def read_bruker(args):
"""
:param args:
:return list imageOut:
:return list fileoutNames:
"""
imageOut = []
fileoutNames = []
# for all Bruker datasets compliant all queries
for data, properties in yield_bruker(args):
orientation = NIFTIOrient(np.reshape(np.array(properties['affine']), (4,4)))
imageOut.append(
nifti_mrs.NIfTI_MRS(data,
orientation.Q44,
properties['dwell_s'],
nifti_mrs.hdr_ext(
properties['SpectrometerFrequency'],
properties['ResonantNucleus']
))
)
fileoutNames.append(properties['id'])
return imageOut, fileoutNames
def jmrui_hdr_to_obj(header):
"""Translate jMRUI txt header to NIfTI MRS"""
if 'TypeOfNucleus' in header:
nucleus = id_nucleus(header['TypeOfNucleus'],
header['TransmitterFrequency'],
header['MagneticField'])
else:
nucleus = id_nucleus(None, header['TransmitterFrequency'],
header['MagneticField'])
meta = nifti_mrs.hdr_ext(float(header['TransmitterFrequency']), nucleus)
if 'Spectrometer' in header:
meta.set_standard_def('ManufacturersModelName', header['Spectrometer'])
if 'NameOfPatient' in header:
meta.set_standard_def('PatientName', header['NameOfPatient'])
meta.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
meta.set_standard_def('ConversionTime', conversion_time)
if 'AdditionalInformation' in header:
meta.set_user_def(key='AdditionalInformation',
value=header['AdditionalInformation'],
doc='jMRUI AdditionalInformation field.')
if 'SignalNames' in header:
meta.set_user_def(key='SignalNames',
value=header['SignalNames'],
doc='jMRUI SignalNames field.')
return meta
def lcm_raw(args):
'''Processing for LCModel .RAW (and .H2O) files.
Currently only handles one FID per file.
'''
# Read data from file
data, header = readLCModelRaw(args.file, conjugate=True)
newshape = (1, 1, 1) + data.shape
data = data.reshape(newshape)
# meta
dwelltime = header['dwelltime']
meta = nifti_mrs.hdr_ext(header['centralFrequency'],
args.nucleus)
meta.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
conversion_time = datetime.now().isoformat(sep='T', timespec='milliseconds')
meta.set_standard_def('ConversionTime', conversion_time)
meta.set_standard_def('OriginalFile', [basename(args.file), ])
# Read optional affine file
if args.affine:
affine = np.loadtxt(args.affine)
else:
tmp = np.array([10000, 10000, 10000, 1])
affine = np.diag(tmp)
nifti_orientation = NIFTIOrient(affine)
img_out = [nifti_mrs.NIfTI_MRS(data,
nifti_orientation.Q44,
dwelltime,
meta), ]
# File names
if args.fileout:
fname_out = [args.fileout, ]
else:
fname_out = [splitext(basename(args.file))[0], ]
# Place in data output format
return img_out, fname_out
def text(args):
'''Processing for simple ascii formatted columns of data.'''
# Read text from file
data = np.loadtxt(args.file)
data = data[:, 0] + 1j * data[:, 1]
newshape = (1, 1, 1) + data.shape
data = data.reshape(newshape)
# Interpret required arguments (frequency and bandwidth)
dwelltime = 1.0 / args.bandwidth
meta = nifti_mrs.hdr_ext(args.imagingfreq,
args.nucleus)
meta.set_standard_def('ConversionMethod', 'spec2nii')
conversion_time = datetime.now().isoformat(sep='T', timespec='milliseconds')
meta.set_standard_def('ConversionTime', conversion_time)
meta.set_standard_def('OriginalFile', [basename(args.file), ])
# Read optional affine file
if args.affine:
affine = np.loadtxt(args.affine)
else:
tmp = np.array([10000, 10000, 10000, 1])
affine = np.diag(tmp)
nifti_orientation = NIFTIOrient(affine)
img_out = [nifti_mrs.NIfTI_MRS(data,
nifti_orientation.Q44,
dwelltime,
meta), ]
# File names
if args.fileout:
fname_out = [args.fileout, ]
else:
fname_out = [splitext(basename(args.file))[0], ]
# Place in data output format
return img_out, fname_out
def jmrui_hdr_to_obj_mrui(header, str_info):
"""Translate jMRUI mrui header to NIfTI MRS"""
nucleus = id_nucleus(header['type_of_nucleus'],
header['transmitter_frequency'],
header['magnetic_field'])
meta = nifti_mrs.hdr_ext(header['transmitter_frequency'], nucleus)
# meta.set_standard_def('ManufacturersModelName', header['Spectrometer'])
# meta.set_standard_def('PatientName', header['NameOfPatient'])
meta.set_standard_def('TxOffset', header['reference_frequency_ppm'])
meta.set_standard_def('ConversionMethod', 'spec2nii')
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
meta.set_standard_def('ConversionTime', conversion_time)
meta.set_user_def(key='AdditionalInformation',
value=str_info,
doc='jMRUI .mrui string field.')
return meta
def extractTwixMetadata(mapVBVDHdr, orignal_file):
""" Extract information from the pymapVBVD header to insert into the json sidecar.
