def plot_two_pc(x, y, point_size=0.005, c1='g', c2='r'):
if c1 == 'b':
k = 245
elif c1 == 'g':
k = 25811000
elif c1 == 'r':
k = 11801000
elif c1 == 'black':
k = 2580
else:
k = 2580
if c2 == 'b':
k2 = 245
elif c2 == 'g':
k2 = 25811000
elif c2 == 'r':
k2 = 11801000
elif c2 == 'black':
k2 = 2580
else:
k2 = 2580
col1 = np.ones(x.shape[0]) * k
col2 = np.ones(y.shape[0]) * k2
plot = k3d.plot(name='points')
plt_points = k3d.points(x, col1.astype(np.uint32), point_size=point_size)
plot += plt_points
plt_points = k3d.points(y, col2.astype(np.uint32), point_size=point_size)
plot += plt_points
plt_points.shader = '3d'
plot.display()
def Icosahedron(origin, size=1):
if np.shape(origin) == (3, ):
fi = (1 + np.sqrt(5)) / 2
icosahedron_vertices = k3d.points([(1, fi, 0),
(1, -fi, 0), (-1, fi, 0),
(-1, -fi, 0), (fi, 0, 1),
(fi, 0, -1), (-fi, 0, 1),
(-fi, 0, -1), (0, 1, fi),
(0, 1, -fi), (0, -1, fi),
(0, -1, -fi)],
point_size=0.1)
icosahedron_vertices.positions = np.float32(
size * np.array(icosahedron_vertices.positions) + np.array(origin))
icosahedron_mesh = k3d.mesh(icosahedron_vertices.positions,
indices=[
0, 2, 8, 0, 4, 8, 0, 2, 9, 0, 5, 9, 2,
6, 8, 2, 7, 9, 2, 6, 7, 0, 4, 5, 1, 4,
5, 1, 5, 11, 7, 9, 11, 3, 7, 11, 3, 6,
7, 3, 6, 10, 4, 8, 10, 6, 8, 10, 1, 4,
10, 1, 3, 11, 1, 3, 10, 5, 9, 11
])
else:
raise TypeError('Origin attribute should have 3 coordinates.')
return [icosahedron_vertices, icosahedron_mesh]
def vis_pcloud_interactive(res, img):
import k3d
from colormap import rgb2hex
color_vals = np.zeros((img.shape[0], img.shape[1]))
for i in range(img.shape[0]):
for j in range(img.shape[1]):
color_vals[i, j] = int(
rgb2hex(img[i, j, 0], img[i, j, 1],
img[i, j, 2]).replace('#', '0x'), 0)
colors = color_vals.flatten()
points = np.stack(
(res['X'].flatten(), res['Y'].flatten(), res['Z'].flatten()), axis=1)
invalid_inds = np.any(np.isnan(points), axis=1)
points_valid = points[invalid_inds == False]
colors_valid = colors[invalid_inds == False]
plot = k3d.plot(grid_auto_fit=True, camera_auto_fit=False)
plot += k3d.points(points_valid,
colors_valid,
point_size=0.01,
compression_level=9,
shader='flat')
plot.display()
plot.camera = [
-0.3568942548181382, -0.12775125650240726, 3.5390732533009452,
0.33508163690567017, 0.3904658555984497, -0.0499117374420166,
0.11033077266672488, 0.9696364582197756, 0.2182481603445357
]
return plot
def illustrate_points(points, plot=None, size=0.1):
if plot is None:
plot = k3d.plot(name='points')
plt_points = k3d.points(positions=points, point_size=size)
plot += plt_points
plt_points.shader = '3d'
return plot
def scatter2k3d(x, **kwargs):
"""Convert DataFrame with x,y,z columns to plotly scatter plot."""
