# TODO: Materials, Lights
import base64
import copy
import os
from typing import Dict # noqa
from PIL import Image
import numpy as np
import pygltflib as gltflib
from pygltflib.utils import glb2gltf, gltf2glb
from fury import actor, io, transform, utils
from fury.animation import Animation
from fury.animation.interpolator import (
linear_interpolator,
slerp,
step_interpolator,
tan_cubic_spline_interpolator,
)
from fury.decorators import warn_on_args_to_kwargs
from fury.lib import Camera, Matrix4x4, Texture, Transform, numpy_support
comp_type = {
5120: {"size": 1, "dtype": np.byte},
5121: {"size": 1, "dtype": np.ubyte},
5122: {"size": 2, "dtype": np.short},
5123: {"size": 2, "dtype": np.ushort},
5125: {"size": 4, "dtype": np.uint},
5126: {"size": 4, "dtype": np.float32},
}
acc_type = {"SCALAR": 1, "VEC2": 2, "VEC3": 3, "VEC4": 4, "MAT4": 16}
[docs]
class glTF:
@warn_on_args_to_kwargs()
def __init__(self, filename, *, apply_normals=False):
"""Read and generate actors from glTF files.
Parameters
----------
filename : str
Path of the gltf file
apply_normals : bool, optional
If `True` applies normals to the mesh.
"""
if filename in ["", None]:
raise IOError("Filename cannot be empty or None!")
name, extension = os.path.splitext(filename)
if extension == ".glb":
fname_gltf = f"{name}.gltf"
if not os.path.exists(fname_gltf):
glb2gltf(filename)
filename = fname_gltf
self.gltf = gltflib.GLTF2().load(filename)
self.pwd = os.path.dirname(filename)
self.apply_normals = apply_normals
self.cameras = {}
self.materials = []
self.nodes = []
self.transformations = []
self.polydatas = []
self.init_transform = np.identity(4)
self.node_transform = []
self.animation_channels = {}
self.sampler_matrices = {}
# Skinning Information
self.bone_tranforms = {}
self.keyframe_transforms = []
self.joints_0 = []
self.weights_0 = []
self.bones = []
self.ibms = {}
self._vertices = None
self._vcopy = None
self._bvertices = {}
self._bvert_copy = {}
self.show_bones = False
# morphing inofrmations
self.morph_vertices = []
self.morph_weights = []
self.inspect_scene(scene_id=0)
self._actors = []
self._bactors = {}
[docs]
def actors(self):
"""Generate actors from glTF file.
Returns
-------
actors : list
List of vtkActors with texture.
"""
for i, polydata in enumerate(self.polydatas):
actor = utils.get_actor_from_polydata(polydata)
transform_mat = self.transformations[i]
_transform = Transform()
_matrix = Matrix4x4()
_matrix.DeepCopy(transform_mat.ravel())
_transform.SetMatrix(_matrix)
actor.SetUserTransform(_transform)
if self.materials[i] is not None:
base_col_tex = self.materials[i]["baseColorTexture"]
actor.SetTexture(base_col_tex)
base_color = self.materials[i]["baseColor"]
actor.GetProperty().SetColor(tuple(base_color[:3]))
self._actors.append(actor)
return self._actors
[docs]
@warn_on_args_to_kwargs()
def inspect_scene(self, *, scene_id=0):
"""Loop over nodes in a scene.
Parameters
----------
scene_id : int, optional
scene index of the glTF.
"""
scene = self.gltf.scenes[scene_id]
nodes = scene.nodes
for node_id in nodes:
self.transverse_node(node_id, self.init_transform)
for i, animation in enumerate(self.gltf.animations):
self.transverse_channels(animation, i)
[docs]
@warn_on_args_to_kwargs()
def transverse_node(self, nextnode_id, matrix, *, parent=None, is_joint=False):
"""Load mesh and generates transformation matrix.
Parameters
----------
nextnode_id : int
Index of the node
matrix : ndarray (4, 4)
Transformation matrix
parent : list, optional
List of indices of parent nodes
Default: None.
is_joint : Bool
To determine if the current node is a joint/bone of skins.
Default: False
"""
node = self.gltf.nodes[nextnode_id]
if parent is None:
parent = [nextnode_id]
else:
parent.append(nextnode_id)
matnode = np.identity(4)
if node.matrix is not None:
matnode = np.array(node.matrix)
matnode = matnode.reshape(-1, 4).T
else:
if node.translation is not None:
trans = node.translation
translate = transform.translate(trans)
matnode = np.dot(matnode, translate)
if node.rotation is not None:
rot = node.rotation
rotate = transform.rotate(rot)
matnode = np.dot(matnode, rotate)
if node.scale is not None:
scales = node.scale
scale = transform.scale(scales)
matnode = np.dot(matnode, scale)
next_matrix = np.dot(matrix, matnode)
if node.skin is not None:
if (
nextnode_id in self.gltf.skins[0].joints
and nextnode_id not in self.bone_tranforms
):
self.bone_tranforms[nextnode_id] = next_matrix[:]
if is_joint:
if nextnode_id not in self.bone_tranforms:
self.bone_tranforms[nextnode_id] = next_matrix[:]
if node.mesh is not None:
mesh_id = node.mesh
self.load_mesh(mesh_id, next_matrix, parent)
if node.skin is not None:
skin_id = node.skin
joints, ibms = self.get_skin_data(skin_id)
for bone, ibm in zip(joints, ibms):
self.bones.append(bone)
self.ibms[bone] = ibm
self.transverse_node(
joints[0], np.identity(4), parent=parent, is_joint=True
)
if node.camera is not None:
camera_id = node.camera
self.load_camera(camera_id, next_matrix)
if node.children:
for child_id in node.children:
self.transverse_node(
child_id,
next_matrix,
parent=parent,
is_joint=is_joint,
)
[docs]
def load_mesh(self, mesh_id, transform_mat, parent):
"""Load the mesh data from accessor and applies the transformation.
