alisterburt

import os
from pathlib import Path
from typing import Tuple, Optional

import einops
import fast_histogram
import mmdf
import mrcfile
import numpy as np
from scipy.stats import special_ortho_group

alisterburt

from pathlib import Path

import einops
import mrcfile
import numpy as np
import torch

import typer

cli = typer.Typer(add_completion=False)

alisterburt

import os
from pathlib import Path

import einops
import mmdf
import mrcfile
import numpy as np
import typer

cli = typer.Typer(add_completion=False)

alisterburt

alisterburt

alisterburt

from typing import Tuple

import starfile
import numpy as np
import einops

from scipy.spatial.transform import Rotation as R

CHIMERAX_VIEW_MATRIX_OUTPUT_FILE = 'chimerax/view_matrix_output_origin_at_rotation_center.txt'
PARTICLE_STAR_FILE = 'class3d_dir/run_it025_data.star'

alisterburt

from enum import Enum

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

PARTICLE_STAR_FILE = 'ricardo_data.star'

alisterburt

import pandas as pd
import einops
import numpy as np


def Rx(angles_degrees: np.ndarray) -> np.ndarray:
    """Affine matrix for a rotation around the X-axis."""
    angles_degrees = np.asarray(angles_degrees).reshape(-1)
    c = np.cos(np.deg2rad(angles_degrees))
    s = np.sin(np.deg2rad(angles_degrees))

alisterburt

from typing import Sequence, Tuple, Literal
import einops
import mrcfile
import napari
from magicgui import magicgui
from napari.types import ImageData

import numpy as np
import torch
from torch.nn import functional as F

alisterburt

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

# set up initial orientations of two particles
p0 = np.eye(3)  # oriented same as basis vectors of coord system
p1 = R.from_euler(seq='XYZ', angles=[10, 10, 60], degrees=True)  # slightly rotated out of plane, in plane quite different

# take y vector from p0, project onto y and y from p1
# take y vector because is easier for construction of x-vector with the cross product
p0_y = p0[:, 1]