.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_experiments/legacy_preprocessing.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_legacy_preprocessing.py>`
        to download the full example code.

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

.. _sphx_glr_auto_experiments_legacy_preprocessing.py:


Legacy Preprocessing Pipeline
=============================

This notebook demonstrates reproducing preprocessing results from the
legacy ASPIRE MATLAB workflow system for the EMPIAR 10028 ribosome
dataset.

https://www.ebi.ac.uk/empiar/EMPIAR-10028

.. GENERATED FROM PYTHON SOURCE LINES 13-28

Source data and Preprocessing
-----------------------------

Load the data and apply preprocessing steps corresponding to the MATLAB prompts:

>>> Phaseflip projections? (Y/N)? [Y] Y
>>> Enter pixel size in Angstrom (-1 to read from STAR file): [-1.000000]
>>> Number of projections to read? [105247]
>>> Crop? (Y/N)? [Y] Y
>>> Crop to size? [360]359
>>> Downsample? (Y/N)? [Y] Y
>>> Downsample to size? [360]179
>>> Normalize background of images to variance 1? (Y/N)? [Y]
>>> Prewhiten? (Y/N)? [Y]
>>> Split data into groups? (Y/N)? [Y] N

.. GENERATED FROM PYTHON SOURCE LINES 28-48

.. code-block:: Python


    from aspire.source import RelionSource

    # Inputs
    # Note the published ``shiny_2sets.star`` requires removal of a stray '9' character on line 5476.
    starfile_in = "10028/data/shiny_2sets_fixed9.star"
    # Caching, while not required, will increase speed in exchange for potentially increased memory usage.
    src = RelionSource(starfile_in).cache()

    # Define preprocessing steps.
    src = src.phase_flip().cache()
    src = src.crop_pad(359).cache()
    src = src.legacy_downsample(179).cache()
    src = src.legacy_normalize_background().cache()
    src = src.legacy_whiten().cache()
    src = src.invert_contrast().cache()

    # Save the preprocessed images.
    # `save_mode=single` will save a STAR file and single mrcs holding the image stack.
    src.save("10028_legacy_preprocessed_179px.star", save_mode="single", overwrite=True)


.. _sphx_glr_download_auto_experiments_legacy_preprocessing.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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