def compute(self):
k = self.getVal('kernel size')
r = self.getVal('calibration region size')
kspace = self.getData('kspace')
# load up arguments list
args = [base_path + '/bart calmat']
args += ['-r ' + str(r)]
args += ['-k ' + str(k)]
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [in1]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('output', out.data())
out.close()
return 0
def compute(self):
kspace = self.getData('kspace')
# load up arguments list
args = [base_path+'/bart nlinv']
if self.getVal('regularization') == 0:
args += ['-l1']
else:
args += ['-l2']
args += ['-i {}'.format(self.getVal('iterations'))]
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl','.hdr'])
args += [in1]
out1 = OFilePath(cfl.readcfl, asuffix=['.cfl','.hdr'])
args += [out1]
out2 = OFilePath(cfl.readcfl, asuffix=['.cfl','.hdr'])
args += [out2]
# run commandline
print(Command(*args))
self.setData('out', out1.data())
self.setData('sensitivities', out2.data())
in1.close()
out1.close()
out2.close()
return 0
def compute(self):
reg = self.getVal('Regularization:')
alpha = self.getVal('regularization parameter')
kspace = self.getData('kspace')
inmaps = self.getData('sensitivities')
# load up arguments list
args = [base_path + '/bart pocsense']
if reg == 0:
args += ['-l1']
else:
args += ['-l2']
args += ['-r ' + str(alpha)]
# setup file for passing data to external command
coords = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [coords]
sens = IFilePath(cfl.writecfl, inmaps, asuffix=['.cfl', '.hdr'])
args += [sens]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('output', out.data())
out.close()
return 0
def compute(self):
x = self.getVal('readout samples')
y = self.getVal('phase encoding lines')
a = self.getVal('acceleration')
t = self.getVal('turns')
r = self.getVal('radial')
g = self.getVal('golden-ratio sampling')
d = self.getVal('double base angle')
# load up arguments list
args = [base_path + '/bart traj']
args += ['-x ' + str(x)]
args += ['-y ' + str(y)]
args += ['-a ' + str(a)]
args += ['-t ' + str(t)]
args += r * ['-r']
args += g * ['-G']
args += d * ['-D']
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('out1', out.data())
out.close()
return 0
def compute(self):
e = self.getVal('SVD Econ')
inp = self.getData('input')
# load up arguments list
args = [base_path + '/bart svd']
if e:
args += ['-e']
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, inp, asuffix=['.cfl', '.hdr'])
args += [in1]
# setup file for getting data from external command
out1 = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out1]
out2 = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out2]
out3 = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out3]
# run commandline
print(Command(*args))
self.setData('U', out1.data())
self.setData('S', out2.data())
self.setData('VH', out3.data())
out1.close()
out2.close()
out3.close()
return 0
def compute(self):
if self.getVal('compute'):
direction = self.getVal('direction')
bm = self.getVal('bitmask')
kspace = self.getData('input')
# load up arguments list
args = [base_path + '/cdf97']
if direction != 0:
args += ['-i']
args += [str(bm)]
in1 = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [in1]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('output', out.data())
out.close()
return 0
def compute(self):
kspace = self.getData('kspace')
# load up arguments list
args = [base_path + '/bart homodyne']
args += [str(self.getVal('dim'))]
args += [str(self.getVal('fraction'))]
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [in1]
out1 = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out1]
# run commandline
print(Command(*args))
self.setData('out', out1.data())
in1.close()
out1.close()
return 0
def compute(self):
j = self.getVal('thresholding bitmask')
lamda = self.getVal('lambda')
inp = self.getData('input')
# load up arguments list
args = [base_path + '/bart threshold']
args += ['-j ' + str(j)]
args += [str(lamda)]
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, inp, asuffix=['.cfl', '.hdr'])
args += [in1]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('output', out.data())
out.close()
return 0
def compute(self):
# load up arguments list
args = [base_path + '/bart poisson']
args += ['-Y {}'.format(self.getVal('y size'))]
args += ['-Z {}'.format(self.getVal('z size'))]
args += ['-y {}'.format(self.getVal('y accel'))]
args += ['-z {}'.format(self.getVal('z accel'))]
args += ['-C {}'.format(self.getVal('cal size'))]
if self.getVal('variable density'):
args += ['-v']
if self.getVal('elliptical'):
args += ['-e']
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('out', out.data())
out.close()
return 0
def compute(self):
i = self.getVal('iterations')
s = self.getVal('relative subspace size')
kspace = self.getData('kspace')
# load up arguments list
args = [base_path + '/bart sake']
args += [str(i)]
args += [str(s)]
