def _renderer_default(self):
center = tuple(self.ds.domain_center.in_units("code_length").d)
right = tuple((self.ds.domain_right_edge +
(self.ds.domain_right_edge - self.ds.domain_center) *
2.0).in_units("code_length").d)
camera = pythreejs.PerspectiveCamera(
position=right, fov=20, children=[pythreejs.AmbientLight()])
scene = pythreejs.Scene(
children=[camera, pythreejs.AmbientLight(color="#dddddd")] +
self.grid_views)
orbit_control = pythreejs.OrbitControls(controlling=camera)
renderer = pythreejs.Renderer(
scene=scene,
camera=camera,
controls=[orbit_control],
width=400,
height=400,
background="black",
background_opacity=1,
antialias=True,
)
camera.lookAt(center)
orbit_control.target = center
renderer.layout.border = "1px solid darkgrey"
return renderer
def view_3js(sheet, coords=['x', 'y', 'z'], **draw_specs):
"""
Creates a javascript renderer of the edge lines to be displayed
in Jupyter Notebooks
Returns
-------
renderer: a :class:`pythreejs.pythreejs.Renderer` instance
lines: a :class:`pythreejs.pythreejs.Line` object
Example
-------
>>> from IPython import display
>>> renderer, lines = view_3js(eptm)
>>> display(renderer)
"""
lines = edge_lines(sheet, coords, **draw_specs)
scene = py3js.Scene(children=[
lines,
py3js.DirectionalLight(color='#ccaabb', position=[0, 5, 0]),
py3js.AmbientLight(color='#cccccc')
])
c = py3js.PerspectiveCamera(position=[0, 5, 5])
renderer = py3js.Renderer(camera=c,
scene=scene,
controls=[py3js.OrbitControls(controlling=c)])
return renderer, lines
def plot_voxelgrid_with_pythreejs(voxel_centers, voxel_colors, width, height,
**kwargs):
if pythreejs is None:
raise ImportError(
"pythreejs is needed for plotting with pythreejs backend.")
if display is None:
raise ImportError(
"IPython is needed for plotting with pythreejs backend.")
centroid, camera_position = get_centroid_and_camera_position(voxel_centers)
camera = pythreejs.PerspectiveCamera(fov=90,
aspect=width / height,
position=camera_position,
up=[0, 0, 1])
mesh = get_voxelgrid_pythreejs(voxel_centers, voxel_colors)
scene = pythreejs.Scene(children=[camera, mesh], background=None)
controls = pythreejs.OrbitControls(controlling=camera,
target=tuple(centroid))
camera.lookAt(tuple(centroid))
renderer = pythreejs.Renderer(scene=scene,
camera=camera,
controls=[controls],
width=width,
height=height)
display(renderer)
def _ipython_display_(self):
# This needs to actually display, which is not the same as returning a display.
cam = pythreejs.PerspectiveCamera(
position=[25, 35, 100],
fov=20,
children=[pythreejs.AmbientLight()],
)
children = [cam, pythreejs.AmbientLight(color="#dddddd")]
material = pythreejs.MeshBasicMaterial(color="#ff0000",
vertexColors="VertexColors",
side="DoubleSide")
for model in self.components:
mesh = pythreejs.Mesh(geometry=model.geometry,
material=material,
position=[0, 0, 0])
children.append(mesh)
scene = pythreejs.Scene(children=children)
rendererCube = pythreejs.Renderer(
camera=cam,
background="white",
background_opacity=1,
scene=scene,
controls=[pythreejs.OrbitControls(controlling=cam)],
width=800,
height=800,
)
return rendererCube
def __init__(self, obj, width=512, height=512, textureMap=None, scalarField=None, vectorField=None):
# Note: subclass's constructor should define
# self.MeshConstructor and self.isLineMesh, which will
# determine how the geometry is interpreted.
if (self.isLineMesh is None):
self.isLineMesh = False
if (self.MeshConstructor is None):
self.MeshConstructor = pythreejs.Mesh
light = pythreejs.PointLight(color='white', position=[0, 0, 5])
light.intensity = 0.6
self.cam = pythreejs.PerspectiveCamera(position = [0, 0, 5], up = [0, 1, 0], aspect=width / height,
children=[light])
self.avoidRedrawFlicker = False
self.objects = pythreejs.Group()
self.meshes = pythreejs.Group()
self.ghostMeshes = pythreejs.Group() # Translucent meshes kept around by preserveExisting
self.materialLibrary = MaterialLibrary(self.isLineMesh)
# Sometimes we do not use a particular attribute buffer, e.g. the index buffer when displaying
# per-face scalar fields. But to avoid reallocating these buffers when
# switching away from these cases, we need to preserve the buffers
# that may have previously been allocated. This is done with the bufferAttributeStash.
# A buffer attribute, if it exists, must always be attached to the
# current BufferGeometry or in this stash (but not both!).
self.bufferAttributeStash = {}
self.currMesh = None # The main mesh being viewed
self.wireframeMesh = None # Wireframe for the main visualization mesh
self.pointsMesh = None # Points for the main visualization mesh
self.vectorFieldMesh = None
self.cachedWireframeMaterial = None
self.cachedPointsMaterial = None
self.objects.add([self.meshes, self.ghostMeshes])
self.shouldShowWireframe = False
self.scalarField = None
self.vectorField = None
self.arrowMaterial = None # Will hold this viewer's instance of the special vector field shader
self._arrowSize = 60
# Camera needs to be part of the scene because the scene light is its child
# (so that it follows the camera).
self.scene = pythreejs.Scene(children=[self.objects, self.cam, pythreejs.AmbientLight(intensity=0.5)])
# Sane trackball controls.
self.controls = pythreejs.TrackballControls(controlling=self.cam)
self.controls.staticMoving = True
self.controls.rotateSpeed = 2.0
self.controls.zoomSpeed = 2.0
self.controls.panSpeed = 1.0
self.renderer = pythreejs.Renderer(camera=self.cam, scene=self.scene, controls=[self.controls], width=width, height=height)
self.update(True, obj, updateModelMatrix=True, textureMap=textureMap, scalarField=scalarField, vectorField=vectorField)
def _default_camera(self):
# see https://github.com/maartenbreddels/ipyvolume/pull/40 for an explanation
z = 2 * np.tan(45.0 / 2.0 * np.pi / 180) / np.tan(
self.camera_fov / 2.0 * np.pi / 180)
return pythreejs.PerspectiveCamera(fov=self.camera_fov,
position=(0, 0, z),
width=400,
height=500)
def __initialize_camera(self, width, height):
camera_target = np.mean([drawable.center for drawable in self.drawables], axis=0)
camera_position = tuple(camera_target + [0, 0, np.mean([drawable.scale for drawable in self.drawables])])
directional_light = three.DirectionalLight(color = '#ffffff', position = [0, 10, 0], intensity = 1)
camera = three.PerspectiveCamera(
position=camera_position, aspect=width/height, lookAt=camera_target, fov=50, near=.1, far=20000,
children=[directional_light]
)
return camera
def __init__(self, width=600, height=400):
light = p3js.DirectionalLight(color='#ffffff', position=[0, 0, 1], intensity=0.5)
self.camera = p3js.PerspectiveCamera(position=[2.0, 5.0, 2.0], fov=50, children=[light], aspect=width/float(height))
self.camera.up = (0.0, 0.0, 1.0)
self.width = 600
self.height = 400
self.geometry = []
self.draw_axes(size=1)
def get_camera_pythreejs(centroid, xyz, width, height):
camera = pythreejs.PerspectiveCamera(
fov=90,
aspect=width / height,
position=tuple(centroid +
[0, abs(xyz.max(0)[1]),
abs(xyz.max(0)[2]) * 1.5]),
up=[0, 0, 1])
camera.lookAt(tuple(centroid))
return camera
def display_jupyter(self, window_size=(800, 600), axes_arrow_length=None):
"""Returns a PyThreeJS Renderer and AnimationAction for displaying and
animating the scene inside a Jupyter notebook.
