Module vedo.tetmesh

Work with tetrahedral meshes

Expand source code 
import vtk
import vedo
from vedo import utils
from vedo.base import BaseGrid
from vedo.mesh import Mesh
from vedo.io import download, loadUnStructuredGrid

__doc__ = """
Work with tetrahedral meshes

.. image:: https://vedo.embl.es/images/volumetric/82767107-2631d500-9e25-11ea-967c-42558f98f721.jpg
"""

__all__ = ["TetMesh", "delaunay3D"]


##########################################################################
def delaunay3D(mesh, alphaPar=0, tol=None, boundary=False):
    """Create 3D Delaunay triangulation of input points."""
    deln = vtk.vtkDelaunay3D()
    if utils.isSequence(mesh):
        pd = vtk.vtkPolyData()
        vpts = vtk.vtkPoints()
        vpts.SetData(utils.numpy2vtk(mesh, dtype=float))
        pd.SetPoints(vpts)
        deln.SetInputData(pd)
    else:
        deln.SetInputData(mesh.GetMapper().GetInput())
    deln.SetAlpha(alphaPar)
    deln.AlphaTetsOn()
    deln.AlphaTrisOff()
    deln.AlphaLinesOff()
    deln.AlphaVertsOff()
    if tol:
        deln.SetTolerance(tol)
    deln.SetBoundingTriangulation(boundary)
    deln.Update()
    m = TetMesh(deln.GetOutput())
    return m


def _buildtetugrid(points, cells):
    ug = vtk.vtkUnstructuredGrid()

    if len(points) == 0:
        return ug
    if not utils.isSequence(points[0]):
        return ug

    if len(cells) == 0:
        return ug

    if not utils.isSequence(cells[0]):
        tets = []
        nf = cells[0] + 1
        for i, cl in enumerate(cells):
            if i in (nf, 0):
                k = i + 1
                nf = cl + k
                cell = [cells[j + k] for j in range(cl)]
                tets.append(cell)
        cells = tets

    sourcePoints = vtk.vtkPoints()
    varr = utils.numpy2vtk(points, dtype=float)
    sourcePoints.SetData(varr)
    ug.SetPoints(sourcePoints)

    sourceTets = vtk.vtkCellArray()
    for f in cells:
        ele = vtk.vtkTetra()
        pid = ele.GetPointIds()
        for i, fi in enumerate(f):
            pid.SetId(i, fi)
        sourceTets.InsertNextCell(ele)
    ug.SetCells(vtk.VTK_TETRA, sourceTets)
    return ug


##########################################################################
class TetMesh(vtk.vtkVolume, BaseGrid):
    """The class describing tetrahedral meshes."""

    def __init__(
        self,
        inputobj=None,
        c=("r", "y", "lg", "lb", "b"),  # ('b','lb','lg','y','r')
        alpha=(0.5, 1),
        alphaUnit=1,
        mapper="tetra",
    ):

        BaseGrid.__init__(self)

        self.useArray = 0

        # inputtype = str(type(inputobj))
        # print('TetMesh inputtype', inputtype)

        ###################
        if inputobj is None:
            self._data = vtk.vtkUnstructuredGrid()

        elif isinstance(inputobj, vtk.vtkUnstructuredGrid):
            self._data = inputobj

        elif isinstance(inputobj, vtk.vtkRectilinearGrid):
            r2t = vtk.vtkRectilinearGridToTetrahedra()
            r2t.SetInputData(inputobj)
            r2t.RememberVoxelIdOn()
            r2t.SetTetraPerCellTo6()
            r2t.Update()
            self._data = r2t.GetOutput()

        elif isinstance(inputobj, vtk.vtkDataSet):
            r2t = vtk.vtkDataSetTriangleFilter()
            r2t.SetInputData(inputobj)
            # r2t.TetrahedraOnlyOn()
            r2t.Update()
            self._data = r2t.GetOutput()

        elif isinstance(inputobj, str):
            if "https://" in inputobj:
                inputobj = download(inputobj, verbose=False)
            ug = loadUnStructuredGrid(inputobj)
            tt = vtk.vtkDataSetTriangleFilter()
            tt.SetInputData(ug)
            tt.SetTetrahedraOnly(True)
            tt.Update()
            self._data = tt.GetOutput()

        elif utils.isSequence(inputobj):
            # if "ndarray" not in inputtype:
            #     inputobj = np.array(inputobj)
            self._data = _buildtetugrid(inputobj[0], inputobj[1])