Parameters
----------
mesh_id : int
Mesh index to be loaded
transform_mat : ndarray (4, 4)
Transformation matrix.
"""
primitives = self.gltf.meshes[mesh_id].primitives
for primitive in primitives:
attributes = primitive.attributes
vertices = self.get_acc_data(attributes.POSITION)
self.transformations.append(transform_mat)
polydata = utils.PolyData()
utils.set_polydata_vertices(polydata, vertices)
if attributes.NORMAL is not None and self.apply_normals:
normals = self.get_acc_data(attributes.NORMAL)
normals = transform.apply_transformation(normals, transform_mat)
utils.set_polydata_normals(polydata, normals)
if attributes.TEXCOORD_0 is not None:
tcoords = self.get_acc_data(attributes.TEXCOORD_0)
utils.set_polydata_tcoords(polydata, tcoords)
if attributes.COLOR_0 is not None:
color = self.get_acc_data(attributes.COLOR_0)
color = color[:, :-1] * 255
utils.set_polydata_colors(polydata, color)
if primitive.indices is not None:
indices = self.get_acc_data(primitive.indices).reshape(-1, 3)
else:
indices = np.arange(0, len(vertices)).reshape((-1, 3))
utils.set_polydata_triangles(polydata, indices)
if attributes.JOINTS_0 is not None:
vertex_joints = self.get_acc_data(attributes.JOINTS_0)
self.joints_0.append(vertex_joints)
vertex_weight = self.get_acc_data(attributes.WEIGHTS_0)
self.weights_0.append(vertex_weight)
material = None
if primitive.material is not None:
material = self.get_materials(primitive.material)
self.polydatas.append(polydata)
self.nodes.append(parent[:])
self.materials.append(material)
if primitive.targets is not None:
prim_morphdata = []
for target in primitive.targets:
prim_morphdata.append(self.get_morph_data(target, mesh_id))
self.morph_vertices.append(prim_morphdata)
[docs]
def get_acc_data(self, acc_id):
"""Get the correct data from buffer using accessors and bufferviews.
Parameters
----------
acc_id : int
Accessor index
Returns
-------
buffer_array : ndarray
Numpy array extracted from the buffer.
"""
accessor = self.gltf.accessors[acc_id]
buffview_id = accessor.bufferView
acc_byte_offset = accessor.byteOffset
count = accessor.count
d_type = comp_type.get(accessor.componentType)
d_size = d_type["size"]
a_type = acc_type.get(accessor.type)
buffview = self.gltf.bufferViews[buffview_id]
buff_id = buffview.buffer
byte_offset = buffview.byteOffset
byte_stride = buffview.byteStride
byte_stride = byte_stride if byte_stride else (a_type * d_size)
byte_length = count * byte_stride
total_byte_offset = byte_offset + acc_byte_offset
buff_array = self.get_buff_array(
buff_id, d_type["dtype"], byte_length, total_byte_offset, byte_stride
)
return buff_array[:, :a_type]
[docs]
def get_buff_array(self, buff_id, d_type, byte_length, byte_offset, byte_stride):
"""Extract the mesh data from buffer.
Parameters
----------
buff_id : int
Buffer Index
d_type : type
Element data type
byte_length : int
The length of the buffer data
byte_offset : int
The offset into the buffer in bytes
byte_stride : int
The stride, in bytes
Returns
-------
out_arr : ndarray
Numpy array of size byte_length from buffer.
"""
buffer = self.gltf.buffers[buff_id]
uri = buffer.uri
if d_type == np.short or d_type == np.ushort or d_type == np.uint16:
byte_length = int(byte_length / 2)
byte_stride = int(byte_stride / 2)
elif d_type == np.float32:
byte_length = int(byte_length / 4)
byte_stride = int(byte_stride / 4)
try:
if uri.startswith("data:application/octet-stream;base64") or uri.startswith(
"data:application/gltf-buffer;base64"
):
buff_data = uri.split(",")[1]
buff_data = base64.b64decode(buff_data)
elif uri.endswith(".bin"):
with open(os.path.join(self.pwd, uri), "rb") as f:
buff_data = f.read(-1)
out_arr = np.frombuffer(
buff_data, dtype=d_type, count=byte_length, offset=byte_offset
)
out_arr = out_arr.reshape(-1, byte_stride)
return out_arr
except IOError:
print("Failed to read ! Error in opening file:")
[docs]
def get_materials(self, mat_id):
"""Get the material data.