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [in1]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('output', out.data())
out.close()
return 0
def compute(self):
f = self.getVal('factor')
indata = self.getData('in')
# load up arguments list
args = [base_path+'/bart scale']
args += [str(f)]
# setup file for passing data to external command
inp = IFilePath(cfl.writecfl, indata, asuffix=['.cfl','.hdr'])
args += [inp]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl','.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('out', out.data())
out.close()
inp.close()
return 0
def compute(self):
t = self.getVal('threshold')
c = self.getVal('crop value')
k = self.getVal('kernel size')
r = self.getVal('calibration size')
m = self.getVal('number maps')
I = self.getVal('intensity correction')
first = self.getVal('1st part only')
kspace = self.getData('kspace')
# load up arguments list
args = [base_path+'/bart ecalib']
args += ['-t '+str(t)]
args += ['-c '+str(c)]
args += ['-k '+str(k)]
args += ['-r '+str(r)]
args += ['-m '+str(m)]
if I:
args += ['-I']
if first:
args += ['-1']
# setup file for passing data to external command
in1 = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl','.hdr'])
args += [in1]
out1 = OFilePath(cfl.readcfl, asuffix=['.cfl','.hdr'])
args += [out1]
if not first:
out2 = OFilePath(cfl.readcfl, asuffix=['.cfl','.hdr'])
args += [out2]
# run commandline
print(Command(*args))
if first:
self.setData('imgcov', out1.data())
else:
self.setData('sensitivities', out1.data())
out1.close()
if not first:
self.setData('ev_maps', out2.data())
out2.close()
in1.close()
return 0
def compute(self):
adjoint = self.getVal('adjoint')
inverse = self.getVal('inverse')
dimensions = self.getVal('dimensions')
toeplitz = self.getVal('toeplitz')
lmbda = self.getVal('lambda')
kspace = self.getData('input')
traj = self.getData('traj')
# load up arguments list
args = [base_path + '/bart nufft']
args += ['-l ' + str(lmbda)]
if adjoint:
args += ['-a']
if inverse:
args += ['-i']
if toeplitz:
args += ['-t']
if dimensions != '':
try:
dims = re.search('^([0-9]*):([0-9]*):([0-9]*)$',
dimensions).groups()
args += ['-d ' + ':'.join(dims)]
except:
self.log.warn(
'\'dimensions\' must be a list of positive integers delimited by colons (i.e. int:int:int), skipping...'
)
# setup file for passing data to external command
in_traj = IFilePath(cfl.writecfl, traj, asuffix=['.cfl', '.hdr'])
in_kspc = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [in_traj, in_kspc]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('output', out.data())
out.close()
in_traj.close()
in_kspc.close()
return 0
def compute(self):
kspace = self.getData('kspace')
coil_maps = self.getData('coil_maps')
trajectory = self.getData('traj')
reg = self.getVal('regularization')
lamb = self.getVal('lamb')
# load up arguments list
args = [base_path + '/bart pics']
if reg == 0:
args += ['-l1']
else:
args += ['-l2']
args += ['-r {}'.format(lamb)]
args += ['-e -i 100']
# setup file for getting data from external command
if trajectory is not None:
traj = IFilePath(cfl.writecfl,
trajectory,
asuffix=['.cfl', '.hdr'])
args += ['-t', traj]
kspace = IFilePath(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
coil_maps = IFilePath(cfl.writecfl,
coil_maps,
asuffix=['.cfl', '.hdr'])
output = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [kspace, coil_maps, output]
print(Command(*args))
self.setData('output', output.data())
if trajectory is not None:
traj.close()
kspace.close()
coil_maps.close()
output.close()
return 0
def compute(self):
p = self.getVal('virtual channels')
r = self.getVal('calibration size')
a = self.getVal('Use All Data')
comptype = self.getVal('Compression Type:')
kspace = self.getData('kspace')
coeff = self.getData('coeff')
# load up arguments list
args = [base_path + '/bart cc']
args += ['-P ' + str(p)]
args += ['-r ' + str(r)]
if a:
args += ['-A']
if comptype == 0:
args += ['-S']
elif comptype == 1:
args += ['-G']
else:
args += ['-E']
# setup file for passing data to external command
in1 = IFile(cfl.writecfl, kspace, asuffix=['.cfl', '.hdr'])
args += [in1]
in2 = IFile(cfl.writecfl, coeff, asuffix=['.cfl', '.hdr'])
args += [in2]
# setup file for getting data from external command
out = OFile(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('proj_kspace', out.data())
out.close()
return 0
def compute(self):
# load up arguments list
args = [base_path + '/bart phantom']
args += ['-s {}'.format(self.getVal('num_coils'))]
if self.getVal('kspace'):
args += ['-k']
traj = self.getData('traj')
if traj is not None:
traj_file = IFilePath(cfl.writecfl, traj, asuffix=['.cfl', '.hdr'])
args += ['-t', traj_file]
# setup file for getting data from external command
out = OFilePath(cfl.readcfl, asuffix=['.cfl', '.hdr'])
args += [out]
# run commandline
print(Command(*args))
self.setData('out1', out.data())
out.close()
return 0