Args:
dcmdata (dict): Twix headers
Returns:
obj (hdr_ext): NIfTI MRS hdr ext object.
"""
# Extract required metadata and create hdr_ext object
obj = nifti_mrs.hdr_ext(mapVBVDHdr['Meas'][('Frequency')] / 1E6,
mapVBVDHdr['Meas'][('ResonantNucleus')])
# Standard defined metadata
# # 5.1 MRS specific Tags
# 'EchoTime'
obj.set_standard_def('EchoTime',
mapVBVDHdr['Phoenix'][('alTE', '0')] * 1E-6)
# 'RepetitionTime'
if ('TR_Time') in mapVBVDHdr['Meas']:
tr = mapVBVDHdr['Meas'][('TR_Time')] / 1E6
else:
tr = mapVBVDHdr['Meas'][('TR')] / 1E6
obj.set_standard_def('RepetitionTime', float(tr))
# 'InversionTime'
if ('InversionTime') in mapVBVDHdr['Meas']:
obj.set_standard_def('InversionTime',
float(mapVBVDHdr['Meas'][('TI_Time')]))
# 'MixingTime'
# 'ExcitationFlipAngle'
obj.set_standard_def('ExcitationFlipAngle',
float(mapVBVDHdr['Meas'][('FlipAngle')]))
# 'TxOffset'
obj.set_standard_def(
'TxOffset',
empty_str_to_0float(mapVBVDHdr['Meas'][('dDeltaFrequency')]))
# 'VOI'
# 'WaterSuppressed'
# TO DO
# 'WaterSuppressionType'
# 'SequenceTriggered'
# # 5.2 Scanner information
# 'Manufacturer'
obj.set_standard_def('Manufacturer', mapVBVDHdr['Dicom'][('Manufacturer')])
# 'ManufacturersModelName'
obj.set_standard_def('ManufacturersModelName',
mapVBVDHdr['Dicom'][('ManufacturersModelName')])
# 'DeviceSerialNumber'
obj.set_standard_def('DeviceSerialNumber',
str(mapVBVDHdr['Dicom'][('DeviceSerialNumber')]))
# 'SoftwareVersions'
obj.set_standard_def('SoftwareVersions',
mapVBVDHdr['Dicom'][('SoftwareVersions')])
# 'InstitutionName'
obj.set_standard_def('InstitutionName',
mapVBVDHdr['Dicom'][('InstitutionName')])
# 'InstitutionAddress'
obj.set_standard_def('InstitutionAddress',
mapVBVDHdr['Dicom'][('InstitutionAddress')])
# 'TxCoil'
# 'RxCoil'
rx_coil_1 = ('sCoilSelectMeas', 'aRxCoilSelectData', '0', 'asList', '0',
'sCoilElementID', 'tCoilID')
rx_coil_2 = ('asCoilSelectMeas', '0', 'asList', '0', 'sCoilElementID',
'tCoilID')
if rx_coil_1 in mapVBVDHdr['MeasYaps']:
obj.set_standard_def('RxCoil', mapVBVDHdr['MeasYaps'][rx_coil_1])
elif rx_coil_2 in mapVBVDHdr['MeasYaps']:
obj.set_standard_def('RxCoil', mapVBVDHdr['MeasYaps'][rx_coil_2])
# # 5.3 Sequence information
# 'SequenceName'
obj.set_standard_def('SequenceName',
mapVBVDHdr['Meas'][('tSequenceString')])
# 'ProtocolName'
obj.set_standard_def('ProtocolName',
mapVBVDHdr['Dicom'][('tProtocolName')])
# # 5.4 Sequence information
# 'PatientPosition'
obj.set_standard_def('PatientPosition',
mapVBVDHdr['Meas'][('PatientPosition')])
# 'PatientName'
obj.set_standard_def('PatientName', mapVBVDHdr['Meas'][('PatientName')])
# 'PatientID'
# 'PatientWeight'
obj.set_standard_def('PatientWeight',
mapVBVDHdr['Meas'][('flUsedPatientWeight')])
# 'PatientDoB'
obj.set_standard_def('PatientDoB',
str(mapVBVDHdr['Meas'][('PatientBirthDay')]))
# 'PatientSex'
if mapVBVDHdr['Meas'][('PatientSex')] == 1:
sex_str = 'M'
elif mapVBVDHdr['Meas'][('PatientSex')] == 2:
sex_str = 'F'
else:
sex_str = 'O'
obj.set_standard_def('PatientSex', sex_str)
# # 5.5 Provenance and conversion metadata
# 'ConversionMethod'
obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
obj.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
obj.set_standard_def('OriginalFile', [
orignal_file,
])
# # 5.6 Spatial information
# 'kSpace'
obj.set_standard_def('kSpace', [False, False, False])
# Some additional information
obj.set_user_def(key='PulseSequenceFile',
value=mapVBVDHdr['Config'][('SequenceFileName')],
doc='Sequence binary path.')
