alisterburt

import einops
import numpy as np
import torch
import mrcfile
import napari
from torch_fourier_slice import project_3d_to_2d
from torch_image_lerp import sample_image_2d
from torch_grid_utils import coordinate_grid
from scipy.spatial.transform import Rotation as R

alisterburt

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

# set up rotation matrices for rotations around X axis
rotation_angles = np.linspace(0, 90, 50)
Rx = R.from_euler('x', angles=rotation_angles, degrees=True).as_matrix()
print(Rx.shape)

# set up column vector which points along y
z_vec = np.array([0, 0, 1]).reshape((3, 1))

alisterburt

https://docs.google.com/presentation/d/1QD6J1SR2_Q_7DivvtIE_P1ScrFGcU9yk-46ZmVavmf0/edit#slide=id.g27333d73966_0_16

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.