def tractography_from_trackvis_file(filename):
tracts_and_data, header = trackvis.read(filename, points_space='rasmm')
tracts, scalars, properties = izip(*tracts_and_data)
scalar_names = [n for n in header['scalar_name'] if len(n) > 0]
#scalar_names_unique = []
#scalar_names_subcomp = {}
#for sn in scalar_names:
# if re.match('.*_[0-9]{2}', sn):
# prefix = sn[:sn.rfind('_')]
# if prefix not in scalar_names_unique:
# scalar_names_unique.append(prefix)
# scalar_names_subcomp[prefix] = int(sn[-2:])
# scalar_names_subcomp[prefix] = max(sn[-2:], scalar_names_subcomp[prefix])
# else:
# scalar_names_unique.append(sn)
tracts_data = {}
for i, sn in enumerate(scalar_names):
tracts_data[sn] = [scalar[:, i][:, None] for scalar in scalars]
affine = header['vox_to_ras']
image_dims = header['dim']
tr = Tractography(tracts, tracts_data)
tr.affine = affine
tr.image_dims = image_dims
return tr
def tractography_from_vtk_files(vtk_file_names):
tr = Tractography()
if isinstance(vtk_file_names, str):
vtk_file_names = [vtk_file_names]
for file_name in vtk_file_names:
tracts = read_vtkPolyData(file_name)
tr.append(tracts.tracts(), tracts.tracts_data())
return tr
def tractography_from_vtk_files(vtk_file_names):
tr = Tractography()
if isinstance(vtk_file_names, str):
vtk_file_names = [vtk_file_names]
for file_name in vtk_file_names:
tracts = read_vtkPolyData(file_name)
tr.append(tracts.tracts(), tracts.tracts_data())
return tr
def vtkPolyData_to_tracts(polydata, return_tractography_object=True):
r'''
Reads a VTKPolyData object and outputs a tracts/tracts_data pair
Parameters
----------
polydata : vtkPolyData
VTKPolyData Object
Returns
-------
tracts : list of float array N_ix3
Each element of the list is a tract represented as point array,
the length of the i-th tract is N_i
tract_data : dict of <data name>= list of float array of N_ixM
Each element in the list corresponds to a tract,
N_i is the length of the i-th tract and M is the
number of components of that data type.
'''
result = {}
result['lines'] = ns.vtk_to_numpy(polydata.GetLines().GetData())
result['points'] = ns.vtk_to_numpy(polydata.GetPoints().GetData())
result['numberOfLines'] = polydata.GetNumberOfLines()
data = {}
if polydata.GetPointData().GetScalars():
data['ActiveScalars'] = polydata.GetPointData().GetScalars().GetName()
if polydata.GetPointData().GetVectors():
data['ActiveVectors'] = polydata.GetPointData().GetVectors().GetName()
if polydata.GetPointData().GetTensors():
data['ActiveTensors'] = polydata.GetPointData().GetTensors().GetName()
for i in xrange(polydata.GetPointData().GetNumberOfArrays()):
array = polydata.GetPointData().GetArray(i)
np_array = ns.vtk_to_numpy(array)
if np_array.ndim == 1:
np_array = np_array.reshape(len(np_array), 1)
data[polydata.GetPointData().GetArrayName(i)] = np_array
result['pointData'] = data
tracts, data = vtkPolyData_dictionary_to_tracts_and_data(result)
if return_tractography_object:
tr = Tractography()
tr.append(tracts, data)
return tr
else:
return tracts, data
def vtkPolyData_to_tracts(polydata, return_tractography_object=True):
r'''
Reads a VTKPolyData object and outputs a tracts/tracts_data pair
Parameters
----------
polydata : vtkPolyData
VTKPolyData Object
Returns
-------
tracts : list of float array N_ix3
Each element of the list is a tract represented as point array,
the length of the i-th tract is N_i
tract_data : dict of <data name>= list of float array of N_ixM
Each element in the list corresponds to a tract,
N_i is the length of the i-th tract and M is the
number of components of that data type.
'''
result = {}
result['lines'] = ns.vtk_to_numpy(polydata.GetLines().GetData())
result['points'] = ns.vtk_to_numpy(polydata.GetPoints().GetData())
result['numberOfLines'] = polydata.GetNumberOfLines()
data = {}
if polydata.GetPointData().GetScalars():
data['ActiveScalars'] = polydata.GetPointData().GetScalars().GetName()
if polydata.GetPointData().GetVectors():
data['ActiveVectors'] = polydata.GetPointData().GetVectors().GetName()
if polydata.GetPointData().GetTensors():
data['ActiveTensors'] = polydata.GetPointData().GetTensors().GetName()
for i in xrange(polydata.GetPointData().GetNumberOfArrays()):
array = polydata.GetPointData().GetArray(i)
np_array = ns.vtk_to_numpy(array)
if np_array.ndim == 1:
np_array = np_array.reshape(len(np_array), 1)
data[polydata.GetPointData().GetArrayName(i)] = np_array
result['pointData'] = data
tracts, data = vtkPolyData_dictionary_to_tracts_and_data(result)
if return_tractography_object:
tr = Tractography()
tr.append(tracts, data)
return tr
else:
return tracts, data
def tractography_from_vtkPolyData(polydata):
tractography = Tractography()
tractography._originalFibers = []
tractography._tractData = {}
tractography._originalLines = []
tractography._originalData = {}
tractography._tracts = []
lines, lines_ids, point_data = vtkPolyData_to_lines(polydata)
tractography._tracts = lines
tractography._tractData = point_data
tractography._originalFibers = np.vstack(lines)
tractography._originalLines = lines_ids
tractography._originalData = dict(
((key, np.vstack(value)) for key, value in tractography._tractData))
def tractography_from_vtkPolyData(polydata):
tractography = Tractography()
tractography._originalFibers = []
tractography._tractData = {}
tractography._originalLines = []
tractography._originalData = {}
tractography._tracts = []
lines, lines_ids, point_data = vtkPolyData_to_lines(polydata)
tractography._tracts = lines
tractography._tractData = point_data
tractography._originalFibers = np.vstack(lines)
tractography._originalLines = lines_ids
tractography._originalData = dict((
(key, np.vstack(value))
for key, value in tractography._tractData
))