Parameters
==========
window_size : 2-tuple of integers
2-tuple containing the width and height of the renderer window in
pixels.
axes_arrow_length : float
If a positive value is supplied a red (x), green (y), and blue (z)
arrows of the supplied length will be displayed as arrows for the
global axes.
Returns
=======
vbox : widgets.VBox
A vertical box containing the action (pythreejs.AnimationAction)
and renderer (pythreejs.Renderer).
"""
if p3js is None:
raise ImportError('pythreejs needs to be installed.')
self._generate_meshes_tracks()
view_width = window_size[0]
view_height = window_size[1]
camera = p3js.PerspectiveCamera(position=[1, 1, 1],
aspect=view_width / view_height)
key_light = p3js.DirectionalLight()
ambient_light = p3js.AmbientLight()
children = self._meshes + [camera, key_light, ambient_light]
if axes_arrow_length is not None:
children += [p3js.AxesHelper(size=abs(axes_arrow_length))]
scene = p3js.Scene(children=children)
controller = p3js.OrbitControls(controlling=camera)
renderer = p3js.Renderer(camera=camera,
scene=scene,
controls=[controller],
width=view_width,
height=view_height)
clip = p3js.AnimationClip(tracks=self._tracks, duration=self.times[-1])
action = p3js.AnimationAction(p3js.AnimationMixer(scene), clip, scene)
return widgets.VBox([action, renderer])
def __init__(self, eye_pos, obj_pos, obj, up=(0, 1, 0)):
self.camera = three.PerspectiveCamera(
position=tuple(eye_pos),
lookAt=tuple(obj_pos),
fov=30,
)
self.camera.up = up
self.light = three.PointLight(
color="white",
position=(-eye_pos[0], eye_pos[1], eye_pos[2]),
)
self.obj = obj
self.scene = three.Scene(children=[self.obj, self.light, self.camera])
def __init__(self, settings):
self.__update_settings(settings)
self._light = p3s.DirectionalLight(color='white', position=[0, 0, 1], intensity=0.6)
self._light2 = p3s.AmbientLight(intensity=0.5)
self._cam = p3s.PerspectiveCamera(position=[0, 0, 1], lookAt=[0, 0, 0], fov=self.__s["fov"],
aspect=self.__s["width"]/self.__s["height"], children=[self._light])
self._orbit = p3s.OrbitControls(controlling=self._cam)
self._scene = p3s.Scene(children=[self._cam, self._light2], background=self.__s["background"])#"#4c4c80"
self._renderer = p3s.Renderer(camera=self._cam, scene = self._scene, controls=[self._orbit],
width=self.__s["width"], height=self.__s["height"], antialias=self.__s["antialias"])
self.__objects = {}
self.__cnt = 0
def pvcamera_to_threejs_camera(pv_camera, lights, aspect):
"""Return an ipygany camera dict from a ``pyvista.Plotter`` object."""
# scene will be centered at focal_point, so adjust the position
position = np.array(pv_camera.position) - np.array(pv_camera.focal_point)
far = np.linalg.norm(position) * 100000
return tjs.PerspectiveCamera(
up=pv_camera.up,
children=lights,
position=position.tolist(),
fov=pv_camera.view_angle,
aspect=aspect,
far=far,
near=0.01,
)
def __init__(self):
# TODO: arguments for width/height
self._width = 600
self._height = 400
self._ball = _three.Mesh(
geometry=_three.SphereGeometry(
radius=1,
widthSegments=30,
heightSegments=20,
),
material=_three.MeshLambertMaterial(color='lightgray'),
)
self._axes = _three.AxesHelper(size=1.2)
self._ambient_light = _three.AmbientLight(
intensity=0.5,
)
self._directional_light1 = _three.DirectionalLight(
position=[0, 0, 1],
intensity=0.6,
)
self._directional_light2 = _three.DirectionalLight(
position=[0, 0, -1],
intensity=0.6,
)
self._scene = _three.Scene(
children=[
self._ball,
self._axes,
self._ambient_light,
self._directional_light1,
self._directional_light2,
],
)
self._camera = _three.PerspectiveCamera(
position=[0, 0, 2.4],
up=[0, 0, 1],
aspect=self._width/self._height,
)
self._controls = _three.OrbitControls(controlling=self._camera)
self._renderer = _three.Renderer(
camera=self._camera,
scene=self._scene,
controls=[self._controls],
width=self._width,
height=self._height,
#alpha=True,
#clearOpacity=0.5,
)
def viewer_cloth(cloth):
view_width = 800
view_height = 600
camera = THREE.PerspectiveCamera(position=[20, 5, 30],
aspect=view_width / view_height)
key_light = THREE.DirectionalLight(position=[10, 10, 10])
ambient_light = THREE.AmbientLight()
axes_helper = THREE.AxesHelper(0.5)
scene = THREE.Scene()
controller = THREE.OrbitControls(controlling=camera)
renderer = THREE.Renderer(camera=camera,
scene=scene,
controls=[controller],
width=view_width,
height=view_height)
scene.children = [cloth, axes_helper, camera, key_light, ambient_light]
return renderer
def getView(self, regenerateView=False, viewWidth=600, viewHeight=400):
if regenerateView or self.view is None:
center = self.model.get_center()
camera = three.PerspectiveCamera(
position=(center + np.array([0, 200, 0])).tolist(),
aspect=viewWidth / viewHeight)
key_light = three.DirectionalLight(position=[0, 10, 10])
ambient_light = three.AmbientLight()
scene = three.Scene(
children=[self.selectable, camera, key_light, ambient_light])
three.Picker(controlling=scene, event='mousemove')
controller = three.OrbitControls(controlling=camera,
screenSpacePanning=True,
target=center.tolist())
camera.lookAt(center.tolist())
self.coord_label = HTML('Select beads by double-clicking')
selIncrButton = Button(description='Increase selection')
selIncrButton.on_click(self.increaseSelection)
selDecrButton = Button(description='Decrease selection')
selDecrButton.on_click(self.decreaseSelection)
click_picker = three.Picker(controlling=self.selectable,
event='dblclick')
click_picker.observe(self.selectBead, names=['point'])
renderer = three.Renderer(camera=camera,
scene=scene,
controls=[controller, click_picker],
width=viewWidth,
height=viewHeight,
antialias=True)
self.view = VBox([
self.coord_label, renderer,
HBox([selDecrButton, selIncrButton])
])
return self.view
def _setup_scene(self, bounding_box, render_size):
self.min_width = render_size[0]
self.min_height = render_size[1]
fov_angle = 60
if len(bounding_box[0]) == 2:
lower = np.array([bounding_box[0][0], bounding_box[0][1], 0])
upper = np.array([bounding_box[1][0], bounding_box[1][1], 0])
bounding_box = (lower, upper)
combined_bounds = np.hstack(bounding_box)
absx = np.abs(combined_bounds[0] - combined_bounds[3])
