.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/04-drift_correction.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_auto_examples_04-drift_correction.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_04-drift_correction.py:


Drift correction
================

This example demonstrates how to correct for sample drift in a movie using
the :func:`massphoto.correct_drift` function.

This correction is automatically applied when using :func:`massphoto.fit` with the
`movie_correct_drift=True` argument, but here we show how to do it manually and
visualize the results.

.. GENERATED FROM PYTHON SOURCE LINES 12-16

.. code-block:: Python


    import matplotlib.pyplot as plt
    import numpy as np








.. GENERATED FROM PYTHON SOURCE LINES 17-22

Download example data
---------------------

This tutorial uses a short example movie from Zenodo. You can replace this
block with a direct file path once you have a local file.

.. GENERATED FROM PYTHON SOURCE LINES 22-40

.. code-block:: Python

    from zenodozipdownloader import ZenodoZipDownloader

    import massphoto as mp

    files = ZenodoZipDownloader(
        doi="10.5281/zenodo.15800729",
        download_dir="example_data",
    ).download(inner_pattern="005_mfp1_500x.mp")
    if not files:
        raise RuntimeError(
            "Failed to download example data. Please download it manually from https://zenodo.org/record/15800729 "
            "or set path_movie to your own movie file."
        )
    path_movie = files[0]

    print(f"Using movie: {path_movie}")






.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Using movie: /home/runner/work/massphoto/massphoto/docs/source/_examples/example_data/005_mfp1_500x.mp




.. GENERATED FROM PYTHON SOURCE LINES 41-46

Determine and correct drift
---------------------------

Load the movie and choose a template image used for alignment. A robust choice
is the mean image over time (also the default template in `correct_drift`).

.. GENERATED FROM PYTHON SOURCE LINES 46-54

.. code-block:: Python


    movie, metadata = mp.read_movie(path_movie, convert_metadata=True)
    movie = movie.astype(float)

    template = np.mean(movie, axis=0)

    movie_corrected, drift = mp.correct_drift(movie, template=template, return_drift=True)








.. GENERATED FROM PYTHON SOURCE LINES 55-60

Plot drift over time
--------------------

`drift` contains the per-frame translation (in pixels) applied to align each
frame to the template.

.. GENERATED FROM PYTHON SOURCE LINES 60-70

.. code-block:: Python

    plt.figure(figsize=(10, 5))
    plt.plot(drift[:, 0], label="Y drift")
    plt.plot(drift[:, 1], label="X drift")
    plt.xlabel("Frame")
    plt.ylabel("Drift (pixels)")
    plt.legend()
    plt.title("Sample Drift Over Time")
    plt.grid(True)
    plt.tight_layout()




.. image-sg:: /auto_examples/images/sphx_glr_04-drift_correction_001.png
   :alt: Sample Drift Over Time
   :srcset: /auto_examples/images/sphx_glr_04-drift_correction_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 71-77

Visual sanity check (before/after)
----------------------------------

Compare the difference between the first and last frame. With drift, the
difference image often shows edge-like structures; after correction, these
should be reduced.

.. GENERATED FROM PYTHON SOURCE LINES 77-92

.. code-block:: Python


    diff_before = movie[-1] - movie[0]
    diff_after = movie_corrected[-1] - movie_corrected[0]

    vmin, vmax = np.quantile(diff_before, [0.01, 0.99])
    plt.figure(figsize=(12, 6))
    plt.subplot(2, 1, 1)
    plt.imshow(diff_before, cmap="bwr", vmin=vmin, vmax=vmax)
    plt.title("Difference Before Drift Correction")
    plt.colorbar(label="Intensity difference (counts)")
    plt.subplot(2, 1, 2)
    plt.imshow(diff_after, cmap="bwr", vmin=vmin, vmax=vmax)
    plt.title("Difference After Drift Correction")
    plt.colorbar(label="Intensity difference (counts)")
    plt.tight_layout()



.. image-sg:: /auto_examples/images/sphx_glr_04-drift_correction_002.png
   :alt: Difference Before Drift Correction, Difference After Drift Correction
   :srcset: /auto_examples/images/sphx_glr_04-drift_correction_002.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 12.895 seconds)


.. _sphx_glr_download_auto_examples_04-drift_correction.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: 04-drift_correction.ipynb <04-drift_correction.ipynb>`

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

      :download:`Download Python source code: 04-drift_correction.py <04-drift_correction.py>`

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

      :download:`Download zipped: 04-drift_correction.zip <04-drift_correction.zip>`


.. only:: html

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

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