c = eval_color(kwargs.get('color', kwargs.get('c', (100, 100, 100))),
color_range=255)
c = color_to_int(c)
s = kwargs.get('size', kwargs.get('s', 1))
name = kwargs.get('name', None)
trace_data = []
for scatter in x:
if isinstance(scatter, pd.DataFrame):
if not all([c in scatter.columns for c in ['x', 'y', 'z']]):
raise ValueError('DataFrame must have x, y and z columns')
scatter = [['x', 'y', 'z']].values
if not isinstance(scatter, np.ndarray):
scatter = np.array(scatter)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
trace_data.append(k3d.points(positions=scatter,
name=name,
color=c,
point_size=s,
shader='dot'))
return trace_data
def setup_plot(self, pb):
super(WBShellFETriangularMesh, self).setup_plot(pb)
X_Id = self.X_Id.astype(np.float32)
fixed_nodes = self.bc_fixed_nodes
loaded_nodes = self.bc_loaded_nodes
X_Ma = X_Id[fixed_nodes]
k3d_fixed_nodes = k3d.points(X_Ma, color=0x22ffff, point_size=100)
pb.plot_fig += k3d_fixed_nodes
pb.objects['fixed_nodes'] = k3d_fixed_nodes
X_Ma = X_Id[loaded_nodes]
k3d_loaded_nodes = k3d.points(X_Ma, color=0xff22ff, point_size=100)
pb.plot_fig += k3d_loaded_nodes
pb.objects['loaded_nodes'] = k3d_loaded_nodes
def k3d(self, point_size=.8, color=True):
'''makes a 3d plot of the lattice using k3d visualization'''
import k3d
plot = k3d.plot(name='lattice_plot')
if not color:
for layer in range(self.n_layers):
plot += k3d.points(positions=self.layer_coords(layer, z=True),
point_size=point_size)
if color:
color_list = [
0x0054a7, 0xe41134, 0x75ac4f, 0xf4ea19, 0xffaff8, 0xa35112,
0x15e3f4, 0xcfc7ff
]
for layer in range(self.n_layers):
plot += k3d.points(positions=self.layer_coords(layer, z=True),
point_size=point_size,
color=color_list[layer % 8])
plot.display()
def setup_plot(self, pb):
X_Ia = self.mesh.X_Ia.astype(np.float32)
I_Fi = self.mesh.I_Fi.astype(np.uint32)
X_Ma = X_Ia[self.bc_J_xyz]
self.k3d_fixed_xyz = k3d.points(X_Ma)
pb.plot_fig += self.k3d_fixed_xyz
X_Ma = X_Ia[self.bc_J_x]
self.k3d_fixed_x = k3d.points(X_Ma, color=0x22ffff)
pb.plot_fig += self.k3d_fixed_x
X_Ma = X_Ia[self.bc_J_F_xyz]
self.k3d_load_z = k3d.points(X_Ma, color=0xff22ff)
pb.plot_fig += self.k3d_load_z
self.k3d_mesh = k3d.mesh(X_Ia, I_Fi, color=0x999999, side='double')
pb.plot_fig += self.k3d_mesh
def __get_joint_points(self) -> List[Points]:
skeleton_joint_colors: np.ndarray = self.__get_joint_colors()
return [
k3d.points(positions=self.joint_positions[line_index],
point_size=self.part_size,
shader='mesh',
color=int(skeleton_joint_colors[line_index]))
for line_index in range(self.joint_set.number_of_joints)
]
def points(plot_array, point_size=0.1, color=0x99bbff, plot=None, **kwargs):
plot_array = plot_array.astype(np.float32) # to avoid k3d warning
if plot is None:
plot = k3d.plot()
plot.display()
plot += k3d.points(plot_array,
point_size=point_size,
color=color,
**kwargs)
return plot
def __get_joint_points_for_video(self) -> List[Points]:
skeleton_joint_colors: np.ndarray = self.__get_joint_colors()
return [
k3d.points(positions={
current_timestamp[0]: current_timestamp[1][line_index]
for current_timestamp in self.joint_positions.items()
},
color=int(skeleton_joint_colors[line_index]),
point_size=self.part_size,
shader='mesh')
for line_index in range(self.joint_set.number_of_joints)
]
def new_plot(self, bs=1.0):
points_number = 1
positions = 50 * np.random.random_sample((points_number, 3)) - 25
colors = np.random.randint(0, 0x777777, points_number)
self.plot = k3d.plot()
self.pkts = k3d.points(positions, colors, point_size=.3)
self.plot += self.pkts
self.plot.camera_auto_fit = False
self.plot.grid_auto_fit = False
self.box = k3d.line(self.box_coords(bs=bs))
self.plot += self.box
def test_drawable_notification(self):
# given
transform = Transform()
points = k3d.points([0, 0, 1])
transform.add_drawable(points)
# when
transform.scaling = [1., 2., 3.]
# then
self.assertTrue((points.model_matrix == np.array([[1., 0., 0., 0.],
[0., 2., 0., 0.],
[0., 0., 3., 0.],
[0., 0., 0.,
1.]])).all())
def visualization_inter3D_xyz(pa):
if (pa.shape[1] == 4):
pa = np.delete(pa, (3), axis=1)
plot = k3d.plot()
print(pa.shape[0])
points_number = pa.shape[0]
colors = np.random.randint(0, 0xFFFFFF, points_number)
points = k3d.points(pa, colors, point_size=0.01, shader='3d')
plot += points
plot.camera_auto_fit = False
plot.display()
print("(x) : {:2.1f}m".format(pa[:, 0:1].max() - pa[:, 0:1].min()))
print("(y) : {:2.1f}m".format(pa[:, 1:2].max() - pa[:, 1:2].min()))
print("(z) : {:2.1f}m".format(pa[:, 2:3].max() - pa[:, 2:3].min()))
def visualize_pointcloud(point_cloud,
point_size,
flip_axes=False,
name='point_cloud'):
plot = k3d.plot(name=name,
grid_visible=False,
grid=(-0.55, -0.55, -0.55, 0.55, 0.55, 0.55))
if flip_axes:
point_cloud[:, 2] = point_cloud[:, 2] * -1
point_cloud[:, [0, 1, 2]] = point_cloud[:, [0, 2, 1]]
plt_points = k3d.points(positions=point_cloud.astype(np.float32),
point_size=point_size,
color=0xd0d0d0)
plot += plt_points
plt_points.shader = '3d'
plot.display()
def viz_dimer_positions_k3d(positions,
size=5,
cmap_name="tab20c",
color_feature_name=None):
try:
import k3d
except ImportError:
mess = "YOu need to install the k3d library. "
mess += (
"Please follow the official instructions at https://github.com/K3D-tools/K3D-jupyter/."
