alisterburt

import numpy as np
import einops
import starfile

from yet_another_imod_wrapper.utils.io import read_xf, read_tlt


XF_FILE = 'imod_TS_01/TS_01.xf'
TLT_FILE = 'imod_TS_01/TS_01.tlt'
TILT_IMAGE_DIMENSIONS = (3710, 3838)  # (x, y)

alisterburt

from pathlib import Path
from typing import Tuple

import eulerangles
import imodmodel
import numpy as np
import pandas as pd
import starfile as starfile
from pydantic import BaseModel

biochem-fan

RELION interoperabiity with Warp and M

This document examines how to use RELION 4.0 (beta2 as of writing) with Warp 1.09 and M 1.09 for single particle analysis.

Special thanks to Alister Burt, Pranav Shah and Dimitry Tegunov for discussion on this Twitter thread.

Download the movies

We use the RELION tutorial dataset (beta-galactosidase collected on JEOL CRYO ARM 200, a subset of EMPIAR-10204).

Edenhofer

#!/usr/bin/env python3

from jax import numpy as jnp
import numpy as np
from scipy.interpolate import RegularGridInterpolator as _si_RegularGridInterpolator


class RegularGridInterpolator:
    # Based on SciPy's implementation which in turn is originally based on an
    # implementation by Johannes Buchner

hanjinliu

from __future__ import annotations
import inspect
from magicgui import magicgui
import napari
from qtpy.QtWidgets import QPushButton, QWidget, QVBoxLayout

# Usage:
# >>> viewer = napari.Viewer()
# >>> cgui = ClassGui(viewer)
# >>> @cgui.from_class

YoraiLevi

<#
.SYNOPSIS
    Requires powershell 5 or later
    Provides Get and Set functions for KnownFolders
.EXAMPLE
    PS> Set-KnownFolderPath Desktop $ENV:USERPROFILE/Desktop
.EXAMPLE
    PS> $Path=""
    PS> Get-KnownFolderPath Desktop ([ref]$Path)
.LINK

alisterburt

function table = vll2table(vll_file)
    %%% Convert a vll file into a table and corresponding tomogram table-map file
    
    % Read volume list file
    volume_list = ptdb.volumelisttext2object(vll_file).volumes;
    
    % Prepare output filenames
    table_file_name = strrep(vll_file, '.vll', '.tbl');
    table_map_file_name = strrep(vll_file, '.vll', '_tablemap.doc');
    

alisterburt

function dms2mod(markers_dms_file, model_file, image_file)
    %%%%% Convert Dynamo markers (.dms files) into IMOD format model files (.mod)
    %%%%% Requires MATLAB >= r2019a
    %%%%% Requires Dynamo >= 1.1.478
    %%%%% Requires IMOD >= 4.10.37
    %%% Reading marker file
    m = dread(markers_dms_file);
    
    %%% Extract useful objects
    markers = m.shapes;

biochem-fan

/*  BoxNet2D runner
 *   Based on Warp 1.0.7 by Dimitry Tegunov https://github.com/cramerlab/warp/
 *   Command line interface and Linux port by @biochem_fan
 *   Licensed under GPLv3
 */

using System;
using System.IO;
using System.Linq; // for toList()
using System.Diagnostics; // for Stopwatch

DustinMorado

#!/bin/bash

if [[ ! -d 3DEM ]]
then
    mkdir 3DEM
fi

cd 3DEM

curl -s http://mail.ncmir.ucsd.edu/pipermail/3dem/ |\