def add_line_at_point(self,
point,
axis,
color="blackboard",
lw=3,
**kwargs):
"""
Adds a line oriented on a given axis at a point
:param point:list or 1d np array with coordinates of point where crosshair is centered
:param replace_coord: index of the coordinate to replace (i.e. along which axis is the line oriented)
:param bounds: list of two floats with lower and upper bound for line, determins the extent of the line
:param kwargs: dictionary with arguments to specify how lines should look like
"""
# TODO bgspace could be used here
axis_dict = dict(rostrocaudal=0, dorsoventral=1, mediolateral=2)
replace_coord = axis_dict[axis]
bounds = self.atlas._root_bounds[replace_coord]
# Get line coords
p0, p1 = point.copy(), point.copy()
p0[replace_coord] = bounds[0]
p1[replace_coord] = bounds[1]
# Create line actor
line = Line(p0, p1, c=color, lw=lw, **kwargs)
line.name = f"line through {point}"
line._br_class = "line"
return self.add_actor(line)
def _onMouseMove(self, evt):
if self.drawmode:
cpt = self.computeWorldPosition(
evt.picked2d) # make this 2d-screen point 3d
if self.cpoints and mag(cpt - self.cpoints[-1]
) < self.mesh.diagonalSize() * 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 = Line(self.top_pts)
# self.topline.lw(self.linewidth-1).c(self.linecolor).pickable(False)
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 ruler(p1, p2, unit_scale=1, units=None, s=50):
actors = []
# Make two line segments
midpoint = np.array([(x + y) / 2 for x, y in zip(p1, p2)])
gap1 = ((midpoint - p1) * 0.8) + p1
gap2 = ((midpoint - p2) * 0.8) + p2
actors.append(Line(p1, gap1, lw=200))
actors.append(Line(gap2, p2, lw=200))
# Add label
if units is None:
units = ""
dist = mag(p2 - p1) * unit_scale
label = precision(dist, 3) + " " + units
lbl = Text(label, pos=midpoint, s=s + 100, justify="center")
lbl.SetOrientation([0, 0, 180])
actors.append(lbl)
# Add spheres add end
actors.append(Sphere(p1, r=s, c=[0.3, 0.3, 0.3]))
actors.append(Sphere(p2, r=s, c=[0.3, 0.3, 0.3]))
acts = merge(*actors).c((0.3, 0.3, 0.3)).alpha(1).lw(2)
acts.name = "Ruler"
acts.bg_class = "Ruler"
return acts
def _onRightClick(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 init(self, initpoints):
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 ruler(p1, p2, unit_scale=1, units=None, s=50):
"""
Creates a ruler showing the distance between two points.
The ruler is composed of a line between the points and
a text indicating the distance.
:param p1: list, np.ndarray with coordinates of first point
:param p2: list, np.ndarray with coordinates of second point
:param unit_scale: float. To scale the units (e.g. show mm instead of µm)
:param units: str, name of unit (e.g. 'mm')
:param s: float size of text
"""
actors = []
# Make two line segments
midpoint = np.array([(x + y) / 2 for x, y in zip(p1, p2)])
gap1 = ((midpoint - p1) * 0.8) + p1
gap2 = ((midpoint - p2) * 0.8) + p2
actors.append(Line(p1, gap1, lw=200))
actors.append(Line(gap2, p2, lw=200))
# Add label
if units is None: # pragma: no cover
units = "" # pragma: no cover
dist = mag(p2 - p1) * unit_scale
label = precision(dist, 3) + " " + units
lbl = Text(label, pos=midpoint, s=s + 100, justify="center")
lbl.SetOrientation([0, 0, 180])
actors.append(lbl)
# Add spheres add end
actors.append(Sphere(p1, r=s, c=[0.3, 0.3, 0.3]))
actors.append(Sphere(p2, r=s, c=[0.3, 0.3, 0.3]))
act = Actor(merge(*actors), name="Ruler", br_class="Ruler")
act.c((0.3, 0.3, 0.3)).alpha(1).lw(2)
return act
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, optional
join points with a spline or a simple line. The default is True.
font : str, optional
Font name for the instructions. The default is "Bongas".
alpha : float, optional
transparency of the instruction message panel. The default is 0.9.
lw : str, optional
selection line width. The default is 3.
lc : str, optional
selection line color. The default is "red5".
pc : str, optional
selection points color. The default is "black".
c : str, optional
backgound color of instructions. The default is "green3".
tc : str, optional
text color of instructions. The default is "white".
tol : int, optional
tolerance of the point proximity. Default is 5.
"""
# 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,
):
if not isinstance(mesh, Points):
printc("FreeHandCutPlotter input must be Points or Mesh.", c='r')
raise RuntimeError()
Plotter.__init__(self, title="Free-hand mesh cutter")
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.addCallback('KeyPress', self._onKeyPress)
self.idrightclck = self.addCallback('RightButton', self._onRightClick)
self.idmousemove = self.addCallback('MouseMove', self._onMouseMove)
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):
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 _onRightClick(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 _onMouseMove(self, evt):
if self.drawmode:
cpt = self.computeWorldPosition(
evt.picked2d) # make this 2d-screen point 3d
if self.cpoints and mag(cpt - self.cpoints[-1]
) < self.mesh.diagonalSize() * 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 = Line(self.top_pts)
# self.topline.lw(self.linewidth-1).c(self.linecolor).pickable(False)
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 _onKeyPress(self, evt):
if evt.keyPressed.lower(
) == 'z' and self.spline: # Cut mesh with a ribbon-like surface
inv = False
if evt.keyPressed == 'Z':
inv = True
self.txt2d.background('red8').text(" ... working ... ")
self.render()
self.mesh_prev = self.mesh.clone()
tol = self.mesh.diagonalSize() / 2 # size of ribbon (not shown)
pts = self.spline.points()
n = fitPlane(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._onRightClick(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.keyPressed == '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.extractLargestRegion()
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.keyPressed == 'u': # Undo last action
if self.drawmode:
self._onRightClick(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.keyPressed == 'c' or evt.keyPressed == '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.keyPressed == 'r': # reset camera and axes
try:
self.remove(self.axes_instances[0])
self.axes_instances[0] = None
self.addGlobalAxes(axtype=1, c=None)
self.renderer.ResetCamera()
self.interactor.Render()
except:
pass
elif evt.keyPressed == '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"):
self.mesh.write(filename)
printc("\save saved to file:", filename, c='lb', invert=True)
return self
def start(self, *args, **kwargs):
acts = [self.txt2d, self.mesh, self.points, self.spline, self.jline]
self.show(acts + list(args), **kwargs)
return self