        ###################
        if "tetra" in mapper:
            self._mapper = vtk.vtkProjectedTetrahedraMapper()
        elif "ray" in mapper:
            self._mapper = vtk.vtkUnstructuredGridVolumeRayCastMapper()
        elif "zs" in mapper:
            self._mapper = vtk.vtkUnstructuredGridVolumeZSweepMapper()
        elif isinstance(mapper, vtk.vtkMapper):
            self._mapper = mapper
        else:
            vedo.logger.error(f"Unknown mapper type {type(mapper)}")
            raise RuntimeError()

        self._mapper.SetInputData(self._data)
        self.SetMapper(self._mapper)
        self.color(c).alpha(alpha)
        if alphaUnit:
            self.GetProperty().SetScalarOpacityUnitDistance(alphaUnit)

        # remember stuff:
        self._color = c
        self._alpha = alpha
        self._alphaUnit = alphaUnit
        # -----------------------------------------------------------

    def _update(self, data):
        self._data = data
        self.mapper().SetInputData(data)
        self.mapper().Modified()
        return self

    def clone(self):
        """Clone the ``TetMesh`` object to yield an exact copy."""
        ugCopy = vtk.vtkUnstructuredGrid()
        ugCopy.DeepCopy(self._data)

        cloned = TetMesh(ugCopy)
        pr = vtk.vtkVolumeProperty()
        pr.DeepCopy(self.GetProperty())
        cloned.SetProperty(pr)

        # assign the same transformation to the copy
        cloned.SetOrigin(self.GetOrigin())
        cloned.SetScale(self.GetScale())
        cloned.SetOrientation(self.GetOrientation())
        cloned.SetPosition(self.GetPosition())

        cloned.mapper().SetScalarMode(self.mapper().GetScalarMode())
        cloned.name = self.name
        return cloned

    def addQuality(self, measure=7):
        """
        Calculate functions of quality for the elements of a triangular mesh.
        This method adds to the mesh a cell array named "Quality".

        Parameters
        ----------
        measure : int
            type of estimator

                - EDGE RATIO, 0
                - ASPECT RATIO, 1
                - RADIUS RATIO, 2
                - ASPECT FROBENIUS, 3
                - MIN_ANGLE, 4
                - COLLAPSE RATIO, 5
                - ASPECT GAMMA, 6
                - VOLUME, 7
                - ...
                See class [vtkMeshQuality](https://vtk.org/doc/nightly/html/classvtkMeshQuality.html)
                for explanation.

        .. hint:: meshquality.py
            .. image:: https://vedo.embl.es/images/advanced/meshquality.png
        """
        qf = vtk.vtkMeshQuality()
        qf.SetInputData(self._data)
        qf.SetTetQualityMeasure(measure)
        qf.SaveCellQualityOn()
        qf.Update()
        return self._update(qf.GetOutput())

    def threshold(self, name=None, above=None, below=None, on="cells"):
        """
        Threshold the tetrahedral mesh by a cell scalar value.
        Reduce to only tets which satisfy the threshold limits.
        If ``above==below`` will only select tets with that specific value.
        If ``above > below`` selection range is "flipped" (vtk_version>8).

        Set keyword `on` either to a "cells" or "points".
        """
        th = vtk.vtkThreshold()
        th.SetInputData(self._data)

        if name is None:
            if self.celldata.keys():
                name = self.celldata.keys()[0]
                th.SetInputArrayToProcess(0, 0, 0, 1, name)
            elif self.pointdata.keys():
                name = self.pointdata.keys()[0]
                th.SetInputArrayToProcess(0, 0, 0, 0, name)
            if name is None:
                vedo.logger.warning("cannot find active array. Skip.")
                return self
        else:
            if on.startswith("c"):
                th.SetInputArrayToProcess(0, 0, 0, 1, name)
            else:
                th.SetInputArrayToProcess(0, 0, 0, 0, name)

        if above is not None and below is not None:
            if above > below:
                if vedo.vtk_version[0] >= 9:
                    th.SetInvert(True)
                    th.ThresholdBetween(below, above)
                else:
                    vedo.logger.error("in vtk<9, above cannot be larger than below. Skip")
                    return self
            else:
                th.ThresholdBetween(above, below)

        elif above is not None:
            th.ThresholdByUpper(above)

        elif below is not None:
            th.ThresholdByLower(below)

        th.Update()
        return self._update(th.GetOutput())

    def decimate(self, scalarsName, fraction=0.5, N=None):
        """
        Downsample the number of tets in a TetMesh to a specified fraction.

