Note

This page was generated from Animation.ipynb. Interactive online version: . Some tutorial content may look better in light mode.

Animation of 3D models generated by spateo

import io, warnings
import base64
from IPython.display import HTML

import spateo as st
warnings.filterwarnings('ignore')

2023-07-26 18:08:19.246980: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT

Load the data

cpo = [(553, 1098, 277), (1.967, -6.90, -2.21), (0, 0, 1)]

# embryo mesh，see also ``3D Rconstruction.ipynb``
embryo_mesh = st.tdr.read_model(f"E7-9h_embryo_mesh_model.vtk")
st.tdr.scale_model(model=embryo_mesh, scale_factor=1.05, inplace=True)

# tissue mesh，see also ``3D Rconstruction.ipynb``
tissues_name = ["amnioserosa", "CNS", "midgut", "salivary gland", "muscle", "epidermis"]
tissues_mesh = [st.tdr.read_model(f"E7-9h_mesh_model_{tissue_name}.vtk") for tissue_name in tissues_name]

Visualize the 3D models of each tissue individually

st.pl.three_d_multi_plot(
    model=st.tdr.collect_models([st.tdr.collect_models([embryo_mesh, tm]) for tm in tissues_mesh]),
    key="tissue", model_style="surface", cpo=[cpo], shape=(2, 3), jupyter="static",
)

Integrate 3D models of all tissues

integrated_meshes = tissues_mesh.copy()
integrated_meshes.append(embryo_mesh)
st.pl.three_d_plot(model=st.tdr.collect_models(integrated_meshes), key="tissue", model_style="surface", cpo=cpo, jupyter="static",)

Animate 3D models

st.pl.three_d_plot(
    model=st.tdr.collect_models(integrated_meshes),
    key="tissue",
    filename=f"E7-9h_completed_model_animation1.mp4",
    model_style="surface",
    show_legend=True,
    off_screen=False,
    jupyter="static",
    background="white",
    window_size=(1024, 1024),
    cpo=cpo,
    text=f"\nAxis of rotation: D-V",
    view_up=(0, 0, 1),
    framerate=6)

st.pl.three_d_plot(
    model=st.tdr.collect_models(integrated_meshes),
    key="tissue",
    filename=f"E7-9h_completed_model_animation2.mp4",
    model_style="surface",
    show_legend=True,
    off_screen=False,
    jupyter="static",
    background="white",
    window_size=(1024, 1024),
    cpo=cpo,
    text=f"\nAxis of rotation: A-P",
    view_up=(1, 0, 0),
    framerate=6)

st.pl.merge_animations(
    mp4_files=[
        f"E7-9h_completed_model_animation1.mp4",
        f"E7-9h_completed_model_animation2.mp4"
    ],
    filename=f"E7-9h_merged_completed_model_animation.mp4"
)

Moviepy - Building video visualize_sample/E7-9h_merged_completed_model_animation.mp4.
Moviepy - Writing video visualize_sample/E7-9h_merged_completed_model_animation.mp4

Moviepy - Done !
Moviepy - video ready visualize_sample/E7-9h_merged_completed_model_animation.mp4

vedio_path = "./video/E7-9h_merged_completed_model_animation.mp4"
video = io.open(vedio_path, 'r+b').read()
encoded = base64.b64encode(video)
HTML(
    data=
    '''
    <video width="500" height="500"  controls>
    <source src="data:video/mp4;base64,{0}" type="video/mp4" />
    </video>
    '''.format(encoded.decode('ascii'))
)