not_mathematical_distance_scaling = 1.2
self.camera_distance = np.sin(
(90 - fov_angle / 2) * np.pi / 180) * 0.5 * absx / np.sin(
fov_angle / 2 * np.pi / 180)
self.camera_distance *= not_mathematical_distance_scaling
xhalf = (combined_bounds[0] + combined_bounds[3]) / 2
yhalf = (combined_bounds[1] + combined_bounds[4]) / 2
zhalf = (combined_bounds[2] + combined_bounds[5]) / 2
self.mesh_center = (xhalf, yhalf, zhalf)
self.cam = p3js.PerspectiveCamera(
aspect=render_size[0] / render_size[1],
position=[0, 0, 0 + self.camera_distance])
self.light = p3js.AmbientLight(color='white', intensity=1.0)
self.scene = p3js.Scene(children=[self.cam, self.light],
background='white')
self.controller = p3js.OrbitControls(
controlling=self.cam,
position=[0, 0, 0 + self.camera_distance],
target=[0, 0, 0])
self.freeze_camera(True)
self.renderer = p3js.Renderer(camera=self.cam,
scene=self.scene,
controls=[self.controller],
webgl_version=1,
width=render_size[0],
height=render_size[1])
def display_scene(lm_scene):
"""Display Lightmetrica scene."""
# Scene
scene = three.Scene()
# Camera
# Get lm camera information
lm_main_camera = lm_scene.camera()
lm_camera_params = lm_main_camera.underlying_value()
camera = three.PerspectiveCamera(fov=lm_camera_params['vfov'],
aspect=lm_camera_params['aspect'],
near=0.1,
far=10000)
camera.position = lm_camera_params['eye']
camera.up = lm_camera_params['up']
scene.add(camera)
# Mesh
def add_lm_scene_mesh():
# Default material
mat_default = three.MeshBasicMaterial(color='#000000',
wireframe=True,
transparent=True,
opacity=0.2,
depthTest=False)
# Convert lm mesh
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)
lm_scene.traverse_primitive_nodes(traverse_func)
add_lm_scene_mesh()
# View frustum
def add_view_frustum():
position = np.array(lm_camera_params['eye'])
center = np.array(lm_camera_params['center'])
up = np.array(lm_camera_params['up'])
aspect = lm_camera_params['aspect']
fov = math.radians(lm_camera_params['vfov'])
M = lookat_matrix(position, center, up)
z = 5
half_fov = fov * .5
y = math.tan(half_fov) * z
x = aspect * y
p = list(position)
p1 = list(position + np.dot(M, [-x, -y, -z]))
p2 = list(position + np.dot(M, [x, -y, -z]))
p3 = list(position + np.dot(M, [x, y, -z]))
p4 = list(position + np.dot(M, [-x, y, -z]))
# Add mesh
geom = three.Geometry(
vertices=[p, p1, p2, p, p2, p3, p, p3, p4, p, p4, p1])
mat = three.MeshBasicMaterial(color='#00ff00',
wireframe=True,
side='DoubleSide')
mesh = three.Line(geometry=geom, material=mat)
scene.add(mesh)
add_view_frustum()
# Axis
axes = three.AxesHelper(size=1)
scene.add(axes)
# Renderer
controls = three.OrbitControls(controlling=camera)
# Rendered image size
w = 1000
h = w / lm_camera_params['aspect']
# We need to set both target and lookAt in this order.
# Otherwise the initial target position becomes wrong.
# cf. https://github.com/jupyter-widgets/pythreejs/issues/200
controls.target = lm_camera_params['center']
camera.lookAt(lm_camera_params['center'])
renderer = three.Renderer(camera=camera,
scene=scene,
width=w,
height=h,
controls=[controls])
# Button to reset camera configuration
# Note that we need to press the button twice to reset the control
# to the correct target possibly due to the bug of pythreejs.
reset_camera_button = widgets.Button(description="Reset Camera")
@reset_camera_button.on_click
def reset_camera_button_on_click(b):
controls.reset()
controls.target = lm_camera_params['center']
camera.lookAt(lm_camera_params['center'])
# Display all
display(reset_camera_button)
display(renderer)
return scene, camera, renderer
def create_jsrenderer(scene,
height=400,
width=400,
background='gray',
orthographic=False,
camera_position=(0, 0, -10),
view=(10, -10, -10, 10),
fov=50):
"""
Properties
----------
orthographic : bool
use orthographic camera (True) or perspective (False)
camera_position : tuple
position of camera in scene
view : tuple
view extents: (top, bottom, left, right) (orthographic only)
fov : float
camera field of view (perspective only)
Returns
-------
camera : pythreejs.Camera
renderer : pythreejs.Renderer
Examples
--------
>>> import pythreejs as js
>>> scene = js.Scene(children=[js.AmbientLight(color='#777777')])
>>> camera, renderer = create_jsrenderer(scene,200,200, 'gray', (1,-1,-1,1))
>>> type(renderer)
<class 'pythreejs.pythreejs.Renderer'>
>>> type(camera)
<class 'pythreejs.pythreejs.OrthographicCamera'>
"""
if orthographic:
top, bottom, left, right = view
camera = js.OrthographicCamera(position=camera_position,
up=[0, 0, 1],
top=top,
bottom=bottom,
left=left,
right=right,
near=.1,
far=2000)
else:
camera = js.PerspectiveCamera(position=camera_position,
up=[0, 0, 1],
far=2000,
near=.1,
fov=fov,
aspect=width / float(height))
camera.children = [
js.DirectionalLight(color='white', position=[3, 5, 1], intensity=0.5)
]
control = js.OrbitControls(controlling=camera)
renderer = js.Renderer(camera=camera,
background=background,
background_opacity=.1,
height=str(height),
width=str(width),
scene=scene,
controls=[control])
return camera, renderer
def cqdisplay(result, color='#708090', scale=1.0):
'display CQ object in a ThreeJS Webgl context'
# Open stream
output = StringIO.StringIO()
# cadquery will stream a ThreeJS JSON (using old v3 schema, which is deprecated)
exporters.exportShape(result.shape.findSolid().scale(scale), 'TJS', output)
# store stream to a variable
contents = output.getvalue()
# Close stream
output.close()
# Overwrite the JSON color portion with user defined color. Disallows NAMED colors
col = list(matplotlib.colors.hex2color(color))
old_col_str = '"colorDiffuse" : [0.6400000190734865, 0.10179081114814892, 0.126246120426746]'
new_col_str = '"colorDiffuse" : ' + str(col)
new_contents = contents.replace(old_col_str, new_col_str)
# Take the string and create a proper json object
contents = json.loads(contents)
# Vertices and Faces are both flat lists, but the pythreejs module requires list of lists
old_v = contents['vertices']
old_f = contents['faces']
# Splits the list up in 3s, to produce a list of lists representing the vertices
vertices = [old_v[i:i+3] for i in range(0, len(old_v), 3)]