)
raise ImportError(mess)
# Only show visible dimers
selected_dimers = positions[positions["visible"]]
coordinates = selected_dimers[["x", "y", "z"]].values.astype("float")
coordinates = coordinates.astype("float32")
if color_feature_name:
# TODO: that code should be much simpler...
cmap = matplotlib.cm.get_cmap(cmap_name)
categories = selected_dimers[color_feature_name].unique()
color_indices = cmap([i / len(categories) for i in categories])
colors = np.zeros((len(selected_dimers[color_feature_name]), ),
dtype="uint32")
for color_index, _ in enumerate(categories):
mask = selected_dimers[color_feature_name] == categories[
color_index]
color = color_indices[color_index]
color = "".join([format(int(x * 255), "02X") for x in color[:-1]])
color = int(color, 16)
colors[mask] = color
else:
colors = "#e4191b"
plot = k3d.plot()
plt_points = k3d.points(positions=coordinates,
point_size=size,
colors=colors)
plot += plt_points
plot.display()
return plot
def Tetrahedron(origin, size=1):
if np.shape(origin) == (3, ):
tetrahedron_vertices = k3d.points(positions=[(1, 1, 1), (1, -1, -1),
(-1, 1, -1), (-1, -1, 1)],
point_size=0.1)
tetrahedron_vertices.positions = np.float32(
size * np.array(tetrahedron_vertices.positions) +
np.array(origin, np.float32))
tetrahedron_mesh = k3d.mesh(
tetrahedron_vertices.positions,
indices=[0, 1, 2, 0, 1, 3, 1, 2, 3, 0, 2, 3])
else:
raise TypeError('Origin attribute should have 3 coordinates.')
return [tetrahedron_vertices, tetrahedron_mesh]
def Octahedron(origin, size=1):
if np.shape(origin) == (3, ):
octahedron_vertices = k3d.points([(1, 0, 0), (0, 1, 0), (0, 0, 1),
(-1, 0, 0), (0, -1, 0), (0, 0, -1)],
point_size=0.1)
octahedron_vertices.positions = np.float32(
size * np.array(octahedron_vertices.positions) + np.array(origin))
octahedron_mesh = k3d.mesh(octahedron_vertices.positions,
indices=[
0, 1, 2, 0, 1, 5, 1, 2, 3, 1, 3, 5, 0,
4, 5, 0, 2, 4, 2, 3, 4, 3, 4, 5
])
else:
raise TypeError('Origin attribute should have 3 coordinates.')
return [octahedron_vertices, octahedron_mesh]
def create(self, data):
self.plot = k3d.plot()
self.data = data
# Equatorial slice
self.equatorial_slice \
= k3d.vtk_poly_data(serpentine.tools.extract_plane(data, [0, 0, 0], [0, 0, 1]),
color_attribute=self.color_attribute,
color_map=self.color_map)
# Meridional slice
self.meridional_slice \
= k3d.vtk_poly_data(serpentine.tools.extract_plane(data, [0, 0, 0], [0, 1, 0]),
color_attribute=self.color_attribute,
color_map=self.color_map)
# Spherical slice
self.spherical_slice \
= k3d.vtk_poly_data(serpentine.tools.extract_sphere(data, [0, 0, 0], 0.105),
color_attribute=self.color_attribute,
color_map=self.color_map)
self.boundary_sphere = k3d.points([0, 0, 0],
point_size=0.2,
shader="mesh",
color=0xffffff,
mesh_detail=3)
# Get rmin and rmax
x, y, z = np.split(self.equatorial_slice.vertices.T, 1, axis=0)[0]
rsqr = x**2 + y**2 + z**2
self.r_bounds = (np.sqrt(min(rsqr)), np.sqrt(max(rsqr)))
# Add to plot
self.plot += self.equatorial_slice
self.plot += self.meridional_slice
self.plot += self.spherical_slice
self.plot += self.boundary_sphere
# Modify defaults
self.plot.grid_auto_fit = False
self.initialize_sliders()
def display_3d(K,show_labels=False):
"""display a 3d simplicial complex using k3d, in jupyter
to install it:
sudo pip install k3d
sudo jupyter nbextension install --py k3d
sudo jupyter nbextension enable --py k3d
"""
import k3d
if not isinstance(K.vertices[0] ,Point):
raise Exception("Can display only Point-class vertices of dim 3!!!")
