def isosurface(self, threshold=True):
"""Return a ``Mesh`` isosurface.
:param float,list threshold: value or list of values to draw the isosurface(s)
"""
if not self._data.GetPointData().GetScalars():
self.mapCellsToPoints()
scrange = self._data.GetPointData().GetScalars().GetRange()
cf = vtk.vtkContourFilter() #vtk.vtkContourGrid()
cf.SetInputData(self._data)
if utils.isSequence(threshold):
cf.SetNumberOfContours(len(threshold))
for i, t in enumerate(threshold):
cf.SetValue(i, t)
cf.Update()
else:
if threshold is True:
threshold = (2 * scrange[0] + scrange[1]) / 3.0
#print('automatic threshold set to ' + utils.precision(threshold, 3), end=' ')
#print('in [' + utils.precision(scrange[0], 3) + ', ' + utils.precision(scrange[1], 3)+']')
cf.SetValue(0, threshold)
cf.Update()
clp = vtk.vtkCleanPolyData()
clp.SetInputData(cf.GetOutput())
clp.Update()
msh = Mesh(clp.GetOutput(), c=None).phong()
msh._mapper.SetLookupTable(utils.ctf2lut(self))
return msh
def slice(self, origin=(0, 0, 0), normal=(1, 0, 0)):
"""Return a 2D slice of the mesh by a plane passing through origin and
assigned normal."""
strn = str(normal)
if strn == "x": normal = (1, 0, 0)
elif strn == "y": normal = (0, 1, 0)
elif strn == "z": normal = (0, 0, 1)
elif strn == "-x": normal = (-1, 0, 0)
elif strn == "-y": normal = (0, -1, 0)
elif strn == "-z": normal = (0, 0, -1)
plane = vtk.vtkPlane()
plane.SetOrigin(origin)
plane.SetNormal(normal)
cc = vtk.vtkCutter()
cc.SetInputData(self._data)
cc.SetCutFunction(plane)
cc.Update()
msh = Mesh(cc.GetOutput()).flat().lighting('ambient')
msh._mapper.SetLookupTable(utils.ctf2lut(self))
return msh
def __init__(self, inputobj=None):
vtk.vtkImageSlice.__init__(self)
Base3DProp.__init__(self)
BaseVolume.__init__(self)
self._mapper = vtk.vtkImageResliceMapper()
self._mapper.SliceFacesCameraOn()
self._mapper.SliceAtFocalPointOn()
self._mapper.SetAutoAdjustImageQuality(False)
self._mapper.BorderOff()
self.lut = None
self.property = vtk.vtkImageProperty()
self.property.SetInterpolationTypeToLinear()
self.SetProperty(self.property)
###################
if isinstance(inputobj, str):
if "https://" in inputobj:
from vedo.io import download
inputobj = download(inputobj, verbose=False) # fpath
elif os.path.isfile(inputobj):
pass
else:
inputobj = sorted(glob.glob(inputobj))
###################
inputtype = str(type(inputobj))
if inputobj is None:
img = vtk.vtkImageData()
if isinstance(inputobj, Volume):
img = inputobj.imagedata()
self.lut = utils.ctf2lut(inputobj)
elif utils.isSequence(inputobj):
if isinstance(inputobj[0], str): # scan sequence of BMP files
ima = vtk.vtkImageAppend()
ima.SetAppendAxis(2)
pb = utils.ProgressBar(0, len(inputobj))
for i in pb.range():
f = inputobj[i]
picr = vtk.vtkBMPReader()
picr.SetFileName(f)
picr.Update()
mgf = vtk.vtkImageMagnitude()
mgf.SetInputData(picr.GetOutput())
mgf.Update()
ima.AddInputData(mgf.GetOutput())
pb.print('loading...')
ima.Update()
img = ima.GetOutput()
else:
if "ndarray" not in inputtype:
inputobj = np.array(inputobj)
if len(inputobj.shape) == 1:
varr = utils.numpy2vtk(inputobj, dtype=float)
else:
if len(inputobj.shape) > 2:
inputobj = np.transpose(inputobj, axes=[2, 1, 0])
varr = utils.numpy2vtk(inputobj.ravel(order='F'),
dtype=float)
varr.SetName('input_scalars')
img = vtk.vtkImageData()
img.SetDimensions(inputobj.shape)
img.GetPointData().AddArray(varr)
img.GetPointData().SetActiveScalars(varr.GetName())
elif "ImageData" in inputtype:
img = inputobj
elif isinstance(inputobj, Volume):
img = inputobj.inputdata()
elif "UniformGrid" in inputtype:
img = inputobj
elif hasattr(
inputobj,
"GetOutput"): # passing vtk object, try extract imagdedata
if hasattr(inputobj, "Update"):
inputobj.Update()
img = inputobj.GetOutput()
elif isinstance(inputobj, str):
from vedo.io import loadImageData, download
if "https://" in inputobj:
inputobj = download(inputobj, verbose=False)
img = loadImageData(inputobj)
else:
colors.printc("VolumeSlice: cannot understand input type:\n",
inputtype,
c='r')
return
self._data = img
self._mapper.SetInputData(img)
self.SetMapper(self._mapper)