alisterburt’s gists

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

alisterburt / dynamo2warp.py

Created February 3, 2025 18:15

standalone dynamo to warp particle metadata conversion, to run `uv run dynamo2warp.py`

alisterburt / dynamo2warp.py

Created February 3, 2025 18:15

standalone dynamo -> warp particle metadata conversion

alisterburt / cuzco.py

Created February 3, 2025 06:07

	from functools import partial

	import napari
	from magicgui.widgets import Button, Container
	from scipy.spatial.transform import Rotation as R
	from skimage import data

	viewer = napari.Viewer(ndisplay=3)
	blobs = data.binary_blobs(n_dim=3, length=32, volume_fraction=0.1)
	viewer.add_image(blobs)