alisterburt

from lxml import etree

json_file = "/Users/burta2/data/fakery/MotionAndCTF2D/average/20170629_00021_frameImage_motion.json"

# <GridMovementX Width="1" Height="1" Depth="3" MarginX="0" MarginY="0" MarginZ="0">
# 		<Node X="0" Y="0" Z="0" Value="-5.1639977" />
# 		<Node X="0" Y="0" Z="1" Value="0.7089546" />
# 		<Node X="0" Y="0" Z="2" Value="4.455043" />
# 	</GridMovementX>
# 	<GridMovementY Width="1" Height="1" Depth="3" MarginX="0" MarginY="0" MarginZ="0">

alisterburt

import os
from concurrent.futures import ThreadPoolExecutor, as_completed
from pathlib import Path


def find_relion_dirs(root_dir):
    """
    Recursively walks through the directory and finds all directories that contain a 'Refine3D' or 'Class3D' subdirectory.

    Args:

alisterburt

import ast

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

DO_VIS = True

particle_star = starfile.read('matching.star')

alisterburt

import numpy as np
import h3
import einops


def get_h3_grid_at_resolution(resolution: int) -> list[str]:
    """Get h3 cells (their h3 index) at a given resolution.
    Each cell appears once
    - resolution 0:       122 cells, every   ~20 degrees
    - resolution 1:       842 cells, every  ~7.5 degrees

alisterburt

from enum import Enum
from pathlib import Path

import starfile
import mrcfile
import napari
import numpy as np
from magicgui import magicgui, widgets

RECONSTRUCTION_DIR = '/Users/burta2/Downloads/10499/reconstruction'

alisterburt

from pathlib import Path
from typing import Sequence

import dask
import mrcfile
import numpy as np
import torch
import pandas as pd
import dask.array as da

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()