def _grid_views_default(self):
# This needs to generate the geometries and access the materials
grid_views = []
cmap = mcm.get_cmap("inferno")
for level in range(self.ds.max_level + 1):
# We truncate at half of the colormap so that we just get a slight
# linear progression
color = mcolors.to_hex(
cmap(self.cmap_truncate * level / self.ds.max_level))
# Corners is shaped like 8, 3, NGrids
this_level = self.ds.index.grid_levels[:, 0] == level
corners = np.rollaxis(self.ds.index.grid_corners[:, :, this_level],
2).astype("float32")
indices = (((np.arange(corners.shape[0]) * 8)[:, None] +
_CORNER_INDICES[None, :]).ravel().astype("uint32"))
corners.shape = (corners.size // 3, 3)
geometry = pythreejs.BufferGeometry(attributes=dict(
position=pythreejs.BufferAttribute(array=corners,
normalized=False),
index=pythreejs.BufferAttribute(array=indices,
normalized=False),
))
material = pythreejs.LineBasicMaterial(color=color,
linewidth=1,
linecap="round",
linejoin="round")
segments = pythreejs.LineSegments(geometry=geometry,
material=material)
grid_views.append(segments)
return grid_views
def mesh(self, colors={}):
import pythreejs as js
import numpy as np
lines = []
line_colors = []
red = [1, 0, 0]
green = [0, 1, 0]
exterior = self.project(exterior=True)
interior = self.project(exterior=False)
for color, polygons in zip([green, red], [exterior, interior]):
for polygon in polygons:
for segment in polygon.segments():
lines.extend([segment.p1, segment.p2])
line_colors.extend([color, color])
lines = np.array(lines, dtype=np.float32)
line_colors = np.array(line_colors, dtype=np.float32)
geometry = js.BufferGeometry(attributes={
'position':
js.BufferAttribute(lines, normalized=False),
'color':
js.BufferAttribute(line_colors, normalized=False),
}, )
material = js.LineBasicMaterial(vertexColors='VertexColors',
linewidth=1)
return js.LineSegments(geometry, material)
def __add_line_geometry(self, lines, shading, obj=None):
lines = lines.astype("float32", copy=False)
mi = np.min(lines, axis=0)
ma = np.max(lines, axis=0)
geometry = p3s.BufferGeometry(
attributes={
'position': p3s.BufferAttribute(lines, normalized=False)
})
material = p3s.LineBasicMaterial(linewidth=shading["line_width"],
color=shading["line_color"])
#, vertexColors='VertexColors'),
lines = p3s.LineSegments(geometry=geometry,
material=material) #type='LinePieces')
line_obj = {
"geometry": geometry,
"mesh": lines,
"material": material,
"max": ma,
"min": mi,
"type": "Lines",
"wireframe": None
}
if obj:
return self.__add_object(line_obj, obj), line_obj
else:
return self.__add_object(line_obj)
def build_geometry(triangles, positions, normals=None, colors=None):
attributes = {
"position": three.BufferAttribute(
np.array(positions, dtype="float32").reshape(-1, 3),
normalized=False,
),
"index": three.BufferAttribute(
np.array(triangles, dtype="uint32"),
normalized=False,
),
}
if normals:
attributes["normal"] = three.BufferAttribute(
np.array(normals, dtype="float32").reshape(-1, 3),
normalized=False,
)
if colors:
attributes["color"] = three.BufferAttribute(
np.array(colors, dtype="uint8").reshape(-1, 4),
normalized=False,
)
geometry = three.BufferGeometry(attributes=attributes)
# Compute normals from face geometry if they were not specified.
if not normals:
geometry.exec_three_obj_method("computeVertexNormals")
return geometry
def _make_threejs_primitive(self):
geometry = pythreejs.BufferGeometry()
material = pythreejs.MeshStandardMaterial(
vertexColors=pythreejs.enums.Colors.VertexColors, metalness=0.05, roughness=.9)
result = pythreejs.Mesh(geometry, material)
return result
def traverse_func(node, trans):
# Underlying mesh
mesh = node.primitive.mesh
if mesh is None:
return
# Iterate through all triangles
vs = []
def process_triangle(face_index, tri):
vs.append(list(tri.p1.p))
vs.append(list(tri.p2.p))
vs.append(list(tri.p3.p))
mesh.foreach_triangle(process_triangle)
# Create geometry
ps_attr = three.BufferAttribute(array=vs, normalized=False)
geom = three.BufferGeometry(attributes={'position': ps_attr})
# Create mesh
mesh = three.Mesh(geometry=geom, material=mat_default)
mesh.matrixAutoUpdate = False
mesh.matrix = trans.T.flatten().tolist()
scene.add(mesh)
def __get_points_from_pointcloud(self):
vertices = self.geometry.vertices.astype(np.float32)
buffer = np.empty((int(vertices.shape[0] * 3), 3), dtype=np.float32).reshape(-1, 3)
buffer[:vertices.shape[0]] = vertices
vertex_buffer = self.__as_buffer_attr(buffer)
points = three.BufferGeometry(attributes={'position': vertex_buffer})
points.exec_three_obj_method("setDrawRange", 0, vertices.shape[0])
return points
def scatter_children(points, color="red", size=4):
scene_children = []
geometry_point = p3js.BufferGeometry(
attributes={"position": p3js.BufferAttribute(array=points)})
material_point = p3js.PointsMaterial(color=color, size=size)
pts = p3js.Points(geometry_point, material_point)
scene_children.append(pts)
return scene_children
def get_pointcloud_pythreejs(xyz, colors):
points_geometry = pythreejs.BufferGeometry(attributes=dict(
position=pythreejs.BufferAttribute(xyz, normalized=False),
color=pythreejs.BufferAttribute(list(map(tuple, colors)))))
points_material = pythreejs.PointsMaterial(vertexColors='VertexColors')
return pythreejs.Points(geometry=points_geometry, material=points_material)
def __get_wireframe_from_boundary(self):
edges = self.geometry.vertices[self.geometry.as_edges_flat()].astype(
np.float32)
buffer = np.empty((int(edges.shape[0] * 3), 3),
dtype=np.float32).reshape(-1, 3)
buffer[:edges.shape[0]] = edges
vertices = self.__as_buffer_attr(buffer)
