Added actual code

angdist.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import starfile as star
+import matplotlib.pyplot as plt
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+import click
+
+# Building blocks
+
+def load_angles(starfile):
+    """Load rlnAngleRot and rlnAngleTilt from a run_data.star file."""
+    star_data = star.open(starfile)
+    angles = star_data[1][['rlnAngleRot', 'rlnAngleTilt']]
+    return angles
+
+def build_histogram(angles, title, colormap, gridsize):
+    """Builds a 2D histogram of number of particles per Euler angle pair."""
+    fig, ax = plt.subplots()
+    hb = ax.hexbin(angles.rlnAngleRot, angles.rlnAngleTilt, bins='log', cmap=colormap, gridsize=gridsize)
+    ax.set(xlim=(-180, 180), ylim=(0, 180))
+    ax.set_xlabel('$\phi$ (rlnAngleRot, deg)')
+    ax.set_xticks(range(-180, 181, 45))
+    ax.set_ylabel('$\\theta$ (rlnAngleTilt, deg)')
+    ax.set_yticks(range(0, 181, 45))
+    ax.set_title(title)
+    fig.gca().set_aspect('equal', adjustable='box')
+    divider = make_axes_locatable(ax)
+    cax = divider.append_axes('right', size='5%', pad=0.1)
+    cb = fig.colorbar(hb, ax=ax, cax=cax)
+    cb.set_label('Number of particles')
+    fig.tight_layout()
+    return fig
+
+# Command-line tool made from the buidling blocks
+
+@click.command(context_settings = dict(help_option_names = ['-h', '--help']))
+@click.argument('starfile', metavar = '<run_data.star>')
+@click.option('-t', '--title', 'title', default = '', type = str, help = 'Title of the histogram (default: no title).')
+@click.option('-c', '--colormap', 'colormap', default = 'viridis', type = str, help = 'A color map supported by matplotlib (default: "viridis").')
+@click.option('-g', '--gridsize', 'gridsize', default = 50, type = int, help = 'Number of hexagonal bins along the x axis (default: 50).')
+@click.option('-o', '--output', 'output_file', default = '', type = str, help = 'File name to save the histogram (optional: with no file name, simply display the histogram on screen without saving it; recommended file formats: .png, .pdf, .svg or any format supported by matplotlib).')
+def cli(starfile, title, colormap, gridsize, output_file):
+    """Plots a 2D histogram of Euler angles distribution from a run_data.star file produced by RELION."""
+    angles = load_angles(starfile)
+    histogram = build_histogram(angles, title, colormap, gridsize)
+    if output_file:
+        histogram.figsize = (11.80, 8.85)
+        histogram.dpi = 300
+        plt.savefig(output_file)
+    else:
+        plt.show()
+
+if __name__ == '__main__':
+    cli()

setup.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from setuptools import setup
+from os import path
+
+# Get the long description from the README file
+here = path.abspath(path.dirname(__file__))
+with open(path.join(here, 'README.md'), encoding = 'utf-8') as f:
+    readme = f.read()
+
+setup(
+    name = 'angdist',
+    version = '1.0',
+
+    description = 'Plot the 2D histogram of Euler angles covered by a set of cryo-EM particles.',
+    long_description = readme,
+    long_description_content_type = 'text/markdown',
+    url = 'https://github.com/Guillawme/angdist',
+
+    author = 'Guillaume Gaullier',
+    author_email = '[email protected]',
+
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Visualization',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3',
+        'Operating System :: OS Independent',
+        'Environment :: Console',
+        'Natural Language :: English'
+    ],
+    keywords = 'cryo-EM Euler angle histogram visualization',
+
+    py_modules = ["angdist"],
+
+    python_requires = '>=3.8.5',
+    install_requires = [
+        'click>=7.1.2',
+        'matplotlib>=3.3.1',
+        'starfile>=0.3.1'
+    ],
+
+    entry_points = {
+        'console_scripts': [
+            'angdist=angdist:cli'
+        ]
+    },
+
+    project_urls = {
+        'Bug Reports': 'https://github.com/Guillawme/angdist/issues',
+        'Source': 'https://github.com/Guillawme/angdist'
+    }
+)