Parameters
----------
mat_id : int
Material index
Returns
-------
materials : dict
Dictionary of all textures.
"""
material = self.gltf.materials[mat_id]
bct = None
pbr = material.pbrMetallicRoughness
if pbr.baseColorTexture is not None:
bct = pbr.baseColorTexture.index
bct = self.get_texture(bct)
colors = pbr.baseColorFactor
return {"baseColorTexture": bct, "baseColor": colors}
[docs]
def get_texture(self, tex_id):
"""Read and convert image into vtk texture.
Parameters
----------
tex_id : int
Texture index
Returns
-------
atexture : Texture
Returns flipped vtk texture from image.
"""
texture = self.gltf.textures[tex_id].source
image = self.gltf.images[texture]
file = image.uri
bv_index = image.bufferView
if file is None:
mimetype = image.mimeType
if file is not None and file.startswith("data:image"):
buff_data = file.split(",")[1]
buff_data = base64.b64decode(buff_data)
extension = ".png" if file.startswith("data:image/png") else ".jpg"
image_path = os.path.join(self.pwd, str("b64texture" + extension))
with open(image_path, "wb") as image_file:
image_file.write(buff_data)
elif bv_index is not None:
bv = self.gltf.bufferViews[bv_index]
buffer = bv.buffer
bo = bv.byteOffset
bl = bv.byteLength
uri = self.gltf.buffers[buffer].uri
with open(os.path.join(self.pwd, uri), "rb") as f:
f.seek(bo)
img_binary = f.read(bl)
extension = ".png" if mimetype == "images/png" else ".jpg"
image_path = os.path.join(self.pwd, str("bvtexture" + extension))
with open(image_path, "wb") as image_file:
image_file.write(img_binary)
else:
image_path = os.path.join(self.pwd, file)
rgb = io.load_image(image_path)
grid = utils.rgb_to_vtk(np.flipud(rgb))
atexture = Texture()
atexture.InterpolateOn()
atexture.EdgeClampOn()
atexture.SetInputDataObject(grid)
return atexture
[docs]
def load_camera(self, camera_id, transform_mat):
"""Load the camera data of a node.
Parameters
----------
camera_id : int
Camera index of a node.
transform_mat : ndarray (4, 4)
Transformation matrix of the camera.
"""
camera = self.gltf.cameras[camera_id]
vtk_cam = Camera()
position = vtk_cam.GetPosition()
position = np.asarray([position])
new_position = transform.apply_transformation(position, transform_mat)
vtk_cam.SetPosition(tuple(new_position[0]))
if camera.type == "orthographic":
orthographic = camera.orthographic
vtk_cam.ParallelProjectionOn()
zfar = orthographic.zfar
znear = orthographic.znear
vtk_cam.SetClippingRange(znear, zfar)
else:
perspective = camera.perspective
vtk_cam.ParallelProjectionOff()
zfar = perspective.zfar if perspective.zfar else 1000.0
znear = perspective.znear
vtk_cam.SetClippingRange(znear, zfar)
angle = perspective.yfov * 180 / np.pi if perspective.yfov else 30.0
vtk_cam.SetViewAngle(angle)
if perspective.aspectRatio:
vtk_cam.SetExplicitAspectRatio(perspective.aspectRatio)
self.cameras[camera_id] = vtk_cam
[docs]
def transverse_channels(self, animation: gltflib.Animation, count: int):
"""Loop over animation channels and sets animation data.
Parameters
----------
animation : glTflib.Animation
pygltflib animation object.
count : int
Animation count.
"""
name = animation.name
if name is None:
name = str(f"anim_{count}")
anim_channel = {} # type: Dict[int, np.ndarray]
for channel in animation.channels:
sampler = animation.samplers[channel.sampler]
node_id = channel.target.node
path = channel.target.path
anim_data = self.get_sampler_data(sampler, node_id, path)
self.node_transform.append(anim_data)
sampler_data = self.get_matrix_from_sampler(
path, node_id, anim_channel, sampler
)
anim_channel[node_id] = sampler_data
self.animation_channels[name] = anim_channel
[docs]
def get_sampler_data(self, sampler: gltflib.Sampler, node_id: int, transform_type):
"""Get the animation and transformation data from sampler.
Parameters
----------
sampler : glTFlib.Sampler
pygltflib sampler object.
node_id : int
Node index of the current animation channel.
transform_type : str
Property of the node to be transformed.
Returns
-------
sampler_data : dict
dictionary of data containing timestamps, node transformations and
interpolation type.
"""
time_array = self.get_acc_data(sampler.input)
transform_array = self.get_acc_data(sampler.output)
interpolation = sampler.interpolation
return {
"node": node_id,
"input": time_array,
"output": transform_array,
"interpolation": interpolation,
"property": transform_type,
}
[docs]
def get_matrix_from_sampler(
self, prop, node, anim_channel, sampler: gltflib.Sampler
):
"""Return transformation matrix for a given timestamp from Sampler
data. Combine matrices for a given common timestamp.