dim=K.vertices[0].dim
if dim != 3:
sys.stderr.write("Not yet implemented display in dim = %s\n" % dim )
return None
vertices = [v.coords for v in K.vertices]
edges = [ s for s in K.simplices[1] ]
faces = []
if 2 in K.simplices:
faces = [ s for s in K.simplices[2] ]
plt=k3d.plot(name='points')
plt_points = k3d.points( positions=vertices , point_size=0.05)
plt_points.shader ='3dSpecular'
plt_points.color = 14
plt += plt_points
# now lines:
for s in edges:
plt_line = k3d.line([vertices[s[0]],vertices[s[1]] ],shader='mesh', width=0.01,
color=0xff0000)
plt += plt_line
# now convert all faces to a mesh
plt_mesh = k3d.mesh(vertices,faces,color=0xff, wireframe=False, opacity=0.7, name="Simplicial Complex")
plt += plt_mesh
# now add the text
for P in K.vertices:
if show_labels and P.label is not None:
plt_text = k3d.text("%s" % repr(P), position = P.coords, color=0x7700,size=1)
plt += plt_text
#finally display
plt.display()
def show_points(points,
colors=[],
normals=None,
point_size=0.1,
line_width=0.00001):
plot = k3d.plot(grid_visible=False, axes_helper=0)
if normals is not None:
normal_vectors = k3d.vectors(points,
normals,
line_width=line_width,
use_head=False)
plot += normal_vectors
point_cloud = k3d.points(points,
colors=colors,
point_size=point_size,
shader='flat')
plot += point_cloud
plot.display()
return None
def plot_pcd(x, point_size=0.005, c='g'):
"""
x: point_nr,3
"""
if c == 'b':
k = 245
elif c == 'g':
k = 25811000
elif c == 'r':
k = 11801000
elif c == 'black':
k = 2580
else:
k = 2580
colors = np.ones(x.shape[0]) * k
plot = k3d.plot(name='points')
plt_points = k3d.points(x, colors.astype(np.uint32), point_size=point_size)
plot += plt_points
plt_points.shader = '3d'
plot.display()
def Cube(origin, size=1):
if np.shape(origin) == (3, ):
cube_vertices = np.array(list(product([1, -1], [1, -1], [1, -1])),
np.float32)
cube_vertices = k3d.points(positions=cube_vertices, point_size=0.1)
cube_vertices.positions = np.float32(size * cube_vertices.positions +
np.array(origin))
cube_mesh = k3d.mesh(cube_vertices.positions,
indices=[
0, 1, 2, 1, 2, 3, 0, 1, 4, 1, 4, 5, 1, 3, 5,
3, 5, 7, 0, 2, 4, 2, 4, 6, 2, 3, 7, 2, 6, 7,
4, 5, 6, 5, 6, 7
])
else:
raise TypeError('Origin attribute should have 3 coordinates.')
return [cube_vertices, cube_mesh]
def Dodecahedron(origin, size=1):
origin = np.array(origin, dtype=np.float32)
if np.shape(origin) == (3, ):
fi = (1 + np.sqrt(5)) / 2
dodecahedron_vertices = list(product([-1, 1], [-1, 1], [-1, 1]))
dodecahedron_vertices += [(0, fi, 1 / fi), (0, -fi, 1 / fi),
(0, -fi, -1 / fi), (0, fi, -1 / fi),
(1 / fi, 0, fi), (-1 / fi, 0, fi),
(-1 / fi, 0, -fi), (1 / fi, 0, -fi),
(fi, 1 / fi, 0), (-fi, 1 / fi, 0),
(-fi, -1 / fi, 0), (fi, -1 / fi, 0)]
dodecahedron_vertices = np.float32(size *
np.array(dodecahedron_vertices) +
origin)
dodecahedron_vertices = k3d.points(dodecahedron_vertices,
point_size=0.1,
visible=False)
indices = [
0, 1, 18, 0, 1, 10, 1, 9, 10, 0, 10, 14, 10, 14, 15, 4, 10, 15, 4,
9, 10, 4, 5, 9, 4, 5, 19, 4, 15, 19, 6, 15, 19, 6, 16, 19, 6, 7,
16, 6, 7, 8, 6, 8, 11, 2, 3, 17, 2, 3, 8, 2, 8, 11, 1, 3, 13, 1, 3,
18, 3, 17, 18, 1, 9, 13, 9, 12, 13, 5, 9, 12, 5, 12, 19, 12, 16,
19, 7, 12, 16, 3, 7, 8, 3, 7, 12, 3, 12, 13, 14, 6, 15, 14, 6, 11,
2, 11, 14, 0, 17, 18, 0, 2, 17, 0, 2, 14
]
dodecahedron_mesh = k3d.mesh(dodecahedron_vertices.positions,
indices=indices,
wireframe=False)
else:
raise TypeError('Origin attribute should have 3 coordinates.')
return [dodecahedron_vertices, dodecahedron_mesh]
def plot_pcd(x, point_size=0.005, c='g'):
"""[summary]
Args:
x ([type]): point_nr,3
point_size (float, optional): [description]. Defaults to 0.005.
c (str, optional): [description]. Defaults to 'g'.
"""
if c == 'b':
k = 245
elif c == 'g':
k = 25811000
elif c == 'r':
k = 11801000
elif c == 'black':
k = 2580
else:
k = 2580
colors = np.ones(x.shape[0]) * k
plot = k3d.plot(name='points')
plt_points = k3d.points(x, colors.astype(np.uint32), point_size=point_size)
plot += plt_points
plt_points.shader = '3d'
plot.display()
def __init__(
self,
data: Union[np.ndarray, geo.SpatialData],
name: str,
reference_system: str,
plot: k3d.Plot = None,
color: int = None,
visualization_method: str = "auto",
show_wireframe: bool = False,
):
"""Create a ``SpatialDataVisualizer`` instance.
