def save_polydata(polydata, file_name, binary=False, color_array_name=None):
"""Save a vtk polydata to a supported format file.
Save formats can be VTK, FIB, PLY, STL and XML.
Parameters
----------
polydata : vtkPolyData
file_name : string
"""
# get file extension (type)
file_extension = file_name.split(".")[-1].lower()
if file_extension == "vtk":
writer = vtk.vtkPolyDataWriter()
elif file_extension == "fib":
writer = vtk.vtkPolyDataWriter()
elif file_extension == "ply":
writer = vtk.vtkPLYWriter()
elif file_extension == "stl":
writer = vtk.vtkSTLWriter()
elif file_extension == "xml":
writer = vtk.vtkXMLPolyDataWriter()
elif file_extension == "obj":
raise Exception("mni obj or Wavefront obj ?")
# writer = utils.set_input(vtk.vtkMNIObjectWriter(), polydata)
writer.SetFileName(file_name)
writer = utils.set_input(writer, polydata)
if color_array_name is not None:
writer.SetArrayName(color_array_name)
if binary:
writer.SetFileTypeToBinary()
writer.Update()
writer.Write()
def save_polydata(polydata, file_name, binary=False, color_array_name=None):
"""Save a vtk polydata to a supported format file.
Save formats can be VTK, FIB, PLY, STL and XML.
Parameters
----------
polydata : vtkPolyData
file_name : string
"""
# get file extension (type)
file_extension = file_name.split(".")[-1].lower()
if file_extension == "vtk":
writer = vtk.vtkPolyDataWriter()
elif file_extension == "fib":
writer = vtk.vtkPolyDataWriter()
elif file_extension == "ply":
writer = vtk.vtkPLYWriter()
elif file_extension == "stl":
writer = vtk.vtkSTLWriter()
elif file_extension == "xml":
writer = vtk.vtkXMLPolyDataWriter()
elif file_extension == "obj":
raise Exception("mni obj or Wavefront obj ?")
# writer = utils.set_input(vtk.vtkMNIObjectWriter(), polydata)
writer.SetFileName(file_name)
writer = utils.set_input(writer, polydata)
if color_array_name is not None:
writer.SetArrayName(color_array_name)
if binary:
writer.SetFileTypeToBinary()
writer.Update()
writer.Write()
def save_vtk_streamlines(streamlines, filename, to_lps=True, binary=False):
"""Save streamlines as vtk polydata to a supported format file.
File formats can be VTK, FIB
Parameters
----------
streamlines : list
list of 2D arrays or ArraySequence
filename : string
output filename (.vtk or .fib)
to_lps : bool
Default to True, will follow the vtk file convention for streamlines
Will be supported by MITKDiffusion and MI-Brain
binary : bool
save the file as binary
"""
if to_lps:
# ras (mm) to lps (mm)
to_lps = np.eye(4)
to_lps[0, 0] = -1
to_lps[1, 1] = -1
streamlines = transform_streamlines(streamlines, to_lps)
# Get the 3d points_array
nb_lines = len(streamlines)
points_array = np.vstack(streamlines)
# Get lines_array in vtk input format
lines_array = []
current_position = 0
for i in range(nb_lines):
current_len = len(streamlines[i])
end_position = current_position + current_len
lines_array.append(current_len)
lines_array.extend(range(current_position, end_position))
current_position = end_position
# Set Points to vtk array format
vtk_points = vtk.vtkPoints()
vtk_points.SetData(
ns.numpy_to_vtk(points_array.astype(np.float32), deep=True))
# Set Lines to vtk array format
vtk_lines = vtk.vtkCellArray()
vtk_lines.SetNumberOfCells(nb_lines)
vtk_lines.GetData().DeepCopy(
ns.numpy_to_vtk(np.array(lines_array), deep=True))
# Create the poly_data
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
polydata.SetLines(vtk_lines)
writer = vtk.vtkPolyDataWriter()
writer.SetFileName(filename)
writer = utils.set_input(writer, polydata)
if binary:
writer.SetFileTypeToBinary()
writer.Update()
writer.Write()