Parameters
----------
prop : str
Property of the array ('translation', 'rotation' or 'scale')
node : int
Node index of the sampler data.
anim_channel : dict
Containing previous animations with node as keys.
sampler : gltflib.Sampler
Sampler object for an animation channel.
"""
time_array = self.get_acc_data(sampler.input)
tran_array = self.get_acc_data(sampler.output)
if prop == "weights":
tran_array = tran_array.reshape(
-1,
)
tran_matrix = []
if node in anim_channel:
prev_arr = anim_channel[node]["matrix"]
else:
prev_arr = [np.identity(4) for i in range(len(tran_array))]
for i, arr in enumerate(tran_array):
temp = self.generate_tmatrix(arr, prop)
if temp.shape == (4, 4):
tran_matrix.append(np.dot(prev_arr[i], temp))
else:
tran_matrix.append(temp)
data = {"timestamps": time_array, "matrix": tran_matrix}
self.sampler_matrices[node] = data
return data
[docs]
def get_morph_data(self, target, mesh_id):
weights_array = self.gltf.meshes[mesh_id].weights
if target.get("POSITION") is not None:
morphed_data = self.get_acc_data(target.get("POSITION"))
self.morph_weights.append(weights_array)
return morphed_data
[docs]
def get_skin_data(self, skin_id):
"""Get the inverse bind matrix for each bone in the skin.
Parameters
----------
skin_id : int
Index of the skin.
Returns
-------
joint_nodes : list
List of bones in the skin.
inv_bind_matrix : ndarray
Numpy array containing inverse bind pose for each bone.
"""
skin = self.gltf.skins[skin_id]
inv_bind_matrix = self.get_acc_data(skin.inverseBindMatrices)
inv_bind_matrix = inv_bind_matrix.reshape((-1, 4, 4))
joint_nodes = skin.joints
return joint_nodes, inv_bind_matrix
[docs]
def generate_tmatrix(self, transf, prop):
"""Create transformation matrix from TRS array.
Parameters
----------
transf : ndarray
Array containing translation, rotation or scale values.
prop : str
String that defines the type of array
(values: translation, rotation or scale).
Returns
-------
matrix : ndarray (4, 4)
ransformation matrix of shape (4, 4) with respective transforms.
"""
if prop == "translation":
matrix = transform.translate(transf)
elif prop == "rotation":
matrix = transform.rotate(transf)
elif prop == "scale":
matrix = transform.scale(transf)
else:
matrix = transf
return matrix
[docs]
@warn_on_args_to_kwargs()
def transverse_animations(
self,
animation,
bone_id,
timestamp,
joint_matrices,
*,
parent_bone_deform=None,
):
"""Calculate skinning matrix (Joint Matrices) and transform bone for
each animation.
Parameters
----------
animation : Animation
Animation object.
bone_id : int
Bone index of the current transform.
timestamp : float
Current timestamp of the animation.
joint_matrices : dict
Empty dictionary that will contain joint matrices.
parent_bone_transform : ndarray (4, 4)
Transformation matrix of the parent bone.
(default=np.identity(4))
"""
if parent_bone_deform is None:
parent_bone_deform = np.identity(4)
deform = animation.get_value("transform", timestamp)
new_deform = np.dot(parent_bone_deform, deform)
ibm = self.ibms[bone_id].T
skin_matrix = np.dot(new_deform, ibm)
joint_matrices[bone_id] = skin_matrix
node = self.gltf.nodes[bone_id]
if self.show_bones:
actor_transform = self.transformations[0]
bone_transform = np.dot(actor_transform, new_deform)
self._bvertices[bone_id][:] = transform.apply_transformation(
self._bvert_copy[bone_id], bone_transform
)
utils.update_actor(self._bactors[bone_id])
if node.children:
c_animations = animation.child_animations
c_bones = node.children
for c_anim, c_bone in zip(c_animations, c_bones):
self.transverse_animations(
c_anim,
c_bone,
timestamp,
joint_matrices,
parent_bone_deform=new_deform,
)
[docs]
def update_skin(self, animation):
"""Update the animation and actors with skinning data.
Parameters
----------
animation : Animation
Animation object.
"""
animation.update_animation()
timestamp = animation.current_timestamp
joint_matrices = {}
root_bone = self.gltf.skins[0].skeleton
root_bone = root_bone if root_bone else self.bones[0]
if not root_bone == self.bones[0]:
_animation = animation.child_animations[0]
parent_transform = self.transformations[root_bone].T
else:
_animation = animation
parent_transform = np.identity(4)
for child in _animation.child_animations:
self.transverse_animations(
child,
self.bones[0],
timestamp,
joint_matrices,
parent_bone_deform=parent_transform,
)
for i, vertex in enumerate(self._vertices):
vertex[:] = self.apply_skin_matrix(
self._vcopy[i],
joint_matrices,
actor_index=i,
)
actor_transf = self.transformations[i]
vertex[:] = transform.apply_transformation(vertex, actor_transf)
utils.update_actor(self._actors[i])
utils.compute_bounds(self._actors[i])
[docs]
@warn_on_args_to_kwargs()
def initialize_skin(self, animation, *, bones=False, length=0.2):
"""Create bones and add to the animation and initialise `update_skin`
Parameters
----------
animation : Animation
Skin animation object.
bones : bool
Switches the visibility of bones in scene.