        Parameters
        ----------
        fraction : float
            the desired final fraction of the total.

        N : int
            the desired number of final tets

        .. note:: Setting ``fraction=0.1`` leaves 10% of the original nr of tets.
        """
        decimate = vtk.vtkUnstructuredGridQuadricDecimation()
        decimate.SetInputData(self._data)
        decimate.SetScalarsName(scalarsName)

        if N:  # N = desired number of points
            decimate.SetNumberOfTetsOutput(N)
        else:
            decimate.SetTargetReduction(1 - fraction)
        decimate.Update()
        return self._update(decimate.GetOutput())

    def subdvide(self):
        """
        Increase the number of tets of a TetMesh.
        Subdivide one tetrahedron into twelve for every tetra.
        """
        sd = vtk.vtkSubdivideTetra()
        sd.SetInputData(self._data)
        sd.Update()
        return self._update(sd.GetOutput())

    def isosurface(self, threshold=True):
        """
        Return a ``Mesh`` isosurface.

        Set `threshold` to a single value or list of values to compute 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

Functions

def delaunay3D(mesh, alphaPar=0, tol=None, boundary=False)

Create 3D Delaunay triangulation of input points.

Expand source code 
def delaunay3D(mesh, alphaPar=0, tol=None, boundary=False):
    """Create 3D Delaunay triangulation of input points."""
    deln = vtk.vtkDelaunay3D()
    if utils.isSequence(mesh):
        pd = vtk.vtkPolyData()
        vpts = vtk.vtkPoints()
        vpts.SetData(utils.numpy2vtk(mesh, dtype=float))
        pd.SetPoints(vpts)
        deln.SetInputData(pd)
    else:
        deln.SetInputData(mesh.GetMapper().GetInput())
    deln.SetAlpha(alphaPar)
    deln.AlphaTetsOn()
    deln.AlphaTrisOff()
    deln.AlphaLinesOff()
    deln.AlphaVertsOff()
    if tol:
        deln.SetTolerance(tol)
    deln.SetBoundingTriangulation(boundary)
    deln.Update()
    m = TetMesh(deln.GetOutput())
    return m

Classes

class TetMesh (inputobj=None, c=('r', 'y', 'lg', 'lb', 'b'), alpha=(0.5, 1), alphaUnit=1, mapper='tetra')

The class describing tetrahedral meshes.

Expand source code 
class TetMesh(vtk.vtkVolume, BaseGrid):
    """The class describing tetrahedral meshes."""

    def __init__(
        self,
        inputobj=None,
        c=("r", "y", "lg", "lb", "b"),  # ('b','lb','lg','y','r')
        alpha=(0.5, 1),
        alphaUnit=1,
        mapper="tetra",
    ):

        BaseGrid.__init__(self)

        self.useArray = 0

        # inputtype = str(type(inputobj))
        # print('TetMesh inputtype', inputtype)

        ###################
        if inputobj is None:
            self._data = vtk.vtkUnstructuredGrid()

        elif isinstance(inputobj, vtk.vtkUnstructuredGrid):
            self._data = inputobj

        elif isinstance(inputobj, vtk.vtkRectilinearGrid):
            r2t = vtk.vtkRectilinearGridToTetrahedra()
            r2t.SetInputData(inputobj)
            r2t.RememberVoxelIdOn()
            r2t.SetTetraPerCellTo6()
            r2t.Update()
            self._data = r2t.GetOutput()

        elif isinstance(inputobj, vtk.vtkDataSet):
            r2t = vtk.vtkDataSetTriangleFilter()
            r2t.SetInputData(inputobj)
            # r2t.TetrahedraOnlyOn()
            r2t.Update()
            self._data = r2t.GetOutput()

        elif isinstance(inputobj, str):
            if "https://" in inputobj:
                inputobj = download(inputobj, verbose=False)
            ug = loadUnStructuredGrid(inputobj)
            tt = vtk.vtkDataSetTriangleFilter()
            tt.SetInputData(ug)
            tt.SetTetrahedraOnly(True)
            tt.Update()
            self._data = tt.GetOutput()

        elif utils.isSequence(inputobj):
            # if "ndarray" not in inputtype:
            #     inputobj = np.array(inputobj)
            self._data = _buildtetugrid(inputobj[0], inputobj[1])

