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June 23, 2022 05:07
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Make a microtubule in napari, for illustration.
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import napari | |
import numpy as np | |
class MtModel: | |
def __init__( | |
self, | |
npf: int = 13, | |
start: int = 3, | |
space: float = 4.0, | |
radius: float = 9.8, | |
): | |
self.npf = npf | |
self.start = start | |
self.space = space | |
self.radius = radius | |
def _make_a_ring(self, offset: int): | |
theta = np.linspace(0, 2*np.pi, self.npf, endpoint=False) | |
coords = [ | |
np.linspace(0, self.space*self.start, self.npf, endpoint=False) + self.space*offset, | |
self.radius * np.cos(theta), | |
self.radius * np.sin(theta), | |
] | |
return np.stack(coords, axis=1) | |
def polymerize(self, edges: tuple[int, int]) -> np.ndarray: | |
start, stop = edges | |
tub_a = np.concatenate([self._make_a_ring(offset=2*i) for i in range(start, stop)], axis=0) | |
tub_b = np.concatenate([self._make_a_ring(offset=2*i + 1) for i in range(start, stop)], axis=0) | |
mt = np.concatenate([tub_a, tub_b], axis=0) | |
return mt | |
def add_mt( | |
self, | |
viewer, | |
edges: tuple[int, int], | |
colors=("magenta", "#f693ff"), | |
name: str = None, | |
): | |
mt = self.polymerize(edges) | |
n = mt.shape[0] // 2 | |
face_color = [colors[0]] * n + [colors[1]] * n | |
return viewer.add_points( | |
mt, face_color=face_color, edge_width=0.1, size=5, name=name | |
) | |
viewer = napari.Viewer() | |
model = MtModel() | |
model.add_mt(viewer, (0, 8)) |
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