alisterburt’s gists

alisterburt / sympy_matrix_decomp.ipynb

Last active April 17, 2023 13:20

Decomposing a RELION projection matrix for James Hooker

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alisterburt / raps_3d.py

Last active March 28, 2023 19:32

Rotational average 3D for Pranav

	from pathlib import Path
	from typing import List, Sequence, Tuple

	import einops
	import mrcfile
	import numpy as np
	import torch
	import typer

	cli = typer.Typer(name='raps_3d', no_args_is_help=True, add_completion=False)

alisterburt / motioncor_fourier_space.py

Created March 24, 2023 20:59

motioncor implementation in libtilt - fourier space

	import torch
	import numpy as np
	import mrcfile
	import einops

	import torch.nn.functional as F
	from torch_cubic_spline_grids import CubicBSplineGrid3d

	from libtilt.rotational_average import rotational_average_2d
	from libtilt.utils.coordinates import array_to_grid_sample

alisterburt / motioncor_real_space.py

Last active March 24, 2023 20:58

libtilt motion estimation first pass

	import torch
	import numpy as np
	import mrcfile
	import einops

	import torch.nn.functional as F
	from torch_cubic_spline_grids import CubicBSplineGrid3d

	from libtilt.utils.coordinates import array_to_grid_sample
	from libtilt.shift.phase_shift_2d import phase_shift_images_2d, phase_shift_dfts_2d

alisterburt / point_oversample_in_mask.py

Created February 22, 2023 19:43

For Matteo picking crystals

	import einops
	import numpy as np
	import napari
	import imageio

	# variables to be set by user
	SPACING = 28

	# load data
	labels = imageio.imread('matteo_labels_example.tif')

alisterburt / proj_bproj_cycle_libtilt.py

Created February 22, 2023 15:28

projection backprojection cycle in torch

	import sys

	import mrcfile
	import napari
	import torch
	import torch.nn.functional as F
	import numpy as np
	from scipy.stats import special_ortho_group

	from libtilt.utils.coordinates import generate_rotated_slice_coordinates

alisterburt / relion31_particle_pose.py

Created February 11, 2023 14:24

Extract particles poses from a RELION 3.1 STAR file

	import starfile
	from scipy.spatial.transform import Rotation as R

	particle_star_file = 'hiv/01_10.00Apx_particles.star'

	star = starfile.read(particle_star_file)

	df = df = star['particles'].merge(star['optics'], on='rlnOpticsGroup')

	# get necessary info from dataframes

alisterburt / relion30_particle_pose.py

Last active February 11, 2023 14:16

RELION 3.0 particle pose from STAR file

	import starfile
	from scipy.spatial.transform import Rotation as R

	particle_star_file = 'hiv/01_10.00Apx_particles.star'

	df = starfile.read(particle_star_file)

	# get necessary info from dataframe
	xyz = df[['rlnCoordinateX', 'rlnCoordinateY', 'rlnCoordinateZ']].to_numpy() # (n, 3)
	shifts = df[['rlnOriginX', 'rlnOriginY', 'rlnOriginZ']].to_numpy() # (n, 3)

alisterburt / point_in_masked_region.py

Created January 10, 2023 11:46

point in masked region (for Shen Han)

	import numpy as np
	import napari
	from skimage import data

	# fake tomogram
	tomogram = np.random.random((300, 300, 300))

	# fake mask
	mask = data.binary_blobs(
	length=300, n_dim=3, blob_size_fraction=0.3, volume_fraction=0.1

alisterburt / projection_geometry_example_for_tf.py

Created December 15, 2022 18:35

projection geometry example for thomas frosio

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

	import einops
	import fast_histogram
	import mmdf
	import mrcfile
	import napari

Alister Burt alisterburt