# JSON Schema has first position in the face's list reserved to indicate type.
# Cadquery returns Triangle mesh, so we know that we must split list into lists of length 4
# 1st entry to indicate triangle, next 3 to specify vertices
three_faces = [old_f[i:i+4] for i in range(0, len(old_f), 4)]
faces = []
# Drop the first entry in the face list
for entry in three_faces:
entry.pop(0)
faces.append(entry)
# Cadquery does not supply face normals in the JSON,
# and we cannot use THREE.JS built in 'computefaceNormals'
# (at least, not easily)
# Instead, we just calculate the face normals ourselves.
# It is just the cross product of 2 vectors in the triangle.
# TODO: see if there is a better way to achieve this result
face_normals = []
for entry in faces:
v_a = np.asarray(vertices[entry[0]])
v_b = np.asarray(vertices[entry[1]])
v_c = np.asarray(vertices[entry[2]])
vec_a = v_b - v_a
vec_b = v_c - v_a
cross = np.cross(vec_a, vec_b)
face_normals.append([cross[0], cross[1], cross[2]])
# set up geometry
geom = pythreejs.PlainGeometry(vertices=vertices, faces=faces, faceNormals=face_normals)
mtl = pythreejs.LambertMaterial(color=color, shading='FlatShading')
obj = pythreejs.Mesh(geometry=geom, material=mtl)
# set up scene and camera
cam_dist = 50
fov = 35
cam = pythreejs.PerspectiveCamera(
position=[cam_dist, cam_dist, cam_dist], fov=fov,
children=[pythreejs.DirectionalLight(color='#ffffff', position=[-3, 5, 1], intensity=0.45)])
scn_chld = [
obj,
pythreejs.AmbientLight(color='#dddddd')
]
scn = pythreejs.Scene(children=scn_chld)
render = pythreejs.Renderer(
width='830'.decode('utf-8'),
height='553'.decode('utf-8'),
camera=cam,
scene=scn,
controls=[pythreejs.OrbitControls(controlling=cam)]
)
return render
def __init__(self,
scipp_obj_dict=None,
positions=None,
axes=None,
masks=None,
cmap=None,
log=None,
vmin=None,
vmax=None,
color=None,
aspect=None,
background=None,
nan_color=None,
pixel_size=None,
tick_size=None,
show_outline=True):
super().__init__(scipp_obj_dict=scipp_obj_dict,
positions=positions,
axes=axes,
masks=masks,
cmap=cmap,
log=log,
vmin=vmin,
vmax=vmax,
color=color,
aspect=aspect,
button_options=['X', 'Y', 'Z'])
self.vslice = None
self.current_cut_surface_value = None
self.cut_slider_steps = 10.
self.cbar_image = widgets.Image()
self.cut_options = {
"Xplane": 0,
"Yplane": 1,
"Zplane": 2,
"Xcylinder": 3,
"Ycylinder": 4,
"Zcylinder": 5,
"Sphere": 6,
"Value": 7
}
# Prepare colormaps
self.cmap = copy(cm.get_cmap(self.params["values"][self.name]["cmap"]))
self.cmap.set_bad(color=nan_color)
self.scalar_map = cm.ScalarMappable(
norm=self.params["values"][self.name]["norm"], cmap=self.cmap)
self.masks_scalar_map = None
if self.params["masks"][self.name]["show"]:
self.masks_cmap = copy(
cm.get_cmap(self.params["masks"][self.name]["cmap"]))
self.masks_cmap.set_bad(color=nan_color)
self.masks_scalar_map = cm.ScalarMappable(
norm=self.params["values"][self.name]["norm"],
cmap=self.masks_cmap)
# Generate the colorbar image
self.create_colorbar()
# Useful variables
self.permutations = {"x": ["y", "z"], "y": ["x", "z"], "z": ["x", "y"]}
self.remaining_inds = [0, 1]
# Search the coordinates to see if one contains vectors. If so, it will
# be used as position vectors.
self.axlabels = {"x": "", "y": "", "z": ""}
self.positions = None
self.pixel_size = pixel_size
self.tick_size = tick_size
if positions is not None:
coord = self.data_array.coords[positions]
self.positions = np.array(coord.values, dtype=np.float32)
self.axlabels.update({
"x": name_with_unit(coord, name="X"),
"y": name_with_unit(coord, name="Y"),
"z": name_with_unit(coord, name="Z")
})
else:
# If no positions are supplied, create a meshgrid from coordinate
# axes.
coords = []
labels = []
for dim, val in self.slider.items():
if val.disabled:
arr = self.slider_coord[self.name][dim]
if self.histograms[self.name][dim][dim]:
arr = to_bin_centers(arr, dim)
coords.append(arr.values)
labels.append(
name_with_unit(self.slider_coord[self.name][dim]))
z, y, x = np.meshgrid(*coords, indexing='ij')
self.positions = np.array(
[x.ravel(), y.ravel(), z.ravel()], dtype=np.float32).T
if self.pixel_size is None:
self.pixel_size = coords[0][1] - coords[0][0]
self.axlabels.update({
"z": labels[0],
"y": labels[1],
"x": labels[2]
})
# Find spatial and value limits
self.xminmax, self.center_of_mass = self.get_spatial_extents()
self.vminmax = [
sc.min(self.data_array.data).value,
sc.max(self.data_array.data).value
]
# Create the point cloud with pythreejs
self.points_geometry, self.points_material, self.points = \
self.create_points_geometry()
# Create outline around point positions
self.outline, self.axticks = self.create_outline()
# Save the size of the outline box for later
self.box_size = np.diff(list(self.xminmax.values()), axis=1).ravel()
# Define camera: look at the centre of mass of the points
camera_lookat = self.center_of_mass
camera_pos = np.array(self.center_of_mass) + 1.2 * self.box_size
self.camera = p3.PerspectiveCamera(position=list(camera_pos),
aspect=config.plot.width /
config.plot.height)
# Add red/green/blue axes helper
self.axes_3d = p3.AxesHelper(10.0 * np.linalg.norm(camera_pos))
# Create the pythreejs scene
self.scene = p3.Scene(children=[
self.camera, self.axes_3d, self.points, self.outline, self.axticks
],
background=background)
# Add camera controller
self.controller = p3.OrbitControls(controlling=self.camera,
target=camera_lookat)
self.camera.lookAt(camera_lookat)
# Render the scene into a widget
self.renderer = p3.Renderer(camera=self.camera,
scene=self.scene,
controls=[self.controller],
width=config.plot.width,
height=config.plot.height)
