Module vedo.applications

This module contains vedo applications which provide some ready-to-use funcionalities

Expand source code
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import time
import os
import numpy as np

import vedo
from vedo.colors import color_map
from vedo.colors import get_color
from vedo.utils import is_sequence
from vedo.utils import lin_interpolate
from vedo.utils import mag
from vedo.utils import precision
from vedo.plotter import Plotter
from vedo.pointcloud import fit_plane
from vedo.pointcloud import Points
from vedo.shapes import Line
from vedo.shapes import Ribbon
from vedo.shapes import Spline
from vedo.shapes import Text2D
from vedo.pyplot import CornerHistogram

__doc__ = """
This module contains vedo applications which provide some *ready-to-use* funcionalities
.. image:: https://vedo.embl.es/images/advanced/app_raycaster.gif
"""


__all__ = [
    "Browser",
    "IsosurfaceBrowser",
    "FreeHandCutPlotter",
    "RayCastPlotter",
    "Slicer3DPlotter",
    "Slicer2DPlotter",
    "SplinePlotter",
    "Clock",
]


#################################
class Slicer3DPlotter(Plotter):
    """
    Generate a ``Plotter`` window with slicing planes for the input Volume.

    Returns the ``Plotter`` object.

    Parameters
    ----------
    alpha : float
        transparency of the slicing planes

    cmaps : list
        list of color maps names to cycle when clicking button

    map2cells : bool
        scalars are mapped to cells, not interpolated

    clamp : bool
        clamp scalar to reduce the effect of tails in color mapping

    use_slider3d : bool
        show sliders attached along the axes

    show_histo : bool
        show histogram on bottom left

    show_icon : bool
        show a small 3D rendering icon of the volume

    draggable : bool
        make the icon draggable

    .. hint:: examples/volumetric/slicer1.py
        .. image:: https://vedo.embl.es/images/volumetric/slicer1.jpg
    """

    def __init__(
            self,
            volume,
            alpha=1,
            cmaps=('gist_ncar_r', "hot_r", "bone_r", "jet", "Spectral_r"),
            map2cells=False,  # buggy
            clamp=True,
            use_slider3d=False,
            show_histo=True,
            show_icon=True,
            draggable=False,
            pos=(0, 0),
            size="auto",
            screensize="auto",
            title="",
            bg="white",
            bg2="lightblue",
            axes=7,
            resetcam=True,
            interactive=True,
        ):
        self._cmap_slicer= 'gist_ncar_r'

        if not title:
            if volume.filename:
                title = volume.filename
            else:
                title = "Volume Slicer"

        ################################
        Plotter.__init__(
            self,
            pos=pos,
            bg=bg,
            bg2=bg2,
            size=size,
            screensize=screensize,
            title=title,
            interactive=interactive,
            axes=axes,
        )
        ################################
        box = volume.box().wireframe().alpha(0.1)

        self.show(box, viewup="z", resetcam=resetcam, interactive=False)
        if show_icon:
            self.add_inset(
                volume,
                pos=(0.85, 0.85),
                size=0.15, c="w",
                draggable=draggable,
            )

        # inits
        la, ld = 0.7, 0.3  # ambient, diffuse
        dims = volume.dimensions()
        data = volume.pointdata[0]
        rmin, rmax = volume.imagedata().GetScalarRange()
        if clamp:
            hdata, edg = np.histogram(data, bins=50)
            logdata = np.log(hdata + 1)
            # mean  of the logscale plot
            meanlog = np.sum(np.multiply(edg[:-1], logdata)) / np.sum(logdata)
            rmax = min(rmax, meanlog + (meanlog - rmin) * 0.9)
            rmin = max(rmin, meanlog - (rmax - meanlog) * 0.9)
            vedo.logger.debug(
                "scalar range clamped to range: ("
                + precision(rmin, 3)
                + ", "
                + precision(rmax, 3)
                + ")"
            )
        self._cmap_slicer = cmaps[0]
        visibles = [None, None, None]
        msh = volume.zslice(int(dims[2] / 2))
        msh.alpha(alpha).lighting("", la, ld, 0)
        msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
        if map2cells:
            msh.mapPointsToCells()
        self.renderer.AddActor(msh)
        visibles[2] = msh
        msh.add_scalarbar(pos=(0.04, 0.0), horizontal=True, font_size=0)

        def sliderfunc_x(widget, event):
            i = int(widget.GetRepresentation().GetValue())
            msh = volume.xslice(i).alpha(alpha).lighting("", la, ld, 0)
            msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
            if map2cells:
                msh.mapPointsToCells()
            self.renderer.RemoveActor(visibles[0])
            if i and i < dims[0]:
                self.renderer.AddActor(msh)
            visibles[0] = msh

        def sliderfunc_y(widget, event):
            i = int(widget.GetRepresentation().GetValue())
            msh = volume.yslice(i).alpha(alpha).lighting("", la, ld, 0)
            msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
            if map2cells:
                msh.mapPointsToCells()
            self.renderer.RemoveActor(visibles[1])
            if i and i < dims[1]:
                self.renderer.AddActor(msh)
            visibles[1] = msh

        def sliderfunc_z(widget, event):
            i = int(widget.GetRepresentation().GetValue())
            msh = volume.zslice(i).alpha(alpha).lighting("", la, ld, 0)
            msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
            if map2cells:
                msh.mapPointsToCells()
            self.renderer.RemoveActor(visibles[2])
            if i and i < dims[2]:
                self.renderer.AddActor(msh)
            visibles[2] = msh

        cx, cy, cz, ch = "dr", "dg", "db", (0.3, 0.3, 0.3)
        if np.sum(self.renderer.GetBackground()) < 1.5:
            cx, cy, cz = "lr", "lg", "lb"
            ch = (0.8, 0.8, 0.8)

        if not use_slider3d:
            self.add_slider(
                sliderfunc_x,
                0,
                dims[0],
                title="X",
                title_size=0.5,
                pos=[(0.8, 0.12), (0.95, 0.12)],
                show_value=False,
                c=cx,
            )
            self.add_slider(
                sliderfunc_y,
                0,
                dims[1],
                title="Y",
                title_size=0.5,
                pos=[(0.8, 0.08), (0.95, 0.08)],
                show_value=False,
                c=cy,
            )
            self.add_slider(
                sliderfunc_z,
                0,
                dims[2],
                title="Z",
                title_size=0.6,
                value=int(dims[2] / 2),
                pos=[(0.8, 0.04), (0.95, 0.04)],
                show_value=False,
                c=cz,
            )
        else:  # 3d sliders attached to the axes bounds
            bs = box.bounds()
            self.add_slider3d(
                sliderfunc_x,
                pos1=(bs[0], bs[2], bs[4]),
                pos2=(bs[1], bs[2], bs[4]),
                xmin=0,
                xmax=dims[0],
                t=box.diagonal_size() / mag(box.xbounds()) * 0.6,
                c=cx,
                show_value=False,
            )
            self.add_slider3d(
                sliderfunc_y,
                pos1=(bs[1], bs[2], bs[4]),
                pos2=(bs[1], bs[3], bs[4]),
                xmin=0,
                xmax=dims[1],
                t=box.diagonal_size() / mag(box.ybounds()) * 0.6,
                c=cy,
                show_value=False,
            )
            self.add_slider3d(
                sliderfunc_z,
                pos1=(bs[0], bs[2], bs[4]),
                pos2=(bs[0], bs[2], bs[5]),
                xmin=0,
                xmax=dims[2],
                value=int(dims[2] / 2),
                t=box.diagonal_size() / mag(box.zbounds()) * 0.6,
                c=cz,
                show_value=False,
            )

        #################
        def buttonfunc():
            bu.switch()
            self._cmap_slicer = bu.status()
            for mesh in visibles:
                if mesh:
                    mesh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
                    if map2cells:
                        mesh.mapPointsToCells()
            self.renderer.RemoveActor(mesh.scalarbar)
            mesh.add_scalarbar(pos=(0.04, 0.0), horizontal=True, title_font_size=0)

        bu = self.add_button(
            buttonfunc,
            pos=(0.27, 0.005),
            states=cmaps,
            c=["db"] * len(cmaps),
            bc=["lb"] * len(cmaps),  # colors of states
            size=14,
            bold=True,
        )

        #################
        hist = None
        if show_histo:
            hist = CornerHistogram(
                data,
                s=0.2,
                bins=25,
                logscale=1,
                pos=(0.02, 0.02),
                c=ch,
                bg=ch,
                alpha=0.7,
            )

        self.add([msh, hist], resetcam=False)
        if interactive:
            self.interactive()


########################################################################################
class Slicer2DPlotter(Plotter):
    """
    Create a ``Plotter`` with a single slice of a Volume which always faces the camera,
    but at the same time can be oriented arbitrarily in space.

    Parameters
    ----------
    levels : list
        window and color level

    .. image:: https://vedo.embl.es/images/volumetric/read_volume3.jpg
    """

    def __init__(
        self,
        volume,
        levels=(None, None),
        axes=None,
        zoom=1.2,
        pos=(0, 0),
        size="auto",
        screensize="auto",
        title="",
        bg="white",
        bg2=None,
        interactive=True,
    ):
        custom_shape = [  # define here the 2 rendering rectangle spaces
            dict(bottomleft=(0.0, 0.0), topright=(1, 1), bg="k9"),  # the full window
            dict(bottomleft=(0.8, 0.8), topright=(1, 1), bg="k8", bg2="lb"),
        ]

        if not title:
            if volume.filename:
                title = volume.filename[:80]
            else:
                title = "Volume Slicer2D"

        Plotter.__init__(
            self,
            shape=custom_shape,
            title=title,
            pos=pos,
            screensize=screensize,
            size=size,
            bg=bg,
            bg2=bg2,
            axes=0,
            interactive=False,
        )

        vsl = vedo.volume.VolumeSlice(
            volume
        )  # reuse the same underlying data as in vol

        # no argument will grab the existing cmap in vol (or use build_lut())
        vsl.colorize()

        if levels[0] and levels[1]:
            vsl.lighting(window=levels[0], level=levels[1])

        usage = Text2D((
            "SHIFT+Left click   \rightarrow rotate camera for oblique slicing\n"
            "SHIFT+Middle click \rightarrow slice perpendicularly through image\n"
            "Left click & drag  \rightarrow modify luminosity and contrast\n"
            "R                  \rightarrow Reset the Window/Color levels\n"
            "X                  \rightarrow Reset to sagittal view\n"
            "Y                  \rightarrow Reset to coronal view\n"
            "Z                  \rightarrow Reset to axial view"),
            font="Calco",
            pos="top-left",
            s=0.8,
            bg="yellow",
            alpha=0.25,
        )

        hist = CornerHistogram(
            volume.pointdata[0],
            bins=25,
            logscale=1,
            pos=(0.02, 0.02),
            s=0.175,
            c="dg",
            bg="k",
            alpha=1,
        )
        ax = None
        if axes == 7:
            ax = vedo.addons.RulerAxes(vsl, xtitle="x - ", ytitle="y - ", ztitle="z - ")

        box = vsl.box().alpha(0.1)
        self.show(vsl, box, ax, usage, hist, at=0, mode="image", zoom=zoom)
        self.show(volume, at=1, interactive=interactive)


########################################################################
class RayCastPlotter(Plotter):
    """
    Generate a ``Plotter`` window for Volume rendering using ray casting.

    Returns the ``Plotter`` object.