obj.set_user_def(key='IceProgramFile',
value=mapVBVDHdr['Meas'][('tICEProgramName')],
doc='Reconstruction binary path.')
return obj
def extractDicomMetadata(dcmdata):
""" Extract information from the nibabel DICOM object to insert into the json header ext.
Args:
dcmdata: nibabel.nicom image object
Returns:
obj (hdr_ext): NIfTI MRS hdr ext object.
"""
# Extract required metadata and create hdr_ext object
obj = nifti_mrs.hdr_ext(
dcmdata.csa_header['tags']['ImagingFrequency']['items'][0],
dcmdata.csa_header['tags']['ImagedNucleus']['items'][0])
# Standard defined metadata
def set_standard_def(nifti_mrs_key, location, key, cast=None):
try:
if cast is not None:
obj.set_standard_def(nifti_mrs_key,
cast(getattr(location, key)))
else:
obj.set_standard_def(nifti_mrs_key, getattr(location, key))
except AttributeError:
pass
# # 5.1 MRS specific Tags
# 'EchoTime'
obj.set_standard_def(
'EchoTime',
float(dcmdata.csa_header['tags']['EchoTime']['items'][0] * 1E-3))
# 'RepetitionTime'
obj.set_standard_def(
'RepetitionTime',
float(dcmdata.csa_header['tags']['RepetitionTime']['items'][0] / 1E3))
# 'InversionTime'
if dcmdata.csa_header['tags']['InversionTime']['n_items'] > 0:
obj.set_standard_def(
'InversionTime',
float(dcmdata.csa_header['tags']['InversionTime']['items'][0]))
# 'MixingTime'
# 'ExcitationFlipAngle'
obj.set_standard_def(
'ExcitationFlipAngle',
float(dcmdata.csa_header['tags']['FlipAngle']['items'][0]))
# 'TxOffset'
# 'VOI'
# 'WaterSuppressed'
# 'WaterSuppressionType'
# 'SequenceTriggered'
# # 5.2 Scanner information
# 'Manufacturer'
set_standard_def('Manufacturer', dcmdata.dcm_data, 'Manufacturer')
# 'ManufacturersModelName'
set_standard_def('ManufacturersModelName', dcmdata.dcm_data,
'ManufacturerModelName')
# 'DeviceSerialNumber'
set_standard_def('DeviceSerialNumber',
dcmdata.dcm_data,
'DeviceSerialNumber',
cast=str)
# 'SoftwareVersions'
set_standard_def('SoftwareVersions', dcmdata.dcm_data, 'SoftwareVersions')
# 'InstitutionName'
set_standard_def('InstitutionName', dcmdata.dcm_data, 'InstitutionName')
# 'InstitutionAddress'
set_standard_def('InstitutionAddress', dcmdata.dcm_data,
'InstitutionAddress')
# 'TxCoil'
# 'RxCoil'
if len(dcmdata.csa_header['tags']['ReceivingCoil']['items']) > 0:
obj.set_standard_def(
'RxCoil', dcmdata.csa_header['tags']['ReceivingCoil']['items'][0])
else:
obj.set_standard_def(
'RxCoil', dcmdata.csa_header['tags']['ImaCoilString']['items'][0])
# # 5.3 Sequence information
# 'SequenceName'
obj.set_standard_def(
'SequenceName', dcmdata.csa_header['tags']['SequenceName']['items'][0])
# 'ProtocolName'
set_standard_def('ProtocolName', dcmdata.dcm_data, 'ProtocolName')
# # 5.4 Sequence information
# 'PatientPosition'
set_standard_def('PatientPosition', dcmdata.dcm_data, 'PatientPosition')
# 'PatientName'
set_standard_def('PatientName', dcmdata.dcm_data.PatientName,
'family_name')
# 'PatientID'
# 'PatientWeight'
set_standard_def('PatientWeight',
dcmdata.dcm_data,
'PatientWeight',
cast=float)
# 'PatientDoB'
set_standard_def('PatientDoB', dcmdata.dcm_data, 'PatientBirthDate')
# 'PatientSex'
set_standard_def('PatientSex', dcmdata.dcm_data, 'PatientSex')
# # 5.5 Provenance and conversion metadata
obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
obj.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
# Set elsewhere
# # 5.6 Spatial information
# 'kSpace'
obj.set_standard_def('kSpace', [False, False, False])
# Some additional sequence information
obj.set_user_def(
key='PulseSequenceFile',
value=dcmdata.csa_header['tags']['SequenceName']['items'][0],
doc='Sequence binary path.')