Parameters
----------
data :
The data that should be visualized
name :
Name of the data
reference_system :
Name of the data's reference system
plot :
A k3d plotting widget.
color :
The RGB color of the coordinate system (affects trace and label) as a 24 bit
integer value.
visualization_method :
The initial data visualization method. Options are ``point``, ``mesh``,
``both``and ``auto``. If ``auto`` is selected, a mesh will be drawn if
triangle data is available and points if not.
show_wireframe :
If `True`, meshes will be drawn as wireframes
"""
if not isinstance(data, geo.SpatialData):
data = geo.SpatialData(coordinates=data)
colors = []
if color is None or isinstance(color, str):
if isinstance(color, str):
colors = data.attributes[color]
color = RGB_GREY
if data.triangles is not None:
triangles = data.triangles.astype(np.uint32)
else:
triangles = None
self._reference_system = reference_system
self._label_pos = data.coordinates.mean(dim=data.additional_dims).data
if isinstance(self._label_pos, Q_):
self._label_pos = self._label_pos.to(_DEFAULT_LEN_UNIT).m
self._label = None
if name is not None:
self._label = k3d.text(
text=name,
position=self._label_pos,
reference_point="cc",
color=color,
size=0.5,
label_box=True,
name=name if name is None else f"{name} (text)",
)
coordinates = data.coordinates.data
if isinstance(coordinates, Q_):
coordinates = coordinates.to(_DEFAULT_LEN_UNIT).m
self._points = k3d.points(
coordinates,
point_size=0.05,
color=color,
name=name if name is None else f"{name} (points)",
)
self._mesh = None
if data.triangles is not None:
self._mesh = k3d.mesh(
coordinates.astype(np.float32).reshape(-1, 3),
triangles,
side="double",
color=color,
attribute=colors,
color_map=k3d.colormaps.matplotlib_color_maps.Viridis,
wireframe=show_wireframe,
name=name if name is None else f"{name} (mesh)",
)
self.set_visualization_method(visualization_method)
if plot is not None:
plot += self._points
if self._mesh is not None:
plot += self._mesh
if self._label is not None:
plot += self._label
self.data = data
def _add_nodes_to_fig(self, pb, X_Ma):
k3d_points = k3d.points(X_Ma, point_size=300)
pb.objects[self.NODES] = k3d_points
pb.plot_fig += k3d_points
def getNotebookBackend(actors2show, zoom, viewup):
vp = settings.plotter_instance
if isinstance(vp.shape, str) or sum(vp.shape) > 2:
colors.printc("Multirendering is not supported in jupyter.", c=1)
return
####################################################################################
# https://github.com/InsightSoftwareConsortium/itkwidgets
# /blob/master/itkwidgets/widget_viewer.py
if 'itk' in settings.notebookBackend:
from itkwidgets import view
settings.notebook_plotter = view(actors=actors2show,
cmap='jet', ui_collapsed=True,
gradient_opacity=False)
####################################################################################
elif settings.notebookBackend == 'k3d':
try:
import k3d # https://github.com/K3D-tools/K3D-jupyter
except:
print("Cannot find k3d, install with: pip install k3d")
return
actors2show2 = []
for ia in actors2show:
if not ia:
continue
if isinstance(ia, vtk.vtkAssembly): #unpack assemblies
acass = ia.unpack()
actors2show2 += acass
else:
actors2show2.append(ia)
# vbb, sizes, _, _ = addons.computeVisibleBounds()
# kgrid = vbb[0], vbb[2], vbb[4], vbb[1], vbb[3], vbb[5]
settings.notebook_plotter = k3d.plot(axes=[vp.xtitle, vp.ytitle, vp.ztitle],
menu_visibility=True,
# height=int(vp.size[1]/2),
)
# settings.notebook_plotter.grid = kgrid
settings.notebook_plotter.lighting = 1.2
# set k3d camera
settings.notebook_plotter.camera_auto_fit = True
if settings.plotter_instance and settings.plotter_instance.camera:
k3dc = utils.vtkCameraToK3D(settings.plotter_instance.camera)
if zoom:
k3dc[0] /= zoom
k3dc[1] /= zoom
k3dc[2] /= zoom
settings.notebook_plotter.camera = k3dc
# else:
# vsx, vsy, vsz = vbb[0]-vbb[1], vbb[2]-vbb[3], vbb[4]-vbb[5]
# vss = numpy.linalg.norm([vsx, vsy, vsz])
# if zoom:
# vss /= zoom
# vfp = (vbb[0]+vbb[1])/2, (vbb[2]+vbb[3])/2, (vbb[4]+vbb[5])/2 # camera target
# if viewup == 'z':
# vup = (0,0,1) # camera up vector
# vpos= vfp[0] + vss/1.9, vfp[1] + vss/1.9, vfp[2]+vss*0.01 # camera position
# elif viewup == 'x':
# vup = (1,0,0)
# vpos= vfp[0]+vss*0.01, vfp[1] + vss/1.5, vfp[2] # camera position
# else:
# vup = (0,1,0)
# vpos= vfp[0]+vss*0.01, vfp[1]+vss*0.01, vfp[2] + vss/1.5 # camera position
# settings.notebook_plotter.camera = [vpos[0], vpos[1], vpos[2],
# vfp[0], vfp[1], vfp[2],
# vup[0], vup[1], vup[2] ]
if not vp.axes:
