alisterburt’s gists

alisterburt / barrett.py

Created September 18, 2024 22:08

R5 parsing for Barrett

	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 / h3_utils.py

Created August 29, 2024 13:21

	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 / warp_tm_vis.py

Created August 2, 2024 11:00

warp template matching visualisation

	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 / spencer_dask.py

Created July 23, 2024 04:24

spencer dask

alisterburt / 3d_correlation_from_2d_correlations.py

Created June 13, 2024 00:20

3D correlations from multiple 2D correlations for Will Wan

	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 / aysecan.py

Created June 11, 2024 21:50

constructing rotation matrices and generating RELION compatible euler angles from them

	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 / gist:90fb9e3329e6315b1eecee53df32964d

Created June 10, 2024 15:47

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

alisterburt / eric_bogdan_thing.py

Created May 17, 2024 11:06

Interpret/visualise composition of prior and pose in RELION

	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 / mpl_gradient_overlay.py

Last active May 7, 2024 17:24

matplotlib gradient overlays - gradient resolution is different from image resolution

	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 / josh.py

Last active March 13, 2024 01:05

recentering/reorienting RELION particles for Josh Hutchings

	"""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