03 - Dynamic: export video
This demo show how to do a 4DCT reconstruction and export a video of the reconstructed object afterwards.
demo/03_dynamic_reconstruction_video.py
"""
Demo 03: Reconstruct a dynamic volume from an array and export a video of the reconstruction."""
from pathlib import Path
from nect.download_demo_data import download_demo_data, get_demo_data_path
import nect
demo_dir = get_demo_data_path("SimulatedFluidInvasion")
download_demo_data("SimulatedFluidInvasion")
geometry = nect.Geometry.from_yaml(demo_dir / "geometry.yaml")
reconstruction_path = nect.reconstruct(
geometry=geometry,
projections=demo_dir / "projections.npy",
quality="high",
mode="dynamic",
exp_name="SimulatedFluidInvasion", # optional, name of the experiment
config_override={
"epochs": "1x", # a multiplier of base-epochs. Base-epochs is: floor(49 / num_projections * max(nDetector))
"checkpoint_interval": 1800, # How often to save the model in seconds
"image_interval": 30, # How often to save images in seconds
"plot_type": "XZ", # XZ or XY, YZ
},
)
nect.export_video(reconstruction_path, add_scale_bar=True, acquisition_time_minutes=60)