    .. hint:: examples/volumetric/app_raycaster.py
        .. image:: https://vedo.embl.es/images/advanced/app_raycaster.gif
    """

    def __init__(self, volume, **kwargs):

        Plotter.__init__(self, **kwargs)

        self.alphaslider0 = 0.33
        self.alphaslider1 = 0.66
        self.alphaslider2 = 1

        volumeProperty = volume.GetProperty()
        img = volume.imagedata()

        if volume.dimensions()[2] < 3:
            vedo.logger.error("RayCastPlotter: not enough z slices.")
            raise RuntimeError

        smin, smax = img.GetScalarRange()
        x0alpha = smin + (smax - smin) * 0.25
        x1alpha = smin + (smax - smin) * 0.5
        x2alpha = smin + (smax - smin) * 1.0

        ############################## color map slider
        # Create transfer mapping scalar value to color
        cmaps = [
            "jet",
            "viridis",
            "bone",
            "hot",
            "plasma",
            "winter",
            "cool",
            "gist_earth",
            "coolwarm",
            "tab10",
        ]
        cols_cmaps = []
        for cm in cmaps:
            cols = color_map(range(0, 21), cm, 0, 20)  # sample 20 colors
            cols_cmaps.append(cols)
        Ncols = len(cmaps)
        csl = (0.9, 0.9, 0.9)
        if sum(get_color(self.renderer.GetBackground())) > 1.5:
            csl = (0.1, 0.1, 0.1)

        def sliderColorMap(widget, event):
            sliderRep = widget.GetRepresentation()
            k = int(sliderRep.GetValue())
            sliderRep.SetTitleText(cmaps[k])
            volume.color(cmaps[k])

        w1 = self.add_slider(
            sliderColorMap,
            0,
            Ncols - 1,
            value=0,
            show_value=0,
            title=cmaps[0],
            c=csl,
            pos=[(0.8, 0.05), (0.965, 0.05)],
        )
        w1.GetRepresentation().SetTitleHeight(0.018)

        ############################## alpha sliders
        # Create transfer mapping scalar value to opacity
        opacityTransferFunction = volumeProperty.GetScalarOpacity()

        def setOTF():
            opacityTransferFunction.RemoveAllPoints()
            opacityTransferFunction.AddPoint(smin, 0.0)
            opacityTransferFunction.AddPoint(smin + (smax - smin) * 0.1, 0.0)
            opacityTransferFunction.AddPoint(x0alpha, self.alphaslider0)
            opacityTransferFunction.AddPoint(x1alpha, self.alphaslider1)
            opacityTransferFunction.AddPoint(x2alpha, self.alphaslider2)

        setOTF()

        def sliderA0(widget, event):
            self.alphaslider0 = widget.GetRepresentation().GetValue()
            setOTF()

        self.add_slider(
            sliderA0,
            0,
            1,
            value=self.alphaslider0,
            pos=[(0.84, 0.1), (0.84, 0.26)],
            c=csl,
            show_value=0,
        )

        def sliderA1(widget, event):
            self.alphaslider1 = widget.GetRepresentation().GetValue()
            setOTF()

        self.add_slider(
            sliderA1,
            0,
            1,
            value=self.alphaslider1,
            pos=[(0.89, 0.1), (0.89, 0.26)],
            c=csl,
            show_value=0,
        )

        def sliderA2(widget, event):
            self.alphaslider2 = widget.GetRepresentation().GetValue()
            setOTF()

        w2 = self.add_slider(
            sliderA2,
            0,
            1,
            value=self.alphaslider2,
            pos=[(0.96, 0.1), (0.96, 0.26)],
            c=csl,
            show_value=0,
            title="Opacity levels",
        )
        w2.GetRepresentation().SetTitleHeight(0.016)

        # add a button
        def button_func_mode():
            s = volume.mode()
            snew = (s + 1) % 2
            volume.mode(snew)
            bum.switch()

        bum = self.add_button(
            button_func_mode,
            pos=(0.7, 0.035),
            states=["composite", "max proj."],
            c=["bb", "gray"],
            bc=["gray", "bb"],  # colors of states
            font="",
            size=16,
            bold=0,
            italic=False,
        )
        bum.status(volume.mode())

        # add histogram of scalar
        plot = CornerHistogram(
            volume,
            bins=25,
            logscale=1,
            c=(0.7, 0.7, 0.7),
            bg=(0.7, 0.7, 0.7),
            pos=(0.78, 0.065),
            lines=True,
            dots=False,
            nmax=3.1415e06,  # subsample otherwise is too slow
        )

        plot.GetPosition2Coordinate().SetValue(0.197, 0.20, 0)
        plot.GetXAxisActor2D().SetFontFactor(0.7)
        plot.GetProperty().SetOpacity(0.5)
        self.add([plot, volume])


#####################################################################################
class IsosurfaceBrowser(Plotter):
    """
    Generate a ``Plotter`` for Volume isosurfacing using a slider.

    Set ``delayed=True`` to delay slider update on mouse release.

    Set ``res`` to set the resolution, e.g. the number of desired isosurfaces to be
    generated on the fly.

    Set ``precompute=True`` to precompute the isosurfaces (so slider browsing will be smoother).

    .. hint:: examples/volumetric/app_isobrowser.py
        .. image:: https://vedo.embl.es/images/advanced/app_isobrowser.gif
    """

    def __init__(
            self,
            volume,
            threshold=None,
            c=None,
            alpha=1,
            lego=False,
            res=50,
            precompute=False,
            progress=False,
            cmap='hot',
            delayed=False,
            sliderpos=4,
            pos=(0,0),
            size="auto",
            screensize="auto",
            title="",
            bg="white",
            bg2=None,
            axes=1,
            interactive=True,
        ):

        Plotter.__init__(
            self,
            pos=pos,
            bg=bg,
            bg2=bg2,
            size=size,
            screensize=screensize,
            title=title,
            interactive=interactive,
            axes=axes,
        )

        self._prev_value = 1e30

        scrange = volume.scalar_range()
        delta = scrange[1] - scrange[0]
        if not delta:
            return

        if lego:
            res = int(res / 2)  # because lego is much slower
            slidertitle = ""
        else:
            slidertitle = "threshold"

        allowed_vals = np.linspace(scrange[0], scrange[1], num=res)

        bacts = {}  # cache the meshes so we dont need to recompute
        if precompute:
            delayed = False  # no need to delay the slider in this case
            if progress:
                pb = vedo.ProgressBar(0, len(allowed_vals))

            for value in allowed_vals:
                value_name = precision(value, 2)
                if lego:
                    mesh = volume.legosurface(vmin=value)
                    if mesh.NCells():
                        mesh.cmap(cmap, vmin=scrange[0], vmax=scrange[1], on="cells")
                else:
                    mesh = volume.isosurface(threshold=value).color(c).alpha(alpha)
                bacts.update({value_name: mesh})  # store it
                if progress:
                    pb.print("isosurfacing volume..")

        ############################## threshold slider callback
        def sliderThres(widget, event):

            prevact = self.actors[0]
            if isinstance(widget, float):
                value = widget
            else:
                value = widget.GetRepresentation().GetValue()

            # snap to the closest
            idx = (np.abs(allowed_vals - value)).argmin()
            value = allowed_vals[idx]

            if abs(value - self._prev_value) / delta < 0.001:
                return
            self._prev_value = value

            value_name = precision(value, 2)
            if value_name in bacts:  # reusing the already existing mesh
                # print('reusing')
                mesh = bacts[value_name]
            else:  # else generate it
                # print('generating', value)
                if lego:
                    mesh = volume.legosurface(vmin=value)
                    if mesh.NCells():
                        mesh.cmap(cmap, vmin=scrange[0], vmax=scrange[1], on="cells")
                else:
                    mesh = volume.isosurface(threshold=value).color(c).alpha(alpha)
                bacts.update({value_name: mesh})  # store it

            self.renderer.RemoveActor(prevact)
            self.renderer.AddActor(mesh)
            self.actors[0] = mesh

        ################################################

        if threshold is None:
            threshold = delta / 3.0 + scrange[0]

        self.actors = [None]
        sliderThres(threshold, "")  # init call
        if lego:
            self.actors[0].add_scalarbar(pos=(0.8, 0.12))

        self.add_slider(
            sliderThres,
            scrange[0] + 0.02 * delta,
            scrange[1] - 0.02 * delta,
            value=threshold,
            pos=sliderpos,
            title=slidertitle,
            show_value=True,
            delayed=delayed,
        )


##############################################################################
class Browser(Plotter):
    """
    Browse a serie of vedo objects by using a simple slider.

    Example:
        .. code-block:: python

            import vedo
            from vedo.applications import Browser
            meshes = vedo.load("data/2*0.vtk") # a python list
            plt = Browser(meshes, resetcam=1, axes=4) # a vedo.Plotter
            plt.show()

    .. hint:: examples/other/morphomatics_tube.py
    """
    def __init__(
            self,
            objects=(),
            sliderpos=((0.55, 0.07),(0.96, 0.07)),
            c=None,  # slider color
            prefix="",
            pos=(0, 0),
            size="auto",
            screensize="auto",
            title="Browser",
            bg="white",
            bg2=None,
            axes=4,
            resetcam=False,
            interactive=True,
        ):

        Plotter.__init__(
            self,
            pos=pos,
            size=size,
            screensize=screensize,
            title=title,
            bg=bg,
            bg2=bg2,
            axes=axes,
            interactive=interactive,
        )

        self += objects

        self.slider = None

        # define the slider
        def sliderfunc(widget, event=None):
            k = int(widget.GetRepresentation().GetValue())
            ak = self.actors[k]
            for a in self.actors:
                if a == ak:
                    a.on()
                else:
                    a.off()
            if resetcam:
                self.resetCamera()
            tx = str(k)
            if ak.filename:
                tx = ak.filename.split("/")[-1]
                tx = tx.split("\\")[-1]  # windows os
            elif ak.name:
                tx = ak.name
            widget.GetRepresentation().SetTitleText(prefix + tx)

        self.slider = self.add_slider(
            sliderfunc,
            0.5,
            len(objects) - 0.5,
            pos=sliderpos,
            font="courier",
            c=c,
            show_value=False,
        )
        self.slider.GetRepresentation().SetTitleHeight(0.020)
        sliderfunc(self.slider)  # init call


#############################################################################################
class FreeHandCutPlotter(Plotter):
    """
    A ``Plotter`` derived class which edits polygonal meshes interactively.
    Can also be invoked from command line. E.g. with:

    ``vedo --edit https://vedo.embl.es/examples/data/porsche.ply``

    Usage
    -----
        - Left-click and hold to rotate
        - Right-click and move to draw line
        - Second right-click to stop drawing
        - Press c to clear points
        -       z/Z to cut mesh (Z inverts inside-out the selection area)
        -       L to keep only the largest connected surface
        -       s to save mesh to file (tag _edited is appended to filename)
        -       u to undo last action
        -       h for help, i for info

    Parameters
    ----------
    mesh : Mesh, Points
        The input Mesh or pointcloud.

    splined : bool
        join points with a spline or a simple line.

    font : str
        Font name for the instructions.

    alpha : float
        transparency of the instruction message panel.

    lw : str
        selection line width.

    lc : str
        selection line color.

    pc : str
        selection points color.

    c : str
        backgound color of instructions.

    tc : str
        text color of instructions.

    tol : int
        tolerance of the point proximity.

