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 from_mrfile(cls, mrfile):
subj_code, group_name, exp_name = nimsutil.parse_patient_id(mrfile.patient_id, ResearchGroup.all_ids())
query = cls.query.join(Experiment, cls.experiment).filter(Experiment.name == exp_name)
query = query.join(ResearchGroup, Experiment.owner).filter(ResearchGroup.gid == group_name)
if subj_code:
subject = query.filter(cls.code==subj_code).first()
elif mrfile.subj_firstname and mrfile.subj_lastname:
subject = query.filter(cls.firstname==unicode(mrfile.subj_firstname)).filter(cls.lastname==unicode(mrfile.subj_lastname)).filter(cls.dob==mrfile.subj_dob).first()
else:
subject = None
if not subject:
owner = ResearchGroup.query.filter_by(gid=group_name).one()
experiment = Experiment.from_owner_name(owner, exp_name)
subject = cls(
experiment=experiment,
person=Person(),
code=subj_code[:31] or experiment.next_subject_code,
firstname=(unicode(mrfile.subj_firstname) or u'')[:63],
lastname=(unicode(mrfile.subj_lastname) or u'')[:63],
dob=mrfile.subj_dob,
)
return subject
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
