def get_database_xml_from_path(server,token,pathname) :
# is it a valid dicom directory?
# is it a braink parameters.txt file?
# is it an unknown file?
# if it is a directory, assume it is a dicom directory
# if it is a file, check if it is a brainK parameters.txt file
# otherwise, for now assume it is a raw file
if not os.path.exists(pathname) :
object_xml=None
if os.path.isdir(pathname) :
if do.isvaliddicom(pathname) :
df=do.getfirstdicomfile(pathname)
object_xml=do.checkdicomexistence(server,token,df.SeriesInstanceUID)
if os.path.isfile(pathname) :
if pathname.endswith('.Parameters.txt') :
bkstub=pathname.replace('.Parameters.txt','')
bkhash=bko.brainkhash(bkstub)
object_xml=bko.checkbrainkexistence(server,token,bkhash)
else :
# 'raw' file case
rawhash=rawfilehash(pathname)
object_xml=checkrawfileexistence(server,token,rawhash)
#raise Exception('raw file case not implemented yet')
return object_xml
def upload_nii_with_dicom_reference(server,token,nii_path,reference_dicom_path) :
""" Extract subject from dicom, upload nii file using this
subject. Use with care! This routine cannot verify that the nii
and dicom actually correspond"""
if not dicomobject.isvaliddicom(reference_dicom_path) :
raise Exception('Invalid dicom path ' +reference_dicom_path+' given')
subject=dicomobject.DicomSubject(dicomobject.getfirstdicomfile(reference_dicom_path))
# this will add subject to database, if it isn't there already
subject_parsed_xml=dicomobject.uploadsubject(server,token,subject)
subject_id=common.get_id_from_parsed_xml(subject_parsed_xml)
nii_parsed_xml=uploadnii(server,token,nii_path,subject_id)
return nii_parsed_xml
def determine_file_type(pathname) :
# file could be an .nii file, or a .gps file, or unknown
if os.path.isfile(pathname) :
if pathname.endswith('.nii') or pathname.endswith('.nii.gz') :
return 'nii'
elif pathname.endswith('.sfp') or pathname.endswith('.gps') :
return 'gps'
elif pathname.endswith('.Parameters.txt') :
return 'bkparam'
elif pathname.endswith('.hdr') :
D=lfmobject.parselfmheader(pathname)
if 'LFM format' in D :
return 'lfm'
else :
raise Exception('.hdr file ' +pathname +' does not look like an lfm header')
else :
pass
if os.path.isdir(pathname) :
if do.isvaliddicom(pathname):
return 'dicomdir'
return 'unknown'