    .. hint:: examples/basic/cutFreeHand.py
        .. image:: https://vedo.embl.es/images/basic/cutFreeHand.gif
    """

    # thanks to Jakub Kaminski for the original version of this script
    def __init__(
            self,
            mesh,
            splined=True,
            font="Bongas",
            alpha=0.9,
            lw=4,
            lc="red5",
            pc="red4",
            c="green3",
            tc="k9",
            tol=0.008,
            **options
        ):

        if not isinstance(mesh, Points):
            vedo.logger.error("FreeHandCutPlotter input must be Points or Mesh")
            raise RuntimeError()

        super().__init__(**options)

        self.mesh = mesh
        self.mesh_prev = mesh
        self.splined = splined
        self.linecolor = lc
        self.linewidth = lw
        self.pointcolor = pc
        self.color = c
        self.alpha = alpha

        self.msg = "Right-click and move to draw line\n"
        self.msg += "Second right-click to stop drawing\n"
        self.msg += "Press L to extract largest surface\n"
        self.msg += "        z/Z to cut mesh (s to save)\n"
        self.msg += "        c to clear points, u to undo"
        self.txt2d = Text2D(self.msg, pos="top-left", font=font, s=0.9)
        self.txt2d.c(tc).background(c, alpha).frame()

        self.idkeypress = self.add_callback("KeyPress", self._on_keypress)
        self.idrightclck = self.add_callback("RightButton", self._on_right_click)
        self.idmousemove = self.add_callback("MouseMove", self._on_mouse_move)
        self.drawmode = False
        self.tol = tol  # tolerance of point distance
        self.cpoints = []
        self.points = None
        self.spline = None
        self.jline = None
        self.topline = None
        self.top_pts = []

    def init(self, initpoints):
        """Set an initial number of points to define a region"""
        if isinstance(initpoints, Points):
            self.cpoints = initpoints.points()
        else:
            self.cpoints = np.array(initpoints)
        self.points = Points(self.cpoints, r=self.linewidth).c(self.pointcolor).pickable(0)
        if self.splined:
            self.spline = Spline(self.cpoints, res=len(self.cpoints) * 4)
        else:
            self.spline = Line(self.cpoints)
        self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
        self.jline = Line(self.cpoints[0], self.cpoints[-1], lw=1, c=self.linecolor).pickable(0)
        self.add([self.points, self.spline, self.jline], render=False)
        return self

    def _on_right_click(self, evt):
        self.drawmode = not self.drawmode  # toggle mode
        if self.drawmode:
            self.txt2d.background(self.linecolor, self.alpha)
        else:
            self.txt2d.background(self.color, self.alpha)
            if len(self.cpoints) > 2:
                self.remove([self.spline, self.jline])
                if self.splined:  # show the spline closed
                    self.spline = Spline(
                        self.cpoints, closed=True, res=len(self.cpoints) * 4
                    )
                else:
                    self.spline = Line(self.cpoints, closed=True)
                self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
                self.add(self.spline)

    def _on_mouse_move(self, evt):
        if self.drawmode:
            cpt = self.compute_world_position(evt.picked2d) # make this 2d-screen point 3d
            if self.cpoints and mag(cpt - self.cpoints[-1]) < self.mesh.diagonal_size()*self.tol:
                return  # new point is too close to the last one. skip
            self.cpoints.append(cpt)
            if len(self.cpoints) > 2:
                self.remove([self.points, self.spline, self.jline, self.topline])
                self.points = Points(self.cpoints, r=self.linewidth).c(self.pointcolor).pickable(0)
                if self.splined:
                    self.spline = Spline(self.cpoints, res=len(self.cpoints)*4) # not closed here
                else:
                    self.spline = Line(self.cpoints)

                if evt.actor:
                    self.top_pts.append(evt.picked3d)
                    self.topline = Points(self.top_pts, r=self.linewidth)
                    self.topline.c(self.linecolor).pickable(False)

                self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
                self.txt2d.background(self.linecolor)
                self.jline = Line(self.cpoints[0], self.cpoints[-1], lw=1, c=self.linecolor).pickable(0)
                self.add([self.points, self.spline, self.jline, self.topline])

    def _on_keypress(self, evt):
        if evt.keypress.lower() == 'z' and self.spline: # Cut mesh with a ribbon-like surface
            inv = False
            if evt.keypress == "Z":
                inv = True
            self.txt2d.background("red8").text("  ... working ...  ")
            self.render()
            self.mesh_prev = self.mesh.clone()
            tol = self.mesh.diagonal_size() / 2  # size of ribbon (not shown)
            pts = self.spline.points()
            n = fit_plane(pts, signed=True).normal  # compute normal vector to points
            rb = Ribbon(pts - tol * n, pts + tol * n, closed=True)
            self.mesh.cutWithMesh(rb, invert=inv)  # CUT
            self.txt2d.text(self.msg)  # put back original message
            if self.drawmode:
                self._on_right_click(evt)  # toggle mode to normal
            else:
                self.txt2d.background(self.color, self.alpha)
            self.remove([self.spline, self.points, self.jline, self.topline]).render()
            self.cpoints, self.points, self.spline = [], None, None
            self.top_pts, self.topline = [], None

        elif evt.keypress == "L":
            self.txt2d.background("red8")
            self.txt2d.text(" ... removing smaller ... \n ... parts of the mesh ... ")
            self.render()
            self.remove(self.mesh)
            self.mesh_prev = self.mesh
            mcut = self.mesh.extract_largest_region()
            mcut.filename = self.mesh.filename          # copy over various properties
            mcut.name = self.mesh.name
            mcut.scalarbar = self.mesh.scalarbar
            mcut.info = self.mesh.info
            self.mesh = mcut                            # discard old mesh by overwriting it
            self.txt2d.text(self.msg).background(self.color)   # put back original message
            self.add(mcut)

        elif evt.keypress == 'u':                     # Undo last action
            if self.drawmode:
                self._on_right_click(evt)                 # toggle mode to normal
            else:
                self.txt2d.background(self.color, self.alpha)
            self.remove([self.mesh, self.spline, self.jline, self.points, self.topline])
            self.mesh = self.mesh_prev
            self.cpoints, self.points, self.spline = [], None, None
            self.top_pts, self.topline = [], None
            self.add(self.mesh)

        elif evt.keypress in ('c', 'Delete'):
            # clear all points
            self.remove([self.spline, self.points, self.jline, self.topline]).render()
            self.cpoints, self.points, self.spline = [], None, None
            self.top_pts, self.topline = [], None

        elif evt.keypress == "r":  # reset camera and axes
            try:
                self.remove(self.axes_instances[0])
                self.axes_instances[0] = None
                self.add_global_axes(axtype=1, c=None)
                self.renderer.ResetCamera()
                self.interactor.Render()
            except:
                pass

        elif evt.keypress == "s":
            if self.mesh.filename:
                fname = os.path.basename(self.mesh.filename)
                fname, extension = os.path.splitext(fname)
                fname = fname.replace("_edited", "")
                fname = f"{fname}_edited{extension}"
            else:
                fname = "mesh_edited.vtk"
            self.write(fname)

    def write(self, filename="mesh_edited.vtk"):
        """Save the resulting mesh to file"""
        self.mesh.write(filename)
        vedo.logger.info(f"mesh saved to file {filename}")
        return self

    def start(self, *args, **kwargs):
        """Start window interaction (with mouse and keyboard)"""
        acts = [self.txt2d, self.mesh, self.points, self.spline, self.jline]
        self.show(acts + list(args), **kwargs)
        return self

########################################################################
class SplinePlotter(Plotter):
    """
    Create an interactive application that allows the user to click points and
    retrieve the coordinates of such points and optionally a spline or line
    (open or closed).

    Input object can be a image file name or a 3D mesh.
    """
    def __init__(self, obj, initpoints=(), **kwargs):

        super().__init__(**kwargs)

        self.mode    = 'trackball'
        self.verbose = True
        self.splined = True
        self.closed  = False
        self.lcolor  = 'yellow4'
        self.lwidth  = 3
        self.pcolor  = 'purple5'
        self.psize   = 10

        self.cpoints = list(initpoints)
        self.vpoints = None
        self.line = None

        if isinstance(obj, str):
            self.object = vedo.Picture(obj, channels=(0,1,2))
            # keep rgb but drop alpha channel
            self.mode = 'image'
        else:
            self.object = obj

        t = """Click to add a point
        Right-click to remove it
        Drag mouse to change constrast
        Press c to clear points
        Press q to continue""".replace("  ","")
        self.instructions = Text2D(t, pos='bottom-left', c='white', bg='green', font='Calco')

        self.callid1 = self.add_callback('KeyPress', self._key_press)
        self.callid2 = self.add_callback('LeftButtonPress', self._onLeftClick)
        self.callid3 = self.add_callback('RightButtonPress', self._on_right_click)

    def points(self, newpts=None):
        """Retrieve the 3D coordinates of the clicked points"""
        if newpts is not None:
            self.cpoints = newpts
            self._update()
            return self
        return np.array(self.cpoints)

    def _onLeftClick(self, evt):
        if not evt.actor: return
        p = evt.picked3d
        self.cpoints.append(p)
        self._update()
        if self.verbose:
            vedo.colors.printc("Added point:", precision(p,4), c='g')

    def _on_right_click(self, evt):
        if evt.actor and len(self.cpoints)>0:
            self.cpoints.pop() # pop removes from the list the last pt
            self._update()
            if self.verbose:
                vedo.colors.printc("Deleted last point", c="r")

    def _update(self):
        self.remove(self.line, self.vpoints)  # remove old points and spline
        self.vpoints = Points(self.cpoints).ps(self.psize).c(self.pcolor)
        self.vpoints.pickable(False)  # avoid picking the same point
        minnr = 1
        if self.splined:
            minnr = 2
        if len(self.cpoints) > minnr:
            if self.splined:
                try:
                    self.line = Spline(self.cpoints, closed=self.closed)
                except ValueError:
                    # if clicking too close splining might fail
                    self.cpoints.pop()
                    return
            else:
                self.line = Line(self.cpoints, closed=self.closed)
            self.line.c(self.lcolor).lw(3).pickable(False)
            self.add(self.vpoints, self.line)
        else:
            self.add(self.vpoints)

    def _key_press(self, evt):
        if evt.keypress == 'c':
            self.cpoints = []
            self.remove(self.line, self.vpoints).render()
            if self.verbose:
                vedo.colors.printc("==== Cleared all points ====", c="r", invert=True)

    def start(self):
        """Start the interaction"""
        self.show(self.object, self.instructions, mode=self.mode)
        return self


########################################################################
class Animation(Plotter):
    """
    A ``Plotter`` derived class that allows to animate simultaneously various objects
    by specifying event times and durations of different visual effects.

    Parameters
    ----------
    total_duration : float
        expand or shrink the total duration of video to this value

    time_resolution : float
        in seconds, save a frame at this rate

    show_progressbar : bool
        whether to show a progress bar or not

    video_filename : str
        output file name of the video

    video_fps : int
        desired value of the nr of frames per second

    .. warning:: this is still an experimental feature at the moment.
    """

    def __init__(
        self,
        total_duration=None,
        time_resolution=0.02,
        show_progressbar=True,
        video_filename="animation.mp4",
        video_fps=12,
    ):
        Plotter.__init__(self)
        self.resetcam = True

        self.events = []
        self.time_resolution = time_resolution
        self.total_duration = total_duration
        self.show_progressbar = show_progressbar
        self.video_filename = video_filename
        self.video_fps = video_fps
        self.bookingMode = True
        self._inputvalues = []
        self._performers = []
        self._lastT = None
        self._lastDuration = None
        self._lastActs = None
        self.eps = 0.00001

    def _parse(self, objs, t, duration):
        if t is None:
            if self._lastT:
                t = self._lastT
            else:
                t = 0.0
        if duration is None:
            if self._lastDuration:
                duration = self._lastDuration
            else:
                duration = 0.0
        if objs is None:
            if self._lastActs:
                objs = self._lastActs
            else:
                vedo.logger.error("Need to specify actors!")
                raise RuntimeError

        objs2 = objs

        if is_sequence(objs):
            objs2 = objs
        else:
            objs2 = [objs]

