def get_phase_encoding_direction(self, dicom_path):
dcm = pydicom.read_file(dicom_path)
inplane_pe_dir = dcm[int('00181312', 16)].value
csa_str = dcm[int('00291010', 16)].value
csa_tr = csareader.read(csa_str)
pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]
sign = PEDP_TO_SIGN[pedp]
return sign, inplane_pe_dir
def test_simplify(self):
eq_(extract.simplify_csa_dict(None), None)
csa_dict = csareader.read(self.data[pydicom.tag.Tag(0x29, 0x1010)].value)
simp_dict = extract.simplify_csa_dict(csa_dict)
for tag in csa_dict['tags']:
items = csa_dict['tags'][tag]['items']
if len(items) == 0:
ok_(not tag in simp_dict)
elif len(items) == 1:
eq_(simp_dict[tag], items[0])
else:
eq_(simp_dict[tag], items)
def test_simplify(self):
eq_(extract.simplify_csa_dict(None), None)
csa_dict = csareader.read(self.data[pydicom.tag.Tag(0x29, 0x1010)].value)
simp_dict = extract.simplify_csa_dict(csa_dict)
for tag in csa_dict['tags']:
items = csa_dict['tags'][tag]['items']
if len(items) == 0:
ok_(not tag in simp_dict)
elif len(items) == 1:
eq_(simp_dict[tag], items[0])
else:
eq_(simp_dict[tag], items)
def get_bids_phase_encoding_direction(dicom_path):
"""Return BIDS PhaseEncodingDirection string (i, j, k, i-, j-, k-) for DICOM at dicom_path.
NOTE: work-in-progress
"""
dcm = pydicom.read_file(dicom_path)
inplane_pe_dir = dcm_pa[int('00181312', 16)].value
csa_str = dcm[int('00291010', 16)].value
csa_tr = csareader.read(csa_str)
pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]
ij = rowcol_to_niftidim[inplane_pe_dir]
sign = pedp_to_sign[pedp]
return '{}{}'.format(ij, sign)
def csa_series_trans_func(elem):
'''Function for parsing the CSA series sub header.'''
csa_dict = simplify_csa_dict(csareader.read(elem.value))
#If there is a phoenix protocol, parse it and dump it into the csa_dict
phx_src = None
if 'MrPhoenixProtocol' in csa_dict:
phx_src = 'MrPhoenixProtocol'
elif 'MrProtocol' in csa_dict:
phx_src = 'MrProtocol'
if not phx_src is None:
phoenix_dict = parse_phoenix_prot(phx_src, csa_dict[phx_src])
del csa_dict[phx_src]
for key, val in iteritems(phoenix_dict):
new_key = '%s.%s' % ('MrPhoenixProtocol', key)
csa_dict[new_key] = val
return csa_dict
def csa_series_trans_func(elem):
'''Function for parsing the CSA series sub header.'''
csa_dict = simplify_csa_dict(csareader.read(elem.value))
#If there is a phoenix protocol, parse it and dump it into the csa_dict
phx_src = None
if 'MrPhoenixProtocol' in csa_dict:
phx_src = 'MrPhoenixProtocol'
elif 'MrProtocol' in csa_dict:
phx_src = 'MrProtocol'
if not phx_src is None:
phoenix_dict = parse_phoenix_prot(phx_src, csa_dict[phx_src])
del csa_dict[phx_src]
for key, val in phoenix_dict.iteritems():
new_key = '%s.%s' % ('MrPhoenixProtocol', key)
csa_dict[new_key] = val
return csa_dict
def csa_image_trans_func(elem):
'''Function for translating the CSA image sub header.'''
return simplify_csa_dict(csareader.read(elem.value))
def csa_image_trans_func(elem):
'''Function for translating the CSA image sub header.'''
return simplify_csa_dict(csareader.read(elem.value))