(default=False)
length : float
Length of the bones.
(default=0.2)
"""
self.show_bones = bones
if bones:
self.get_joint_actors(length=length, with_transforms=False)
animation.add_actor(list(self._bactors.values()))
self.update_skin(animation)
[docs]
@warn_on_args_to_kwargs()
def apply_skin_matrix(self, vertices, joint_matrices, *, actor_index=0):
"""Apply the skinnig matrix, that transform the vertices.
Parameters
----------
vertices : ndarray
Vertices of an actor.
join_matrices : list
List of skinning matrix to calculate the weighted transformation.
Returns
-------
vertices : ndarray
Modified vertices.
"""
clone = np.copy(vertices)
weights = self.weights_0[actor_index]
joints = self.joints_0[actor_index]
for i, xyz in enumerate(clone):
a_joint = joints[i]
a_joint = [self.bones[i] for i in a_joint]
a_weight = weights[i]
skin_mat = (
np.multiply(a_weight[0], joint_matrices[a_joint[0]])
+ np.multiply(a_weight[1], joint_matrices[a_joint[1]])
+ np.multiply(a_weight[2], joint_matrices[a_joint[2]])
+ np.multiply(a_weight[3], joint_matrices[a_joint[3]])
)
xyz = np.dot(skin_mat, np.append(xyz, [1.0]))
clone[i] = xyz[:3]
return clone
[docs]
def transverse_bones(self, bone_id, channel_name, parent_animation: Animation):
"""Loop over the bones and add child bone animation to their parent
animation.
Parameters
----------
bone_id : int
Index of the bone.
channel_name : str
Animation name.
parent_animation : Animation
The animation of the parent bone. Should be `root_animation` by
default.
"""
node = self.gltf.nodes[bone_id]
animation = Animation()
if bone_id in self.bone_tranforms.keys():
orig_transform = self.bone_tranforms[bone_id]
else:
orig_transform = np.identity(4)
if bone_id in self.animation_channels[channel_name]:
transforms = self.animation_channels[channel_name][bone_id]
timestamps = transforms["timestamps"]
matrices = transforms["matrix"]
for time, matrix in zip(timestamps, matrices):
animation.set_keyframe("transform", time[0], matrix)
else:
animation.set_keyframe("transform", 0.0, orig_transform)
parent_animation.add(animation)
if node.children:
for child_bone in node.children:
self.transverse_bones(child_bone, channel_name, animation)
[docs]
def skin_animation(self):
"""One animation for each bone, contains parent transforms.
Returns
-------
root_animations : Dict
An animation containing all the child animations for bones.
"""
root_animations = {}
self._vertices = [utils.vertices_from_actor(act) for act in self.actors()]
self._vcopy = [np.copy(vert) for vert in self._vertices]
for name in self.animation_channels.keys():
root_animation = Animation()
root_bone = self.gltf.skins[0].skeleton
root_bone = root_bone if root_bone else self.bones[0]
self.transverse_bones(root_bone, name, root_animation)
root_animations[name] = root_animation
root_animation.add_actor(self._actors)
return root_animations
[docs]
@warn_on_args_to_kwargs()
def get_joint_actors(self, *, length=0.5, with_transforms=False):
"""Create an arrow actor for each bone in a skinned model.
Parameters
----------
length : float (default = 0.5)
Length of the arrow actor
with_transforms : bool (default = False)
Applies respective transformations to bone. Bones will be at origin
if set to `False`.
"""
origin = np.zeros((3, 3))
parent_transforms = self.bone_tranforms
for bone in self.bones:
arrow = actor.arrow(origin, [0, 1, 0], [1, 1, 1], scales=length)
verts = utils.vertices_from_actor(arrow)
if with_transforms:
verts[:] = transform.apply_transformation(
verts, parent_transforms[bone]
)
utils.update_actor(arrow)
self._bactors[bone] = arrow
self._bvertices[bone] = verts
self._bvert_copy = copy.deepcopy(self._bvertices)
[docs]
def update_morph(self, animation):
"""Update the animation and actors with morphing.
Parameters
----------
animation : Animation
Animation object.
"""
animation.update_animation()
timestamp = animation.current_timestamp
for i, vertex in enumerate(self._vertices):
weights = animation.child_animations[0].get_value("morph", timestamp)
vertex[:] = self.apply_morph_vertices(self._vcopy[i], weights, i)
vertex[:] = transform.apply_transformation(vertex, self.transformations[i])
utils.update_actor(self._actors[i])
utils.compute_bounds(self._actors[i])
[docs]
def apply_morph_vertices(self, vertices, weights, cnt):
"""Calculate weighted vertex from the morph data.
Parameters
----------
vertices : ndarray
Vertices of a actor.
weights : ndarray
Morphing weights used to calculate the weighted average of new
vertex.
cnt : int
Count of the actor.