        # quantize time steps and duration
        t = int(t / self.time_resolution + 0.5) * self.time_resolution
        nsteps = int(duration / self.time_resolution + 0.5)
        duration = nsteps * self.time_resolution

        rng = np.linspace(t, t + duration, nsteps + 1)

        self._lastT = t
        self._lastDuration = duration
        self._lastActs = objs2

        for a in objs2:
            if a not in self.actors:
                self.actors.append(a)

        return objs2, t, duration, rng

    def switch_on(self, acts=None, t=None):
        """Switch on the input list of meshes."""
        return self.fade_in(acts, t, 0)

    def switch_off(self, acts=None, t=None):
        """Switch off the input list of meshes."""
        return self.fade_out(acts, t, 0)

    def fade_in(self, acts=None, t=None, duration=None):
        """Gradually switch on the input list of meshes by increasing opacity."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)
            for tt in rng:
                alpha = lin_interpolate(tt, [t, t + duration], [0, 1])
                self.events.append((tt, self.fade_in, acts, alpha))
        else:
            for a in self._performers:
                if hasattr(a, "alpha"):
                    if a.alpha() >= self._inputvalues:
                        continue
                    a.alpha(self._inputvalues)
        return self

    def fade_out(self, acts=None, t=None, duration=None):
        """Gradually switch off the input list of meshes by increasing transparency."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)
            for tt in rng:
                alpha = lin_interpolate(tt, [t, t + duration], [1, 0])
                self.events.append((tt, self.fade_out, acts, alpha))
        else:
            for a in self._performers:
                if a.alpha() <= self._inputvalues:
                    continue
                a.alpha(self._inputvalues)
        return self

    def change_alpha_between(self, alpha1, alpha2, acts=None, t=None, duration=None):
        """Gradually change transparency for the input list of meshes."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)
            for tt in rng:
                alpha = lin_interpolate(tt, [t, t + duration], [alpha1, alpha2])
                self.events.append((tt, self.fade_out, acts, alpha))
        else:
            for a in self._performers:
                a.alpha(self._inputvalues)
        return self

    def change_color(self, c, acts=None, t=None, duration=None):
        """Gradually change color for the input list of meshes."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)

            col2 = get_color(c)
            for tt in rng:
                inputvalues = []
                for a in acts:
                    col1 = a.color()
                    r = lin_interpolate(tt, [t, t + duration], [col1[0], col2[0]])
                    g = lin_interpolate(tt, [t, t + duration], [col1[1], col2[1]])
                    b = lin_interpolate(tt, [t, t + duration], [col1[2], col2[2]])
                    inputvalues.append((r, g, b))
                self.events.append((tt, self.change_color, acts, inputvalues))
        else:
            for i, a in enumerate(self._performers):
                a.color(self._inputvalues[i])
        return self

    def change_backcolor(self, c, acts=None, t=None, duration=None):
        """Gradually change backface color for the input list of meshes.
        An initial backface color should be set in advance."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)

            col2 = get_color(c)
            for tt in rng:
                inputvalues = []
                for a in acts:
                    if a.GetBackfaceProperty():
                        col1 = a.backColor()
                        r = lin_interpolate(tt, [t, t + duration], [col1[0], col2[0]])
                        g = lin_interpolate(tt, [t, t + duration], [col1[1], col2[1]])
                        b = lin_interpolate(tt, [t, t + duration], [col1[2], col2[2]])
                        inputvalues.append((r, g, b))
                    else:
                        inputvalues.append(None)
                self.events.append((tt, self.change_backcolor, acts, inputvalues))
        else:
            for i, a in enumerate(self._performers):
                a.backColor(self._inputvalues[i])
        return self

    def change_to_wireframe(self, acts=None, t=None):
        """Switch representation to wireframe for the input list of meshes at time `t`."""
        if self.bookingMode:
            acts, t, _, _ = self._parse(acts, t, None)
            self.events.append((t, self.change_to_wireframe, acts, True))
        else:
            for a in self._performers:
                a.wireframe(self._inputvalues)
        return self

    def change_to_surface(self, acts=None, t=None):
        """Switch representation to surface for the input list of meshes at time `t`."""
        if self.bookingMode:
            acts, t, _, _ = self._parse(acts, t, None)
            self.events.append((t, self.change_to_surface, acts, False))
        else:
            for a in self._performers:
                a.wireframe(self._inputvalues)
        return self

    def change_line_width(self, lw, acts=None, t=None, duration=None):
        """Gradually change line width of the mesh edges for the input list of meshes."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)
            for tt in rng:
                inputvalues = []
                for a in acts:
                    newlw = lin_interpolate(tt, [t, t + duration], [a.lw(), lw])
                    inputvalues.append(newlw)
                self.events.append((tt, self.changeLineWidth, acts, inputvalues))
        else:
            for i, a in enumerate(self._performers):
                a.lw(self._inputvalues[i])
        return self

    def change_line_color(self, c, acts=None, t=None, duration=None):
        """Gradually change line color of the mesh edges for the input list of meshes."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)
            col2 = get_color(c)
            for tt in rng:
                inputvalues = []
                for a in acts:
                    col1 = a.linecolor()
                    r = lin_interpolate(tt, [t, t + duration], [col1[0], col2[0]])
                    g = lin_interpolate(tt, [t, t + duration], [col1[1], col2[1]])
                    b = lin_interpolate(tt, [t, t + duration], [col1[2], col2[2]])
                    inputvalues.append((r, g, b))
                self.events.append((tt, self.change_line_color, acts, inputvalues))
        else:
            for i, a in enumerate(self._performers):
                a.linecolor(self._inputvalues[i])
        return self

    def change_lighting(self, style, acts=None, t=None, duration=None):
        """Gradually change the lighting style for the input list of meshes.

        Allowed styles are: [metallic, plastic, shiny, glossy, default].
        """
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)

            c = (1,1,0.99)
            if   style=='metallic': pars = [0.1, 0.3, 1.0, 10, c]
            elif style=='plastic' : pars = [0.3, 0.4, 0.3,  5, c]
            elif style=='shiny'   : pars = [0.2, 0.6, 0.8, 50, c]
            elif style=='glossy'  : pars = [0.1, 0.7, 0.9, 90, c]
            elif style=='default' : pars = [0.1, 1.0, 0.05, 5, c]
            else:
                vedo.logger.error(f"Unknown lighting style {style}")

            for tt in rng:
                inputvalues = []
                for a in acts:
                    pr = a.GetProperty()
                    aa = pr.GetAmbient()
                    ad = pr.GetDiffuse()
                    asp = pr.GetSpecular()
                    aspp = pr.GetSpecularPower()
                    naa  = lin_interpolate(tt, [t,t+duration], [aa,  pars[0]])
                    nad  = lin_interpolate(tt, [t,t+duration], [ad,  pars[1]])
                    nasp = lin_interpolate(tt, [t,t+duration], [asp, pars[2]])
                    naspp= lin_interpolate(tt, [t,t+duration], [aspp,pars[3]])
                    inputvalues.append((naa, nad, nasp, naspp))
                self.events.append((tt, self.change_lighting, acts, inputvalues))
        else:
            for i, a in enumerate(self._performers):
                pr = a.GetProperty()
                vals = self._inputvalues[i]
                pr.SetAmbient(vals[0])
                pr.SetDiffuse(vals[1])
                pr.SetSpecular(vals[2])
                pr.SetSpecularPower(vals[3])
        return self

    def move(self, act=None, pt=(0, 0, 0), t=None, duration=None, style="linear"):
        """Smoothly change the position of a specific object to a new point in space."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(act, t, duration)
            if len(acts) != 1:
                vedo.logger.error("in move(), can move only one object.")
            cpos = acts[0].pos()
            pt = np.array(pt)
            dv = (pt - cpos) / len(rng)
            for j, tt in enumerate(rng):
                i = j + 1
                if "quad" in style:
                    x = i / len(rng)
                    y = x * x
                    self.events.append((tt, self.move, acts, cpos + dv * i * y))
                else:
                    self.events.append((tt, self.move, acts, cpos + dv * i))
        else:
            self._performers[0].pos(self._inputvalues)
        return self

    def rotate(self, act=None, axis=(1, 0, 0), angle=0, t=None, duration=None):
        """Smoothly rotate a specific object by a specified angle and axis."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(act, t, duration)
            if len(acts) != 1:
                vedo.logger.error("in rotate(), can move only one object.")
            for tt in rng:
                ang = angle / len(rng)
                self.events.append((tt, self.rotate, acts, (axis, ang)))
        else:
            ax = self._inputvalues[0]
            if ax == "x":
                self._performers[0].rotate_x(self._inputvalues[1])
            elif ax == "y":
                self._performers[0].rotate_y(self._inputvalues[1])
            elif ax == "z":
                self._performers[0].rotate_z(self._inputvalues[1])
        return self

    def scale(self, acts=None, factor=1, t=None, duration=None):
        """Smoothly scale a specific object to a specified scale factor."""
        if self.bookingMode:
            acts, t, duration, rng = self._parse(acts, t, duration)
            for tt in rng:
                fac = lin_interpolate(tt, [t, t + duration], [1, factor])
                self.events.append((tt, self.scale, acts, fac))
        else:
            for a in self._performers:
                a.scale(self._inputvalues)
        return self

    def mesh_erode(self, act=None, corner=6, t=None, duration=None):
        """Erode a mesh by removing cells that are close to one of the 8 corners
        of the bounding box.
        """
        if self.bookingMode:
            acts, t, duration, rng = self._parse(act, t, duration)
            if len(acts) != 1:
                vedo.logger.error("in meshErode(), can erode only one object.")
            diag = acts[0].diagonal_size()
            x0, x1, y0, y1, z0, z1 = acts[0].GetBounds()
            corners = [
                (x0, y0, z0),
                (x1, y0, z0),
                (x1, y1, z0),
                (x0, y1, z0),
                (x0, y0, z1),
                (x1, y0, z1),
                (x1, y1, z1),
                (x0, y1, z1),
            ]
            pcl = acts[0].closestPoint(corners[corner])
            dmin = np.linalg.norm(pcl - corners[corner])
            for tt in rng:
                d = lin_interpolate(tt, [t, t + duration], [dmin, diag * 1.01])
                if d > 0:
                    ids = acts[0].closestPoint(
                        corners[corner], radius=d, returnPointId=True
                    )
                    if len(ids) <= acts[0].npoints:
                        self.events.append((tt, self.meshErode, acts, ids))
        return self

    def play(self):
        """Play the internal list of events and save a video."""

        self.events = sorted(self.events, key=lambda x: x[0])
        self.bookingMode = False

        if self.show_progressbar:
            pb = vedo.ProgressBar(0, len(self.events), c="g")

        if self.total_duration is None:
            self.total_duration = self.events[-1][0] - self.events[0][0]

        if self.video_filename:
            vd = vedo.Video(self.video_filename, fps=self.video_fps, duration=self.total_duration)

        ttlast = 0
        for e in self.events:

            tt, action, self._performers, self._inputvalues = e
            action(0, 0)

            dt = tt - ttlast
            if dt > self.eps:
                self.show(interactive=False, resetcam=self.resetcam)
                if self.video_filename: vd.add_frame()

                if dt > self.time_resolution+self.eps:
                    if self.video_filename: vd.pause(dt)

            ttlast = tt

            if self.show_progressbar:
                pb.print("t=" + str(int(tt * 100) / 100) + "s,  " + action.__name__)

        self.show(interactive=False, resetcam=self.resetcam)
        if self.video_filename:
            vd.add_frame()
            vd.close()

        self.show(interactive=True, resetcam=self.resetcam)
        self.bookingMode = True


class Clock(vedo.Assembly):
    """
    Create a clock with current time or user provided time.