wireframe = three.BufferGeometry(attributes={'position': vertices})
wireframe.exec_three_obj_method("setDrawRange", 0, edges.shape[0])
return wireframe
def add_points(self, points, c=None, shading={}, obj=None, **kwargs):
shading.update(kwargs)
if len(points.shape) == 1:
if len(points) == 2:
points = np.array([[points[0], points[1], 0]])
else:
if points.shape[1] == 2:
points = np.append(points, np.zeros([points.shape[0], 1]), 1)
sh = self.__get_shading(shading)
points = points.astype("float32", copy=False)
mi = np.min(points, axis=0)
ma = np.max(points, axis=0)
g_attributes = {
"position": p3s.BufferAttribute(points, normalized=False)
}
m_attributes = {"size": sh["point_size"]}
if sh["point_shape"] == "circle": # Plot circles
tex = p3s.DataTexture(data=gen_circle(16, 16),
format="RGBAFormat",
type="FloatType")
m_attributes["map"] = tex
m_attributes["alphaTest"] = 0.5
m_attributes["transparency"] = True
else: # Plot squares
pass
colors, v_colors = self.__get_point_colors(points, c, sh)
if v_colors: # Colors per point
m_attributes["vertexColors"] = 'VertexColors'
g_attributes["color"] = p3s.BufferAttribute(colors,
normalized=False)
else: # Colors for all points
m_attributes["color"] = colors
material = p3s.PointsMaterial(**m_attributes)
geometry = p3s.BufferGeometry(attributes=g_attributes)
points = p3s.Points(geometry=geometry, material=material)
point_obj = {
"geometry": geometry,
"mesh": points,
"material": material,
"max": ma,
"min": mi,
"type": "Points",
"wireframe": None
}
if obj:
return self.__add_object(point_obj, obj), point_obj
else:
return self.__add_object(point_obj)
def create_points_geometry(self):
"""
Make a PointsGeometry using pythreejs
"""
points_geometry = p3.BufferGeometry(
attributes={
'position': p3.BufferAttribute(array=self.positions),
'rgba_color': p3.BufferAttribute(array=self.slice_data(None))
})
points_material = self.create_points_material()
points = p3.Points(geometry=points_geometry, material=points_material)
return points_geometry, points_material, points
def __get_wireframe_from_boundary(self):
#edges in the boundary box
edges = self.geometry.vertices[self.geometry.as_edges_flat()].astype(np.float32)
#The function empty returns an array without values initialized
buffer = np.empty((int(edges.shape[0] * 3), 3), dtype=np.float32).reshape(-1, 3)
buffer[:edges.shape[0]] = edges
vertices = self.__as_buffer_attr(buffer)
wireframe = three.BufferGeometry(attributes={'position': vertices})
#Excute the method specified by `method_name` on the three object, with arguments `args`
#SetDrawRange is a function that sets the attribute DrawRange which determines the part of the geometry to render. (start, end)
wireframe.exec_three_obj_method("setDrawRange", 0, edges.shape[0])
return wireframe
def _create_point_cloud(self, pos_array):
"""
Make a PointsGeometry using pythreejs
"""
rgba_shape = list(pos_array.shape)
rgba_shape[1] += 1
self.points_geometry = p3.BufferGeometry(
attributes={
'position':
p3.BufferAttribute(array=pos_array),
'rgba_color':
p3.BufferAttribute(array=np.ones(rgba_shape, dtype=np.float32))
})
self.point_cloud = p3.Points(geometry=self.points_geometry,
material=self.points_material)
def geometry(self):
attributes = dict(
position=pythreejs.BufferAttribute(self.vertices, normalized=False),
index=pythreejs.BufferAttribute(
self.indices.ravel(order="C").astype("u4"), normalized=False
),
)
if self.attributes is not None:
attributes["color"] = pythreejs.BufferAttribute(self.attributes)
# Face colors requires
# https://speakerdeck.com/yomotsu/low-level-apis-using-three-dot-js?slide=22
# and
# https://github.com/mrdoob/three.js/blob/master/src/renderers/shaders/ShaderLib.js
geometry = pythreejs.BufferGeometry(attributes=attributes)
geometry.exec_three_obj_method("computeFaceNormals")
return geometry
def mesh(self):
import numpy as np
import pythreejs as js
wireframe = self.view_data.get('wireframe', False)
def triangles(polygon):
points = polygon.points
return [(points[0], points[ix], points[ix + 1])
for ix in range(1, len(polygon.points) - 1)]
def _ba(vs):
points = np.array(vs, dtype=np.float32)
return js.BufferAttribute(array=points, normalized=False)
vertices = [
list(p.xyz) for polygon in self.polygons
for t in triangles(polygon)
for p in t
]
normals = [
list(polygon.plane.normal.xyz) for polygon in self.polygons
for t in triangles(polygon)
for p in t
]
geometry = js.BufferGeometry(
attributes={
'position': _ba(vertices),
'normal': _ba(normals)
},
)
if not wireframe:
color = self.view_data.get('color', 'white')
material = material=js.MeshLambertMaterial(color=color)
opacity = self.view_data.get('opacity')
if opacity is not None:
material.opacity = opacity
material.transparent = True
return js.Mesh(geometry, material)
else:
color = self.view_data.get('color', '#00ff00')
material = js.MeshBasicMaterial(color=color, wireframe=True)
return js.Mesh(geometry, material)
def _get_mesh(self, u):
if self.codim == 2:
u = u[self.entity_map]
elif self.grid.reference_element == triangle:
u = np.repeat(u, 3)
else:
u = np.tile(np.repeat(u, 3), 2)
data = p3js.BufferAttribute(_normalize(u, self.vmin, self.vmax),
normalized=True)
geo = p3js.BufferGeometry(
index=self.buffer_faces,
attributes=dict(position=self.buffer_vertices, data=data))
mesh = p3js.Mesh(geometry=geo, material=self.material)
mesh.visible = False
# translate to origin where the camera is looking by default, avoids camera not updating in nbconvert run
mesh.position = tuple(p - i
for p, i in zip(mesh.position, self.mesh_center))
return mesh
def display_portal(th_scene, portal):
"""Display portal."""