        ###################
        if "tetra" in mapper:
            self._mapper = vtk.vtkProjectedTetrahedraMapper()
        elif "ray" in mapper:
            self._mapper = vtk.vtkUnstructuredGridVolumeRayCastMapper()
        elif "zs" in mapper:
            self._mapper = vtk.vtkUnstructuredGridVolumeZSweepMapper()
        elif isinstance(mapper, vtk.vtkMapper):
            self._mapper = mapper
        else:
            vedo.logger.error(f"Unknown mapper type {type(mapper)}")
            raise RuntimeError()

        self._mapper.SetInputData(self._data)
        self.SetMapper(self._mapper)
        self.color(c).alpha(alpha)
        if alphaUnit:
            self.GetProperty().SetScalarOpacityUnitDistance(alphaUnit)

        # remember stuff:
        self._color = c
        self._alpha = alpha
        self._alphaUnit = alphaUnit
        # -----------------------------------------------------------

    def _update(self, data):
        self._data = data
        self.mapper().SetInputData(data)
        self.mapper().Modified()
        return self

    def clone(self):
        """Clone the ``TetMesh`` object to yield an exact copy."""
        ugCopy = vtk.vtkUnstructuredGrid()
        ugCopy.DeepCopy(self._data)

        cloned = TetMesh(ugCopy)
        pr = vtk.vtkVolumeProperty()
        pr.DeepCopy(self.GetProperty())
        cloned.SetProperty(pr)

        # assign the same transformation to the copy
        cloned.SetOrigin(self.GetOrigin())
        cloned.SetScale(self.GetScale())
        cloned.SetOrientation(self.GetOrientation())
        cloned.SetPosition(self.GetPosition())

        cloned.mapper().SetScalarMode(self.mapper().GetScalarMode())
        cloned.name = self.name
        return cloned

    def addQuality(self, measure=7):
        """
        Calculate functions of quality for the elements of a triangular mesh.
        This method adds to the mesh a cell array named "Quality".

        Parameters
        ----------
        measure : int
            type of estimator

                - EDGE RATIO, 0
                - ASPECT RATIO, 1
                - RADIUS RATIO, 2
                - ASPECT FROBENIUS, 3
                - MIN_ANGLE, 4
                - COLLAPSE RATIO, 5
                - ASPECT GAMMA, 6
                - VOLUME, 7
                - ...
                See class [vtkMeshQuality](https://vtk.org/doc/nightly/html/classvtkMeshQuality.html)
                for explanation.

        .. hint:: meshquality.py
            .. image:: https://vedo.embl.es/images/advanced/meshquality.png
        """
        qf = vtk.vtkMeshQuality()
        qf.SetInputData(self._data)
        qf.SetTetQualityMeasure(measure)
        qf.SaveCellQualityOn()
        qf.Update()
        return self._update(qf.GetOutput())

    def threshold(self, name=None, above=None, below=None, on="cells"):
        """
        Threshold the tetrahedral mesh by a cell scalar value.
        Reduce to only tets which satisfy the threshold limits.
        If ``above==below`` will only select tets with that specific value.
        If ``above > below`` selection range is "flipped" (vtk_version>8).