    Parameters
    ----------
    h : int
        hours in range [0,23]

    m : int
        minutes in range [0,59]

    s : int
        seconds in range [0,59]

    font : str
        font type

    title : str
        some extra text to show on the clock

    c : str
        color of the numbers


    Example:
        .. code-block:: python

            import time
            from vedo import show
            from vedo.applications import Clock
            clock = Clock()
            plt = show(clock, interactive=False)
            for i in range(10):
                time.sleep(1)
                clock.update()
                plt.render()
            plt.close()
    """
    def __init__(
            self,
            h=None,
            m=None,
            s=None,
            font="Quikhand",
            title="",
            c="k",
        ):
        self.elapsed = 0
        self._start = time.time()

        wd = ""
        if h is None and m is None:
            t = time.localtime()
            h = t.tm_hour
            m = t.tm_min
            s = t.tm_sec
            if not title:
                d = ["Mon","Tue","Wed","Thu","Fri","Sat","Sun"]
                wd = d[t.tm_wday] + " "

        h = int(h) % 24
        m = int(m) % 60
        t = (h*60+m) / 12 / 60

        if not title:
            if h<10:
                h = f"0{h}"
            if m<10:
                m = f"0{m}"
            title = f"{h}:{m}"

        alpha = 2*np.pi*t + np.pi/2
        beta  = 12*2*np.pi*t + np.pi/2

        x1,y1 = np.cos(alpha), np.sin(alpha)
        x2,y2 = np.cos(beta),  np.sin(beta)
        if s is not None:
            s = int(s) % 60
            gamma = s*2*np.pi /60 + np.pi/2
            x3,y3 = np.cos(gamma), np.sin(gamma)

        ore = Line([0,0], [x1,y1], lw=14, c='red4').scale(0.5).mirror()
        minu= Line([0,0], [x2,y2], lw=7, c='blue3').scale(0.75).mirror()
        secs = None
        if s is not None:
            secs= Line([0,0], [x3,y3], lw=1, c='k').scale(0.95).mirror()
            secs.z(0.003)
        back1 = vedo.shapes.Circle(res=180, c="k6").lw(1)
        back2 = vedo.shapes.Circle(res=12).mirror().scale(0.86).rotate_z(-360/12)
        labels = back2.labels(
            range(1,13),
            justify="center",
            font=font,
            c=c,
        )
        txt = vedo.shapes.Text3D(wd+title,
            font="VictorMono",
            justify="top-center",
            s=.1,
            c=c,
        )
        txt.pos(0,-0.25, 0.001)
        labels.z(0.001)
        minu.z(0.002)
        vedo.Assembly.__init__(self, [back1, labels, ore, minu, secs, txt])
        self.name = "Clock"

    def update(self, h=None, m=None, s=None):
        """Update clock with current or user time"""
        parts = self.unpack()
        self.elapsed = time.time() - self._start

        if h is None and m is None:
            t = time.localtime()
            h = t.tm_hour
            m = t.tm_min
            s = t.tm_sec

        h = int(h) % 24
        m = int(m) % 60
        t = (h*60+m) / 12 / 60

        alpha = 2*np.pi*t + np.pi/2
        beta  = 12*2*np.pi*t + np.pi/2

        x1,y1 = np.cos(alpha), np.sin(alpha)
        x2,y2 = np.cos(beta),  np.sin(beta)
        if s is not None:
            s = int(s) % 60
            gamma = s*2*np.pi /60 + np.pi/2
            x3,y3 = np.cos(gamma), np.sin(gamma)

        pts2 = parts[2].points()
        pts2[1] = [-x1*0.5,y1*0.5, 0.001]
        parts[2].points(pts2)

        pts3 = parts[3].points()
        pts3[1] = [-x2*0.75,y2*0.75, 0.002]
        parts[3].points(pts3)

        if s is not None:
            pts4 = parts[4].points()
            pts4[1] = [-x3*0.95,y3*0.95, 0.003]
            parts[4].points(pts4)

        return self

Classes

class Browser (objects=(), sliderpos=((0.55, 0.07), (0.96, 0.07)), c=None, prefix='', pos=(0, 0), size='auto', screensize='auto', title='Browser', bg='white', bg2=None, axes=4, resetcam=False, interactive=True)

Browse a serie of vedo objects by using a simple slider.

Example

.. code-block:: python

import vedo
from vedo.applications import Browser
meshes = vedo.load("data/2*0.vtk") # a python list
plt = Browser(meshes, resetcam=1, axes=4) # a vedo.Plotter
plt.show()

Hint: examples/other/morphomatics_tube.py

Expand source code
class Browser(Plotter):
    """
    Browse a serie of vedo objects by using a simple slider.

    Example:
        .. code-block:: python

            import vedo
            from vedo.applications import Browser
            meshes = vedo.load("data/2*0.vtk") # a python list
            plt = Browser(meshes, resetcam=1, axes=4) # a vedo.Plotter
            plt.show()

    .. hint:: examples/other/morphomatics_tube.py
    """
    def __init__(
            self,
            objects=(),
            sliderpos=((0.55, 0.07),(0.96, 0.07)),
            c=None,  # slider color
            prefix="",
            pos=(0, 0),
            size="auto",
            screensize="auto",
            title="Browser",
            bg="white",
            bg2=None,
            axes=4,
            resetcam=False,
            interactive=True,
        ):

        Plotter.__init__(
            self,
            pos=pos,
            size=size,
            screensize=screensize,
            title=title,
            bg=bg,
            bg2=bg2,
            axes=axes,
            interactive=interactive,
        )

        self += objects

        self.slider = None

        # define the slider
        def sliderfunc(widget, event=None):
            k = int(widget.GetRepresentation().GetValue())
            ak = self.actors[k]
            for a in self.actors:
                if a == ak:
                    a.on()
                else:
                    a.off()
            if resetcam:
                self.resetCamera()
            tx = str(k)
            if ak.filename:
                tx = ak.filename.split("/")[-1]
                tx = tx.split("\\")[-1]  # windows os
            elif ak.name:
                tx = ak.name
            widget.GetRepresentation().SetTitleText(prefix + tx)

        self.slider = self.add_slider(
            sliderfunc,
            0.5,
            len(objects) - 0.5,
            pos=sliderpos,
            font="courier",
            c=c,
            show_value=False,
        )
        self.slider.GetRepresentation().SetTitleHeight(0.020)
        sliderfunc(self.slider)  # init call

Ancestors

Inherited members

class Clock (h=None, m=None, s=None, font='Quikhand', title='', c='k')

Create a clock with current time or user provided time.

Parameters

h : int
hours in range [0,23]
m : int
minutes in range [0,59]
s : int
seconds in range [0,59]
font : str
font type
title : str
some extra text to show on the clock
c : str
color of the numbers

Example

.. code-block:: python

import time
from vedo import show
from vedo.applications import Clock
clock = Clock()
plt = show(clock, interactive=False)
for i in range(10):
    time.sleep(1)
    clock.update()
    plt.render()
plt.close()
Expand source code
class Clock(vedo.Assembly):
    """
    Create a clock with current time or user provided time.

    Parameters
    ----------
    h : int
        hours in range [0,23]

    m : int
        minutes in range [0,59]

    s : int
        seconds in range [0,59]

    font : str
        font type

    title : str
        some extra text to show on the clock

    c : str
        color of the numbers


    Example:
        .. code-block:: python

            import time
            from vedo import show
            from vedo.applications import Clock
            clock = Clock()
            plt = show(clock, interactive=False)
            for i in range(10):
                time.sleep(1)
                clock.update()
                plt.render()
            plt.close()
    """
    def __init__(
            self,
            h=None,
            m=None,
            s=None,
            font="Quikhand",
            title="",
            c="k",
        ):
        self.elapsed = 0
        self._start = time.time()

        wd = ""
        if h is None and m is None:
            t = time.localtime()
            h = t.tm_hour
            m = t.tm_min
            s = t.tm_sec
            if not title:
                d = ["Mon","Tue","Wed","Thu","Fri","Sat","Sun"]
                wd = d[t.tm_wday] + " "

        h = int(h) % 24
        m = int(m) % 60
        t = (h*60+m) / 12 / 60

        if not title:
            if h<10:
                h = f"0{h}"
            if m<10:
                m = f"0{m}"
            title = f"{h}:{m}"

        alpha = 2*np.pi*t + np.pi/2
        beta  = 12*2*np.pi*t + np.pi/2

        x1,y1 = np.cos(alpha), np.sin(alpha)
        x2,y2 = np.cos(beta),  np.sin(beta)
        if s is not None:
            s = int(s) % 60
            gamma = s*2*np.pi /60 + np.pi/2
            x3,y3 = np.cos(gamma), np.sin(gamma)

        ore = Line([0,0], [x1,y1], lw=14, c='red4').scale(0.5).mirror()
        minu= Line([0,0], [x2,y2], lw=7, c='blue3').scale(0.75).mirror()
        secs = None
        if s is not None:
            secs= Line([0,0], [x3,y3], lw=1, c='k').scale(0.95).mirror()
            secs.z(0.003)
        back1 = vedo.shapes.Circle(res=180, c="k6").lw(1)
        back2 = vedo.shapes.Circle(res=12).mirror().scale(0.86).rotate_z(-360/12)
        labels = back2.labels(
            range(1,13),
            justify="center",
            font=font,
            c=c,
        )
        txt = vedo.shapes.Text3D(wd+title,
            font="VictorMono",
            justify="top-center",
            s=.1,
            c=c,
        )
        txt.pos(0,-0.25, 0.001)
        labels.z(0.001)
        minu.z(0.002)
        vedo.Assembly.__init__(self, [back1, labels, ore, minu, secs, txt])
        self.name = "Clock"

    def update(self, h=None, m=None, s=None):
        """Update clock with current or user time"""
        parts = self.unpack()
        self.elapsed = time.time() - self._start

        if h is None and m is None:
            t = time.localtime()
            h = t.tm_hour
            m = t.tm_min
            s = t.tm_sec

        h = int(h) % 24
        m = int(m) % 60
        t = (h*60+m) / 12 / 60

        alpha = 2*np.pi*t + np.pi/2
        beta  = 12*2*np.pi*t + np.pi/2

        x1,y1 = np.cos(alpha), np.sin(alpha)
        x2,y2 = np.cos(beta),  np.sin(beta)
        if s is not None:
            s = int(s) % 60
            gamma = s*2*np.pi /60 + np.pi/2
            x3,y3 = np.cos(gamma), np.sin(gamma)

        pts2 = parts[2].points()
        pts2[1] = [-x1*0.5,y1*0.5, 0.001]
        parts[2].points(pts2)

        pts3 = parts[3].points()
        pts3[1] = [-x2*0.75,y2*0.75, 0.002]
        parts[3].points(pts3)

        if s is not None:
            pts4 = parts[4].points()
            pts4[1] = [-x3*0.95,y3*0.95, 0.003]
            parts[4].points(pts4)

        return self

Ancestors

  • Assembly
  • vtkmodules.vtkRenderingCore.vtkAssembly
  • vtkmodules.vtkRenderingCore.vtkProp3D
  • vtkmodules.vtkRenderingCore.vtkProp
  • vtkmodules.vtkCommonCore.vtkObject
  • vtkmodules.vtkCommonCore.vtkObjectBase
  • Base3DProp

Methods

def update(self, h=None, m=None, s=None)

Update clock with current or user time

Expand source code
def update(self, h=None, m=None, s=None):
    """Update clock with current or user time"""
    parts = self.unpack()
    self.elapsed = time.time() - self._start

    if h is None and m is None:
        t = time.localtime()
        h = t.tm_hour
        m = t.tm_min
        s = t.tm_sec

    h = int(h) % 24
    m = int(m) % 60
    t = (h*60+m) / 12 / 60

    alpha = 2*np.pi*t + np.pi/2
    beta  = 12*2*np.pi*t + np.pi/2

    x1,y1 = np.cos(alpha), np.sin(alpha)
    x2,y2 = np.cos(beta),  np.sin(beta)
    if s is not None:
        s = int(s) % 60
        gamma = s*2*np.pi /60 + np.pi/2
        x3,y3 = np.cos(gamma), np.sin(gamma)

    pts2 = parts[2].points()
    pts2[1] = [-x1*0.5,y1*0.5, 0.001]
    parts[2].points(pts2)

    pts3 = parts[3].points()
    pts3[1] = [-x2*0.75,y2*0.75, 0.002]
    parts[3].points(pts3)

    if s is not None:
        pts4 = parts[4].points()
        pts4[1] = [-x3*0.95,y3*0.95, 0.003]
        parts[4].points(pts4)

    return self

Inherited members

class FreeHandCutPlotter (mesh, splined=True, font='Bongas', alpha=0.9, lw=4, lc='red5', pc='red4', c='green3', tc='k9', tol=0.008, **options)

A Plotter derived class which edits polygonal meshes interactively. Can also be invoked from command line. E.g. with:

vedo --edit https://vedo.embl.es/examples/data/porsche.ply

Usage

- Left-click and hold to rotate
- Right-click and move to draw line
- Second right-click to stop drawing
- Press c to clear points
-       z/Z to cut mesh (Z inverts inside-out the selection area)
-       L to keep only the largest connected surface
-       s to save mesh to file (tag _edited is appended to filename)
-       u to undo last action
-       h for help, i for info

Parameters

mesh : Mesh, Points
The input Mesh or pointcloud.
splined : bool
join points with a spline or a simple line.
font : str
Font name for the instructions.
alpha : float
transparency of the instruction message panel.
lw : str
selection line width.
lc : str
selection line color.
pc : str
selection points color.
c : str
backgound color of instructions.
tc : str
text color of instructions.
tol : int
tolerance of the point proximity.