# obj.set_user_def(key='IceProgramFile',
# value=mapVBVDHdr['Meas'][('tICEProgramName')],
# doc='Reconstruction binary path.')
return obj
def spar_to_nmrs_hdrext(spar_dict):
""" Extract information from the dict of keys read from the spar file to insert into the json header ext.
:param dict spar_dict: key-value pairs read from spar file
:return: NIfTI MRS hdr ext object.
"""
# Extract required metadata and create hdr_ext object
cf = float(spar_dict["synthesizer_frequency"]) / 1E6
obj = nifti_mrs.hdr_ext(cf, spar_dict["nucleus"])
def set_standard_def(nifti_mrs_key, location, key, cast=None):
try:
if cast is not None:
obj.set_standard_def(nifti_mrs_key,
cast(getattr(location, key)))
else:
obj.set_standard_def(nifti_mrs_key, getattr(location, key))
except AttributeError:
pass
# # 5.1 MRS specific Tags
# 'EchoTime'
obj.set_standard_def('EchoTime', float(spar_dict['echo_time']) * 1E-3)
# 'RepetitionTime'
obj.set_standard_def('RepetitionTime',
float(spar_dict['repetition_time'] / 1E3))
# 'InversionTime'
if spar_dict['spectrum_inversion_time'] > 0:
obj.set_standard_def('InversionTime',
float(spar_dict['spectrum_inversion_time']))
# 'MixingTime'
# 'ExcitationFlipAngle'
# 'TxOffset'
obj.set_standard_def('TxOffset', float(spar_dict['offset_frequency'] / cf))
# 'VOI'
# 'WaterSuppressed'
# No apparent parameter stored in the SPAR info.
# 'WaterSuppressionType'
# 'SequenceTriggered'
# # 5.2 Scanner information
# 'Manufacturer'
obj.set_standard_def('Manufacturer', 'Philips')
# 'ManufacturersModelName'
# 'DeviceSerialNumber'
# 'SoftwareVersions'
set_standard_def('SoftwareVersions', spar_dict, 'equipment_sw_verions')
# 'InstitutionName'
# 'InstitutionAddress'
# 'TxCoil'
# 'RxCoil'
# # 5.3 Sequence information
# 'SequenceName'
# 'ProtocolName'
set_standard_def('ProtocolName', spar_dict, 'scan_id')
# # 5.4 Sequence information
# 'PatientPosition'
try:
obj.set_standard_def(
'PatientPosition', spar_dict['patient_position'] + ' ' +
spar_dict['patient_orientation'])
except AttributeError:
pass
# 'PatientName'
set_standard_def('PatientName', spar_dict, 'patient_name')
# 'PatientID'
# 'PatientWeight'
# 'PatientDoB'
set_standard_def('PatientDoB', spar_dict, 'patient_birth_date')
# 'PatientSex'
# # 5.5 Provenance and conversion metadata
# 'ConversionMethod'
obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
obj.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
# Set elsewhere
# # 5.6 Spatial information
# 'kSpace'
obj.set_standard_def('kSpace', [False, False, False])
return obj
def _populate_metadata(pfile, water_suppressed=True):
''' Populate a nifti-mrs header extension with the requisite information'''
hdr = pfile.hdr
spec_frequency = float(pfile.hdr.rhr_rh_ps_mps_freq) / 1e7
# Use the mps freq and field strength to determine gamma and thus isotope
gamma = (hdr.rhr_rh_ps_mps_freq * 1e-7) / (hdr.rhe_magstrength / 10000.0)
if abs(gamma - 42.57) < 0.3:
nucleus = "1H"
elif abs(gamma - 10.7) < 0.3:
nucleus = "13C"
elif abs(gamma - 17.2) < 0.3:
nucleus = "31P"
else:
nucleus = "1H"
meta = nifti_mrs.hdr_ext(spec_frequency, nucleus)
# Standard defined metadata
# # 5.1 MRS specific Tags
# 'EchoTime'
meta.set_standard_def('EchoTime', float(hdr.rhi_te))
# 'RepetitionTime'
meta.set_standard_def('RepetitionTime', float(hdr.rhi_tr))
# 'InversionTime'
meta.set_standard_def('InversionTime', float(hdr.rhi_ti))
# 'MixingTime'
# Not known
# 'ExcitationFlipAngle'
meta.set_standard_def('ExcitationFlipAngle', float(hdr.rhi_mr_flip))
# 'TxOffset'
# Not known
# 'VOI'
# Not known
# 'WaterSuppressed'
meta.set_standard_def('WaterSuppressed', water_suppressed)
