Created
April 8, 2024 22:27
script to setup point annotator test
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import napari | |
import numpy as np | |
from skimage import data | |
from napari_threedee.annotators import PointAnnotator | |
from napari_threedee.manipulators import RenderPlaneManipulator | |
viewer = napari.Viewer() | |
image_data = data.cells3d()[:,1,...] # just get the one channel | |
image_layer = viewer.add_image(image_data, name="nuclei", colormap="green") | |
image_layer.scale = [.5, .25, .25] | |
viewer.dims.ndisplay = 3 | |
# add_points will yield scale = [1, 1, 1] | |
pts_layer = viewer.add_points(name="Points", ndim=3) | |
# set scale | |
# pts_layer.scale = [.5, .25, .25] | |
# for easier visualization | |
plane_layer = viewer.add_image( | |
image_data, | |
rendering='average', | |
name='plane', | |
colormap='magenta', | |
blending='additive', | |
opacity=0.75, | |
depiction='plane') | |
plane_layer.scale = image_layer.scale | |
# create the point annotator, we will use the plane_layer for locations | |
annotator = PointAnnotator( | |
viewer=viewer, | |
image_layer=plane_layer, | |
points_layer=pts_layer, | |
enabled=True, | |
) | |
# try this plane first, it will work, but if you rotate the points are not on the plane | |
plane_layer.plane.position = (9, 229, 216) | |
plane_layer.plane.normal = (0.3, -.7, .7) | |
napari.run() |
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