Alister Burt alisterburt
alisterburt
/ napari_projector.py
Created
February 28, 2025 17:55
render a projection below a volume in napari
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| 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
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| # /// script | |
| # requires-python = ">=3.11" | |
| # dependencies = [ | |
| # "pandas", | |
| # "scipy", | |
| # "starfile", | |
| # "typer", | |
| # "einops", | |
| # "rich", | |
| # ] |
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| # /// script | |
| # requires-python = ">=3.11" | |
| # dependencies = [ | |
| # "pandas", | |
| # "scipy", | |
| # "starfile", | |
| # "typer", | |
| # "einops", | |
| # ] | |
| # [tool.uv] |
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| # /// script | |
| # requires-python = ">=3.11" | |
| # dependencies = [ | |
| # "pandas", | |
| # "starfile", | |
| # "typer", | |
| # ] | |
| # [tool.uv] | |
| # exclude-newer = "2025-01-01T00:00:00Z" | |
| # /// |
alisterburt
/ dynamo2warp.py
Last active
February 4, 2025 18:03
works on per-tomogram table files and takes corresponding tomostar file name as input
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| # /// script | |
| # requires-python = ">=3.11" | |
| # dependencies = [ | |
| # "dynamotable", | |
| # "pandas", | |
| # "scipy", | |
| # "starfile", | |
| # "typer", | |
| # ] | |
| # [tool.uv] |
alisterburt
/ dynamo2warp.py
Created
February 3, 2025 18:15
standalone dynamo to warp particle metadata conversion, to run `uv run dynamo2warp.py`
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| # /// script | |
| # requires-python = ">=3.11" | |
| # dependencies = [ | |
| # "dynamotable", | |
| # "pandas", | |
| # "scipy", | |
| # "starfile", | |
| # "typer", | |
| # ] | |
| # [tool.uv] |
alisterburt
/ dynamo2warp.py
Created
February 3, 2025 18:15
standalone dynamo -> warp particle metadata conversion
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| # /// script | |
| # requires-python = ">=3.11" | |
| # dependencies = [ | |
| # "dynamotable", | |
| # "pandas", | |
| # "scipy", | |
| # "starfile", | |
| # "typer", | |
| # ] | |
| # [tool.uv] |
alisterburt
/ cuzco.py
Created
February 3, 2025 06:07
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| 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) |
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| 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"> |
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| 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: |