settings.notebook_plotter.grid_visible = False
for ia in actors2show2:
if isinstance(ia, (vtk.vtkCornerAnnotation, vtk.vtkAssembly)):
continue
kobj = None
kcmap= None
name = None
if hasattr(ia, 'filename'):
if ia.filename:
name = os.path.basename(ia.filename)
if ia.name:
name = os.path.basename(ia.name)
#####################################################################scalars
# work out scalars first, Points Lines are also Mesh objs
if isinstance(ia, (Mesh, shapes.Line, Points)):
# print('scalars', ia.name, ia.N())
iap = ia.GetProperty()
if isinstance(ia, (shapes.Line, Points)):
iapoly = ia.polydata()
else:
iapoly = ia.clone().clean().triangulate().computeNormals().polydata()
vtkscals = None
color_attribute = None
if ia.mapper().GetScalarVisibility():
vtkdata = iapoly.GetPointData()
vtkscals = vtkdata.GetScalars()
if vtkscals is None:
vtkdata = iapoly.GetCellData()
vtkscals = vtkdata.GetScalars()
if vtkscals is not None:
c2p = vtk.vtkCellDataToPointData()
c2p.SetInputData(iapoly)
c2p.Update()
iapoly = c2p.GetOutput()
vtkdata = iapoly.GetPointData()
vtkscals = vtkdata.GetScalars()
if vtkscals is not None:
if not vtkscals.GetName():
vtkscals.SetName('scalars')
scals_min, scals_max = ia.mapper().GetScalarRange()
color_attribute = (vtkscals.GetName(), scals_min, scals_max)
lut = ia.mapper().GetLookupTable()
lut.Build()
kcmap=[]
nlut = lut.GetNumberOfTableValues()
for i in range(nlut):
r,g,b,a = lut.GetTableValue(i)
kcmap += [i/(nlut-1), r,g,b]
#####################################################################Volume
if isinstance(ia, Volume):
# print('Volume', ia.name, ia.dimensions())
kx, ky, kz = ia.dimensions()
arr = ia.getPointArray()
kimage = arr.reshape(-1, ky, kx)
colorTransferFunction = ia.GetProperty().GetRGBTransferFunction()
kcmap=[]
for i in range(128):
r,g,b = colorTransferFunction.GetColor(i/127)
kcmap += [i/127, r,g,b]
kbounds = numpy.array(ia.imagedata().GetBounds()) \
+ numpy.repeat(numpy.array(ia.imagedata().GetSpacing()) / 2.0, 2)\
* numpy.array([-1,1] * 3)
kobj = k3d.volume(kimage.astype(numpy.float32),
color_map=kcmap,
#color_range=ia.imagedata().GetScalarRange(),
alpha_coef=10,
bounds=kbounds,
name=name,
)
settings.notebook_plotter += kobj
#####################################################################text
elif hasattr(ia, 'info') and 'formula' in ia.info.keys():
pos = (ia.GetPosition()[0],ia.GetPosition()[1])
kobj = k3d.text2d(ia.info['formula'], position=pos)
settings.notebook_plotter += kobj
#####################################################################Mesh
elif isinstance(ia, Mesh) and ia.N() and len(ia.faces()):
# print('Mesh', ia.name, ia.N(), len(ia.faces()))
kobj = k3d.vtk_poly_data(iapoly,
name=name,
# color=_rgb2int(iap.GetColor()),
color_attribute=color_attribute,
color_map=kcmap,
opacity=iap.GetOpacity(),
wireframe=(iap.GetRepresentation()==1))
if iap.GetInterpolation() == 0:
kobj.flat_shading = True
settings.notebook_plotter += kobj
#####################################################################Points
elif isinstance(ia, Points) or ia.NPoints() == ia.NCells():
# print('Points', ia.name, ia.N())
kcols=[]
if color_attribute is not None:
scals = utils.vtk2numpy(vtkscals)
kcols = k3d.helpers.map_colors(scals, kcmap,
[scals_min,scals_max]).astype(numpy.uint32)
# sqsize = numpy.sqrt(numpy.dot(sizes, sizes))
kobj = k3d.points(ia.points().astype(numpy.float32),
color=_rgb2int(iap.GetColor()),
colors=kcols,
opacity=iap.GetOpacity(),
shader="dot",
point_size=3, # point_size=iap.GetPointSize()*sqsize/800,
name=name,
)
settings.notebook_plotter += kobj
#####################################################################Line
elif ia.polydata(False).GetNumberOfLines():
# print('Line', ia.name, ia.N(), len(ia.faces()),
# ia.polydata(False).GetNumberOfLines(), len(ia.lines()),
# color_attribute, [vtkscals])
# kcols=[]
# if color_attribute is not None:
# scals = utils.vtk2numpy(vtkscals)
# kcols = k3d.helpers.map_colors(scals, kcmap,
# [scals_min,scals_max]).astype(numpy.uint32)
# sqsize = numpy.sqrt(numpy.dot(sizes, sizes))
for i, ln_idx in enumerate(ia.lines()):
if i>200:
print('WARNING: K3D nr of line segments is limited to 200.')