# Update visibility of outline according to keyword arg
self.outline.visible = show_outline
self.axticks.visible = show_outline
# Opacity slider: top value controls opacity if no cut surface is
# active. If a cut curface is present, the upper slider is the opacity
# of the slice, while the lower slider value is the opacity of the
# data not in the cut surface.
self.opacity_slider = widgets.FloatRangeSlider(
min=0.0,
max=1.0,
value=[0.1, 1],
step=0.01,
description="Opacity slider: When no cut surface is active, the "
"max value of the range slider controls the overall opacity, "
"and the lower value has no effect. When a cut surface is "
"present, the max value is the opacity of the slice, while the "
"min value is the opacity of the background.",
continuous_update=True,
style={'description_width': '60px'})
self.opacity_slider.observe(self.update_opacity, names="value")
self.opacity_checkbox = widgets.Checkbox(
value=self.opacity_slider.continuous_update,
description="Continuous update",
indent=False,
layout={"width": "20px"})
self.opacity_checkbox_link = widgets.jslink(
(self.opacity_checkbox, 'value'),
(self.opacity_slider, 'continuous_update'))
self.toggle_outline_button = widgets.ToggleButton(value=show_outline,
description='',
button_style='')
self.toggle_outline_button.observe(self.toggle_outline, names="value")
# Run a trigger to update button text
self.toggle_outline({"new": show_outline})
# Add buttons to provide a choice of different cut surfaces:
# - Cartesian X, Y, Z
# - Cylindrical X, Y, Z (cylinder major axis)
# - Sperical R
# - Value-based iso-surface
# Note additional spaces required in cylindrical names because
# options must be unique.
self.cut_surface_buttons = widgets.ToggleButtons(
options=[('X ', self.cut_options["Xplane"]),
('Y ', self.cut_options["Yplane"]),
('Z ', self.cut_options["Zplane"]),
('R ', self.cut_options["Sphere"]),
(' X ', self.cut_options["Xcylinder"]),
(' Y ', self.cut_options["Ycylinder"]),
(' Z ', self.cut_options["Zcylinder"]),
('', self.cut_options["Value"])],
value=None,
description='Cut surface:',
button_style='',
tooltips=[
'X-plane', 'Y-plane', 'Z-plane', 'Sphere', 'Cylinder-X',
'Cylinder-Y', 'Cylinder-Z', 'Value'
],
icons=(['cube'] * 3) + ['circle-o'] + (['toggle-on'] * 3) +
['magic'],
style={"button_width": "55px"},
layout={'width': '350px'})
self.cut_surface_buttons.observe(self.update_cut_surface_buttons,
names="value")
# Add a capture for a click event: if the active button is clicked,
# this resets the togglebuttons value to None and deletes the cut
# surface.
self.cut_surface_buttons.on_msg(self.check_if_reset_needed)
# Add slider to control position of cut surface
self.cut_slider = widgets.FloatSlider(min=0,
max=1,
description="Position:",
disabled=True,
value=0.5,
layout={"width": "350px"})
self.cut_checkbox = widgets.Checkbox(value=True,
description="Continuous update",
indent=False,
layout={"width": "20px"},
disabled=True)
self.cut_checkbox_link = widgets.jslink(
(self.cut_checkbox, 'value'),
(self.cut_slider, 'continuous_update'))
self.cut_slider.observe(self.update_cut_surface, names="value")
# Allow to change the thickness of the cut surface
self.cut_surface_thickness = widgets.BoundedFloatText(
value=0.05 * self.box_size.max(),
min=0,
layout={"width": "150px"},
disabled=True,
description="Thickness:",
style={'description_width': 'initial'})
self.cut_surface_thickness.observe(self.update_cut_surface,
names="value")
self.cut_thickness_link = widgets.jslink(
(self.cut_slider, 'step'), (self.cut_surface_thickness, 'value'))
self.cut_slider.observe(self.update_cut_surface, names="value")
# Put widgets into boxes
self.cut_surface_controls = widgets.HBox([
self.cut_surface_buttons,
widgets.VBox([
widgets.HBox([self.cut_slider, self.cut_checkbox]),
self.cut_surface_thickness
])
])
self.box = widgets.VBox([
widgets.HBox([self.renderer, self.cbar_image]),
widgets.VBox(self.vbox),
widgets.HBox([
self.opacity_slider, self.opacity_checkbox,
self.toggle_outline_button
]), self.cut_surface_controls
])
# Update list of members to be returned in the SciPlot object
self.members.update({
"camera": self.camera,
"scene": self.scene,
"renderer": self.renderer
})
return
def _default_camera(self):
# return pythreejs.CombinedCamera(fov=46, position=(0, 0, 2), width=400, height=500)
return pythreejs.PerspectiveCamera(fov=46, position=(0, 0, 2), width=400, height=500)
def visualise(mesh,
geometric_field,
number_of_dimensions,
xi_interpolation,
dependent_field=None,
variable=None,
mechanics_animation=False,
colour_map_dependent_component_number=None,
cmap='gist_rainbow',
resolution=1,
node_labels=False):
if number_of_dimensions != 3:
print(
'Warning: Only visualisation of 3D meshes is currently supported.')
return
if xi_interpolation != [1, 1, 1]:
print(
'Warning: Only visualisation of 3D elements with linear Lagrange \
interpolation along all coordinate directions is currently \
supported.')