def portal_vertices(portal):
p1 = np.array(portal[0])
p2 = np.array(portal[1])
p4 = np.array(portal[2])
p3 = p1 + (p2 - p1) + (p4 - p1)
return [p1, p2, p3, p1, p3, p4]
ps_attr = three.BufferAttribute(array=portal_vertices(portal),
normalized=False)
geom = three.BufferGeometry(attributes={'position': ps_attr})
mat = three.MeshBasicMaterial(color='#ff0000',
transparent=True,
opacity=0.1,
side='DoubleSide')
mesh = three.Mesh(geometry=geom, material=mat)
th_scene.add(mesh)
def __get_drawable_from_boundary(self):
geometry_attributes = {}
tris, vtx_normals = self.geometry._as_threejs_triangle_soup()
new_colors = self.geometry_color[
self.geometry._as_threejs_colors()].astype(np.float32)
interleaved_array = np.concatenate((tris, new_colors, vtx_normals),
axis=1)
buffer = three.InterleavedBuffer(array=interleaved_array, stride=3)
geometry_attributes['position'] = three.InterleavedBufferAttribute(
data=buffer, itemSize=3, dynamic=True)
geometry_attributes['color'] = three.InterleavedBufferAttribute(
data=buffer, itemSize=3, offset=3, dynamic=True)
geometry_attributes['normal'] = three.InterleavedBufferAttribute(
data=buffer, itemSize=3, offset=6, dynamic=True)
drawable_geometry = three.BufferGeometry(
attributes=geometry_attributes)
return drawable_geometry
def axes_1d(x, y, color="#000000", linewidth=1.5):
N = len(x)
pts = np.zeros([5, 3])
xmin = np.amin(x)
xmax = np.amax(x)
ymin = np.amin(y)
ymax = np.amax(y)
pts[:, 0] = x
pts[:, 1] = y
geometry = p3.BufferGeometry(attributes={
'position': p3.BufferAttribute(array=pts),
})
material = p3.LineBasicMaterial(color=color, linewidth=linewidth)
line = p3.Line(geometry=geometry, material=material)
width = 800
height = 500
def to_edge_mesh(surf, mapper, prop, use_edge_coloring=True, use_lines=False):
"""Convert a pyvista surface to a three.js edge mesh."""
# extract all edges from the surface. Should not use triangular
# mesh here as mesh may contain more than triangular faces
if use_lines:
edges_mesh = surf
edges = segment_poly_cells(surf)
else:
edges_mesh = surf.extract_all_edges()
edges = edges_mesh.lines.reshape(-1, 3)[:, 1:]
attr = {
'position': array_to_float_buffer(edges_mesh.points),
'index': cast_to_min_size(edges, surf.n_points),
}
# add in colors
coloring = get_coloring(mapper, surf)
if coloring != 'NoColors' and not use_edge_coloring:
if mapper.GetScalarModeAsString() == 'UsePointData':
edge_scalars = edges_mesh.point_data.active_scalars
edge_colors = map_scalars(mapper, edge_scalars)
attr['color'] = array_to_float_buffer(edge_colors)
edge_geo = tjs.BufferGeometry(attributes=attr)
mesh_attr = {}
if coloring != 'NoColors':
mesh_attr['vertexColors'] = coloring
if use_edge_coloring:
edge_color = prop.GetEdgeColor()
else:
edge_color = prop.GetColor()
edge_mat = tjs.LineBasicMaterial(color=color_to_hex(edge_color),
linewidth=prop.GetLineWidth(),
opacity=prop.GetOpacity(),
side='FrontSide',
**mesh_attr)
return tjs.LineSegments(edge_geo, edge_mat)
def to_tjs_points(dataset, mapper, prop):
"""Extract the points from a dataset and return a buffered geometry."""