break
pts = ia.points()[ln_idx]
kobj = k3d.line(pts.astype(numpy.float32),
color=_rgb2int(iap.GetColor()),
# colors=kcols,
opacity=iap.GetOpacity(),
shader="thick",
# width=iap.GetLineWidth()*sqsize/1000,
name=name,
)
settings.notebook_plotter += kobj
####################################################################################
elif settings.notebookBackend == 'panel' and hasattr(vp, 'window') and vp.window:
import panel # https://panel.pyviz.org/reference/panes/VTK.html
vp.renderer.ResetCamera()
settings.notebook_plotter = panel.pane.VTK(vp.window,
width=int(vp.size[0]/1.5),
height=int(vp.size[1]/2))
####################################################################################
elif 'ipyvtk' in settings.notebookBackend and hasattr(vp, 'window') and vp.window:
from ipyvtklink.viewer import ViewInteractiveWidget
vp.renderer.ResetCamera()
settings.notebook_plotter = ViewInteractiveWidget(vp.window)
####################################################################################
elif '2d' in settings.notebookBackend.lower() and hasattr(vp, 'window') and vp.window:
import PIL.Image
try:
import IPython
except ImportError:
raise Exception('IPython not available.')
from vedo.io import screenshot
settings.screeshotLargeImage = True
nn = screenshot(returnNumpy=True, scale=settings.screeshotScale+2)
pil_img = PIL.Image.fromarray(nn)
settings.notebook_plotter = IPython.display.display(pil_img)
return settings.notebook_plotter
xyz1 = xyz + np.array([0.5, 0.5, 0])
xyz2 = xyz + np.array([0.5, 0, 0.5])
xyz3 = xyz + np.array([0, 0.5, 0.5])
XYZ = np.vstack([xyz, xyz1, xyz2, xyz3]).astype(np.float32)
return XYZ
def distance(a, b):
return np.sqrt(np.sum((a - b)**2, axis=1))
### FIRST DRAWING
cubic_system = cubic(0, 0, 0, 3, 3, 3)
red_point = k3d.points(cubic_system[0], point_size=0.2, color=0xff0000)
system = k3d.points(cubic_system[1:], point_size=0.2, color=0)
a_vec = k3d.vectors(red_point.positions,
cubic_system[3],
head_size=1.5,
labels=['a'])
b_vec = k3d.vectors(red_point.positions,
cubic_system[9],
head_size=1.5,
labels=['b'])
c_vec = k3d.vectors(red_point.positions,
cubic_system[1],
head_size=1.5,
labels=['c'])
ab_vec = k3d.vectors(red_point.positions,
cubic_system[3] + 2 * cubic_system[9],
def getNotebookBackend(actors2show, zoom, viewup):
vp = settings.plotter_instance
####################################################################################
# https://github.com/InsightSoftwareConsortium/itkwidgets
# /blob/master/itkwidgets/widget_viewer.py
if 'itk' in settings.notebookBackend:
from itkwidgets import view
if sum(vp.shape) != 2:
colors.printc("Warning: multirendering is not supported in jupyter.", c=1)
settings.notebook_plotter = view(actors=actors2show,
cmap='jet', ui_collapsed=True,
gradient_opacity=False)
####################################################################################
elif settings.notebookBackend == 'k3d':
import k3d # https://github.com/K3D-tools/K3D-jupyter
if vp.shape[0] != 1 or vp.shape[1] != 1:
colors.printc("Warning: multirendering is not supported in jupyter.", c=1)
actors2show2 = []
for ia in actors2show:
if isinstance(ia, vtk.vtkAssembly): #unpack assemblies
acass = ia.unpack()
#for a in acass:
# a.SetScale(ia.GetScale())
actors2show2 += acass
else:
actors2show2.append(ia)
vbb, sizes, min_bns, max_bns = addons.computeVisibleBounds()
kgrid = vbb[0], vbb[2], vbb[4], vbb[1], vbb[3], vbb[5]
settings.notebook_plotter = k3d.plot(axes=[vp.xtitle, vp.ytitle, vp.ztitle],
menu_visibility=True,
height=int(vp.size[1]/2) )
settings.notebook_plotter.grid = kgrid
settings.notebook_plotter.lighting = 1.2
# set k3d camera
settings.notebook_plotter.camera_auto_fit = False
eps = 1 + numpy.random.random()*1.0e-04 # workaround to bug in k3d
# https://github.com/K3D-tools/K3D-jupyter/issues/180
if settings.plotter_instance and settings.plotter_instance.camera:
k3dc = utils.vtkCameraToK3D(settings.plotter_instance.camera)
k3dc[2] = k3dc[2]*eps
settings.notebook_plotter.camera = k3dc
else:
vsx, vsy, vsz = vbb[0]-vbb[1], vbb[2]-vbb[3], vbb[4]-vbb[5]
vss = numpy.linalg.norm([vsx, vsy, vsz])
if zoom:
vss /= zoom
vfp = (vbb[0]+vbb[1])/2, (vbb[2]+vbb[3])/2, (vbb[4]+vbb[5])/2 # camera target
if viewup == 'z':
vup = (0,0,1) # camera up vector