"""
clone = np.copy(vertices)
target_vertices = np.copy(self.morph_vertices[cnt])
for i, weight in enumerate(weights):
target_vertices[i][:] = np.multiply(weight, target_vertices[i])
new_verts = sum(target_vertices)
for i, vertex in enumerate(clone):
clone[i][:] = vertex + new_verts[i]
return clone
[docs]
def morph_animation(self):
"""Create animation for each channel in animations.
Returns
-------
root_animations : Dict
A dictionary containing animations as values and animation name as
keys.
"""
animations = {}
self._vertices = [utils.vertices_from_actor(act) for act in self.actors()]
self._vcopy = [np.copy(vert) for vert in self._vertices]
for name, data in self.animation_channels.items():
root_animation = Animation()
for i, transforms in enumerate(data.values()):
weights = self.morph_weights[i]
animation = Animation()
timestamps = transforms["timestamps"]
matrices = transforms["matrix"]
matrices = np.array(matrices).reshape(-1, len(weights))
for time, weights in zip(timestamps, matrices):
animation.set_keyframe("morph", time[0], weights)
root_animation.add(animation)
root_animation.add_actor(self._actors)
animations[name] = root_animation
return animations
[docs]
def get_animations(self):
"""Return list of animations.
Returns
-------
animations: List
List of animations containing actors.
"""
actors = self.actors()
interpolators = {
"LINEAR": linear_interpolator,
"STEP": step_interpolator,
"CUBICSPLINE": tan_cubic_spline_interpolator,
}
rotation_interpolators = {
"LINEAR": slerp,
"STEP": step_interpolator,
"CUBICSPLINE": tan_cubic_spline_interpolator,
}
animations = []
for transforms in self.node_transform:
target_node = transforms["node"]
for i, nodes in enumerate(self.nodes):
animation = Animation()
transform_mat = self.transformations[i]
position, rot, scale = transform.transform_from_matrix(transform_mat)
animation.set_keyframe("position", 0.0, position)
if target_node in nodes:
animation.add_actor(actors[i])
timestamp = transforms["input"]
node_transform = transforms["output"]
prop = transforms["property"]
interpolation_type = transforms["interpolation"]
interpolator = interpolators.get(interpolation_type)
rot_interp = rotation_interpolators.get(interpolation_type)
timeshape = timestamp.shape
transhape = node_transform.shape
if transforms["interpolation"] == "CUBICSPLINE":
node_transform = node_transform.reshape(
(timeshape[0], -1, transhape[1])
)
for time, trs in zip(timestamp, node_transform):
in_tan, out_tan = None, None
if trs.ndim == 2:
cubicspline = trs
in_tan = cubicspline[0]
trs = cubicspline[1]
out_tan = cubicspline[2]
if prop == "rotation":
animation.set_rotation(
time[0], trs, in_tangent=in_tan, out_tangent=out_tan
)
animation.set_rotation_interpolator(rot_interp)
if prop == "translation":
animation.set_position(
time[0], trs, in_tangent=in_tan, out_tangent=out_tan
)
animation.set_position_interpolator(interpolator)
if prop == "scale":
animation.set_scale(
time[0], trs, in_tangent=in_tan, out_tangent=out_tan
)
animation.set_scale_interpolator(interpolator)
else:
animation.add_static_actor(actors[i])
animations.append(animation)
return animations
[docs]
def main_animation(self):
"""Return main animation with all glTF animations.
Returns
-------
main_animation : Animation
A parent animation containing all child animations for simple
animation.
"""
main_animation = Animation()
animations = self.get_animations()
for animation in animations:
main_animation.add(animation)
return main_animation
[docs]
@warn_on_args_to_kwargs()
def export_scene(scene, *, filename="default.gltf"):
"""Generate gltf from FURY scene.
Parameters
----------
scene: Scene
FURY scene object.
filename: str, optional
Name of the model to be saved
"""
gltf_obj = gltflib.GLTF2()
name, extension = os.path.splitext(filename)
if extension not in [".gltf", ".glb"]:
raise IOError("Filename should be .gltf or .glb")
buffer_file = open(f"{name}.bin", "wb")
primitives = []
buffer_size = 0
bview_count = 0
for act in scene.GetActors():
prim, size, count = _connect_primitives(
gltf_obj, act, buffer_file, buffer_size, bview_count, name
)
primitives.append(prim)
buffer_size = size
bview_count = count
buffer_file.close()
write_mesh(gltf_obj, primitives)
write_buffer(gltf_obj, size, f"{name}.bin")
camera = scene.camera()
cam_id = None
if camera:
write_camera(gltf_obj, camera)
cam_id = 0
write_node(gltf_obj, mesh_id=0, camera_id=cam_id)
write_scene(gltf_obj, [0])
gltf_obj.save(f"{name}.gltf")
if extension == ".glb":
gltf2glb(f"{name}.gltf", destination=filename)
def _connect_primitives(gltf, actor, buff_file, byteoffset, count, name):
"""Create Accessor, BufferViews and writes primitive data to a binary file
Parameters
----------
gltf: Pygltflib.GLTF2
actor: Actor
the fury actor
buff_file: file
filename.bin opened in `wb` mode
byteoffset: int
offset of the bufferview
count: int
BufferView count
name: str
Prefix of the gltf filename
Returns
-------
prim: Pygltflib.Primitive
byteoffset: int
Offset size of a primitive
count: int
BufferView count after adding the primitive.
