def import_interfile_volume_data(
headerfile='',
datafile=''): #FIXME: this should be in the Interfile package
F = Interfile.load(headerfile)
if F.has_key('matrix size[1]'):
Nx = F['matrix size[1]']['value']
Ny = F['matrix size[2]']['value']
Nz = F['matrix size[3]']['value']
else:
Nx = F['matrix size [1]']['value']
Ny = F['matrix size [2]']['value']
Nz = F['matrix size [3]']['value']
if datafile == '':
datafile1 = headerfile.replace(
headerfile.split(os.sep)[-1], F['name of data file']['value'])
datafile2 = headerfile.replace('.v.hdr', '.v')
datafile2 = datafile2.replace('.h33', '.v')
datafile3 = headerfile.replace('.h33', '.v')
try:
data = fromfile(datafile1, dtype=float32)
except:
try:
data = fromfile(datafile2, dtype=float32)
except:
try:
data = fromfile(datafile3, dtype=float32)
except:
print("Data file not found.")
else:
data = fromfile(datafile, dtype=float32)
data = data.reshape([Nz, Ny, Nx])
data = asfortranarray(data.swapaxes(0, 2))
data = transpose(data, [1, 0, 2])
data = data[::-1, :, :]
return data
def import_interfile_projection_data(headerfile='', datafile=''): #FIXME: this should be in the Interfile package
F = Interfile.load(headerfile)
if F.has_key('matrix size[1]'):
N_planes = F['matrix size[1]']['value']
N_axial = F['matrix size[2]']['value']
N_sinograms = F['matrix size[3]']['value']
else:
N_planes = F['matrix size [1]']['value']
N_axial = F['matrix size [2]']['value']
N_sinograms = F['matrix size [3]']['value']
if datafile == '':
datafile1 = headerfile.replace(headerfile.split(os.sep)[-1],F['name of data file']['value'])
datafile2 = headerfile.replace('.s.hdr','.s')
datafile2 = datafile2.replace('.h33','.a')
datafile3 = headerfile.replace('.h33','.s')
try:
data = fromfile(datafile1,dtype=float32)
except:
try:
data = fromfile(datafile2,dtype=float32)
except:
try:
data = fromfile(datafile3,dtype=float32)
except:
print "Data file not found."
else:
data = fromfile(datafile,dtype=float32)
data = data.reshape([N_sinograms,N_axial,N_planes])
return data
def import_interfile_volume_data(headerfile='', datafile=''): #FIXME: this should be in the Interfile package
F = Interfile.load(headerfile)
if F.has_key('matrix size[1]'):
Nx = F['matrix size[1]']['value']
Ny = F['matrix size[2]']['value']
Nz = F['matrix size[3]']['value']
else:
Nx = F['matrix size [1]']['value']
Ny = F['matrix size [2]']['value']
Nz = F['matrix size [3]']['value']
if datafile == '':
datafile1 = headerfile.replace(headerfile.split(os.sep)[-1],F['name of data file']['value'])
datafile2 = headerfile.replace('.v.hdr','.v')
datafile2 = datafile2.replace('.h33','.v')
datafile3 = headerfile.replace('.h33','.v')
try:
data = fromfile(datafile1,dtype=float32)
except:
try:
data = fromfile(datafile2,dtype=float32)
except:
try:
data = fromfile(datafile3,dtype=float32)
except:
print "Data file not found."
else:
data = fromfile(datafile,dtype=float32)
data = data.reshape([Nz,Ny,Nx])
data = asfortranarray(data.swapaxes(0,2))
data = transpose(data,[1,0,2])
data = data[::-1,:,:]
return data
def __get_interfile(self, dcm):
"""
:param dcm:
:return lm_dict, a dictionary of interfile fields:
"""
from interfile import Interfile
try:
lm_dict = Interfile.load(dcm)
except (AttributeError, TypeError):
raise AssertionError('dcm must be a filename')
return lm_dict
def import_interfile_volume(headerfile='', datafile=''):
# Load ndarray data
data = import_interfile_volume_data(headerfile, datafile)
# Load other information - e.g. pixels size
F = Interfile.load(headerfile)
if F.has_key('scale factor (mm/pixel) [1]'):
pixsize_x = F['scale factor (mm/pixel) [1]']['value']
pixsize_y = F['scale factor (mm/pixel) [2]']['value']
pixsize_z = F['scale factor (mm/pixel) [3]']['value']
# Create Image3D
T_pix_to_world = Transform_Scale(int32([pixsize_x,pixsize_y,pixsize_z]), map_from='pixels_PET', map_to='world')
volume = Image3D(data=data, affine=T_pix_to_world, space='world')
return volume
def import_interfile_volume(headerfile='', datafile=''):
# Load ndarray data
data = import_interfile_volume_data(headerfile, datafile)
# Load other information - e.g. pixels size
F = Interfile.load(headerfile)
if F.has_key('scale factor (mm/pixel) [1]'):
pixsize_x = F['scale factor (mm/pixel) [1]']['value']
pixsize_y = F['scale factor (mm/pixel) [2]']['value']
pixsize_z = F['scale factor (mm/pixel) [3]']['value']
# Create Image3D
T_pix_to_world = Transform_Scale(int32([pixsize_x, pixsize_y, pixsize_z]),
map_from='pixels_PET',
map_to='world')
volume = Image3D(data=data, affine=T_pix_to_world, space='world')
return volume
def import_interfile_projection_data(
headerfile='',
datafile='',
load_time=False): #FIXME: this should be in the Interfile package
F = Interfile.load(headerfile)
if F.has_key('matrix size[1]'):
N_planes = F['matrix size[1]']['value']
N_axial = F['matrix size[2]']['value']
N_sinograms = F['matrix size[3]']['value']
else:
N_planes = F['matrix size [1]']['value']
N_axial = F['matrix size [2]']['value']
N_sinograms = F['matrix size [3]']['value']
if datafile == '':
datafile1 = headerfile.replace(
headerfile.split(os.sep)[-1], F['name of data file']['value'])
datafile2 = headerfile.replace('.s.hdr', '.s')
datafile2 = datafile2.replace('.h33', '.a')
datafile3 = headerfile.replace('.h33', '.s')
try:
data = fromfile(datafile1, dtype=float32)
except:
try:
data = fromfile(datafile2, dtype=float32)
except:
try:
data = fromfile(datafile3, dtype=float32)
except:
print("Data file not found.")
else:
data = fromfile(datafile, dtype=float32)
data = data.reshape([N_sinograms, N_axial, N_planes])
if load_time:
try:
duration = int32([0, F['image duration']['value']]) * 1000
except:
print(
"Unable to load image (sinogram) duration. "
"This may determine an incorrect scale and use of randoms and scatter when reconstructing. "
"Set .time_bins manually. ")
duration = int32([0, 0])
else:
duration = int32([0, 0])
return data, duration
def test_sinogram_parse(self):
"""Parse a simple interfile. """
with open('../examples/parsed_sinogram.pickle', 'rb') as handle:
sino_ref = pickle.load(handle)
sino = Interfile.load('../examples/pet_sinogram.s.hdr')
self.assertEqual(sino_ref, sino)
def test_listmode_parse(self):
"""Parse a simple interfile. """
with open('../examples/parsed_listmode.pickle', 'rb') as handle:
listmode_ref = pickle.load(handle)
listmode = Interfile.load('../examples/pet_listmode.l.hdr')
self.assertEqual(listmode_ref, listmode)