Hint: examples/basic/cutFreeHand.py

Expand source code
class FreeHandCutPlotter(Plotter):
    """
    A ``Plotter`` derived class which edits polygonal meshes interactively.
    Can also be invoked from command line. E.g. with:

    ``vedo --edit https://vedo.embl.es/examples/data/porsche.ply``

    Usage
    -----
        - Left-click and hold to rotate
        - Right-click and move to draw line
        - Second right-click to stop drawing
        - Press c to clear points
        -       z/Z to cut mesh (Z inverts inside-out the selection area)
        -       L to keep only the largest connected surface
        -       s to save mesh to file (tag _edited is appended to filename)
        -       u to undo last action
        -       h for help, i for info

    Parameters
    ----------
    mesh : Mesh, Points
        The input Mesh or pointcloud.

    splined : bool
        join points with a spline or a simple line.

    font : str
        Font name for the instructions.

    alpha : float
        transparency of the instruction message panel.

    lw : str
        selection line width.

    lc : str
        selection line color.

    pc : str
        selection points color.

    c : str
        backgound color of instructions.

    tc : str
        text color of instructions.

    tol : int
        tolerance of the point proximity.

    .. hint:: examples/basic/cutFreeHand.py
        .. image:: https://vedo.embl.es/images/basic/cutFreeHand.gif
    """

    # thanks to Jakub Kaminski for the original version of this script
    def __init__(
            self,
            mesh,
            splined=True,
            font="Bongas",
            alpha=0.9,
            lw=4,
            lc="red5",
            pc="red4",
            c="green3",
            tc="k9",
            tol=0.008,
            **options
        ):

        if not isinstance(mesh, Points):
            vedo.logger.error("FreeHandCutPlotter input must be Points or Mesh")
            raise RuntimeError()

        super().__init__(**options)

        self.mesh = mesh
        self.mesh_prev = mesh
        self.splined = splined
        self.linecolor = lc
        self.linewidth = lw
        self.pointcolor = pc
        self.color = c
        self.alpha = alpha

        self.msg = "Right-click and move to draw line\n"
        self.msg += "Second right-click to stop drawing\n"
        self.msg += "Press L to extract largest surface\n"
        self.msg += "        z/Z to cut mesh (s to save)\n"
        self.msg += "        c to clear points, u to undo"
        self.txt2d = Text2D(self.msg, pos="top-left", font=font, s=0.9)
        self.txt2d.c(tc).background(c, alpha).frame()

        self.idkeypress = self.add_callback("KeyPress", self._on_keypress)
        self.idrightclck = self.add_callback("RightButton", self._on_right_click)
        self.idmousemove = self.add_callback("MouseMove", self._on_mouse_move)
        self.drawmode = False
        self.tol = tol  # tolerance of point distance
        self.cpoints = []
        self.points = None
        self.spline = None
        self.jline = None
        self.topline = None
        self.top_pts = []

    def init(self, initpoints):
        """Set an initial number of points to define a region"""
        if isinstance(initpoints, Points):
            self.cpoints = initpoints.points()
        else:
            self.cpoints = np.array(initpoints)
        self.points = Points(self.cpoints, r=self.linewidth).c(self.pointcolor).pickable(0)
        if self.splined:
            self.spline = Spline(self.cpoints, res=len(self.cpoints) * 4)
        else:
            self.spline = Line(self.cpoints)
        self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
        self.jline = Line(self.cpoints[0], self.cpoints[-1], lw=1, c=self.linecolor).pickable(0)
        self.add([self.points, self.spline, self.jline], render=False)
        return self

    def _on_right_click(self, evt):
        self.drawmode = not self.drawmode  # toggle mode
        if self.drawmode:
            self.txt2d.background(self.linecolor, self.alpha)
        else:
            self.txt2d.background(self.color, self.alpha)
            if len(self.cpoints) > 2:
                self.remove([self.spline, self.jline])
                if self.splined:  # show the spline closed
                    self.spline = Spline(
                        self.cpoints, closed=True, res=len(self.cpoints) * 4
                    )
                else:
                    self.spline = Line(self.cpoints, closed=True)
                self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
                self.add(self.spline)

    def _on_mouse_move(self, evt):
        if self.drawmode:
            cpt = self.compute_world_position(evt.picked2d) # make this 2d-screen point 3d
            if self.cpoints and mag(cpt - self.cpoints[-1]) < self.mesh.diagonal_size()*self.tol:
                return  # new point is too close to the last one. skip
            self.cpoints.append(cpt)
            if len(self.cpoints) > 2:
                self.remove([self.points, self.spline, self.jline, self.topline])
                self.points = Points(self.cpoints, r=self.linewidth).c(self.pointcolor).pickable(0)
                if self.splined:
                    self.spline = Spline(self.cpoints, res=len(self.cpoints)*4) # not closed here
                else:
                    self.spline = Line(self.cpoints)

                if evt.actor:
                    self.top_pts.append(evt.picked3d)
                    self.topline = Points(self.top_pts, r=self.linewidth)
                    self.topline.c(self.linecolor).pickable(False)

                self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
                self.txt2d.background(self.linecolor)
                self.jline = Line(self.cpoints[0], self.cpoints[-1], lw=1, c=self.linecolor).pickable(0)
                self.add([self.points, self.spline, self.jline, self.topline])

    def _on_keypress(self, evt):
        if evt.keypress.lower() == 'z' and self.spline: # Cut mesh with a ribbon-like surface
            inv = False
            if evt.keypress == "Z":
                inv = True
            self.txt2d.background("red8").text("  ... working ...  ")
            self.render()
            self.mesh_prev = self.mesh.clone()
            tol = self.mesh.diagonal_size() / 2  # size of ribbon (not shown)
            pts = self.spline.points()
            n = fit_plane(pts, signed=True).normal  # compute normal vector to points
            rb = Ribbon(pts - tol * n, pts + tol * n, closed=True)
            self.mesh.cutWithMesh(rb, invert=inv)  # CUT
            self.txt2d.text(self.msg)  # put back original message
            if self.drawmode:
                self._on_right_click(evt)  # toggle mode to normal
            else:
                self.txt2d.background(self.color, self.alpha)
            self.remove([self.spline, self.points, self.jline, self.topline]).render()
            self.cpoints, self.points, self.spline = [], None, None
            self.top_pts, self.topline = [], None

        elif evt.keypress == "L":
            self.txt2d.background("red8")
            self.txt2d.text(" ... removing smaller ... \n ... parts of the mesh ... ")
            self.render()
            self.remove(self.mesh)
            self.mesh_prev = self.mesh
            mcut = self.mesh.extract_largest_region()
            mcut.filename = self.mesh.filename          # copy over various properties
            mcut.name = self.mesh.name
            mcut.scalarbar = self.mesh.scalarbar
            mcut.info = self.mesh.info
            self.mesh = mcut                            # discard old mesh by overwriting it
            self.txt2d.text(self.msg).background(self.color)   # put back original message
            self.add(mcut)

        elif evt.keypress == 'u':                     # Undo last action
            if self.drawmode:
                self._on_right_click(evt)                 # toggle mode to normal
            else:
                self.txt2d.background(self.color, self.alpha)
            self.remove([self.mesh, self.spline, self.jline, self.points, self.topline])
            self.mesh = self.mesh_prev
            self.cpoints, self.points, self.spline = [], None, None
            self.top_pts, self.topline = [], None
            self.add(self.mesh)

        elif evt.keypress in ('c', 'Delete'):
            # clear all points
            self.remove([self.spline, self.points, self.jline, self.topline]).render()
            self.cpoints, self.points, self.spline = [], None, None
            self.top_pts, self.topline = [], None

        elif evt.keypress == "r":  # reset camera and axes
            try:
                self.remove(self.axes_instances[0])
                self.axes_instances[0] = None
                self.add_global_axes(axtype=1, c=None)
                self.renderer.ResetCamera()
                self.interactor.Render()
            except:
                pass

        elif evt.keypress == "s":
            if self.mesh.filename:
                fname = os.path.basename(self.mesh.filename)
                fname, extension = os.path.splitext(fname)
                fname = fname.replace("_edited", "")
                fname = f"{fname}_edited{extension}"
            else:
                fname = "mesh_edited.vtk"
            self.write(fname)

    def write(self, filename="mesh_edited.vtk"):
        """Save the resulting mesh to file"""
        self.mesh.write(filename)
        vedo.logger.info(f"mesh saved to file {filename}")
        return self

    def start(self, *args, **kwargs):
        """Start window interaction (with mouse and keyboard)"""
        acts = [self.txt2d, self.mesh, self.points, self.spline, self.jline]
        self.show(acts + list(args), **kwargs)
        return self

Ancestors

Methods

def init(self, initpoints)

Set an initial number of points to define a region

Expand source code
def init(self, initpoints):
    """Set an initial number of points to define a region"""
    if isinstance(initpoints, Points):
        self.cpoints = initpoints.points()
    else:
        self.cpoints = np.array(initpoints)
    self.points = Points(self.cpoints, r=self.linewidth).c(self.pointcolor).pickable(0)
    if self.splined:
        self.spline = Spline(self.cpoints, res=len(self.cpoints) * 4)
    else:
        self.spline = Line(self.cpoints)
    self.spline.lw(self.linewidth).c(self.linecolor).pickable(False)
    self.jline = Line(self.cpoints[0], self.cpoints[-1], lw=1, c=self.linecolor).pickable(0)
    self.add([self.points, self.spline, self.jline], render=False)
    return self
def start(self, *args, **kwargs)

Start window interaction (with mouse and keyboard)

Expand source code
def start(self, *args, **kwargs):
    """Start window interaction (with mouse and keyboard)"""
    acts = [self.txt2d, self.mesh, self.points, self.spline, self.jline]
    self.show(acts + list(args), **kwargs)
    return self
def write(self, filename='mesh_edited.vtk')

Save the resulting mesh to file

Expand source code
def write(self, filename="mesh_edited.vtk"):
    """Save the resulting mesh to file"""
    self.mesh.write(filename)
    vedo.logger.info(f"mesh saved to file {filename}")
    return self

Inherited members

class IsosurfaceBrowser (volume, threshold=None, c=None, alpha=1, lego=False, res=50, precompute=False, progress=False, cmap='hot', delayed=False, sliderpos=4, pos=(0, 0), size='auto', screensize='auto', title='', bg='white', bg2=None, axes=1, interactive=True)

Generate a Plotter for Volume isosurfacing using a slider.

Set delayed=True to delay slider update on mouse release.

Set res to set the resolution, e.g. the number of desired isosurfaces to be generated on the fly.

Set precompute=True to precompute the isosurfaces (so slider browsing will be smoother).

Hint: examples/volumetric/app_isobrowser.py

Expand source code
class IsosurfaceBrowser(Plotter):
    """
    Generate a ``Plotter`` for Volume isosurfacing using a slider.

    Set ``delayed=True`` to delay slider update on mouse release.

    Set ``res`` to set the resolution, e.g. the number of desired isosurfaces to be
    generated on the fly.

    Set ``precompute=True`` to precompute the isosurfaces (so slider browsing will be smoother).