# 'WaterSuppressionType'
# Not Known
# 'SequenceTriggered'
# Not Known
# # 5.2 Scanner information
# 'Manufacturer'
meta.set_standard_def('Manufacturer', 'GE')
# 'ManufacturersModelName'
meta.set_standard_def('ManufacturersModelName',
hdr.rhe_ex_sysid.decode('utf-8'))
# 'DeviceSerialNumber'
meta.set_standard_def('DeviceSerialNumber',
hdr.rhe_uniq_sys_id.decode('utf-8'))
# 'SoftwareVersions'
meta.set_standard_def('SoftwareVersions',
hdr.rhe_ex_verscre.decode('utf-8'))
# 'InstitutionName'
meta.set_standard_def('InstitutionName', hdr.rhe_hospname.decode('utf-8'))
# 'InstitutionAddress'
# Not known
# 'TxCoil'
# Not Known
# 'RxCoil'
meta.set_user_def(key='ReceiveCoilName',
value=hdr.rhi_cname.decode('utf-8'),
doc='Rx coil name.')
# # 5.3 Sequence information
# 'SequenceName'
meta.set_standard_def('SequenceName', hdr.rhi_psdname.decode('utf-8'))
# 'ProtocolName'
meta.set_standard_def('ProtocolName', hdr.rhs_se_desc.decode('utf-8'))
# # 5.4 Sequence information
# 'PatientPosition'
# Not known
# 'PatientName'
meta.set_standard_def('PatientName', hdr.rhe_patname.decode('utf-8'))
# 'PatientID'
# Not known
# 'PatientWeight'
# Not known
# 'PatientDoB'
meta.set_standard_def('PatientDoB', hdr.rhe_dateofbirth.decode('utf-8'))
# 'PatientSex'
if hdr.rhe_patsex == 1:
sex_str = 'M'
elif hdr.rhe_patsex == 2:
sex_str = 'F'
else:
sex_str = 'O'
meta.set_standard_def('PatientSex', sex_str)
# # 5.5 Provenance and conversion metadata
# 'ConversionMethod'
meta.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
meta.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
meta.set_standard_def('OriginalFile', [basename(pfile.file_name)])
# # 5.6 Spatial information
# 'kSpace'
meta.set_standard_def('kSpace', [False, False, False])
return meta
def read_varian(args):
"""read_varian -- load a varian fid.
Note that this format is very flexible and some rather large assumptions are made.
At the moment, this assumes little.
:param file: path to the varian .fid directory, containing fid and procpar files.
returns img_out, fname_out
"""
dic, data = v.read(args.file)
# extract number of coils
number_of_coils = 0
for i in dic['procpar']['rcvrs']['values'][0]:
if re.search(i, 'y'):
number_of_coils += 1
# number of time points -- probably
number_of_time_points = float(
dic['procpar']['arraydim']['values'][0]) / number_of_coils
if (not number_of_time_points.is_integer()):
raise ValueError('Coil reshaping failed')
number_of_time_points = int(number_of_time_points)
# spectral number of points
number_of_spectral_points = int(int(dic['np']) / 2)
# reshape
newshape = (1, 1, 1, number_of_spectral_points, number_of_coils,
number_of_time_points)
data = data.transpose()
data = np.resize(data, newshape)
# extract additional spectral metadata
dwelltime = 1.0 / float(dic['procpar']['sw']['values'][0])
imagingfreq = float(dic['procpar']['sfrq']['values'][0])
nucleus = dic['procpar']['tn']['values'][0]
# reshape to be in the form '13C' rather than 'C13'
nucleus = nucleus[1:] + nucleus[0]
try:
repitition_time = float(dic['procpar']['tr']['values'][0])
except KeyError:
pass
try:
echotime = float(
dic['procpar']['te']['values'][0]) # In ms if 'tis there
except KeyError:
pass
try:
echotime = float(dic['procpar']['pw']['values'][0]) + float(
dic['procpar']['alfa']['values'][0])
except KeyError:
pass
try:
echotime = float(dic['procpar']['p1']['values'][0]) + float(
dic['procpar']['alfa']['values'][0])
except KeyError:
pass
# Parse 3D localisation
sequence_name = dic['procpar']['seqfil']['values'][0]
if (sequence_name.count('press') or sequence_name.count('steam')):
affine = _varian_orientation_3d(dic)
else:
affine = np.diag(np.array([10000, 10000, 10000,
1])) # 10 m slab for now....
