.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_experiments/save_simulation_relion_reconstruct.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_experiments_save_simulation_relion_reconstruct.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_experiments_save_simulation_relion_reconstruct.py:


Simulated Stack to RELION Reconstruction
========================================

This experiment shows how to:

1. build a synthetic dataset with ASPIRE,
2. write the stack via ``ImageSource.save`` so RELION can consume it, and
3. call :code:`relion_reconstruct` on the saved STAR file.

.. GENERATED FROM PYTHON SOURCE LINES 13-15

Imports
-------

.. GENERATED FROM PYTHON SOURCE LINES 15-29

.. code-block:: Python


    import logging
    from pathlib import Path

    import numpy as np

    from aspire.downloader import emdb_2660
    from aspire.noise import WhiteNoiseAdder
    from aspire.operators import RadialCTFFilter
    from aspire.source import Simulation

    logger = logging.getLogger(__name__)



.. GENERATED FROM PYTHON SOURCE LINES 30-35

Configuration
-------------
We set a few parameters to initialize the Simulation.
You can safely alter ``n_particles`` (or change the defocus values, etc.) when
trying this interactively; the defaults here are chosen for demonstrative purposes.

.. GENERATED FROM PYTHON SOURCE LINES 35-47

.. code-block:: Python


    output_dir = Path("relion_save_demo")
    output_dir.mkdir(exist_ok=True)

    n_particles = 512
    snr = 0.5
    defocus = np.linspace(
        15000, 25000, 7
    )  # defocus values for the radial CTF filters (angstroms)
    star_file = f"sim_n{n_particles}.star"
    star_path = output_dir / star_file


.. GENERATED FROM PYTHON SOURCE LINES 48-52

Volume and Filters
------------------
Start from the EMDB-2660 ribosome map and build a small set of radial CTF filters
that RELION will recover as optics groups.

.. GENERATED FROM PYTHON SOURCE LINES 52-57

.. code-block:: Python


    vol = emdb_2660()
    ctf_filters = [RadialCTFFilter(defocus=d) for d in defocus]



.. GENERATED FROM PYTHON SOURCE LINES 58-63

Simulate, Add Noise, Save
-------------------------
Initialize the Simulation:
mix the CTFs across the stack, add white noise at a target SNR,
and write the particles and metadata to a RELION-compatible STAR/MRC stack.

.. GENERATED FROM PYTHON SOURCE LINES 63-73

.. code-block:: Python


    sim = Simulation(
        n=n_particles,
        vols=vol,
        unique_filters=ctf_filters,
        noise_adder=WhiteNoiseAdder.from_snr(snr),
    )
    sim.save(star_path, overwrite=True)



.. GENERATED FROM PYTHON SOURCE LINES 74-79

Running ``relion_reconstruct``
------------------------------
``relion_reconstruct`` is an external RELION command, so we just show the call.
Run this, from the output directory, in a RELION-enabled shell after generating
the STAR file above.

.. GENERATED FROM PYTHON SOURCE LINES 79-81

.. code-block:: Python


    logger.info(f"relion_reconstruct --i {star_file} " f"--o 'relion_recon.mrc' --ctf")


.. _sphx_glr_download_auto_experiments_save_simulation_relion_reconstruct.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: save_simulation_relion_reconstruct.ipynb <save_simulation_relion_reconstruct.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: save_simulation_relion_reconstruct.py <save_simulation_relion_reconstruct.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: save_simulation_relion_reconstruct.zip <save_simulation_relion_reconstruct.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_