        Set keyword `on` either to a "cells" or "points".
        """
        th = vtk.vtkThreshold()
        th.SetInputData(self._data)

        if name is None:
            if self.celldata.keys():
                name = self.celldata.keys()[0]
                th.SetInputArrayToProcess(0, 0, 0, 1, name)
            elif self.pointdata.keys():
                name = self.pointdata.keys()[0]
                th.SetInputArrayToProcess(0, 0, 0, 0, name)
            if name is None:
                vedo.logger.warning("cannot find active array. Skip.")
                return self
        else:
            if on.startswith("c"):
                th.SetInputArrayToProcess(0, 0, 0, 1, name)
            else:
                th.SetInputArrayToProcess(0, 0, 0, 0, name)

        if above is not None and below is not None:
            if above > below:
                if vedo.vtk_version[0] >= 9:
                    th.SetInvert(True)
                    th.ThresholdBetween(below, above)
                else:
                    vedo.logger.error("in vtk<9, above cannot be larger than below. Skip")
                    return self
            else:
                th.ThresholdBetween(above, below)

        elif above is not None:
            th.ThresholdByUpper(above)

        elif below is not None:
            th.ThresholdByLower(below)

        th.Update()
        return self._update(th.GetOutput())

    def decimate(self, scalarsName, fraction=0.5, N=None):
        """
        Downsample the number of tets in a TetMesh to a specified fraction.

        Parameters
        ----------
        fraction : float
            the desired final fraction of the total.

        N : int
            the desired number of final tets

        .. note:: Setting ``fraction=0.1`` leaves 10% of the original nr of tets.
        """
        decimate = vtk.vtkUnstructuredGridQuadricDecimation()
        decimate.SetInputData(self._data)
        decimate.SetScalarsName(scalarsName)

        if N:  # N = desired number of points
            decimate.SetNumberOfTetsOutput(N)
        else:
            decimate.SetTargetReduction(1 - fraction)
        decimate.Update()
        return self._update(decimate.GetOutput())

    def subdvide(self):
        """
        Increase the number of tets of a TetMesh.
        Subdivide one tetrahedron into twelve for every tetra.
        """
        sd = vtk.vtkSubdivideTetra()
        sd.SetInputData(self._data)
        sd.Update()
        return self._update(sd.GetOutput())

    def isosurface(self, threshold=True):
        """
        Return a ``Mesh`` isosurface.

        Set `threshold` to a single value or list of values to compute 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

Ancestors

  • vtkmodules.vtkRenderingCore.vtkVolume
  • vtkmodules.vtkRenderingCore.vtkProp3D
  • vtkmodules.vtkRenderingCore.vtkProp
  • vtkmodules.vtkCommonCore.vtkObject
  • vtkmodules.vtkCommonCore.vtkObjectBase
  • BaseGrid
  • BaseActor
  • Base3DProp

Methods

def addQuality(self, measure=7)

Calculate functions of quality for the elements of a triangular mesh. This method adds to the mesh a cell array named "Quality".

Parameters

measure : int
type of estimator
- EDGE RATIO, 0
- ASPECT RATIO, 1
- RADIUS RATIO, 2
- ASPECT FROBENIUS, 3
- MIN_ANGLE, 4
- COLLAPSE RATIO, 5
- ASPECT GAMMA, 6
- VOLUME, 7
- ...
See class [vtkMeshQuality](https://vtk.org/doc/nightly/html/classvtkMeshQuality.html)
for explanation.

Hint: meshquality.py

Expand source code 
def addQuality(self, measure=7):
    """
    Calculate functions of quality for the elements of a triangular mesh.
    This method adds to the mesh a cell array named "Quality".

    Parameters
    ----------
    measure : int
        type of estimator

            - EDGE RATIO, 0
            - ASPECT RATIO, 1
            - RADIUS RATIO, 2
            - ASPECT FROBENIUS, 3
            - MIN_ANGLE, 4
            - COLLAPSE RATIO, 5
            - ASPECT GAMMA, 6
            - VOLUME, 7
            - ...
            See class [vtkMeshQuality](https://vtk.org/doc/nightly/html/classvtkMeshQuality.html)
            for explanation.

    .. hint:: meshquality.py
        .. image:: https://vedo.embl.es/images/advanced/meshquality.png
    """
    qf = vtk.vtkMeshQuality()
    qf.SetInputData(self._data)
    qf.SetTetQualityMeasure(measure)
    qf.SaveCellQualityOn()
    qf.Update()
    return self._update(qf.GetOutput())
def clone(self)

Clone the TetMesh object to yield an exact copy.