return
view_width = 600
view_height = 600
debug = False
if debug:
vertices = [[0, 0, 0], [0, 0, 1], [0, 1, 0], [0, 1, 1], [1, 0, 0],
[1, 0, 1], [1, 1, 0], [1, 1, 1]]
faces = [[0, 1, 3], [0, 3, 2], [0, 2, 4], [2, 6, 4], [0, 4, 1],
[1, 4, 5], [2, 3, 6], [3, 7, 6], [1, 5, 3], [3, 5, 7],
[4, 6, 5], [5, 6, 7]]
vertexcolors = [
'#000000', '#0000ff', '#00ff00', '#ff0000', '#00ffff', '#ff00ff',
'#ffff00', '#ffffff'
]
else:
# Get mesh topology information.
num_nodes = mesh_tools.num_nodes_get(mesh, mesh_component=1)
node_nums = list(range(1, num_nodes + 1))
num_elements, element_nums = mesh_tools.num_element_get(
mesh, mesh_component=1)
# Convert geometric field to a morphic mesh and export to json
mesh = mesh_tools.OpenCMISS_to_morphic(mesh,
geometric_field,
element_nums,
node_nums,
dimension=3,
interpolation='linear')
vertices, faces, _, xi_element_nums, xis = get_faces(
mesh, res=resolution, exterior_only=True, include_xi=True)
vertices = vertices.tolist()
faces = faces.tolist()
centroid = np.mean(vertices, axis=0)
max_positions = np.max(vertices, axis=0)
min_positions = np.min(vertices, axis=0)
range_positions = max_positions - min_positions
if (dependent_field is not None) and (colour_map_dependent_component_number
is not None):
solution = np.zeros(xis.shape[0])
for idx, (xi, xi_element_num) in enumerate(zip(xis, xi_element_nums)):
solution[idx] = mesh_tools.interpolate_opencmiss_field_xi(
dependent_field,
xi,
element_ids=[xi_element_num],
dimension=3,
deriv=1)[colour_map_dependent_component_number - 1]
minima = min(solution)
maxima = max(solution)
import matplotlib
norm = matplotlib.colors.Normalize(vmin=minima, vmax=maxima, clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap=cm.get_cmap(name=cmap))
vertex_colors = np.zeros((len(vertices), 3), dtype='float32')
for idx, v in enumerate(solution):
vertex_colors[idx, :] = mapper.to_rgba(v, alpha=None)[:3]
# else:
# raise ValueError('Visualisation not supported.')
else:
vertex_colors = np.tile(np.array([0.5, 0.5, 0.5], dtype='float32'),
(len(vertices), 1))
geometry = pjs.BufferGeometry(attributes=dict(
position=pjs.BufferAttribute(vertices, normalized=False),
index=pjs.BufferAttribute(
np.array(faces).astype(dtype='uint16').ravel(), normalized=False),
color=pjs.BufferAttribute(vertex_colors),
))
if mechanics_animation:
deformed_vertices = np.zeros((xis.shape[0], 3), dtype='float32')
for idx, (xi, xi_element_num) in enumerate(zip(xis, xi_element_nums)):
deformed_vertices[idx, :] = \
mesh_tools.interpolate_opencmiss_field_xi(
dependent_field, xi, element_ids=[xi_element_num],
dimension=3,
deriv=1)[0][:3]
geometry.morphAttributes = {
'position': [
pjs.BufferAttribute(deformed_vertices),
]
}
geometry.exec_three_obj_method('computeFaceNormals')
geometry.exec_three_obj_method('computeVertexNormals')
surf1 = pjs.Mesh(geometry,
pjs.MeshPhongMaterial(color='#ff3333',
shininess=150,
morphTargets=True,
side='FrontSide'),
name='A')
surf2 = pjs.Mesh(geometry,
pjs.MeshPhongMaterial(color='#ff3333',
shininess=150,
morphTargets=True,
side='BackSide'),
name='B')
surf = pjs.Group(children=[surf1, surf2])
# camera = pjs.PerspectiveCamera(
# fov=20, position=[range_positions[0] * 10,
# range_positions[1] * 10,
# range_positions[2] * 10],
# width=view_width,
# height=view_height, near=1,
# far=max(range_positions) * 10)
camera = pjs.PerspectiveCamera(position=[
range_positions[0] * 3, range_positions[1] * 3,
range_positions[2] * 3
],
aspect=view_width / view_height)
camera.up = [0, 0, 1]
camera.lookAt(centroid.tolist())
scene3 = pjs.Scene(children=[
surf1, surf2, camera,
pjs.DirectionalLight(position=[3, 5, 1], intensity=0.6),
pjs.AmbientLight(intensity=0.5)
])
axes = pjs.AxesHelper(size=range_positions[0] * 2)
scene3.add(axes)
A_track = pjs.NumberKeyframeTrack(
name='scene/A.morphTargetInfluences[0]',
times=[0, 3],
values=[0, 1])
B_track = pjs.NumberKeyframeTrack(
name='scene/B.morphTargetInfluences[0]',
times=[0, 3],
values=[0, 1])
pill_clip = pjs.AnimationClip(tracks=[A_track, B_track])
pill_action = pjs.AnimationAction(pjs.AnimationMixer(scene3),
pill_clip, scene3)
renderer3 = pjs.Renderer(
camera=camera,
scene=scene3,
controls=[pjs.OrbitControls(controlling=camera)],
width=view_width,
height=view_height)
display(renderer3, pill_action)
else:
geometry.exec_three_obj_method('computeFaceNormals')
geometry.exec_three_obj_method('computeVertexNormals')
surf1 = pjs.Mesh(geometry=geometry,
material=pjs.MeshLambertMaterial(
vertexColors='VertexColors',
side='FrontSide')) # Center the cube.
surf2 = pjs.Mesh(geometry=geometry,
material=pjs.MeshLambertMaterial(
vertexColors='VertexColors',
side='BackSide')) # Center the cube.
surf = pjs.Group(children=[surf1, surf2])
camera = pjs.PerspectiveCamera(position=[
range_positions[0] * 3, range_positions[1] * 3,
range_positions[2] * 3
],
aspect=view_width / view_height)
camera.up = [0, 0, 1]
camera.lookAt(centroid.tolist())
# if perspective:
# camera.mode = 'perspective'
# else:
# camera.mode = 'orthographic'
lights = [
pjs.DirectionalLight(position=[
range_positions[0] * 16, range_positions[1] * 12,
range_positions[2] * 17
],
intensity=0.5),
pjs.AmbientLight(intensity=0.8),
]
orbit = pjs.OrbitControls(controlling=camera,
screenSpacePanning=True,
target=centroid.tolist())
scene = pjs.Scene()
axes = pjs.AxesHelper(size=max(range_positions) * 2)
scene.add(axes)
scene.add(surf1)
scene.add(surf2)
scene.add(lights)
if node_labels:
# Add text labels for each mesh node.
v, ids = mesh.get_node_ids(group='_default')
for idx, v in enumerate(v):
text = make_text(str(ids[idx]), position=(v[0], v[1], v[2]))
scene.add(text)
