tomo2321 / volume-renderer

Volume Renderer with VTK

Volume Renderer with VTK

This is a VTK wrapper of volume renderer, including:

• Volume rendering
• Surface rendering
• Surface distance rendering
• Isosurface rendering

Requirements

• Python 3
• VTK

Installation

Clone this repository

git clone https://github.com/yuta-hi/volume-renderer
cd volume-renderer

Register the preset

You can register own preset files. See the ./pyvr/presets

Install

pip install .

Usage

Console

volume_render --help
surface_render --help
surface_distance_render --help
isosurface_render --help

Python

Volume rendering

from pyvr import volume_render

volume = 'image.mhd'
preset = 'muscle' # ['bone', 'skelton', ...]

proj = volume_render(volume, preset)

Surface rendering

from pyvr import surface_render

volume = 'label.mhd'
preset = 'muscle' # ['bone', 'skin', 'hip_group1', ...]

proj = surface_render(volume, preset)

Surface distance rendering

source = 'label_a.mhd'
target = 'label_b.mhd'

source_index = 1
target_index = 1

clim = (0, 10) # [mm]

proj = surface_distance_render(source, target, source_index, target_index, clim=clim)

Isosurface rendering

from pyvr import isosurface_render

volume = 'label.mhd'
index = 1
rgb = [0., 0., 1.]

proj = isosurface_render(volume, index, rgb=rgb)

Customize

from pyvr.renderer import Renderer
from pyvr.actors import IsosurfaceActor
from pyvr.actors import SurfaceDistanceActor

renderer = Renderer()
renderer.add_actor(IsosurfaceActor(source, index=1, rgb=[1.,1.,1.], alpha=0.3))
renderer.add_actor(IsosurfaceActor(source, index=2, rgb=[1.,1.,1.], alpha=0.3))
renderer.add_actor(IsosurfaceActor(source, index=22, rgb=[0.5,0.5,0.5], alpha=0.3))
renderer.add_actor(SurfaceDistanceActor(source, target, source_index, target_index, clim=clim))
proj = renderer.render(rotate_angles=rotate_angles, bg=bg)

Slice

from pyvr.renderer import Renderer
from pyvr.actors import VolumeActor
from pyvr.actors import SliceActor
from pyvr.data.volume import load_volume

volume = load_volume(volume_file)
clim = (-150, 350)

renderer = Renderer()
renderer.set_camera(pos=(0,-1000,0))
renderer.add_actor(VolumeActor(volume, 'bone'))
renderer.add_actor(SliceActor(volume, normal=(1,0,0), clim=clim))
renderer.add_actor(SliceActor(volume, normal=(0,1,0), clim=clim))
renderer.add_actor(SliceActor(volume, normal=(0,0,1), clim=clim))
proj = renderer.render(rotate_angles=rotate_angles, bg=bg)

Landmark and Line

from pyvr.renderer import Renderer
from pyvr.actors import VolumeActor
from pyvr.actors import LandmarkActor
from pyvr.actors import LineActor

renderer = Renderer()
renderer.set_camera(pos=(0,-1000,0))
renderer.add_actor(VolumeActor(volume, 'bone'))
lt_ASIS = (118.198, -46.615, 187.801)
rt_ASIS = (-119.837, -49.702, 177.924)
pubic_tubercle = (2.919, -44.044, 98.295)
renderer.add_actor(LandmarkActor(lt_ASIS, 7, rgb=(1,0,0)))
renderer.add_actor(LandmarkActor(rt_ASIS, 7, rgb=(0,1,0)))
renderer.add_actor(LandmarkActor(pubic_tubercle, 7, rgb=(0,0,1)))
renderer.add_actor(LineActor(lt_ASIS, rt_ASIS, rgb=(0,0,1)))
renderer.add_actor(LineActor(lt_ASIS, pubic_tubercle, rgb=(0,1,0)))
renderer.add_actor(LineActor(rt_ASIS, pubic_tubercle, rgb=(1,0,0)))
proj = renderer.render(rotate_angles=rotate_angles, bg=bg)

Write projections as video

from pyvr.utils.video import write_video
write_video(proj, 'video.mp4')

Interactive rendering with multiple viewports

from pyvr.renderer import InteractiveMultiViewRenderer
from pyvr.actors import VolumeActor
from pyvr.actors import SurfaceActor

renderer = InteractiveMultiViewRenderer()
renderer.set_camera(pos=(0,-1200,0))
renderer.add_actor(VolumeActor(volume, 'muscle'))
renderer.add_actor(SurfaceActor(label, 'muscle'))
renderer.add_actor(VolumeActor(uncertainty, 'uncertainty'))
renderer.render(bg=(1,1,1))

See also Bayesian U-Net for uncertainty estimates.