# TODO: Jack should implement the affine matrix correctly for all sequences
orientation = NIFTIOrient(affine)
# create object
meta = nifti_mrs.hdr_ext(imagingfreq, nucleus)
meta.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
meta.set_standard_def('EchoTime', echotime)
meta.set_standard_def('RepetitionTime', repitition_time)
meta.set_standard_def('Manufacturer', 'Varian')
meta.set_standard_def('ProtocolName',
dic['procpar']['seqfil']['values'][0])
meta.set_standard_def('PatientName',
dic['procpar']['comment']['values'][0])
# stuff that is nice to have:
try:
meta.set_standard_def('SoftwareVersions',
dic['procpar']['parver']['values'][0])
meta.set_standard_def('TxCoil', dic['procpar']['rfcoil']['values'][0])
meta.set_standard_def('RxCoil', dic['procpar']['rfcoil']['values'][0])
except KeyError:
warnings.warn('Expected standard metadata keying failed')
try:
meta.set_standard_def('InversionTime',
dic['procpar']['ti']['values'][0])
except KeyError:
pass
try:
meta.set_standard_def('ExcitationFlipAngle',
dic['procpar']['flip1']['values'][0])
except KeyError:
pass
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
meta.set_standard_def('ConversionTime', conversion_time)
meta.set_standard_def('OriginalFile', [basename(args.file)])
# k-space
meta.set_standard_def('kSpace', [False, False, False])
# set tag dimensions
meta.set_dim_info(0, "DIM_COIL")
meta.set_dim_info(1, args.tag6)
# Stuff full headers into user fields
if args.dump_headers:
meta.set_user_def(key='VarianProcpar',
doc='Varian procpar metadata.',
value=dic['procpar'])
# File names
if args.fileout:
fname_out = [
args.fileout,
]
else:
fname_out = [
splitext(basename(args.file))[0],
]
return [
nifti_mrs.NIfTI_MRS(data, orientation.Q44, dwelltime, meta),
], fname_out
def _extractDicomMetadata(dcmdata, water_suppressed=True):
""" Extract information from the nibabel DICOM object to insert into the json header ext.
Args:
dcmdata: nibabel.nicom image object
Returns:
obj (hdr_ext): NIfTI MRS hdr ext object.
"""
# Extract required metadata and create hdr_ext object
obj = nifti_mrs.hdr_ext(dcmdata.dcm_data.TransmitterFrequency,
dcmdata.dcm_data.ResonantNucleus)
def set_if_present(tag, val):
if val:
obj.set_standard_def(tag, val)
# Standard metadata
# # 5.1 MRS specific Tags
# 'EchoTime'
echo_time = float(dcmdata.dcm_data.PerFrameFunctionalGroupsSequence[0].
MREchoSequence[0].EffectiveEchoTime) * 1E-3
obj.set_standard_def('EchoTime', echo_time)
# 'RepetitionTime'
rep_tim = float(
dcmdata.dcm_data.PerFrameFunctionalGroupsSequence[0].
MRTimingAndRelatedParametersSequence[0].RepetitionTime) / 1E3
obj.set_standard_def('RepetitionTime', rep_tim)
# 'InversionTime'
# Not known
# 'MixingTime'
# Not known
# 'ExcitationFlipAngle'
fa = float(dcmdata.dcm_data.PerFrameFunctionalGroupsSequence[0].