# Add text for axes labels.
x_axis_label = make_text('x',
position=(max(range_positions) * 2, 0, 0))
y_axis_label = make_text('y',
position=(0, max(range_positions) * 2, 0))
z_axis_label = make_text('z',
position=(0, 0, max(range_positions) * 2))
scene.add(x_axis_label)
scene.add(y_axis_label)
scene.add(z_axis_label)
renderer = pjs.Renderer(scene=scene,
camera=camera,
controls=[orbit],
width=view_width,
height=view_height)
camera.zoom = 1
display(renderer)
return vertices, faces
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 _render_stl(self, stl_file):
vertices, faces = self._conv_stl(stl_file)
# Map the vertex colors into the 'color' slot of the faces
faces = [f + [None, [OBJ_COLOR for i in f], None] for f in faces]
# Create the geometry:
obj_geometry = pjs.Geometry(vertices=vertices,
faces=faces,
colors=[OBJ_COLOR] * len(vertices))
# Calculate normals per face, for nice crisp edges:
obj_geometry.exec_three_obj_method('computeFaceNormals')
# 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], # Center the cube
)
n_vert = len(vertices)
center = [
sum([vertex[i] for vertex in vertices]) / float(n_vert)
for i in range(3)
]
extents = self._get_extents(vertices)
max_delta = max([extent[1] - extent[0] for extent in extents])
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)
scene_things = [
my_object_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)
renderer_obj = pjs.Renderer(
camera=camera,
background='#cccc88',
background_opacity=0,
scene=scene,
controls=[pjs.OrbitControls(controlling=camera)],
width=self.width,
height=self.height)
display_things = [renderer_obj]
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(*display_things)
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))
def __init__(self,
cmap=None,
norm=None,
figsize=None,
unit=None,
log=None,
nan_color=None,
masks=None,
pixel_size=None,
tick_size=None,
background=None,
show_outline=True,
extend=None,
xlabel=None,
ylabel=None,
zlabel=None):
if figsize is None:
figsize = (config.plot.width, config.plot.height)
# Figure toolbar
self.toolbar = PlotToolbar(ndim=3)
# Prepare colormaps
self.cmap = cmap
self.cmap.set_bad(color=nan_color)
self.scalar_map = cm.ScalarMappable(norm=norm, cmap=self.cmap)
self.masks_scalar_map = None
if len(masks) > 0:
self.masks_cmap = masks["cmap"]
self.masks_cmap.set_bad(color=nan_color)
self.masks_scalar_map = cm.ScalarMappable(norm=norm,
cmap=self.masks_cmap)
self.axlabels = {"x": xlabel, "y": ylabel, "z": zlabel}
self.positions = None
self.pixel_size = pixel_size
self.tick_size = tick_size
self.show_outline = show_outline
self.unit = unit
# Create the colorbar image
self.cbar_image = ipw.Image()
self.cbar_fig, self.cbar = self._create_colorbar(figsize, extend)
# Create the point cloud material with pythreejs
self.points_material = self._create_points_material()
self.points_geometry = None
self.point_cloud = None
self.outline = None
self.axticks = None
self.camera_reset = {}
# Define camera
self.camera = p3.PerspectiveCamera(position=[0, 0, 0],
aspect=config.plot.width /
config.plot.height)
# Add red/green/blue axes helper
self.axes_3d = p3.AxesHelper()
# Create the pythreejs scene
self.scene = p3.Scene(children=[self.camera, self.axes_3d],
background=background)
# Add camera controller
self.controls = p3.OrbitControls(controlling=self.camera)
# Render the scene into a widget
self.renderer = p3.Renderer(camera=self.camera,
scene=self.scene,
controls=[self.controls],
width=figsize[0],
height=figsize[1])
def generate_3js_render(
element_groups,
canvas_size,
zoom,
camera_fov=30,
background_color="white",
background_opacity=1.0,
reuse_objects=False,
use_atom_arrays=False,
use_label_arrays=False,
):
"""Create a pythreejs scene of the elements.
Regarding initialisation performance, see: https://github.com/jupyter-widgets/pythreejs/issues/154
"""
import pythreejs as pjs
key_elements = {}
group_elements = pjs.Group()
key_elements["group_elements"] = group_elements
unique_atom_sets = {}
for el in element_groups["atoms"]:
element_hash = (
("radius", el.sradius),
("color", el.color),
("fill_opacity", el.fill_opacity),
("stroke_color", el.get("stroke_color", "black")),
("ghost", el.ghost),
)
unique_atom_sets.setdefault(element_hash, []).append(el)
group_atoms = pjs.Group()
group_ghosts = pjs.Group()
atom_geometries = {}
atom_materials = {}
outline_materials = {}
for el_hash, els in unique_atom_sets.items():
el = els[0]
data = dict(el_hash)
if reuse_objects:
atom_geometry = atom_geometries.setdefault(
el.sradius,
pjs.SphereBufferGeometry(radius=el.sradius,
widthSegments=30,
heightSegments=30),
)
else:
atom_geometry = pjs.SphereBufferGeometry(radius=el.sradius,
widthSegments=30,
heightSegments=30)
if reuse_objects:
atom_material = atom_materials.setdefault(
(el.color, el.fill_opacity),
pjs.MeshLambertMaterial(color=el.color,
transparent=True,
opacity=el.fill_opacity),
)
else:
atom_material = pjs.MeshLambertMaterial(color=el.color,
transparent=True,
opacity=el.fill_opacity)
if use_atom_arrays:
atom_mesh = pjs.Mesh(geometry=atom_geometry,
material=atom_material)
atom_array = pjs.CloneArray(
original=atom_mesh,
positions=[e.position.tolist() for e in els],
merge=False,
)
else:
atom_array = [
pjs.Mesh(
geometry=atom_geometry,
material=atom_material,
position=e.position.tolist(),
name=e.info_string,
) for e in els
]
data["geometry"] = atom_geometry
data["material_body"] = atom_material
if el.ghost:
key_elements["group_ghosts"] = group_ghosts
group_ghosts.add(atom_array)
else:
key_elements["group_atoms"] = group_atoms
group_atoms.add(atom_array)
if el.get("stroke_width", 1) > 0:
if reuse_objects:
outline_material = outline_materials.setdefault(
el.get("stroke_color", "black"),
pjs.MeshBasicMaterial(
color=el.get("stroke_color", "black"),
side="BackSide",
transparent=True,
opacity=el.get("stroke_opacity", 1.0),
),
)
else:
outline_material = pjs.MeshBasicMaterial(
color=el.get("stroke_color", "black"),
side="BackSide",
transparent=True,
opacity=el.get("stroke_opacity", 1.0),
)
# TODO use stroke width to dictate scale
if use_atom_arrays:
outline_mesh = pjs.Mesh(
geometry=atom_geometry,
material=outline_material,
scale=(1.05, 1.05, 1.05),
)
outline_array = pjs.CloneArray(
original=outline_mesh,
positions=[e.position.tolist() for e in els],
merge=False,
)
else:
outline_array = [
pjs.Mesh(
geometry=atom_geometry,
material=outline_material,
position=e.position.tolist(),
scale=(1.05, 1.05, 1.05),
) for e in els
]
data["material_outline"] = outline_material
if el.ghost:
group_ghosts.add(outline_array)
else:
group_atoms.add(outline_array)
key_elements.setdefault("atom_arrays", []).append(data)
group_elements.add(group_atoms)
group_elements.add(group_ghosts)
group_labels = add_labels(element_groups, key_elements, use_label_arrays)
group_elements.add(group_labels)
if len(element_groups["cell_lines"]) > 0:
cell_line_mat = pjs.LineMaterial(
linewidth=1,
color=element_groups["cell_lines"].group_properties["color"])
cell_line_geo = pjs.LineSegmentsGeometry(positions=[
el.position.tolist() for el in element_groups["cell_lines"]
])
cell_lines = pjs.LineSegments2(geometry=cell_line_geo,
material=cell_line_mat)
key_elements["cell_lines"] = cell_lines
group_elements.add(cell_lines)
if len(element_groups["bond_lines"]) > 0:
bond_line_mat = pjs.LineMaterial(
linewidth=element_groups["bond_lines"].
