alisterburt

import numpy as np
import napari
from scipy.interpolate import splprep, splev

n = 10
w = np.linspace(0, 8*np.pi, num=n)
x = [0, 1,  1, 1,]
y = [0,  0, 10, 10]
z = [0, 0, 0, 100]
xyz = np.stack((x, y, z), axis=-1)

alisterburt

from typing import Tuple

import einops
import imageio
import numpy as np
from scipy.interpolate import LSQBivariateSpline
import napari

image = imageio.imread('image/EMPIAR-10164_TS_01_000_0.0.tif')
mask = imageio.imread('mask/EMPIAR-10164_TS_01_000_0.0.tif')

alisterburt

alisterburt

alisterburt

alisterburt

import os

import numpy as np
import pandas as pd
import mrcfile
from pathlib import Path


def components_from_cryosparc(cs_file):
    data = np.load(cs_file)

alisterburt

import gemmi
import numpy as np

pdb = '4v6x-ribo.cif'

structure = gemmi.read_structure(pdb)
model = structure[0]  # assumes one model in the file

ca_coords = np.array([
    [cra.atom.pos.x, cra.atom.pos.y, cra.atom.pos.z]

alisterburt

import numpy as np
import einops
import starfile

from yet_another_imod_wrapper.utils.io import read_xf, read_tlt


XF_FILE = 'imod_TS_01/TS_01.xf'
TLT_FILE = 'imod_TS_01/TS_01.tlt'
TILT_IMAGE_DIMENSIONS = (3710, 3838)  # (x, y)

alisterburt

from typing import Tuple

import napari
import scipy.ndimage as ndi
import numpy as np
from psygnal import EventedModel


viewer = napari.Viewer(ndisplay=3)
mask_layer = viewer.add_image(mask := np.zeros((128, 128, 128)))

alisterburt

import napari
import numpy as np
import scipy.ndimage as ndi


SIZE = 42

# small circle
circle = np.linalg.norm(
    np.indices(dimensions=(SIZE, SIZE)) - (SIZE / 2), axis=0