def loadmod(self):
cmd = '%s modlist ; mv mod.xml %s' % (self.Jcall, workspace())
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, shell=True)
out, err = proc.communicate()
fname = os.path.join(workspace(), 'mod.xml')
mod(fname)
return fname
def __init__(self, fname):
# = DxDy (sometimes given as scalar)
self.RES = np.array([1., 1., 1.])[:, None]
# is a shift in each dimension
self.OFF = np.array([0., 0., 0.])[:, None]
self.labelPhantom = dict()
self.labelPhantom['active'] = False
self.labelMatrix = dict()
self.labelMatrix['active'] = False
self.mapsComputed = False
self.sfacs = dict() # scaling factors
for key in ['M0', 'T1', 'T2', 'T2s', 'CS', 'Xi']:
self.sfacs[key] = 1
if fname is not None:
self.rename(fname)
else:
self.rename(os.path.join(workspace(), 'new_phantom.h5'))
self.tmpname = True
self.geometricPhantoms = ['Sphere', 'Spheres', 'Cylinder', 'Revolver']
print('init', fname)
def __init__(self, fname):
# Defaults.
model = {'name': 'Bloch',
'type': 'CVODE'}
parameter = {'ConcomitantFields': '0',
'EvolutionPrefix': 'evol',
'EvolutionSteps': '0',
'RandomNoise': '0'}
# self.sim = dict()
self.sim = {'sample': dict(),
'sequence': dict(),
'RXcoilarray': dict(),
'TXcoilarray': dict(),
'model': model,
'parameter': parameter}
self.data = None
self.channels = []
if fname is not None:
self.rename(fname)
else:
self.rename(os.path.join(workspace(), 'new_simulation.xml'))
self.tmpname = True
self.setSequence('')
self.setSample('')
self.setTxCoilArray('')
self.setRxCoilArray('')
def updateXML(self):
Instance = self.Instance
tmp = Instance.fname
Instance.rename(os.path.join(workspace(), 'tmp.xml'))
Instance.save()
self.readXML()
Instance.rename(tmp)
def __init__(self, attr, fname=None):
self.attr = attr
self.data = None
if fname is not None:
self.rename(fname)
else:
self.rename(os.path.join(workspace(), 'new_array.xml'))
self.tmpname = True
def __init__(self, attr, fname=None):
self.attr = attr
self.data = None
if fname is not None:
self.rename(fname)
else:
self.rename(os.path.join(workspace(), 'new_sequence.xml'))
self.tmpname = True
self.xml = Element(self.attr, None)