group_properties["stroke_width"],
vertexColors="VertexColors",
)
bond_line_geo = pjs.LineSegmentsGeometry(
positions=[
el.position.tolist() for el in element_groups["bond_lines"]
],
colors=[[Color(c).rgb for c in el.color]
for el in element_groups["bond_lines"]],
)
bond_lines = pjs.LineSegments2(geometry=bond_line_geo,
material=bond_line_mat)
key_elements["bond_lines"] = bond_lines
group_elements.add(bond_lines)
group_millers = pjs.Group()
if len(element_groups["miller_lines"]) or len(
element_groups["miller_planes"]):
key_elements["group_millers"] = group_millers
if len(element_groups["miller_lines"]) > 0:
miller_line_mat = pjs.LineMaterial(
linewidth=3,
vertexColors="VertexColors" # TODO use stroke_width
)
miller_line_geo = pjs.LineSegmentsGeometry(
positions=[
el.position.tolist() for el in element_groups["miller_lines"]
],
colors=[[Color(el.stroke_color).rgb] * 2
for el in element_groups["miller_lines"]],
)
miller_lines = pjs.LineSegments2(geometry=miller_line_geo,
material=miller_line_mat)
group_millers.add(miller_lines)
for el in element_groups["miller_planes"]:
vertices = el.position.tolist()
faces = [(
0,
1,
2,
triangle_normal(vertices[0], vertices[1], vertices[2]),
"black",
0,
)]
if len(vertices) == 4:
faces.append((
2,
3,
0,
triangle_normal(vertices[2], vertices[3], vertices[0]),
"black",
0,
))
elif len(vertices) != 3:
raise NotImplementedError("polygons with more than 4 points")
plane_geom = pjs.Geometry(vertices=vertices, faces=faces)
plane_mat = pjs.MeshBasicMaterial(
color=el.fill_color,
transparent=True,
opacity=el.fill_opacity,
side="DoubleSide",
)
plane_mesh = pjs.Mesh(geometry=plane_geom, material=plane_mat)
group_millers.add(plane_mesh)
group_elements.add(group_millers)
scene = pjs.Scene(background=None)
scene.add([group_elements])
view_width, view_height = canvas_size
minp, maxp = element_groups.get_position_range()
# compute a minimum camera distance, that is guaranteed to encapsulate all elements
camera_dist = maxp[2] + sqrt(maxp[0]**2 + maxp[1]**2) / tan(
radians(camera_fov / 2))
camera = pjs.PerspectiveCamera(
fov=camera_fov,
position=[0, 0, camera_dist],
aspect=view_width / view_height,
zoom=zoom,
)
scene.add([camera])
ambient_light = pjs.AmbientLight(color="lightgray")
key_elements["ambient_light"] = ambient_light
direct_light = pjs.DirectionalLight(position=(maxp * 2).tolist())
key_elements["direct_light"] = direct_light
scene.add([camera, ambient_light, direct_light])
camera_control = pjs.OrbitControls(controlling=camera,
screenSpacePanning=True)
atom_picker = pjs.Picker(controlling=group_atoms, event="dblclick")
key_elements["atom_picker"] = atom_picker
material = pjs.SpriteMaterial(
map=create_arrow_texture(right=False),
transparent=True,
depthWrite=False,
depthTest=False,
)
atom_pointer = pjs.Sprite(material=material,
scale=(4, 3, 1),
visible=False)
scene.add(atom_pointer)
key_elements["atom_pointer"] = atom_pointer
renderer = pjs.Renderer(
camera=camera,
scene=scene,
controls=[camera_control, atom_picker],
width=view_width,
height=view_height,
alpha=True,
clearOpacity=background_opacity,
clearColor=background_color,
)
return renderer, key_elements
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 create_world_axes(camera,
controls,
initial_rotation=np.eye(3),
length=30,
width=3,
camera_fov=10):
"""Create a renderer, containing an axes and camera that is synced to another camera.
adapted from http://jsfiddle.net/aqnL1mx9/
Parameters
----------
camera : pythreejs.PerspectiveCamera
controls : pythreejs.OrbitControls
initial_rotation : list or numpy.array
initial rotation of the axes
length : int
length of axes lines
width : int
line width of axes
Returns
-------
pythreejs.Renderer
"""
import pythreejs as pjs
canvas_width = length * 2
canvas_height = length * 2
ax_scene = pjs.Scene()
group_ax = pjs.Group()
# NOTE: could use AxesHelper, but this does not allow for linewidth seletion
# TODO: add arrow heads (ArrowHelper doesn't seem to work)
ax_line_mat = pjs.LineMaterial(linewidth=width,
vertexColors="VertexColors")
ax_line_geo = pjs.LineSegmentsGeometry(
positions=[[[0, 0, 0], length * r / np.linalg.norm(r)]
for r in initial_rotation],
colors=[[Color(c).rgb] * 2 for c in ("red", "green", "blue")],
)
ax_lines = pjs.LineSegments2(geometry=ax_line_geo, material=ax_line_mat)
group_ax.add(ax_lines)
ax_scene.add([group_ax])
camera_dist = length / tan(radians(camera_fov / 2))
ax_camera = pjs.PerspectiveCamera(fov=camera_fov,
aspect=canvas_width / canvas_height,
near=1,
far=1000)
ax_camera.up = camera.up
ax_renderer = pjs.Renderer(
scene=ax_scene,
camera=ax_camera,
width=canvas_width,
height=canvas_height,
alpha=True,
clearOpacity=0.0,
clearColor="white",
)
def align_axes(change=None):
"""Align axes to world."""
# TODO: this is not working correctly for TrackballControls, when rotated upside-down
# (OrbitControls enforces the camera up direction,
# so does not allow the camera to rotate upside-down).
# TODO how could this be implemented on the client (js) side?
new_position = np.array(camera.position) - np.array(controls.target)
new_position = camera_dist * new_position / np.linalg.norm(
new_position)
ax_camera.position = new_position.tolist()
ax_camera.lookAt(ax_scene.position)
align_axes()
camera.observe(align_axes, names="position")
controls.observe(align_axes, names="target")
ax_scene.observe(align_axes, names="position")
return ax_renderer