def readMeshFile(filename, verbose=False):
"""Read mesh file.
The input format is determined by file name extension. Degenerate data gets
removed and polygons get split into triangles to support varios restrictive
output formats."""
informat = path.splitext(options.infilename)[1].strip('.')
# set reader based on filename extension
if informat == 'stl':
reader = vtk.vtkSTLReader()
elif informat == 'vtk':
reader = vtk.vtkPolyDataReader()
elif informat == 'obj':
reader = vtk.vtkMNIObjectReader()
#elif informat=='tag':
# reader = vtk.vtkMNITagPointReader()
else:
raise ValueError('cannot read input format' + informat)
reader.SetFileName(filename)
# merge duplicate points, and/or remove unused points and/or remove degenerate cells
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(reader.GetOutputPort())
# convert input polygons and strips to triangles
triangles = vtk.vtkTriangleFilter()
triangles.SetInputConnection(clean.GetOutputPort())
#triangles = reader.GetOutputPort() # skipping above 'cleaning' doesn't work
if verbose:
print "read", filename
return triangles
def readMeshFile(filename, verbose=False):
"""Read mesh file.
The input format is determined by file name extension. Degenerate data gets
removed and polygons get split into triangles to support varios restrictive
output formats."""
informat = path.splitext(options.infilename)[1].strip('.')
# set reader based on filename extension
if informat=='stl':
reader = vtk.vtkSTLReader()
elif informat=='vtk':
reader = vtk.vtkPolyDataReader()
elif informat=='obj':
reader = vtk.vtkMNIObjectReader()
#elif informat=='tag':
# reader = vtk.vtkMNITagPointReader()
else:
raise ValueError('cannot read input format' + informat)
reader.SetFileName(filename)
# merge duplicate points, and/or remove unused points and/or remove degenerate cells
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(reader.GetOutputPort())
# convert input polygons and strips to triangles
triangles = vtk.vtkTriangleFilter()
triangles.SetInputConnection(clean.GetOutputPort())
#triangles = reader.GetOutputPort() # skipping above 'cleaning' doesn't work
if verbose:
print "read", filename
return triangles
def load_polydata(file_name, is_mni_obj=False):
"""Load a vtk polydata to a supported format file.
Supported file formats are OBJ, VTK, FIB, PLY, STL and XML
Parameters
----------
file_name : string
is_mni_obj : bool
Returns
-------
output : vtkPolyData
"""
# get file extension (type) lower case
file_extension = file_name.split(".")[-1].lower()
if file_extension == "vtk":
reader = vtk.vtkPolyDataReader()
elif file_extension == "fib":
reader = vtk.vtkPolyDataReader()
elif file_extension == "ply":
reader = vtk.vtkPLYReader()
elif file_extension == "stl":
reader = vtk.vtkSTLReader()
elif file_extension == "xml":
reader = vtk.vtkXMLPolyDataReader()
elif file_extension == "obj" and is_mni_obj:
reader = vtk.vtkMNIObjectReader()
elif file_extension == "obj":
try: # try to read as a normal obj
reader = vtk.vtkOBJReader()
except Exception: # than try load a MNI obj format
reader = vtk.vtkMNIObjectReader()
else:
raise IOError("polydata " + file_extension + " is not suported")
reader.SetFileName(file_name)
reader.Update()
return reader.GetOutput()
def readPolydata(file_name):
""" Load a vtk polydata to a supported format file
Parameters
----------
file_name : string
Returns
-------
output : vtkPolyData
"""
# get file extension (type) lower case
file_extension = file_name.split(".")[-1].lower()
if file_extension == "vtk":
try:
return readLegacyVTK(file_name)[0]
except:
reader = vtk.vtkPolyDataReader()
elif file_extension == "fib":
reader = vtk.vtkPolyDataReader()
elif file_extension == "ply":
reader = vtk.vtkPLYReader()
elif file_extension == "stl":
reader = vtk.vtkSTLReader()
elif file_extension == "vtp":
reader = vtk.vtkXMLPolyDataReader()
elif file_extension == "vti":
return readDataSet(file_name, vtk.vtkXMLImageDataReader)
elif file_extension == "vts":
return readDataSet(file_name, vtk.vtkXMLStructuredGridReader)
elif file_extension == "vtu":
return readDataSet(file_name, vtk.vtkXMLUnstructuredGridReader)
elif file_extension == "vtr":
return readDataSet(file_name, vtk.vtkXMLRectilinearGridReader)
elif file_extension == "xml":
reader = vtk.vtkXMLPolyDataReader()
elif file_extension == "obj":
try: # try to read as a normal obj
reader = vtk.vtkOBJReader()
except: # than try load a MNI obj format
reader = vtk.vtkMNIObjectReader()
else:
raise Exception("polydata " + file_extension + " is not suported")
reader.SetFileName(file_name)
reader.Update()
return reader.GetOutput()
def load_polydata(file_name):
"""Load a vtk polydata to a supported format file.
