alisterburt’s gists

alisterburt / ts_sim.py

Created May 28, 2025 17:48

ts simulation for marten

	from typing import Tuple

	import mmdf
	import numpy as np
	import torch
	from fast_histogram import histogramdd
	import einops
	from scipy.stats import special_ortho_group
	from torch_affine_utils.transforms_3d import Rz, Ry, T
	from torch_affine_utils import homogenise_coordinates

alisterburt / get_contributors.py

Created April 24, 2025 13:52

contributor stats for teamtomo repositories

	import datetime
	import os
	from collections import defaultdict
	from typing import Dict, List, Any

	import requests


	class GitHubContributionsAnalyzer:
	def __init__(self, org_name: str, token: str = None):

alisterburt / warp_particle_vis.py

Last active April 14, 2025 22:23

alisterburt / crop_gain.py

Created March 28, 2025 22:57

	from pathlib import Path

	import mrcfile
	import numpy as np

	image_path = "CountRef_20250327_s004101_75-4_000_Mar27_17.04.37.mrc"
	image = mrcfile.read(image_path)
	image = np.array(image)
	image = image[:, :4031]

alisterburt / simulate_tomogram.py

Created March 12, 2025 15:51

how to simulate tomograms for ayse

	import numpy as np
	from scipy.spatial.transform import Rotation as R
	from torch_fourier_slice import project_3d_to_2d, backproject_2d_to_3d

	tilt_angles = np.linspace(-60, 60, 41, endpoint=True)
	rotation_matrices = R.from_euler('y', angles=tilt_angles, degrees=True).as_matrix()

	volume = simulate_volume()
	projections = project_3d_to_2d(volume, rotation_matrices)
	simulated_tomogram = backproject_2d_to_3d(projections, rotation_matrices)

alisterburt / napari_projector.py

Created February 28, 2025 17:55

render a projection below a volume in napari

	import napari
	import mrcfile
	import torch
	from torch_fourier_slice import project_3d_to_2d

	volume = torch.tensor(mrcfile.read("run_class001.mrc")).float()
	projection = project_3d_to_2d(volume, rotation_matrices=torch.eye(3))

	d, h, w = volume.shape

alisterburt / recenter_3d.py

Created February 7, 2025 18:19

recenter 3D particles in RELION 3.1+ style STAR files

alisterburt / recenter.py

Last active February 6, 2025 22:21

recenter particles r3.1+ for bryce

alisterburt / star_merge.py

Created February 4, 2025 19:08

merge simple one loop block star files

alisterburt / dynamo2warp.py

Last active February 4, 2025 18:03

works on per-tomogram table files and takes corresponding tomostar file name as input

Alister Burt alisterburt