    .. hint:: examples/volumetric/app_isobrowser.py
        .. image:: https://vedo.embl.es/images/advanced/app_isobrowser.gif
    """

    def __init__(
            self,
            volume,
            threshold=None,
            c=None,
            alpha=1,
            lego=False,
            res=50,
            precompute=False,
            progress=False,
            cmap='hot',
            delayed=False,
            sliderpos=4,
            pos=(0,0),
            size="auto",
            screensize="auto",
            title="",
            bg="white",
            bg2=None,
            axes=1,
            interactive=True,
        ):

        Plotter.__init__(
            self,
            pos=pos,
            bg=bg,
            bg2=bg2,
            size=size,
            screensize=screensize,
            title=title,
            interactive=interactive,
            axes=axes,
        )

        self._prev_value = 1e30

        scrange = volume.scalar_range()
        delta = scrange[1] - scrange[0]
        if not delta:
            return

        if lego:
            res = int(res / 2)  # because lego is much slower
            slidertitle = ""
        else:
            slidertitle = "threshold"

        allowed_vals = np.linspace(scrange[0], scrange[1], num=res)

        bacts = {}  # cache the meshes so we dont need to recompute
        if precompute:
            delayed = False  # no need to delay the slider in this case
            if progress:
                pb = vedo.ProgressBar(0, len(allowed_vals))

            for value in allowed_vals:
                value_name = precision(value, 2)
                if lego:
                    mesh = volume.legosurface(vmin=value)
                    if mesh.NCells():
                        mesh.cmap(cmap, vmin=scrange[0], vmax=scrange[1], on="cells")
                else:
                    mesh = volume.isosurface(threshold=value).color(c).alpha(alpha)
                bacts.update({value_name: mesh})  # store it
                if progress:
                    pb.print("isosurfacing volume..")

        ############################## threshold slider callback
        def sliderThres(widget, event):

            prevact = self.actors[0]
            if isinstance(widget, float):
                value = widget
            else:
                value = widget.GetRepresentation().GetValue()

            # snap to the closest
            idx = (np.abs(allowed_vals - value)).argmin()
            value = allowed_vals[idx]

            if abs(value - self._prev_value) / delta < 0.001:
                return
            self._prev_value = value

            value_name = precision(value, 2)
            if value_name in bacts:  # reusing the already existing mesh
                # print('reusing')
                mesh = bacts[value_name]
            else:  # else generate it
                # print('generating', value)
                if lego:
                    mesh = volume.legosurface(vmin=value)
                    if mesh.NCells():
                        mesh.cmap(cmap, vmin=scrange[0], vmax=scrange[1], on="cells")
                else:
                    mesh = volume.isosurface(threshold=value).color(c).alpha(alpha)
                bacts.update({value_name: mesh})  # store it

            self.renderer.RemoveActor(prevact)
            self.renderer.AddActor(mesh)
            self.actors[0] = mesh

        ################################################

        if threshold is None:
            threshold = delta / 3.0 + scrange[0]

        self.actors = [None]
        sliderThres(threshold, "")  # init call
        if lego:
            self.actors[0].add_scalarbar(pos=(0.8, 0.12))

        self.add_slider(
            sliderThres,
            scrange[0] + 0.02 * delta,
            scrange[1] - 0.02 * delta,
            value=threshold,
            pos=sliderpos,
            title=slidertitle,
            show_value=True,
            delayed=delayed,
        )

Ancestors

Inherited members

class RayCastPlotter (volume, **kwargs)

Generate a Plotter window for Volume rendering using ray casting.

Returns the Plotter object.

Hint: examples/volumetric/app_raycaster.py

Expand source code
class RayCastPlotter(Plotter):
    """
    Generate a ``Plotter`` window for Volume rendering using ray casting.

    Returns the ``Plotter`` object.

    .. hint:: examples/volumetric/app_raycaster.py
        .. image:: https://vedo.embl.es/images/advanced/app_raycaster.gif
    """

    def __init__(self, volume, **kwargs):

        Plotter.__init__(self, **kwargs)

        self.alphaslider0 = 0.33
        self.alphaslider1 = 0.66
        self.alphaslider2 = 1

        volumeProperty = volume.GetProperty()
        img = volume.imagedata()

        if volume.dimensions()[2] < 3:
            vedo.logger.error("RayCastPlotter: not enough z slices.")
            raise RuntimeError

        smin, smax = img.GetScalarRange()
        x0alpha = smin + (smax - smin) * 0.25
        x1alpha = smin + (smax - smin) * 0.5
        x2alpha = smin + (smax - smin) * 1.0

        ############################## color map slider
        # Create transfer mapping scalar value to color
        cmaps = [
            "jet",
            "viridis",
            "bone",
            "hot",
            "plasma",
            "winter",
            "cool",
            "gist_earth",
            "coolwarm",
            "tab10",
        ]
        cols_cmaps = []
        for cm in cmaps:
            cols = color_map(range(0, 21), cm, 0, 20)  # sample 20 colors
            cols_cmaps.append(cols)
        Ncols = len(cmaps)
        csl = (0.9, 0.9, 0.9)
        if sum(get_color(self.renderer.GetBackground())) > 1.5:
            csl = (0.1, 0.1, 0.1)

        def sliderColorMap(widget, event):
            sliderRep = widget.GetRepresentation()
            k = int(sliderRep.GetValue())
            sliderRep.SetTitleText(cmaps[k])
            volume.color(cmaps[k])

        w1 = self.add_slider(
            sliderColorMap,
            0,
            Ncols - 1,
            value=0,
            show_value=0,
            title=cmaps[0],
            c=csl,
            pos=[(0.8, 0.05), (0.965, 0.05)],
        )
        w1.GetRepresentation().SetTitleHeight(0.018)

        ############################## alpha sliders
        # Create transfer mapping scalar value to opacity
        opacityTransferFunction = volumeProperty.GetScalarOpacity()

        def setOTF():
            opacityTransferFunction.RemoveAllPoints()
            opacityTransferFunction.AddPoint(smin, 0.0)
            opacityTransferFunction.AddPoint(smin + (smax - smin) * 0.1, 0.0)
            opacityTransferFunction.AddPoint(x0alpha, self.alphaslider0)
            opacityTransferFunction.AddPoint(x1alpha, self.alphaslider1)
            opacityTransferFunction.AddPoint(x2alpha, self.alphaslider2)

        setOTF()

        def sliderA0(widget, event):
            self.alphaslider0 = widget.GetRepresentation().GetValue()
            setOTF()

        self.add_slider(
            sliderA0,
            0,
            1,
            value=self.alphaslider0,
            pos=[(0.84, 0.1), (0.84, 0.26)],
            c=csl,
            show_value=0,
        )

        def sliderA1(widget, event):
            self.alphaslider1 = widget.GetRepresentation().GetValue()
            setOTF()

        self.add_slider(
            sliderA1,
            0,
            1,
            value=self.alphaslider1,
            pos=[(0.89, 0.1), (0.89, 0.26)],
            c=csl,
            show_value=0,
        )

        def sliderA2(widget, event):
            self.alphaslider2 = widget.GetRepresentation().GetValue()
            setOTF()

        w2 = self.add_slider(
            sliderA2,
            0,
            1,
            value=self.alphaslider2,
            pos=[(0.96, 0.1), (0.96, 0.26)],
            c=csl,
            show_value=0,
            title="Opacity levels",
        )
        w2.GetRepresentation().SetTitleHeight(0.016)

        # add a button
        def button_func_mode():
            s = volume.mode()
            snew = (s + 1) % 2
            volume.mode(snew)
            bum.switch()

        bum = self.add_button(
            button_func_mode,
            pos=(0.7, 0.035),
            states=["composite", "max proj."],
            c=["bb", "gray"],
            bc=["gray", "bb"],  # colors of states
            font="",
            size=16,
            bold=0,
            italic=False,
        )
        bum.status(volume.mode())

        # add histogram of scalar
        plot = CornerHistogram(
            volume,
            bins=25,
            logscale=1,
            c=(0.7, 0.7, 0.7),
            bg=(0.7, 0.7, 0.7),
            pos=(0.78, 0.065),
            lines=True,
            dots=False,
            nmax=3.1415e06,  # subsample otherwise is too slow
        )

        plot.GetPosition2Coordinate().SetValue(0.197, 0.20, 0)
        plot.GetXAxisActor2D().SetFontFactor(0.7)
        plot.GetProperty().SetOpacity(0.5)
        self.add([plot, volume])

Ancestors

Inherited members

class Slicer2DPlotter (volume, levels=(None, None), axes=None, zoom=1.2, pos=(0, 0), size='auto', screensize='auto', title='', bg='white', bg2=None, interactive=True)

Create a Plotter with a single slice of a Volume which always faces the camera, but at the same time can be oriented arbitrarily in space.

Parameters

levels : list
window and color level

Expand source code
class Slicer2DPlotter(Plotter):
    """
    Create a ``Plotter`` with a single slice of a Volume which always faces the camera,
    but at the same time can be oriented arbitrarily in space.

    Parameters
    ----------
    levels : list
        window and color level

    .. image:: https://vedo.embl.es/images/volumetric/read_volume3.jpg
    """

    def __init__(
        self,
        volume,
        levels=(None, None),
        axes=None,
        zoom=1.2,
        pos=(0, 0),
        size="auto",
        screensize="auto",
        title="",
        bg="white",
        bg2=None,
        interactive=True,
    ):
        custom_shape = [  # define here the 2 rendering rectangle spaces
            dict(bottomleft=(0.0, 0.0), topright=(1, 1), bg="k9"),  # the full window
            dict(bottomleft=(0.8, 0.8), topright=(1, 1), bg="k8", bg2="lb"),
        ]

        if not title:
            if volume.filename:
                title = volume.filename[:80]
            else:
                title = "Volume Slicer2D"

        Plotter.__init__(
            self,
            shape=custom_shape,
            title=title,
            pos=pos,
            screensize=screensize,
            size=size,
            bg=bg,
            bg2=bg2,
            axes=0,
            interactive=False,
        )

        vsl = vedo.volume.VolumeSlice(
            volume
        )  # reuse the same underlying data as in vol

        # no argument will grab the existing cmap in vol (or use build_lut())
        vsl.colorize()

        if levels[0] and levels[1]:
            vsl.lighting(window=levels[0], level=levels[1])

        usage = Text2D((
            "SHIFT+Left click   \rightarrow rotate camera for oblique slicing\n"
            "SHIFT+Middle click \rightarrow slice perpendicularly through image\n"
            "Left click & drag  \rightarrow modify luminosity and contrast\n"
            "R                  \rightarrow Reset the Window/Color levels\n"
            "X                  \rightarrow Reset to sagittal view\n"
            "Y                  \rightarrow Reset to coronal view\n"
            "Z                  \rightarrow Reset to axial view"),
            font="Calco",
            pos="top-left",
            s=0.8,
            bg="yellow",
            alpha=0.25,
        )

        hist = CornerHistogram(
            volume.pointdata[0],
            bins=25,
            logscale=1,
            pos=(0.02, 0.02),
            s=0.175,
            c="dg",
            bg="k",
            alpha=1,
        )
        ax = None
        if axes == 7:
            ax = vedo.addons.RulerAxes(vsl, xtitle="x - ", ytitle="y - ", ztitle="z - ")

        box = vsl.box().alpha(0.1)
        self.show(vsl, box, ax, usage, hist, at=0, mode="image", zoom=zoom)
        self.show(volume, at=1, interactive=interactive)

Ancestors

Inherited members

class Slicer3DPlotter (volume, alpha=1, cmaps=('gist_ncar_r', 'hot_r', 'bone_r', 'jet', 'Spectral_r'), map2cells=False, clamp=True, use_slider3d=False, show_histo=True, show_icon=True, draggable=False, pos=(0, 0), size='auto', screensize='auto', title='', bg='white', bg2='lightblue', axes=7, resetcam=True, interactive=True)

Generate a Plotter window with slicing planes for the input Volume.

