subj_dob = nimsutil.parse_subject(
dcm.patient_name, dcm.patient_dob
)
md.group_name, md.exp_name = nimsutil.parse_patient_id(dcm.patient_id, ResearchGroup.get_all_ids())
return md
def from_mrfile(cls, mrfile):
uid = nimsutil.pack_dicom_uid(mrfile.series_uid)
epoch = cls.query.filter_by(uid=uid).filter_by(acq=mrfile.acq_no).first()
if not epoch:
session = Session.from_mrfile(mrfile)
if session.timestamp is None or (mrfile.timestamp is not None and session.timestamp > mrfile.timestamp):
session.timestamp = mrfile.timestamp
epoch = cls(
session = session,
timestamp = mrfile.timestamp,
duration = datetime.timedelta(0, mrfile.duration or 0),
prescribed_duration = datetime.timedelta(0, mrfile.prescribed_duration or 0),
uid = uid,
series = mrfile.series_no,
acq = mrfile.acq_no,
description = nimsutil.clean_string(mrfile.series_desc),
psd = unicode(mrfile.psd_name),
physio_recorded = True,
tr = mrfile.tr,
te = mrfile.te,
ti = mrfile.ti,
flip_angle = mrfile.flip_angle,
pixel_bandwidth = mrfile.pixel_bandwidth,
num_slices = mrfile.num_slices,
num_timepoints = mrfile.num_timepoints or 1,
num_averages = mrfile.num_averages,
num_echos = mrfile.num_echos,
receive_coil_name = unicode(mrfile.receive_coil_name),
num_receivers = mrfile.num_receivers,
protocol_name = unicode(mrfile.protocol_name),
scanner_name = unicode(mrfile.scanner_name),
size_x = mrfile.size[0],
size_y = mrfile.size[1],
fov = unicode(str(mrfile.fov)),
mm_per_vox = unicode(str(mrfile.mm_per_vox)),
scan_type = unicode(mrfile.scan_type),
num_bands = mrfile.num_bands,
effective_echo_spacing = mrfile.effective_echo_spacing,
phase_encode_undersample = mrfile.phase_encode_undersample,
slice_encode_undersample = mrfile.slice_encode_undersample,
acquisition_matrix = unicode(str(mrfile.acquisition_matrix)),
num_mux_cal_cycle = mrfile.num_mux_cal_cycle if mrfile.filetype == u'pfile' else None, # hack for pfile
qa_status = u'pending',
# to unpack fov, mm_per_vox, and acquisition_matrix: np.fromstring(str(mm)[1:-1],sep=',')
)
return epoch
def from_mrfile(cls, mrfile, nims_path, archived=True):
series_uid = nimsutil.pack_dicom_uid(mrfile.series_uid)
dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.filetype == mrfile.filetype)
.first())
if not dataset:
alt_dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.kind == u'primary')
.first())
if not alt_dataset:
kind = u'primary'
elif alt_dataset.priority < mrfile.priority:
kind = u'primary'
alt_dataset.kind = u'secondary'
alt_dataset.container.qa_status = u'rerun'
else:
kind = u'secondary'
epoch = Epoch.from_mrfile(mrfile)
dataset = cls(
container=epoch,
priority = mrfile.priority,
filetype=mrfile.filetype,
compressed=mrfile.compressed,
kind=kind,
label=cls.default_labels[mrfile.filetype],
archived=archived,
qa_status=u'pending',
)
transaction.commit()
DBSession.add(dataset)
nimsutil.make_joined_path(nims_path, dataset.relpath)
return dataset
