Affine Transforms 3D

Translate and rotate an object in napari using an affine transformation. Affine for 3D objects is represented as a 4x4 matrix, while affine for 2D objects is represented as a 3x3 matrix. For 3D objects the 4 columns represent the rotate, scale, shear, and translate respectively, and by default, affine is set as a 4x4 identity matrix. By modifying the respective values in this matrix, which is represented as a numpy array, we can move and adjust objects in the napari viewer.

Tags: visualization-advanced

import meshio
import numpy as np
import pooch
from magicgui import magicgui

import napari

cup_path = pooch.retrieve(
    url="https://raw.githubusercontent.com/8bitbiscuit/cup_and_creamer/main/cup.stl",
    known_hash='b6162298f86c94ebb276eb5f0544409996a8ee81fff9627a2bd4b71309835014',
)
creamer_path = pooch.retrieve(
    url="https://raw.githubusercontent.com/8bitbiscuit/cup_and_creamer/main/creamer.stl",
    known_hash='122256d942694cf40fc1a186a346cda0b31a03fbdec61ea8a351c915f3d0d6ed',
)

# Use meshio to read in stl files
cup_mesh = meshio.read(cup_path)
creamer_mesh = meshio.read(creamer_path)

# Create tuples using the data read in from meshio to be viewed by napari as surfaces
cup_data = (cup_mesh.points, cup_mesh.cells[0].data)
creamer_data = (creamer_mesh.points, creamer_mesh.cells[0].data)

viewer = napari.Viewer()

# Define an original affine transformation to be position of surface upon being loaded into viewer
# Otherwise both objects would be loaded in on the origin in the viewer by default and be on top of one another
og_affine = np.array(
    [
        [1.0, 0.0, 0.0, 0.0],
        [0.0, 1.0, 0.0, 0.0],
        [0.0, 0.0, 1.0, -0.1],
        [0.0, 0.0, 0.0, 1.0],
    ]
)

# Add in the two surfaces we read using meshio
viewer.add_surface(cup_data, name="cup")
viewer.add_surface(
    creamer_data, affine=og_affine, opacity=0.5, blending="additive", name="creamer"
)


@magicgui(call_button='POUR!!')
def pour_creamer():
    # Define a new affine transform for the creamer surface, where it is moved up and at an angle to be 'poured' into the cup
    new_affine = np.array(
        [
            [1.0, 0.0, 0.0, 0.0],
            [0.0, 0.23, -0.97, 0.15],
            [0.0, 0.97, 0.23, -0.08],
            [0.0, 0.0, 0.0, 1.0],
        ]
    )

    # Add a transformed surface with the new affine transform
    # This surface is identical to the other creamer object, save for the new affine transformation
    viewer.add_surface(
        creamer_data, affine=new_affine, opacity=0.5, blending="additive", name="pour"
    )


# Set viewer camera angles and zoom
viewer.dims.ndisplay = 3
viewer.camera.angles = (180, 40, 92)
viewer.camera.zoom = 1972

# Add button to create new layer with transformed object using magicgui
viewer.window.add_dock_widget(pour_creamer)

pour_creamer()

if __name__ == "__main__":
    napari.run()