vpos= vfp[0] + vss/1.9, vfp[1] + vss/1.9, vfp[2]+vss*0.01 # camera position
elif viewup == 'x':
vup = (1,0,0)
vpos= vfp[0]+vss*0.01, vfp[1] + vss/1.5, vfp[2] # camera position
else:
vup = (0,1,0)
vpos= vfp[0]+vss*0.01, vfp[1]+vss*0.01, vfp[2] + vss/1.5 # camera position
settings.notebook_plotter.camera = [vpos[0], vpos[1], vpos[2]*eps,
vfp[0], vfp[1], vfp[2],
vup[0], vup[1], vup[2] ]
if not vp.axes:
settings.notebook_plotter.grid_visible = False
for ia in actors2show2:
kobj = None
kcmap= None
if isinstance(ia, Mesh) and ia.N():
iap = ia.GetProperty()
#ia.clean().triangulate().computeNormals()
#ia.triangulate())
iapoly = ia.clone().clean().triangulate().computeNormals().polydata()
vtkscals = None
color_attribute = None
if ia.mapper().GetScalarVisibility():
vtkdata = iapoly.GetPointData()
vtkscals = vtkdata.GetScalars()
if vtkscals is None:
vtkdata = iapoly.GetCellData()
vtkscals = vtkdata.GetScalars()
if vtkscals is not None:
c2p = vtk.vtkCellDataToPointData()
c2p.SetInputData(iapoly)
c2p.Update()
iapoly = c2p.GetOutput()
vtkdata = iapoly.GetPointData()
vtkscals = vtkdata.GetScalars()
if vtkscals is not None:
if not vtkscals.GetName():
vtkscals.SetName('scalars')
scals_min, scals_max = ia.mapper().GetScalarRange()
color_attribute = (vtkscals.GetName(), scals_min, scals_max)
lut = ia.mapper().GetLookupTable()
lut.Build()
kcmap=[]
nlut = lut.GetNumberOfTableValues()
for i in range(nlut):
r,g,b,a = lut.GetTableValue(i)
kcmap += [i/(nlut-1), r,g,b]
if iapoly.GetNumberOfPolys() > 0:
name = None
if ia.filename:
name = os.path.basename(ia.filename)
kobj = k3d.vtk_poly_data(iapoly,
name=name,
color=colors.rgb2int(iap.GetColor()),
color_attribute=color_attribute,
color_map=kcmap,
opacity=iap.GetOpacity(),
wireframe=(iap.GetRepresentation()==1))
if iap.GetInterpolation() == 0:
kobj.flat_shading = True
else:
kcols=[]
if color_attribute is not None:
scals = vtk_to_numpy(vtkscals)
kcols = k3d.helpers.map_colors(scals, kcmap,
[scals_min,scals_max]).astype(numpy.uint32)
sqsize = numpy.sqrt(numpy.dot(sizes, sizes))
if ia.NPoints() == ia.NCells():
kobj = k3d.points(ia.points().astype(numpy.float32),
color=colors.rgb2int(iap.GetColor()),
colors=kcols,
opacity=iap.GetOpacity(),
shader="3d",
point_size=iap.GetPointSize()*sqsize/400,
#compression_level=9,
)
else:
kobj = k3d.line(ia.points().astype(numpy.float32),
color=colors.rgb2int(iap.GetColor()),
colors=kcols,
opacity=iap.GetOpacity(),
shader="thick",
width=iap.GetLineWidth()*sqsize/1000,
)
settings.notebook_plotter += kobj
elif isinstance(ia, Volume):
kx, ky, kz = ia.dimensions()
arr = ia.getPointArray()
kimage = arr.reshape(-1, ky, kx)
colorTransferFunction = ia.GetProperty().GetRGBTransferFunction()
kcmap=[]
for i in range(128):
r,g,b = colorTransferFunction.GetColor(i/127)
kcmap += [i/127, r,g,b]
#print('vol scal range', ia.imagedata().GetScalarRange())
#print(numpy.min(kimage), numpy.max(kimage))
kbounds = numpy.array(ia.imagedata().GetBounds()) \
+ numpy.repeat(numpy.array(ia.imagedata().GetSpacing()) / 2.0, 2)\
* numpy.array([-1,1] * 3)
kobj = k3d.volume(kimage.astype(numpy.float32),
color_map=kcmap,
#color_range=ia.imagedata().GetScalarRange(),
alpha_coef=10,
bounds=kbounds,
)
settings.notebook_plotter += kobj
elif hasattr(ia, 'info') and 'formula' in ia.info.keys():
pos = (ia.GetPosition()[0],ia.GetPosition()[1])
kobj = k3d.text2d(ia.info['formula'], position=pos)
settings.notebook_plotter += kobj
####################################################################################
elif settings.notebookBackend == 'panel' and hasattr(vp, 'window') and vp.window:
import panel # https://panel.pyviz.org/reference/panes/VTK.html
vp.renderer.ResetCamera()
settings.notebook_plotter = panel.pane.VTK(vp.window,
width=int(vp.size[0]/1.5),
height=int(vp.size[1]/2))
####################################################################################
elif '2d' in settings.notebookBackend.lower() and hasattr(vp, 'window') and vp.window:
import PIL.Image
try:
import IPython
except ImportError:
raise Exception('IPython not available.')
return
from vtkplotter.vtkio import screenshot
settings.screeshotLargeImage = True
nn = screenshot(returnNumpy=True, scale=settings.screeshotScale+2)
pil_img = PIL.Image.fromarray(nn)
settings.notebook_plotter = IPython.display.display(pil_img)
return settings.notebook_plotter