attr = {
'position': array_to_float_buffer(dataset.points),
}
coloring = get_coloring(mapper, dataset)
if coloring == 'VertexColors':
colors = map_scalars(mapper, dataset.point_data.active_scalars)
attr['color'] = array_to_float_buffer(colors)
geo = tjs.BufferGeometry(attributes=attr)
m_attr = {
'color': color_to_hex(prop.GetColor()),
'size': prop.GetPointSize() / 100,
'vertexColors': coloring,
}
point_mat = tjs.PointsMaterial(**m_attr)
return tjs.Points(geo, point_mat)
def plot_1d(x, y, color="blue", linewidth=2, background="#DDDDDD"):
if len(x) != len(y):
raise RuntimeError("bad shape")
N = len(x)
dx = config.figure["width"]
dy = config.figure["height"]
xmin = np.amin(x)
ymin = np.amin(y)
scale_x = dx / (np.amax(x) - xmin)
scale_y = dy / (np.amax(y) - ymin)
pts = np.zeros([N, 3], dtype=np.float32)
pts[:, 0] = (x - xmin) * scale_x
pts[:, 1] = (y - ymin) * scale_y
# arr = p3.BufferAttribute(array=pts)
geometry = p3.BufferGeometry(attributes={
'position': p3.BufferAttribute(array=pts),
})
material = p3.LineBasicMaterial(color=color, linewidth=linewidth)
line = p3.Line(geometry=geometry, material=material)
# width = 800
# height= 500
# Create the threejs scene with ambient light and camera
# camera = p3.PerspectiveCamera(position=[0.5*dx, 0.5*dy, 0],
# aspect=dx / dy)
camera = p3.OrthographicCamera(0, dx, dy, 0, 0.5 * dx, -0.5 * dx)
return render(objects=line,
camera=camera,
background=background,
enableRotate=False,
width=dx,
height=dy)
def visualize(self, colors={}):
from ..space import Vector
import pythreejs as js
import numpy as np
prior = Motion(x=0, y=0, z=0, f=0)
lines = []
line_colors = []
for parent, command in self.commands():
if isinstance(command, Motion):
updated = prior.merge(command)
pv = Vector(*prior.xyz)
uv = Vector(*updated.xyz)
delta = pv - uv
start = (uv + pv) / 2
lines.extend([prior.xyz, updated.xyz])
a1 = delta.rotate(Vector(0, 0, 1), tau / 16) * 0.1
a2 = delta.rotate(Vector(0, 0, 1), -tau / 16) * 0.1
lines.extend(
[start, (a1 + start).xyz, start, (a2 + start).xyz])
prior = updated
color = getattr(parent, 'color', [0, 1, 0])
line_colors.extend([color, color])
line_colors.extend([color, color])
line_colors.extend([color, color])
lines = np.array(lines, dtype=np.float32)
line_colors = np.array(line_colors, dtype=np.float32)
geometry = js.BufferGeometry(attributes={
'position':
js.BufferAttribute(lines, normalized=False),
'color':
js.BufferAttribute(line_colors, normalized=False),
}, )
material = js.LineBasicMaterial(vertexColors='VertexColors',
linewidth=1)
return js.LineSegments(geometry, material)
def _render_obj(self, rendered_obj, **kw):
obj_geometry = pjs.BufferGeometry(attributes=dict(
position=pjs.BufferAttribute(rendered_obj.plot_verts),
color=pjs.BufferAttribute(rendered_obj.base_cols),
normal=pjs.BufferAttribute(
rendered_obj.face_normals.astype('float32'))))
vertices = rendered_obj.vertices
# Create a mesh. Note that the material need to be told to use the vertex colors.
my_object_mesh = pjs.Mesh(
geometry=obj_geometry,
material=pjs.MeshLambertMaterial(vertexColors='VertexColors'),
position=[0, 0, 0],
)
line_material = pjs.LineBasicMaterial(color='#ffffff',
transparent=True,
opacity=0.3,
linewidth=1.0)
my_object_wireframe_mesh = pjs.LineSegments(
geometry=obj_geometry,
material=line_material,
position=[0, 0, 0],
)
n_vert = vertices.shape[0]
center = vertices.mean(axis=0)
extents = self._get_extents(vertices)
max_delta = np.max(extents[:, 1] - extents[:, 0])
camPos = [center[i] + 4 * max_delta for i in range(3)]
light_pos = [center[i] + (i + 3) * max_delta for i in range(3)]
# Set up a scene and render it:
camera = pjs.PerspectiveCamera(position=camPos,
fov=20,
children=[
pjs.DirectionalLight(
color='#ffffff',
position=light_pos,
intensity=0.5)
])
camera.up = (0, 0, 1)
v = [0.0, 0.0, 0.0]
if n_vert > 0: v = vertices[0].tolist()
select_point_geom = pjs.SphereGeometry(radius=1.0)
select_point_mesh = pjs.Mesh(
select_point_geom,
material=pjs.MeshBasicMaterial(color=SELECTED_VERTEX_COLOR),
position=v,
scale=(0.0, 0.0, 0.0))
#select_edge_mesh = pjs.ArrowHelper(dir=pjs.Vector3(1.0, 0.0, 0.0), origin=pjs.Vector3(0.0, 0.0, 0.0), length=1.0,
# hex=SELECTED_EDGE_COLOR_INT, headLength=0.1, headWidth=0.05)
arrow_cyl_mesh = pjs.Mesh(geometry=pjs.SphereGeometry(radius=0.01),
material=pjs.MeshLambertMaterial())
arrow_head_mesh = pjs.Mesh(geometry=pjs.SphereGeometry(radius=0.001),
material=pjs.MeshLambertMaterial())
scene_things = [
my_object_mesh, my_object_wireframe_mesh, select_point_mesh,
arrow_cyl_mesh, arrow_head_mesh, camera,
pjs.AmbientLight(color='#888888')