"""
polydata = actor.GetMapper().GetInput()
colors = utils.colors_from_actor(actor)
if colors is not None:
polydata = utils.set_polydata_colors(polydata, colors)
vertices = utils.get_polydata_vertices(polydata)
colors = utils.get_polydata_colors(polydata)
normals = utils.get_polydata_normals(polydata)
tcoords = utils.get_polydata_tcoord(polydata)
try:
indices = utils.get_polydata_triangles(polydata)
except AssertionError as error:
indices = None
print(error)
ispoints = polydata.GetNumberOfVerts()
islines = polydata.GetNumberOfLines()
istraingles = polydata.GetNumberOfPolys()
if ispoints:
mode = 0
elif islines:
mode = 3
elif istraingles:
mode = 4
vertex, index, normal, tcoord, color = (None, None, None, None, None)
if indices is not None and len(indices) != 0:
indices = indices.reshape((-1,))
amax = [np.max(indices)]
amin = [np.min(indices)]
ctype = comp_type.get(gltflib.UNSIGNED_SHORT)
atype = acc_type.get(gltflib.SCALAR)
indices = indices.astype(np.ushort)
blength = len(indices) * ctype["size"]
buff_file.write(indices.tobytes())
write_bufferview(gltf, 0, byteoffset, blength)
write_accessor(
gltf, count, 0, gltflib.UNSIGNED_SHORT, len(indices), gltflib.SCALAR
)
byteoffset += blength
index = count
count += 1
if vertices is not None:
amax = np.max(vertices, 0).tolist()
amin = np.min(vertices, 0).tolist()
ctype = comp_type.get(gltflib.FLOAT)
atype = acc_type.get(gltflib.VEC3)
vertices = vertices.reshape((-1,)).astype(ctype["dtype"])
blength = len(vertices) * ctype["size"]
buff_file.write(vertices.tobytes())
write_bufferview(gltf, 0, byteoffset, blength)
write_accessor(
gltf,
count,
0,
gltflib.FLOAT,
len(vertices) // atype,
gltflib.VEC3,
max=amax,
min=amin,
)
byteoffset += blength
vertex = count
count += 1
if normals is not None:
amax = np.max(normals, 0).tolist()
amin = np.min(normals, 0).tolist()
ctype = comp_type.get(gltflib.FLOAT)
atype = acc_type.get(gltflib.VEC3)
normals = normals.reshape((-1,))
blength = len(normals) * ctype["size"]
buff_file.write(normals.tobytes())
write_bufferview(gltf, 0, byteoffset, blength)
write_accessor(
gltf,
count,
0,
gltflib.FLOAT,
len(normals) // atype,
gltflib.VEC3,
max=amax,
min=amin,
)
byteoffset += blength
normal = count
count += 1
if tcoords is not None:
amax = np.max(tcoords, 0).tolist()
amin = np.min(tcoords, 0).tolist()
ctype = comp_type.get(gltflib.FLOAT)
atype = acc_type.get(gltflib.VEC2)
tcoords = tcoords.reshape((-1,)).astype(ctype["dtype"])
blength = len(tcoords) * ctype["size"]
buff_file.write(tcoords.tobytes())
write_bufferview(gltf, 0, byteoffset, blength)
write_accessor(
gltf, count, 0, gltflib.FLOAT, len(tcoords) // atype, gltflib.VEC2
)
byteoffset += blength
tcoord = count
count += 1
vtk_image = actor.GetTexture().GetInput()
rows, cols, _ = vtk_image.GetDimensions()
scalars = vtk_image.GetPointData().GetScalars()
np_im = numpy_support.vtk_to_numpy(scalars)
np_im = np.reshape(np_im, (rows, cols, -1))
img = Image.fromarray(np_im)
image_path = f"{name}BaseColorTexture.png"
img.save(image_path)
write_material(gltf, 0, image_path)
if colors is not None:
ctype = comp_type.get(gltflib.FLOAT)
atype = acc_type.get(gltflib.VEC3)
shape = colors.shape[0]
colors = np.concatenate((colors, np.full((shape, 1), 255.0)), axis=1)
colors = colors / 255
colors = colors.reshape((-1,)).astype(ctype["dtype"])
blength = len(colors) * ctype["size"]
buff_file.write(colors.tobytes())
write_bufferview(gltf, 0, byteoffset, blength)
write_accessor(gltf, count, 0, gltflib.FLOAT, shape, gltflib.VEC4)
byteoffset += blength
color = count
count += 1
material = None if tcoords is None else 0
prim = get_prim(vertex, index, color, tcoord, normal, material, mode=mode)
return prim, byteoffset, count
[docs]
def write_scene(gltf, nodes):
"""Create scene
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object
nodes: list
List of node indices.