Returns the Plotter object.

Parameters

alpha : float
transparency of the slicing planes
cmaps : list
list of color maps names to cycle when clicking button
map2cells : bool
scalars are mapped to cells, not interpolated
clamp : bool
clamp scalar to reduce the effect of tails in color mapping
use_slider3d : bool
show sliders attached along the axes
show_histo : bool
show histogram on bottom left
show_icon : bool
show a small 3D rendering icon of the volume
draggable : bool
make the icon draggable

Hint: examples/volumetric/slicer1.py

Expand source code
class Slicer3DPlotter(Plotter):
    """
    Generate a ``Plotter`` window with slicing planes for the input Volume.

    Returns the ``Plotter`` object.

    Parameters
    ----------
    alpha : float
        transparency of the slicing planes

    cmaps : list
        list of color maps names to cycle when clicking button

    map2cells : bool
        scalars are mapped to cells, not interpolated

    clamp : bool
        clamp scalar to reduce the effect of tails in color mapping

    use_slider3d : bool
        show sliders attached along the axes

    show_histo : bool
        show histogram on bottom left

    show_icon : bool
        show a small 3D rendering icon of the volume

    draggable : bool
        make the icon draggable

    .. hint:: examples/volumetric/slicer1.py
        .. image:: https://vedo.embl.es/images/volumetric/slicer1.jpg
    """

    def __init__(
            self,
            volume,
            alpha=1,
            cmaps=('gist_ncar_r', "hot_r", "bone_r", "jet", "Spectral_r"),
            map2cells=False,  # buggy
            clamp=True,
            use_slider3d=False,
            show_histo=True,
            show_icon=True,
            draggable=False,
            pos=(0, 0),
            size="auto",
            screensize="auto",
            title="",
            bg="white",
            bg2="lightblue",
            axes=7,
            resetcam=True,
            interactive=True,
        ):
        self._cmap_slicer= 'gist_ncar_r'

        if not title:
            if volume.filename:
                title = volume.filename
            else:
                title = "Volume Slicer"

        ################################
        Plotter.__init__(
            self,
            pos=pos,
            bg=bg,
            bg2=bg2,
            size=size,
            screensize=screensize,
            title=title,
            interactive=interactive,
            axes=axes,
        )
        ################################
        box = volume.box().wireframe().alpha(0.1)

        self.show(box, viewup="z", resetcam=resetcam, interactive=False)
        if show_icon:
            self.add_inset(
                volume,
                pos=(0.85, 0.85),
                size=0.15, c="w",
                draggable=draggable,
            )

        # inits
        la, ld = 0.7, 0.3  # ambient, diffuse
        dims = volume.dimensions()
        data = volume.pointdata[0]
        rmin, rmax = volume.imagedata().GetScalarRange()
        if clamp:
            hdata, edg = np.histogram(data, bins=50)
            logdata = np.log(hdata + 1)
            # mean  of the logscale plot
            meanlog = np.sum(np.multiply(edg[:-1], logdata)) / np.sum(logdata)
            rmax = min(rmax, meanlog + (meanlog - rmin) * 0.9)
            rmin = max(rmin, meanlog - (rmax - meanlog) * 0.9)
            vedo.logger.debug(
                "scalar range clamped to range: ("
                + precision(rmin, 3)
                + ", "
                + precision(rmax, 3)
                + ")"
            )
        self._cmap_slicer = cmaps[0]
        visibles = [None, None, None]
        msh = volume.zslice(int(dims[2] / 2))
        msh.alpha(alpha).lighting("", la, ld, 0)
        msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
        if map2cells:
            msh.mapPointsToCells()
        self.renderer.AddActor(msh)
        visibles[2] = msh
        msh.add_scalarbar(pos=(0.04, 0.0), horizontal=True, font_size=0)

        def sliderfunc_x(widget, event):
            i = int(widget.GetRepresentation().GetValue())
            msh = volume.xslice(i).alpha(alpha).lighting("", la, ld, 0)
            msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
            if map2cells:
                msh.mapPointsToCells()
            self.renderer.RemoveActor(visibles[0])
            if i and i < dims[0]:
                self.renderer.AddActor(msh)
            visibles[0] = msh

        def sliderfunc_y(widget, event):
            i = int(widget.GetRepresentation().GetValue())
            msh = volume.yslice(i).alpha(alpha).lighting("", la, ld, 0)
            msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
            if map2cells:
                msh.mapPointsToCells()
            self.renderer.RemoveActor(visibles[1])
            if i and i < dims[1]:
                self.renderer.AddActor(msh)
            visibles[1] = msh

        def sliderfunc_z(widget, event):
            i = int(widget.GetRepresentation().GetValue())
            msh = volume.zslice(i).alpha(alpha).lighting("", la, ld, 0)
            msh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
            if map2cells:
                msh.mapPointsToCells()
            self.renderer.RemoveActor(visibles[2])
            if i and i < dims[2]:
                self.renderer.AddActor(msh)
            visibles[2] = msh

        cx, cy, cz, ch = "dr", "dg", "db", (0.3, 0.3, 0.3)
        if np.sum(self.renderer.GetBackground()) < 1.5:
            cx, cy, cz = "lr", "lg", "lb"
            ch = (0.8, 0.8, 0.8)

        if not use_slider3d:
            self.add_slider(
                sliderfunc_x,
                0,
                dims[0],
                title="X",
                title_size=0.5,
                pos=[(0.8, 0.12), (0.95, 0.12)],
                show_value=False,
                c=cx,
            )
            self.add_slider(
                sliderfunc_y,
                0,
                dims[1],
                title="Y",
                title_size=0.5,
                pos=[(0.8, 0.08), (0.95, 0.08)],
                show_value=False,
                c=cy,
            )
            self.add_slider(
                sliderfunc_z,
                0,
                dims[2],
                title="Z",
                title_size=0.6,
                value=int(dims[2] / 2),
                pos=[(0.8, 0.04), (0.95, 0.04)],
                show_value=False,
                c=cz,
            )
        else:  # 3d sliders attached to the axes bounds
            bs = box.bounds()
            self.add_slider3d(
                sliderfunc_x,
                pos1=(bs[0], bs[2], bs[4]),
                pos2=(bs[1], bs[2], bs[4]),
                xmin=0,
                xmax=dims[0],
                t=box.diagonal_size() / mag(box.xbounds()) * 0.6,
                c=cx,
                show_value=False,
            )
            self.add_slider3d(
                sliderfunc_y,
                pos1=(bs[1], bs[2], bs[4]),
                pos2=(bs[1], bs[3], bs[4]),
                xmin=0,
                xmax=dims[1],
                t=box.diagonal_size() / mag(box.ybounds()) * 0.6,
                c=cy,
                show_value=False,
            )
            self.add_slider3d(
                sliderfunc_z,
                pos1=(bs[0], bs[2], bs[4]),
                pos2=(bs[0], bs[2], bs[5]),
                xmin=0,
                xmax=dims[2],
                value=int(dims[2] / 2),
                t=box.diagonal_size() / mag(box.zbounds()) * 0.6,
                c=cz,
                show_value=False,
            )

        #################
        def buttonfunc():
            bu.switch()
            self._cmap_slicer = bu.status()
            for mesh in visibles:
                if mesh:
                    mesh.cmap(self._cmap_slicer, vmin=rmin, vmax=rmax)
                    if map2cells:
                        mesh.mapPointsToCells()
            self.renderer.RemoveActor(mesh.scalarbar)
            mesh.add_scalarbar(pos=(0.04, 0.0), horizontal=True, title_font_size=0)

        bu = self.add_button(
            buttonfunc,
            pos=(0.27, 0.005),
            states=cmaps,
            c=["db"] * len(cmaps),
            bc=["lb"] * len(cmaps),  # colors of states
            size=14,
            bold=True,
        )

        #################
        hist = None
        if show_histo:
            hist = CornerHistogram(
                data,
                s=0.2,
                bins=25,
                logscale=1,
                pos=(0.02, 0.02),
                c=ch,
                bg=ch,
                alpha=0.7,
            )

        self.add([msh, hist], resetcam=False)
        if interactive:
            self.interactive()

Ancestors

Inherited members

class SplinePlotter (obj, initpoints=(), **kwargs)

Create an interactive application that allows the user to click points and retrieve the coordinates of such points and optionally a spline or line (open or closed).

Input object can be a image file name or a 3D mesh.

Expand source code
class SplinePlotter(Plotter):
    """
    Create an interactive application that allows the user to click points and
    retrieve the coordinates of such points and optionally a spline or line
    (open or closed).

    Input object can be a image file name or a 3D mesh.
    """
    def __init__(self, obj, initpoints=(), **kwargs):

        super().__init__(**kwargs)

        self.mode    = 'trackball'
        self.verbose = True
        self.splined = True
        self.closed  = False
        self.lcolor  = 'yellow4'
        self.lwidth  = 3
        self.pcolor  = 'purple5'
        self.psize   = 10

        self.cpoints = list(initpoints)
        self.vpoints = None
        self.line = None

        if isinstance(obj, str):
            self.object = vedo.Picture(obj, channels=(0,1,2))
            # keep rgb but drop alpha channel
            self.mode = 'image'
        else:
            self.object = obj

        t = """Click to add a point
        Right-click to remove it
        Drag mouse to change constrast
        Press c to clear points
        Press q to continue""".replace("  ","")
        self.instructions = Text2D(t, pos='bottom-left', c='white', bg='green', font='Calco')

        self.callid1 = self.add_callback('KeyPress', self._key_press)
        self.callid2 = self.add_callback('LeftButtonPress', self._onLeftClick)
        self.callid3 = self.add_callback('RightButtonPress', self._on_right_click)

    def points(self, newpts=None):
        """Retrieve the 3D coordinates of the clicked points"""
        if newpts is not None:
            self.cpoints = newpts
            self._update()
            return self
        return np.array(self.cpoints)

    def _onLeftClick(self, evt):
        if not evt.actor: return
        p = evt.picked3d
        self.cpoints.append(p)
        self._update()
        if self.verbose:
            vedo.colors.printc("Added point:", precision(p,4), c='g')

    def _on_right_click(self, evt):
        if evt.actor and len(self.cpoints)>0:
            self.cpoints.pop() # pop removes from the list the last pt
            self._update()
            if self.verbose:
                vedo.colors.printc("Deleted last point", c="r")

    def _update(self):
        self.remove(self.line, self.vpoints)  # remove old points and spline
        self.vpoints = Points(self.cpoints).ps(self.psize).c(self.pcolor)
        self.vpoints.pickable(False)  # avoid picking the same point
        minnr = 1
        if self.splined:
            minnr = 2
        if len(self.cpoints) > minnr:
            if self.splined:
                try:
                    self.line = Spline(self.cpoints, closed=self.closed)
                except ValueError:
                    # if clicking too close splining might fail
                    self.cpoints.pop()
                    return
            else:
                self.line = Line(self.cpoints, closed=self.closed)
            self.line.c(self.lcolor).lw(3).pickable(False)
            self.add(self.vpoints, self.line)
        else:
            self.add(self.vpoints)

    def _key_press(self, evt):
        if evt.keypress == 'c':
            self.cpoints = []
            self.remove(self.line, self.vpoints).render()
            if self.verbose:
                vedo.colors.printc("==== Cleared all points ====", c="r", invert=True)

    def start(self):
        """Start the interaction"""
        self.show(self.object, self.instructions, mode=self.mode)
        return self

Ancestors

Methods

def points(self, newpts=None)

Retrieve the 3D coordinates of the clicked points

Expand source code
def points(self, newpts=None):
    """Retrieve the 3D coordinates of the clicked points"""
    if newpts is not None:
        self.cpoints = newpts
        self._update()
        return self
    return np.array(self.cpoints)
def start(self)

Start the interaction

Expand source code
def start(self):
    """Start the interaction"""
    self.show(self.object, self.instructions, mode=self.mode)
    return self

Inherited members