Source code for fury.gltf

# 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)