]
if self.draw_grids:
grids, space = self._get_grids(vertices)
scene_things.append(grids)
scene = pjs.Scene(children=scene_things, background=BACKGROUND_COLOR)
click_picker = pjs.Picker(controlling=my_object_mesh, event='dblclick')
out = Output()
top_msg = HTML()
def on_dblclick(change):
if change['name'] == 'point':
try:
point = np.array(change['new'])
face = click_picker.faceIndex
face_points = rendered_obj.face_verts[face]
face_vecs = face_points - np.roll(face_points, 1, axis=0)
edge_lens = np.sqrt((face_vecs**2).sum(axis=1))
point_vecs = face_points - point[np.newaxis, :]
point_dists = (point_vecs**2).sum(axis=1)
min_point = np.argmin(point_dists)
v1s = point_vecs.copy()
v2s = np.roll(v1s, -1, axis=0)
edge_mids = 0.5 * (v2s + v1s)
edge_mid_dists = (edge_mids**2).sum(axis=1)
min_edge_point = np.argmin(edge_mid_dists)
edge_start = min_edge_point
edge = face * 3 + edge_start
close_vert = rendered_obj.face_verts[face, min_point]
edge_start_vert = rendered_obj.face_verts[face, edge_start]
edge_end_vert = rendered_obj.face_verts[face,
(edge_start + 1) %
3]
vertex = face * 3 + min_point
radius = min(
[edge_lens.max() * 0.02, 0.1 * edge_lens.min()])
edge_head_length = radius * 4
edge_head_width = radius * 2
select_point_mesh.scale = (radius, radius, radius)
top_msg.value = '<font color="{}">selected face: {}</font>, <font color="{}">edge: {}</font>, <font color="{}"> vertex: {}</font>'.format(
SELECTED_FACE_COLOR, face, SELECTED_EDGE_COLOR, edge,
SELECTED_VERTEX_COLOR, vertex)
newcols = rendered_obj.base_cols.copy()
newcols[face * 3:(face + 1) * 3] = np.array(
SELECTED_FACE_RGB, dtype='float32')
select_point_mesh.position = close_vert.tolist()
obj_geometry.attributes['color'].array = newcols
with out:
make_arrow(arrow_cyl_mesh, arrow_head_mesh,
edge_start_vert, edge_end_vert, radius / 2,
radius, radius * 3, SELECTED_EDGE_COLOR)
except:
with out:
print(traceback.format_exc())
click_picker.observe(on_dblclick, names=['point'])
renderer_obj = pjs.Renderer(
camera=camera,
background='#cccc88',
background_opacity=0,
scene=scene,
controls=[pjs.OrbitControls(controlling=camera), click_picker],
width=self.width,
height=self.height)
display_things = [top_msg, renderer_obj, out]
if self.draw_grids:
s = """
<svg width="{}" height="30">
<rect width="20" height="20" x="{}" y="0" style="fill:none;stroke-width:1;stroke:rgb(0,255,0)" />
<text x="{}" y="15">={:.1f}</text>
Sorry, your browser does not support inline SVG.
</svg>""".format(self.width, self.width // 2, self.width // 2 + 25, space)
display_things.append(HTML(s))
display(VBox(display_things))
def add_mesh(self, v, f, c=None, uv=None, shading={}, texture_data=None):
sh = self.__get_shading(shading)
mesh_obj = {}
#it is a tet
if v.shape[1] == 3 and f.shape[1] == 4:
f_tmp = np.ndarray([f.shape[0]*4, 3], dtype=f.dtype)
for i in range(f.shape[0]):
f_tmp[i*4+0] = np.array([f[i][1], f[i][0], f[i][2]])
f_tmp[i*4+1] = np.array([f[i][0], f[i][1], f[i][3]])
f_tmp[i*4+2] = np.array([f[i][1], f[i][2], f[i][3]])
f_tmp[i*4+3] = np.array([f[i][2], f[i][0], f[i][3]])
f = f_tmp
if v.shape[1] == 2:
v = np.append(v, np.zeros([v.shape[0], 1]), 1)
# Type adjustment vertices
v = v.astype("float32", copy=False)
# Color setup
colors, coloring = self.__get_colors(v, f, c, sh)
# Type adjustment faces and colors
c = colors.astype("float32", copy=False)
# Material and geometry setup
ba_dict = {"color": p3s.BufferAttribute(c)}
if coloring == "FaceColors":
verts = np.zeros((f.shape[0]*3, 3), dtype="float32")
for ii in range(f.shape[0]):
#print(ii*3, f[ii])
verts[ii*3] = v[f[ii,0]]
verts[ii*3+1] = v[f[ii,1]]
verts[ii*3+2] = v[f[ii,2]]
v = verts
else:
f = f.astype("uint32", copy=False).ravel()
ba_dict["index"] = p3s.BufferAttribute(f, normalized=False)
ba_dict["position"] = p3s.BufferAttribute(v, normalized=False)
if type(uv) != type(None):
uv = (uv - np.min(uv)) / (np.max(uv) - np.min(uv))
if texture_data is None:
texture_data = gen_checkers(20, 20)
tex = p3s.DataTexture(data=texture_data, format="RGBFormat", type="FloatType")
material = p3s.MeshStandardMaterial(map=tex, reflectivity=sh["reflectivity"], side=sh["side"],
roughness=sh["roughness"], metalness=sh["metalness"], flatShading=sh["flat"],
polygonOffset=True, polygonOffsetFactor= 1, polygonOffsetUnits=5)
ba_dict["uv"] = p3s.BufferAttribute(uv.astype("float32", copy=False))
else:
material = p3s.MeshStandardMaterial(vertexColors=coloring, reflectivity=sh["reflectivity"],
side=sh["side"], roughness=sh["roughness"], metalness=sh["metalness"],
flatShading=sh["flat"],
