def writeMeshFile(triangles, filename, binary=True, verbose=False):
"""Write mesh file.
The output format is determined by file name extension. Files can be written
in binary (default) and ASCII format."""
outformat = path.splitext(options.outfilename)[1].strip('.')
# set writer based on filename extension
if outformat=='stl':
write = vtk.vtkSTLWriter()
elif outformat=='vtk':
write = vtk.vtkPolyDataWriter()
elif outformat=='obj':
write = vtk.vtkMNIObjectWriter()
elif outformat=='tag':
write = vtk.vtkMNITagPointWriter()
else:
raise ValueError('cannot write outpur format' + outformat)
write.SetInputConnection(triangles.GetOutputPort())
if outformat!='tag':
if binary:
if verbose: print 'setting ouptut to binary'
write.SetFileTypeToBinary()
else:
if verbose: print 'setting ouptut to ascii'
write.SetFileTypeToASCII()
write.SetFileName(filename)
err = write.Write()
if err != 1:
raise IOError('failed to write')
if verbose:
print "wrote", filename
pass
def writeMeshFile(triangles, filename, binary=True, verbose=False):
"""Write mesh file.
The output format is determined by file name extension. Files can be written
in binary (default) and ASCII format."""
outformat = path.splitext(options.outfilename)[1].strip('.')
# set writer based on filename extension
if outformat == 'stl':
write = vtk.vtkSTLWriter()
elif outformat == 'vtk':
write = vtk.vtkPolyDataWriter()
elif outformat == 'obj':
write = vtk.vtkMNIObjectWriter()
elif outformat == 'tag':
write = vtk.vtkMNITagPointWriter()
else:
raise ValueError('cannot write outpur format' + outformat)
write.SetInputConnection(triangles.GetOutputPort())
if outformat != 'tag':
if binary:
if verbose: print 'setting ouptut to binary'
write.SetFileTypeToBinary()
else:
if verbose: print 'setting ouptut to ascii'
write.SetFileTypeToASCII()
write.SetFileName(filename)
err = write.Write()
if err != 1:
raise IOError('failed to write')
if verbose:
print "wrote", filename
pass
def save_polydata(polydata,
file_name,
binary=False,
color_array_name=None,
is_mni_obj=False):
"""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
binary : bool
color_array_name: ndarray
is_mni_obj : bool
"""
# 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":
if is_mni_obj:
writer = vtk.vtkMNIObjectWriter()
else:
# vtkObjWriter not available on python
# vtk.vtkOBJWriter()
raise IOError("OBJ Writer not available. MNI obj is the only"
" available writer so set mni_tag option to True")
else:
raise IOError("Unknown extension ({})".format(file_extension))
writer.SetFileName(file_name)
writer = set_input(writer, polydata)
if color_array_name is not None and file_extension == "ply":
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
binary : bool
color_array_name: ndarray
"""
# get file extension (type)
file_extension = file_name.split(".")[-1].lower()
poly_writer = {
"vtk": vtk.vtkPolyDataWriter,
"vtp": vtk.vtkXMLPolyDataWriter,
"fib": vtk.vtkPolyDataWriter,
"ply": vtk.vtkPLYWriter,
"stl": vtk.vtkSTLWriter,
"xml": vtk.vtkXMLPolyDataWriter
}
if file_extension in poly_writer.keys():
writer = poly_writer.get(file_extension)()
elif file_extension == "obj":
# Special case, since there is two obj format
find_keyword = file_name.lower().split(".")
if "mni" in find_keyword or "mnc" in find_keyword:
writer = vtk.vtkMNIObjectWriter()
else:
raise IOError("Wavefront obj requires a scene \n"
" for MNI obj, use '.mni.obj' extension")
else:
raise IOError("." + file_extension + " is not supported by FURY")
writer.SetFileName(file_name)
writer = set_input(writer, polydata)
if color_array_name is not None and file_extension == "ply":
writer.SetArrayName(color_array_name)
if binary:
writer.SetFileTypeToBinary()
writer.Update()
writer.Write()
print(n)
# Extract the output and save it to new folder
for i in range(n):
mesh = out_block.GetBlock(i)
# get id of said
id = str(int(df_apoe_f.iloc[i, :].id_alomar))
# save to disk
rd = vtk.vtkPolyDataWriter()
f1 = mesh_aligned_l + 'out_mesh_' + str(id) + '_l.vtk'
rd.SetInputData(mesh)
rd.SetFileName(f1)
rd.Write()
# SAVE IT ALSO AS .OBJ
obj = vtk.vtkMNIObjectWriter()
f1 = mesh_aligned_l + 'out_mesh_' + str(id) + '_l.obj'
obj.SetInputData(mesh)
obj.SetFileName(f1)
obj.Write()
# Get the mean mesh and save it
polydata = vtk.vtkPolyData()
mean_pts_l = pcra.GetMeanPoints()
test = ExtractVTKPoints(mean_pts_l)
np.save("mean_pts_l.npy", test)
polydata.SetPoints(mean_pts_l)
# polydata.SetPoints(points_l)
polydata.SetPolys(X_left[2].GetPolys())
property1 = asciiReader.GetProperty()
if (asciiReader.CanReadFile(str(filename)) != 0):
asciiReader.SetFileName(str(filename))
# this is just to remove the normals, to increase coverage,
# i.e. by forcing the writer to generate normals
removeNormals = vtk.vtkClipClosedSurface()
removeNormals.SetInputConnection(asciiReader.GetOutputPort())
# this is to make triangle strips, also to increase coverage,
# because it forces the writer to decompose the strips
stripper = vtk.vtkStripper()
stripper.SetInputConnection(removeNormals.GetOutputPort())
# test binary writing and reading for polygons
binaryWriter = vtk.vtkMNIObjectWriter()
binaryWriter.SetInputConnection(stripper.GetOutputPort())
binaryWriter.SetFileName("mni-surface-mesh-binary.obj")
binaryWriter.SetProperty(property0)
binaryWriter.SetFileTypeToBinary()
binaryWriter.Write()
binaryReader = vtk.vtkMNIObjectReader()
binaryReader.SetFileName("mni-surface-mesh-binary.obj")
property2 = binaryReader.GetProperty()
# make a polyline object with color scalars
scalars = vtk.vtkCurvatures()
scalars.SetInputConnection(asciiReader.GetOutputPort())
property1 = asciiReader.GetProperty()
if (asciiReader.CanReadFile(str(filename)) != 0):
asciiReader.SetFileName(str(filename))
# this is just to remove the normals, to increase coverage,
# i.e. by forcing the writer to generate normals
removeNormals = vtk.vtkClipClosedSurface()
removeNormals.SetInputConnection(asciiReader.GetOutputPort())
# this is to make triangle strips, also to increase coverage,
# because it forces the writer to decompose the strips
stripper = vtk.vtkStripper()
stripper.SetInputConnection(removeNormals.GetOutputPort())
# test binary writing and reading for polygons
binaryWriter = vtk.vtkMNIObjectWriter()
binaryWriter.SetInputConnection(stripper.GetOutputPort())
binaryWriter.SetFileName("mni-surface-mesh-binary.obj")
binaryWriter.SetProperty(property0)
binaryWriter.SetFileTypeToBinary()
binaryWriter.Write()
binaryReader = vtk.vtkMNIObjectReader()
binaryReader.SetFileName("mni-surface-mesh-binary.obj")
property2 = binaryReader.GetProperty()
# make a polyline object with color scalars
scalars = vtk.vtkCurvatures()
scalars.SetInputConnection(asciiReader.GetOutputPort())