"""
scene = gltflib.Scene()
scene.nodes = nodes
gltf.scenes.append(scene)
[docs]
@warn_on_args_to_kwargs()
def write_node(gltf, *, mesh_id=None, camera_id=None):
"""Create node
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object
mesh_id: int, optional
Mesh index
camera_id: int, optional
Camera index.
"""
node = gltflib.Node()
if mesh_id is not None:
node.mesh = mesh_id
if camera_id is not None:
node.camera = camera_id
gltf.nodes.append(node)
[docs]
def write_mesh(gltf, primitives):
"""Create mesh and add primitive.
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object.
primitives: list
List of Primitive object.
"""
mesh = gltflib.Mesh()
for prim in primitives:
mesh.primitives.append(prim)
gltf.meshes.append(mesh)
[docs]
def write_camera(gltf, camera):
"""Create and add camera.
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object.
camera: vtkCamera
scene camera.
"""
orthographic = camera.GetParallelProjection()
cam = gltflib.Camera()
if orthographic:
cam.type = "orthographic"
else:
clip_range = camera.GetClippingRange()
angle = camera.GetViewAngle()
ratio = camera.GetExplicitAspectRatio()
aspect_ratio = ratio if ratio else 1.0
pers = gltflib.Perspective()
pers.aspectRatio = aspect_ratio
pers.znear, pers.zfar = clip_range
pers.yfov = angle * np.pi / 180
cam.type = "perspective"
cam.perspective = pers
gltf.cameras.append(cam)
[docs]
@warn_on_args_to_kwargs()
def get_prim(vertex, index, color, tcoord, normal, material, *, mode=4):
"""Return a Primitive object.
Parameters
----------
vertex: int
Accessor index for the vertices data.
index: int
Accessor index for the triangles data.
color: int
Accessor index for the colors data.
tcoord: int
Accessor index for the texture coordinates data.
normal: int
Accessor index for the normals data.
material: int
Materials index.
mode: int, optional
The topology type of primitives to render.
Default: 4
Returns
-------
prim: Primitive
pygltflib primitive object.
"""
prim = gltflib.Primitive()
attr = gltflib.Attributes()
attr.POSITION = vertex
attr.NORMAL = normal
attr.TEXCOORD_0 = tcoord
attr.COLOR_0 = color
prim.attributes = attr
prim.indices = index
if material is not None:
prim.material = material
prim.mode = mode
return prim
[docs]
def write_material(gltf, basecolortexture: int, uri: str):
"""Write Material, Images and Textures
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object.
basecolortexture: int
BaseColorTexture index.
uri: str
BaseColorTexture uri.
"""
material = gltflib.Material()
texture = gltflib.Texture()
image = gltflib.Image()
pbr = gltflib.PbrMetallicRoughness()
tinfo = gltflib.TextureInfo()
tinfo.index = basecolortexture
pbr.baseColorTexture = tinfo
pbr.metallicFactor = 0.0
material.pbrMetallicRoughness = pbr
texture.source = basecolortexture
image.uri = uri
gltf.materials.append(material)
gltf.textures.append(texture)
gltf.images.append(image)
[docs]
@warn_on_args_to_kwargs()
def write_accessor(
gltf, bufferview, byte_offset, comp_type, count, accssor_type, *, max=None, min=None
):
"""Write accessor in the gltf.
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 objecomp_type
bufferview: int
BufferView Index
byte_offset: int
ByteOffset of the accessor
comp_type: type
Type of a single component
count: int
Elements count of the accessor
accssor_type: type
Type of the accessor(SCALAR, VEC2, VEC3, VEC4)
max: ndarray, optional
Maximum elements of an array
min: ndarray, optional
Minimum elements of an array
"""
accessor = gltflib.Accessor()
accessor.bufferView = bufferview
accessor.byteOffset = byte_offset
accessor.componentType = comp_type
accessor.count = count
accessor.type = accssor_type
if (max is not None) and (min is not None):
accessor.max = max
accessor.min = min
gltf.accessors.append(accessor)
[docs]
@warn_on_args_to_kwargs()
def write_bufferview(gltf, buffer, byte_offset, byte_length, *, byte_stride=None):
"""Write bufferview in the gltf.
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object
buffer: int
Buffer index
byte_offset: int
Byte offset of the bufferview
byte_length: int
Byte length ie, Length of the data we want to get from
the buffer
byte_stride: int, optional
Byte stride of the bufferview.
"""
buffer_view = gltflib.BufferView()
buffer_view.buffer = buffer
buffer_view.byteOffset = byte_offset
buffer_view.byteLength = byte_length
buffer_view.byteStride = byte_stride
gltf.bufferViews.append(buffer_view)
[docs]
def write_buffer(gltf, byte_length, uri):
"""Write buffer int the gltf
Parameters
----------
gltf: GLTF2
Pygltflib GLTF2 object
byte_length: int
Length of the buffer
uri: str
Path to the external `.bin` file.
"""
buffer = gltflib.Buffer()
buffer.uri = uri
buffer.byteLength = byte_length
gltf.buffers.append(buffer)