polygonOffset=True, polygonOffsetFactor= 1, polygonOffsetUnits=5)
geometry = p3s.BufferGeometry(attributes=ba_dict)
if coloring == "VertexColors":
geometry.exec_three_obj_method('computeVertexNormals')
else:
geometry.exec_three_obj_method('computeFaceNormals')
# Mesh setup
mesh = p3s.Mesh(geometry=geometry, material=material)
# Wireframe setup
mesh_obj["wireframe"] = None
if sh["wireframe"]:
wf_geometry = p3s.WireframeGeometry(mesh.geometry) # WireframeGeometry
wf_material = p3s.LineBasicMaterial(color=sh["wire_color"], linewidth=sh["wire_width"])
wireframe = p3s.LineSegments(wf_geometry, wf_material)
mesh.add(wireframe)
mesh_obj["wireframe"] = wireframe
# Bounding box setup
if sh["bbox"]:
v_box, f_box = self.__get_bbox(v)
_, bbox = self.add_edges(v_box, f_box, sh, mesh)
mesh_obj["bbox"] = [bbox, v_box, f_box]
# Object setup
mesh_obj["max"] = np.max(v, axis=0)
mesh_obj["min"] = np.min(v, axis=0)
mesh_obj["geometry"] = geometry
mesh_obj["mesh"] = mesh
mesh_obj["material"] = material
mesh_obj["type"] = "Mesh"
mesh_obj["shading"] = sh
mesh_obj["coloring"] = coloring
mesh_obj["arrays"] = [v, f, c] # TODO replays with proper storage or remove if not needed
return self.__add_object(mesh_obj)
def __get_drawable_from_boundary(self):
geometry_attributes = {}
tris, vtx_normals = self.geometry._as_threejs_triangle_soup()
new_colors = self.geometry_color[self.geometry._as_threejs_colors()].astype(np.float32)
if self.geometry.uvcoords is not None:
uvcoords = self.geometry.uvcoords.astype(np.float32)
coor = self.geometry.coor
uv = []
if len(uvcoords) != 0:
#corrispondenza delle coordinate uv in triangle soup
#Uv coords in triangle soup
if 'Quadmesh' in self.type:
coor = np.c_[coor[:,:3], coor[:,2:], coor[:,0]]
coor = coor.flatten()
for c in coor:
uv.append(uvcoords[c - 1])
self.faceVertexUvs = np.array(uv).astype(np.float32)
if len(self.faceVertexUvs) != 0 :
interleaved_array = np.concatenate((tris, new_colors, vtx_normals, self.faceVertexUvs), axis=1)
buffer = three.InterleavedBuffer(array=interleaved_array, stride=4)
else:
interleaved_array = np.concatenate((tris, new_colors, vtx_normals), axis=1)
buffer = three.InterleavedBuffer(array=interleaved_array, stride=3)
#Making the interleavedBuffer using the interleaved_array made up of the triangle soup, the color and the vertices' normals, with a stride of 3
#itemsize = item size, dynamic = (is the normalized attribute o f the super class)?, offset = it's the offset from the start item,
geometry_attributes['position'] = three.InterleavedBufferAttribute(data=buffer, itemSize=3, dynamic = True)
geometry_attributes['color'] = three.InterleavedBufferAttribute(data=buffer, itemSize=3, offset=3, dynamic=True)
geometry_attributes['normal'] = three.InterleavedBufferAttribute(data=buffer, itemSize=3, offset=6, dynamic=True)
if self.geometry.material is not {} or self.geometry.texture is not None :
geometry_attributes['uv'] = three.InterleavedBufferAttribute(data=buffer, itemSize=2, offset=9, dynamic=True)
# # Buffer Geometry = an efficient representation of mesh, line, or point geometry
# Includes vertex positions, face indices, normals, colors, UVs, and custom attributes within buffers
drawable_geometry = three.BufferGeometry(attributes=geometry_attributes)
#The multiplier is used because groups need faces' indices in triangle soup and 'count' counts only the number of faces per material
mult = 1
if 'Trimesh' in self.type:
mult = 3
elif 'Quadmesh' in self.type:
mult = 6
if len(self.geometry.material) != 0:
'''
group = { start: Integer, count: Integer, materialIndex: Integer } where:
- start : the first triangle index of the group
- count : how many indices are included
- materialIndex : the material array index to use for this group
'''
i = 0
for g in self.geometry.groups:
if i == 0:
n = copy.copy(g)
drawable_geometry.exec_three_obj_method("addGroup", 0, mult * self.geometry.groups[g], self.search_key(g))
else:
drawable_geometry.exec_three_obj_method("addGroup", mult * self.geometry.groups[n], mult * self.geometry.groups[g],
self.search_key(g))
n = copy.copy(g)
i = i + 1
return drawable_geometry
def setGeometry(self, vertices, idxs, normals, preserveExisting=False, updateModelMatrix=False, textureMap=None, scalarField=None, vectorField=None):
self.scalarField = scalarField
self.vectorField = vectorField
if (updateModelMatrix):
translate = -np.mean(vertices, axis=0)
self.bbSize = np.max(np.abs(vertices + translate))
scaleFactor = 2.0 / self.bbSize
self.objects.scale = [scaleFactor, scaleFactor, scaleFactor]
self.objects.position = tuple(scaleFactor * translate)
