alisterburt

import numpy as np
import starfile
import napari
from scipy.spatial.transform import Rotation as R

df = starfile.read('particles_warp.star')

xyz = df[['rlnCoordinateX', 'rlnCoordinateY', 'rlnCoordinateZ']].to_numpy()
eulers = df[['rlnAngleTiltPrior', 'rlnAnglePsiPrior']].to_numpy()
rotation_matrices = R.from_euler(seq='YZ', degrees=True, angles=eulers).inv().as_matrix()

alisterburt

import matplotlib.pyplot as plt
import numpy as np
from cmap import Colormap


h, w = 512, 868
image = np.random.random(size=(h, w))
defocus = np.array([[0, 1],
                    [1, 0]])

alisterburt

"""Recenter and reorient RELION particles

This shows the gist of how to manually move/reorient RELION particles in 3D.
You define a set of shifts and orientations in the coordinate system of the 
reference for all 'subparticles' you want to generate from each existing particle.
"""
import pandas as pd
import starfile
import numpy as np
from scipy.spatial.transform import Rotation as R

alisterburt

import napari
import numpy as np
from skimage import data

from napari_threedee.manipulators.base_manipulator import BaseManipulator


class FullManipulator(BaseManipulator):

    def __init__(self, viewer, layer=None):

alisterburt

import numpy as np
import torch
import einops
import mmdf

from libtilt.grids._patch_grid_utils import patch_grid_centers
from libtilt.grids import coordinate_grid

RESOLUTION_ANGSTROMS = 3.4
VOLUME_SIZE = (512, 512, 512)

alisterburt

import torch
import einops

def sliding_window_3d(tensor, window_size):
    d, h, w = tensor.shape
    window_depth, window_height, window_width = window_size

    # Calculate the number of windows in each dimension
    new_d = d - window_depth + 1
    new_h = h - window_height + 1

alisterburt

import h3
import torch
import einops
from scipy.spatial.transform import Rotation as R



def get_h3_grid_at_resolution(resolution: int) -> list[str]:
    """Get h3 cells (their h3 index) at a given resolution.

alisterburt

alisterburt

from enum import Enum
from pathlib import Path
from glob import glob

import dynamotable
import mrcfile
import pandas as pd

import napari
import numpy as np

alisterburt

from pathlib import Path

import imageio
import numpy as np
import napari
from napari.utils.notifications import show_info

IMAGE_FILE_PATTERN = 'images/*'
DIRECTORY_FOR_GOOD_IMAGES = 'good_images'