Supported file formats are VTK, VTP, FIB, PLY, STL XML and OBJ
Parameters
----------
file_name : string
Returns
-------
output : vtkPolyData
"""
file_extension = file_name.split(".")[-1].lower()
poly_reader = {
"vtk": vtk.vtkPolyDataReader,
"vtp": vtk.vtkXMLPolyDataWriter,
"fib": vtk.vtkPolyDataReader,
"ply": vtk.vtkPLYReader,
"stl": vtk.vtkSTLReader,
"xml": vtk.vtkXMLPolyDataReader
}
if file_extension in poly_reader.keys():
reader = poly_reader.get(file_extension)()
elif file_extension == "obj":
# Special case, since there is two obj format
reader = vtk.vtkOBJReader()
reader.SetFileName(file_name)
reader.Update()
if reader.GetOutput().GetNumberOfCells() == 0:
reader = vtk.vtkMNIObjectReader()
else:
raise IOError("." + file_extension + " is not supported by FURY")
reader.SetFileName(file_name)
reader.Update()
return reader.GetOutput()
def addColors(infilename, outfilename, colorfilename=None, colorstring=None,
binary=True, verbose=False):
"""add color array"""
outformat = path.splitext(outfilename)[1].strip('.')
if outformat!='ply':
raise ValueError('colors are only supported for PLY format')
informat = path.splitext(infilename)[1].strip('.')
# set reader based on filename extension
if informat=='stl':
reader = vtk.vtkSTLReader()
elif informat=='vtk':
reader = vtk.vtkPolyDataReader()
elif informat=='obj':
reader = vtk.vtkMNIObjectReader()
elif informat=='ply':
reader = vtk.vtkPLYReader()
elif informat=='vtp':
reader = vtk.vtkXMLPolyDataReader()
else:
raise ValueError('cannot read input format: ' + informat)
reader.SetFileName(infilename)
reader.Update()
#N = reader.GetOutput().GetNumberOfPolys()
N = reader.GetOutput().GetNumberOfPoints()
if verbose:
print("read %i points (vertices)" % (N,))
if colorfilename:
colorar = readColorFile(colorfilename)
if N != colorar.shape[0]:
raise ValueError('number of rows in color file does not match' +
'number of points in mesh file')
elif colorstring:
color = [int(i) for i in colorstring.split()]
colorar = np.ones((N,3)) * np.array(color)
Colors = vtk.vtkUnsignedCharArray()
Colors.SetNumberOfComponents(3)
Colors.SetName("Colors")
for i in range(0,N):
Colors.InsertNextTuple3(*colorar[i,:])
polydata = vtk.vtkPolyData()
polydata = reader.GetOutput()
polydata.GetPointData().SetScalars(Colors)
polydata.Modified()
writer = vtk.vtkPLYWriter()
writer.SetArrayName("Colors")
writer.SetInputData(polydata)
writer.SetFileName(outfilename)
if binary:
if verbose: print('setting output to binary')
writer.SetFileTypeToBinary()
else:
if verbose: print('setting output to ascii')
writer.SetFileTypeToASCII()
err = writer.Write()
def readMeshFile(filename, clean=True, verbose=False, recompute_normals=True):
"""Read mesh file.
The input format is determined by file name extension.
Polygons get split into triangles to support various restrictive output
formats.
If clean, degenerate data gets removed."""
informat = path.splitext(options.infilename)[1].strip('.')
# set reader based on filename extension
if informat=='stl':
reader = vtk.vtkSTLReader()
elif informat=='vtk':
reader = vtk.vtkPolyDataReader()
elif informat=='obj':
reader = vtk.vtkMNIObjectReader()
elif informat=='ply':
reader = vtk.vtkPLYReader()
elif informat=='vtp':
reader = vtk.vtkXMLPolyDataReader()
#elif informat=='tag':
# reader = vtk.vtkMNITagPointReader()
else:
raise ValueError('cannot read input format: ' + informat)
reader.SetFileName(filename)
reader.Update()
if verbose:
print("read %i polygons from file %s" % \
(reader.GetOutput().GetNumberOfPolys(), filename))
# merge duplicate points, and/or remove unused points and/or remove degenerate cells
if clean:
polydata = vtk.vtkCleanPolyData()
polydata.SetInputConnection(reader.GetOutputPort())
poly_data_algo = polydata
if verbose:
print("cleaned poly data")
else:
poly_data_algo = reader
# convert input polygons and strips to triangles
triangles = vtk.vtkTriangleFilter()
triangles.SetInputConnection(poly_data_algo.GetOutputPort())
if recompute_normals:
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(triangles.GetOutputPort())
normals.SplittingOff()
normals.ComputePointNormalsOn()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.NonManifoldTraversalOn()
if verbose:
print("recomputed normals")
print("finished reading", filename)
return normals
else:
if verbose:
print("finished reading", filename)
return triangles
ren1 = vtk.vtkRenderer()
ren1.SetViewport(0, 0, 0.33, 1)
ren2 = vtk.vtkRenderer()
ren2.SetViewport(0.33, 0, 0.67, 1)
ren3 = vtk.vtkRenderer()
ren3.SetViewport(0.67, 0, 1, 1)
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600, 200)
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
renWin.SetMultiSamples(0)
property0 = vtk.vtkProperty()
property0.SetDiffuseColor(0.95, 0.90, 0.70)
filename = VTK_DATA_ROOT + "/Data/mni-surface-mesh.obj"
asciiReader = vtk.vtkMNIObjectReader()
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
ren1 = vtk.vtkRenderer()
ren1.SetViewport(0, 0, 0.33, 1)
ren2 = vtk.vtkRenderer()
ren2.SetViewport(0.33, 0, 0.67, 1)
ren3 = vtk.vtkRenderer()
ren3.SetViewport(0.67, 0, 1, 1)
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600, 200)
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
renWin.SetMultiSamples(0)
property0 = vtk.vtkProperty()
property0.SetDiffuseColor(0.95, 0.90, 0.70)
filename = VTK_DATA_ROOT + "/Data/mni-surface-mesh.obj"
asciiReader = vtk.vtkMNIObjectReader()
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
def addColors(infilename,
outfilename,
colorfilename=None,
colorstring=None,
binary=True,
verbose=False):
"""add color array"""
outformat = path.splitext(outfilename)[1].strip('.')