########################################################################
# Construct the raw attributes describing the new mesh.
########################################################################
attrRaw = {'position': vertices,
'index': idxs.ravel(),
'normal': normals}
if (textureMap is not None): attrRaw['uv'] = np.array(textureMap.uv, dtype=np.float32)
useVertexColors = False
if (self.scalarField is not None):
# Construct scalar field from raw data array if necessary
if (not isinstance(self.scalarField, ScalarField)):
self.scalarField = ScalarField(self.mesh, self.scalarField)
self.scalarField.validateSize(vertices.shape[0], idxs.shape[0])
attrRaw['color'] = np.array(self.scalarField.colors(), dtype=np.float32)
if (self.scalarField.domainType == DomainType.PER_TRI):
# Replicate vertex data in the per-face case (positions, normal, uv) and remove index buffer; replicate colors x3
# This is needed according to https://stackoverflow.com/questions/41670308/three-buffergeometry-how-do-i-manually-set-face-colors
# since apparently indexed geometry doesn't support the 'FaceColors' option.
replicateAttributesPerTriCorner(attrRaw)
useVertexColors = True
# Turn the current mesh into a ghost if preserveExisting
if (preserveExisting and (self.currMesh is not None)):
oldMesh = self.currMesh
self.currMesh = None
oldMesh.material = self.materialLibrary.ghostMaterial(oldMesh.material)
self.meshes.remove(oldMesh)
self.ghostMeshes.add(oldMesh)
# Also convert the current vector field into a ghost (if one is displayed)
if (self.vectorFieldMesh in self.meshes.children):
oldVFMesh = self.vectorFieldMesh
self.vectorFieldMesh = None
oldVFMesh.material.transparent = True
colors = oldVFMesh.geometry.attributes['arrowColor'].array
colors[:, 3] = 0.25
oldVFMesh.geometry.attributes['arrowColor'].array = colors
self.meshes.remove(oldVFMesh)
self.ghostMeshes.add(oldVFMesh)
else:
self.__cleanMeshes(self.ghostMeshes)
material = self.materialLibrary.material(useVertexColors, None if textureMap is None else textureMap.dataTex)
########################################################################
# Build or update mesh from the raw attributes.
########################################################################
stashableKeys = ['index', 'color', 'uv']
def allocateUpdateOrStashBufferAttribute(attr, key):
# Verify invariant that attributes, if they exist, must either be
# attached to the current geometry or in the stash (but not both)
assert((key not in attr) or (key not in self.bufferAttributeStash))
if key in attrRaw:
if key in self.bufferAttributeStash:
# Reuse the stashed index buffer
attr[key] = self.bufferAttributeStash[key]
self.bufferAttributeStash.pop(key)
# Update existing attribute or allocate it for the first time
if key in attr:
attr[key].array = attrRaw[key]
else:
attr[key] = pythreejs.BufferAttribute(attrRaw[key])
else:
if key in attr:
# Stash the existing, unneeded attribute
self.bufferAttributeStash[key] = attr[key]
attr.pop(key)
# Avoid flicker/partial redraws during updates
if self.avoidRedrawFlicker:
self.renderer.pauseRendering()
if (self.currMesh is None):
attr = {}
presentKeys = list(attrRaw.keys())
for key in presentKeys:
if key in stashableKeys:
allocateUpdateOrStashBufferAttribute(attr, key)
attrRaw.pop(key)
attr.update({k: pythreejs.BufferAttribute(v) for k, v in attrRaw.items()})
geom = pythreejs.BufferGeometry(attributes=attr)
m = self.MeshConstructor(geometry=geom, material=material)
self.currMesh = m
self.meshes.add(m)
else:
# Update the current mesh...
attr = self.currMesh.geometry.attributes.copy()
attr['position'].array = attrRaw['position']
attr['normal' ].array = attrRaw['normal']
for key in stashableKeys:
allocateUpdateOrStashBufferAttribute(attr, key)
self.currMesh.geometry.attributes = attr
self.currMesh.material = material
# If we reallocated the current mesh (preserveExisting), we need to point
# the wireframe/points mesh at the new geometry.
if self.wireframeMesh is not None:
self.wireframeMesh.geometry = self.currMesh.geometry
if self.pointsMesh is not None:
self.pointsMesh.geometry = self.currMesh.geometry
########################################################################
# Build/update the vector field mesh if requested (otherwise hide it).
########################################################################
if (self.vectorField is not None):
# Construct vector field from raw data array if necessary
if (not isinstance(self.vectorField, VectorField)):
self.vectorField = VectorField(self.mesh, self.vectorField)
self.vectorField.validateSize(vertices.shape[0], idxs.shape[0])
self.vectorFieldMesh = self.vectorField.getArrows(vertices, idxs, material=self.arrowMaterial, existingMesh=self.vectorFieldMesh)
self.arrowMaterial = self.vectorFieldMesh.material
self.arrowMaterial.updateUniforms(arrowSizePx_x = self.arrowSize,
rendererWidth = self.renderer.width,
targetDepth = np.linalg.norm(np.array(self.cam.position) - np.array(self.controls.target)),
arrowAlignment = self.vectorField.align.getRelativeOffset())
self.controls.shaderMaterial = self.arrowMaterial
if (self.vectorFieldMesh not in self.meshes.children):
self.meshes.add(self.vectorFieldMesh)
else:
if (self.vectorFieldMesh in self.meshes.children):
self.meshes.remove(self.vectorFieldMesh)
if self.avoidRedrawFlicker:
# The scene is now complete; reenable rendering and redraw immediatley.
self.renderer.resumeRendering()
def mesh_animation(times, xt, faces):
""" Animate a mesh from a sequence of mesh vertex positions
Args:
times - a list of time values t_i at which the configuration x is specified
xt - i.e., x(t). A list of arrays representing mesh vertex positions at times t_i.