MRTimingAndRelatedParametersSequence[0].RepetitionTime)
obj.set_standard_def('ExcitationFlipAngle', fa)
# 'TxOffset'
# Not known
# 'VOI'
# Not known
# 'WaterSuppressed'
obj.set_standard_def('WaterSuppressed', water_suppressed)
# 'WaterSuppressionType'
# Not known
# 'SequenceTriggered'
# Not known
# # 5.2 Scanner information
# 'Manufacturer'
obj.set_standard_def('Manufacturer', dcmdata.dcm_data.Manufacturer)
# 'ManufacturersModelName'
obj.set_standard_def('ManufacturersModelName',
dcmdata.dcm_data.ManufacturerModelName)
# 'DeviceSerialNumber'
if 'DeviceSerialNumber' in dcmdata.dcm_data:
obj.set_standard_def('DeviceSerialNumber',
str(dcmdata.dcm_data.DeviceSerialNumber))
# 'SoftwareVersions'
obj.set_standard_def('SoftwareVersions',
str(dcmdata.dcm_data.SoftwareVersions))
# 'InstitutionName'
obj.set_standard_def('InstitutionName', dcmdata.dcm_data.InstitutionName)
# 'InstitutionAddress'
if 'InstitutionAddress' in dcmdata.dcm_data:
obj.set_standard_def('InstitutionAddress',
dcmdata.dcm_data.InstitutionAddress)
# 'TxCoil'
# Not known
# 'RxCoil'
# ToDo
# img.dcm_data.SharedFunctionalGroupsSequence[0].MRReceiveCoilSequence[0].ReceiveCoilName
# # 5.3 Sequence information
# 'SequenceName'
obj.set_standard_def('SequenceName', dcmdata.dcm_data.PulseSequenceName)
# 'ProtocolName'
obj.set_standard_def('ProtocolName', dcmdata.dcm_data.ProtocolName)
# # 5.4 Sequence information
# 'PatientPosition'
obj.set_standard_def('PatientPosition', dcmdata.dcm_data.PatientPosition)
# 'PatientName'
if dcmdata.dcm_data.PatientName:
obj.set_standard_def('PatientName',
dcmdata.dcm_data.PatientName.family_name)
# 'PatientID'
# Not known
# 'PatientWeight'
if 'PatientWeight' in dcmdata.dcm_data and dcmdata.dcm_data.PatientWeight:
obj.set_standard_def('PatientWeight',
float(dcmdata.dcm_data.PatientWeight))
# 'PatientDoB'
set_if_present('PatientDoB', dcmdata.dcm_data.PatientBirthDate)
# 'PatientSex'
set_if_present('PatientSex', dcmdata.dcm_data.PatientSex)
# # 5.5 Provenance and conversion metadata
# 'ConversionMethod'
obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T',
timespec='milliseconds')
obj.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
# Added later
# # 5.6 Spatial information
# 'kSpace'
obj.set_standard_def('kSpace', [False, False, False])
return obj
def _fid_meta(d, dump=False):
""" Extract information from method and acqp file into hdr_ext.
:param d: Dataset
:return: NIfTI MRS hdr ext object.
"""
# Extract required metadata and create hdr_ext object
cf = d.SpectrometerFrequency
obj = nifti_mrs.hdr_ext(cf,
d.ResonantNucleus)
# # 5.1 MRS specific Tags
# 'EchoTime'
obj.set_standard_def('EchoTime', float(d.TE * 1E-3))
# 'RepetitionTime'
obj.set_standard_def('RepetitionTime', float(d.TR / 1E3))
# 'InversionTime'
# 'MixingTime'
# 'ExcitationFlipAngle'
# 'TxOffset'
# Bit of a guess, not sure of units.
obj.set_standard_def('TxOffset', float(d.working_offset[0]))
# 'VOI'
# 'WaterSuppressed'
# No apparent parameter stored in the SPAR info.
# 'WaterSuppressionType'
# 'SequenceTriggered'
# # 5.2 Scanner information
# 'Manufacturer'
obj.set_standard_def('Manufacturer', 'Bruker')
# 'ManufacturersModelName'
# 'DeviceSerialNumber'
# 'SoftwareVersions'
obj.set_standard_def('SoftwareVersions', d.PV_version)
# 'InstitutionName'
# 'InstitutionAddress'
# 'TxCoil'
# 'RxCoil'
# # 5.3 Sequence information
# 'SequenceName'
obj.set_standard_def('SequenceName', d.method_desc)
# 'ProtocolName'
# # 5.4 Sequence information
# 'PatientPosition'
# 'PatientName'
obj.set_standard_def('PatientName', d.subj_id)
# 'PatientID'
# 'PatientWeight'
# 'PatientDoB'
# 'PatientSex'
# # 5.5 Provenance and conversion metadata
# 'ConversionMethod'
obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T', timespec='milliseconds')
obj.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
obj.set_standard_def('OriginalFile', [str(d.path), ])
# # 5.6 Spatial information
# 'kSpace'
obj.set_standard_def('kSpace', [False, False, False])
# Stuff full headers into user fields
if dump:
for hdr_file in d.parameters:
obj.set_user_def(key=hdr_file,
doc=f'Bruker {hdr_file} file.',
value=d.parameters[hdr_file].to_dict())
# Tags
unknown_count = 0
for ddx, dim in enumerate(d.dim_type[1:]):
if dim in fid_dimension_defaults:
obj.set_dim_info(ddx, fid_dimension_defaults[dim])
else:
obj.set_dim_info(ddx, f'DIM_USER_{unknown_count}')
unknown_count += 1
return obj
def extractDicomMetadata(dcmdata):
""" Extract information from the nibabel DICOM object to insert into the json header ext.