if outformat != 'ply':
raise ValueError('colors are only supported for PLY format')
informat = path.splitext(infilename)[1].strip('.')
# set reader based on filename extension
if informat == 'stl':
reader = vtk.vtkSTLReader()
elif informat == 'vtk':
reader = vtk.vtkPolyDataReader()
elif informat == 'obj':
reader = vtk.vtkMNIObjectReader()
elif informat == 'ply':
reader = vtk.vtkPLYReader()
elif informat == 'vtp':
reader = vtk.vtkXMLPolyDataReader()
else:
raise ValueError('cannot read input format: ' + informat)
reader.SetFileName(infilename)
reader.Update()
#N = reader.GetOutput().GetNumberOfPolys()
N = reader.GetOutput().GetNumberOfPoints()
if verbose:
print("read %i points (vertices)" % (N, ))
if colorfilename:
colorar = readColorFile(colorfilename)
if N != colorar.shape[0]:
raise ValueError('number of rows in color file does not match' +
'number of points in mesh file')
elif colorstring:
color = [int(i) for i in colorstring.split()]
colorar = np.ones((N, 3)) * np.array(color)
Colors = vtk.vtkUnsignedCharArray()
Colors.SetNumberOfComponents(3)
Colors.SetName("Colors")
for i in range(0, N):
Colors.InsertNextTuple3(*colorar[i, :])
polydata = vtk.vtkPolyData()
polydata = reader.GetOutput()
polydata.GetPointData().SetScalars(Colors)
polydata.Modified()
writer = vtk.vtkPLYWriter()
writer.SetArrayName("Colors")
writer.SetInputData(polydata)
writer.SetFileName(outfilename)
if binary:
if verbose: print('setting output to binary')
writer.SetFileTypeToBinary()
else:
if verbose: print('setting output to ascii')
writer.SetFileTypeToASCII()
err = writer.Write()
def readMeshFile(filename, clean=True, verbose=False, recompute_normals=True):
"""Read mesh file.
The input format is determined by file name extension.
Polygons get split into triangles to support various restrictive output
formats.
If clean, degenerate data gets removed."""
informat = path.splitext(options.infilename)[1].strip('.')
# set reader based on filename extension
if informat == 'stl':
reader = vtk.vtkSTLReader()
elif informat == 'vtk':
reader = vtk.vtkPolyDataReader()
elif informat == 'obj':
reader = vtk.vtkMNIObjectReader()
elif informat == 'ply':
reader = vtk.vtkPLYReader()
elif informat == 'vtp':
reader = vtk.vtkXMLPolyDataReader()
#elif informat=='tag':
# reader = vtk.vtkMNITagPointReader()
else:
raise ValueError('cannot read input format: ' + informat)
reader.SetFileName(filename)
reader.Update()
if verbose:
print("read %i polygons from file %s" % \
(reader.GetOutput().GetNumberOfPolys(), filename))
# merge duplicate points, and/or remove unused points and/or remove degenerate cells
if clean:
polydata = vtk.vtkCleanPolyData()
polydata.SetInputConnection(reader.GetOutputPort())
poly_data_algo = polydata
if verbose:
print("cleaned poly data")
else:
poly_data_algo = reader
# convert input polygons and strips to triangles
triangles = vtk.vtkTriangleFilter()
triangles.SetInputConnection(poly_data_algo.GetOutputPort())
if recompute_normals:
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(triangles.GetOutputPort())
normals.SplittingOff()
normals.ComputePointNormalsOn()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.NonManifoldTraversalOn()
if verbose:
print("recomputed normals")
print("finished reading", filename)
return normals
else:
if verbose:
print("finished reading", filename)
return triangles