Dimensions of each array should be the same as that of mesh.geometry.array
TODO nt - n(t) vertex normals
faces - array of faces, with vertex loop for each face
Side effects:
displays rendering of mesh, with animation action
Returns: None
TODO renderer - THREE.Render to show the default scene
TODO position_action - THREE.AnimationAction IPython widget
"""
position_morph_attrs = []
for pos in xt[
1:]: # xt[0] uses as the Mesh's default/initial vertex position
position_morph_attrs.append(
THREE.BufferAttribute(pos, normalized=False))
# Testing mesh.geometry.morphAttributes = {'position': position_morph_attrs}
geom = THREE.BufferGeometry(
attributes={
'position': THREE.BufferAttribute(xt[0], normalized=False),
'index': THREE.BufferAttribute(faces.ravel())
},
morphAttributes={'position': position_morph_attrs})
matl = THREE.MeshStandardMaterial(side='DoubleSide',
color='red',
wireframe=True,
morphTargets=True)
mesh = THREE.Mesh(geom, matl)
# create key frames
position_track = THREE.NumberKeyframeTrack(
name='.morphTargetInfluences[0]',
times=times,
values=list(range(0, len(times))))
# create animation clip from the morph targets
position_clip = THREE.AnimationClip(tracks=[position_track])
# create animation action
position_action = THREE.AnimationAction(THREE.AnimationMixer(mesh),
position_clip, mesh)
# TESTING
camera = THREE.PerspectiveCamera(position=[2, 1, 2], aspect=600 / 400)
scene = THREE.Scene(children=[
mesh, camera,
THREE.AxesHelper(0.2),
THREE.DirectionalLight(position=[3, 5, 1], intensity=0.6),
THREE.AmbientLight(intensity=0.5)
])
renderer = THREE.Renderer(
camera=camera,
scene=scene,
controls=[THREE.OrbitControls(controlling=camera)],
width=600,
height=400)
display(renderer, position_action)
def plot(self,
backend="pythreejs",
width=800,
height=500,
background="black",
mesh=False,
use_as_color=["red", "green", "blue"],
cmap="hsv",
return_scene=False,
output_name="pyntcloud_plot",
polylines={}):
"""Visualize a PyntCloud using different backends.
Parameters
----------
backend: {"pythreejs", "threejs"}, optional
Default: "pythreejs"
Used to select one of the available libraries for plotting.
width: int, optional
Default: 800
height: int, optional
Default: 500
background: str, optional
Default: "black"
Used to select the default color of the background.
In some backends, i.e "pythreejs" the background can be dynamically changed.
use_as_color: str or ["red", "green", "blue"], optional
Default: ["red", "green", "blue"]
Indicates which scalar fields will be used to colorize the rendered
point cloud.
cmap: str, optional
Default: "hsv"
Color map that will be used to convert a single scalar field into rgb.
Check matplotlib cmaps.
return_scene: bool, optional
Default: False.
Used with "pythreejs" backend in order to return the pythreejs.Scene object
polylines: dict, optional
Default {}.
Mapping hexadecimal colors to a list of list(len(3)) representing the points of the polyline.
Example:
polylines={
"0xFFFFFF": [[0, 0, 0], [0, 0, 1]],
"0xFF00FF": [[1, 0, 0], [1, 0, 1], [1, 1, 1]]
}
Returns
-------
pythreejs.Scene if return_scene else None
"""
try:
colors = self.points[use_as_color].values
except KeyError:
colors = None
if use_as_color != ["red", "green", "blue"] and colors is not None:
import matplotlib.pyplot as plt
s_m = plt.cm.ScalarMappable(cmap=cmap)
colors = s_m.to_rgba(colors)[:, :-1] * 255
elif colors is None:
# default color orange
colors = np.repeat([[255, 125, 0]], self.xyz.shape[0], axis=0)
colors = colors.astype(np.uint8)
ptp = self.xyz.ptp()
if backend == "pythreejs":
import ipywidgets
import pythreejs
from IPython.display import display
if mesh:
raise NotImplementedError(
"Plotting mesh geometry with pythreejs backend is not supported yet."
)
if polylines:
raise NotImplementedError(
"Plotting polylines with pythreejs backend is not supported yet."
)
points_geometry = pythreejs.BufferGeometry(attributes=dict(
position=pythreejs.BufferAttribute(self.xyz, normalized=False),
color=pythreejs.BufferAttribute(list(map(tuple, colors)))))
points_material = pythreejs.PointsMaterial(
vertexColors='VertexColors')
points = pythreejs.Points(geometry=points_geometry,
material=points_material,
position=tuple(self.centroid))
camera = pythreejs.PerspectiveCamera(
fov=90,
aspect=width / height,
position=tuple(
self.centroid +
[0,
abs(self.xyz.max(0)[1]),
abs(self.xyz.max(0)[2]) * 2]),
up=[0, 0, 1])
orbit_control = pythreejs.OrbitControls(controlling=camera)
orbit_control.target = tuple(self.centroid)
camera.lookAt(tuple(self.centroid))
scene = pythreejs.Scene(children=[points, camera],
background=background)
renderer = pythreejs.Renderer(scene=scene,
camera=camera,
controls=[orbit_control],
width=width,
height=height)
display(renderer)
size = ipywidgets.FloatSlider(min=0.,
max=(ptp / 100),
step=(ptp / 1000))
ipywidgets.jslink((size, 'value'), (points_material, 'size'))
color = ipywidgets.ColorPicker()
ipywidgets.jslink((color, 'value'), (scene, 'background'))
display(
ipywidgets.HBox(children=[
ipywidgets.Label('Background color:'), color,
ipywidgets.Label('Point size:'), size
]))
return scene if return_scene else None
elif backend == "threejs":
points = pd.DataFrame(self.xyz, columns=["x", "y", "z"])
for n, i in enumerate(["red", "green", "blue"]):
points[i] = colors[:, n]
new_PyntCloud = PyntCloud(points)
if mesh and self.mesh is not None:
new_PyntCloud.mesh = self.mesh[["v1", "v2", "v3"]]
return plot_PyntCloud(new_PyntCloud,
IFrame_shape=(width, height),
point_size=ptp / 100,
point_opacity=0.9,
output_name=output_name,
polylines=polylines)
else:
raise NotImplementedError(
"{} backend is not supported".format(backend))