There seems to be a large 'uprotocol' in tag 0065,1007 but I don't know how to interpret it.
Args:
dcmdata: nibabel.nicom image object
Returns:
obj (hdr_ext): NIfTI MRS hdr ext object.
"""
# Extract required metadata and create hdr_ext object
obj = nifti_mrs.hdr_ext(dcmdata.dcm_data.TransmitterFrequency,
dcmdata.dcm_data.ResonantNucleus)
def set_if_present(tag, val):
if val:
obj.set_standard_def(tag, val)
# Standard defined
# # 5.1 MRS specific Tags
# 'EchoTime'
obj.set_standard_def('EchoTime', float(dcmdata.dcm_data.EchoTime) * 1E-3)
# 'RepetitionTime'
obj.set_standard_def('RepetitionTime', float(dcmdata.dcm_data.RepetitionTime) / 1E3)
# 'InversionTime'
if 'InversionTime' in dcmdata.dcm_data:
obj.set_standard_def('InversionTime', float(dcmdata.dcm_data.InversionTime) * 1E-3)
# 'MixingTime'
# 'ExcitationFlipAngle'
obj.set_standard_def('ExcitationFlipAngle', float(dcmdata.dcm_data.FlipAngle))
# 'TxOffset'
# 'VOI'
# 'WaterSuppressed'
# TO DO
# 'WaterSuppressionType'
# 'SequenceTriggered'
# # 5.2 Scanner information
# 'Manufacturer'
obj.set_standard_def('Manufacturer', dcmdata.dcm_data.Manufacturer)
# 'ManufacturersModelName'
obj.set_standard_def('ManufacturersModelName', dcmdata.dcm_data.ManufacturerModelName)
# 'DeviceSerialNumber'
obj.set_standard_def('DeviceSerialNumber', str(dcmdata.dcm_data.DeviceSerialNumber))
# 'SoftwareVersions'
obj.set_standard_def('SoftwareVersions', dcmdata.dcm_data.SoftwareVersions)
# 'InstitutionName'
obj.set_standard_def('InstitutionName', dcmdata.dcm_data.InstitutionName)
# 'InstitutionAddress'
obj.set_standard_def('InstitutionAddress', dcmdata.dcm_data.InstitutionAddress)
# 'TxCoil'
# 'RxCoil'
# No apparent coil name in header.
# # 5.3 Sequence information
# 'SequenceName'
obj.set_standard_def('SequenceName', dcmdata.dcm_data.SequenceName)
# 'ProtocolName'
obj.set_standard_def('ProtocolName', dcmdata.dcm_data.ProtocolName)
# # 5.4 Sequence information
# 'PatientPosition'
obj.set_standard_def('PatientPosition', dcmdata.dcm_data.PatientPosition)
# 'PatientName'
if dcmdata.dcm_data.PatientName:
obj.set_standard_def('PatientName', dcmdata.dcm_data.PatientName.family_name)
# 'PatientID'
# 'PatientWeight'
if dcmdata.dcm_data.PatientWeight:
obj.set_standard_def('PatientWeight', float(dcmdata.dcm_data.PatientWeight))
# 'PatientDoB'
set_if_present('PatientDoB', dcmdata.dcm_data.PatientBirthDate)
# 'PatientSex'
set_if_present('PatientSex', dcmdata.dcm_data.PatientSex)
# # 5.5 Provenance and conversion metadata
# 'ConversionMethod'
obj.set_standard_def('ConversionMethod', f'spec2nii v{spec2nii_ver}')
# 'ConversionTime'
conversion_time = datetime.now().isoformat(sep='T', timespec='milliseconds')
obj.set_standard_def('ConversionTime', conversion_time)
# 'OriginalFile'
# Set elsewhere
# # 5.6 Spatial information
# 'kSpace'
obj.set_standard_def('kSpace', [False, False, False])
return obj