Expand source code 
def clone(self):
    """Clone the ``TetMesh`` object to yield an exact copy."""
    ugCopy = vtk.vtkUnstructuredGrid()
    ugCopy.DeepCopy(self._data)

    cloned = TetMesh(ugCopy)
    pr = vtk.vtkVolumeProperty()
    pr.DeepCopy(self.GetProperty())
    cloned.SetProperty(pr)

    # assign the same transformation to the copy
    cloned.SetOrigin(self.GetOrigin())
    cloned.SetScale(self.GetScale())
    cloned.SetOrientation(self.GetOrientation())
    cloned.SetPosition(self.GetPosition())

    cloned.mapper().SetScalarMode(self.mapper().GetScalarMode())
    cloned.name = self.name
    return cloned
def decimate(self, scalarsName, fraction=0.5, N=None)

Downsample the number of tets in a TetMesh to a specified fraction.

Parameters

fraction : float
the desired final fraction of the total.
N : int
the desired number of final tets

Note: Setting fraction=0.1 leaves 10% of the original nr of tets.

Expand source code 
def decimate(self, scalarsName, fraction=0.5, N=None):
    """
    Downsample the number of tets in a TetMesh to a specified fraction.

    Parameters
    ----------
    fraction : float
        the desired final fraction of the total.

    N : int
        the desired number of final tets

    .. note:: Setting ``fraction=0.1`` leaves 10% of the original nr of tets.
    """
    decimate = vtk.vtkUnstructuredGridQuadricDecimation()
    decimate.SetInputData(self._data)
    decimate.SetScalarsName(scalarsName)

    if N:  # N = desired number of points
        decimate.SetNumberOfTetsOutput(N)
    else:
        decimate.SetTargetReduction(1 - fraction)
    decimate.Update()
    return self._update(decimate.GetOutput())
def isosurface(self, threshold=True)

Return a Mesh isosurface.

Set threshold to a single value or list of values to compute the isosurface(s)

Expand source code 
def isosurface(self, threshold=True):
    """
    Return a ``Mesh`` isosurface.

    Set `threshold` to a single value or list of values to compute 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.

Expand source code 
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 subdvide(self)

Increase the number of tets of a TetMesh. Subdivide one tetrahedron into twelve for every tetra.

Expand source code 
def subdvide(self):
    """
    Increase the number of tets of a TetMesh.
    Subdivide one tetrahedron into twelve for every tetra.
    """
    sd = vtk.vtkSubdivideTetra()
    sd.SetInputData(self._data)
    sd.Update()
    return self._update(sd.GetOutput())
def threshold(self, name=None, above=None, below=None, on='cells')

Threshold the tetrahedral mesh by a cell scalar value. Reduce to only tets which satisfy the threshold limits. If above==below will only select tets with that specific value. If above > below selection range is "flipped" (vtk_version>8).

Set keyword on either to a "cells" or "points".

Expand source code 
def threshold(self, name=None, above=None, below=None, on="cells"):
    """
    Threshold the tetrahedral mesh by a cell scalar value.
    Reduce to only tets which satisfy the threshold limits.
    If ``above==below`` will only select tets with that specific value.
    If ``above > below`` selection range is "flipped" (vtk_version>8).

    Set keyword `on` either to a "cells" or "points".
    """
    th = vtk.vtkThreshold()
    th.SetInputData(self._data)

    if name is None:
        if self.celldata.keys():
            name = self.celldata.keys()[0]
            th.SetInputArrayToProcess(0, 0, 0, 1, name)
        elif self.pointdata.keys():
            name = self.pointdata.keys()[0]
            th.SetInputArrayToProcess(0, 0, 0, 0, name)
        if name is None:
            vedo.logger.warning("cannot find active array. Skip.")
            return self
    else:
        if on.startswith("c"):
            th.SetInputArrayToProcess(0, 0, 0, 1, name)
        else:
            th.SetInputArrayToProcess(0, 0, 0, 0, name)

    if above is not None and below is not None:
        if above > below:
            if vedo.vtk_version[0] >= 9:
                th.SetInvert(True)
                th.ThresholdBetween(below, above)
            else:
                vedo.logger.error("in vtk<9, above cannot be larger than below. Skip")
                return self
        else:
            th.ThresholdBetween(above, below)

    elif above is not None:
        th.ThresholdByUpper(above)

    elif below is not None:
        th.ThresholdByLower(below)

    th.Update()
    return self._update(th.GetOutput())

Inherited members