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

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

.. _sphx_glr_auto_examples_ms_figures_plotting.py:

Plotting for manuscript figures
----------------------------------

This script needs to be executed after `ms_figures_simulations.py`.

.. GENERATED FROM PYTHON SOURCE LINES 6-12

.. code-block:: Python


    import os
    from mesocircuit import mesocircuit_framework as mesoframe
    from mesocircuit.plotting import ms_figures as figures



.. GENERATED FROM PYTHON SOURCE LINES 13-15

Load MesocircuitExperiments and pass the respective circuits to the functions
for generating figures.

.. GENERATED FROM PYTHON SOURCE LINES 15-20

.. code-block:: Python


    output_dir = 'ms_figures'
    if not os.path.isdir(output_dir):
        os.makedirs(output_dir)


.. GENERATED FROM PYTHON SOURCE LINES 21-22

Parameters.

.. GENERATED FROM PYTHON SOURCE LINES 22-32

.. code-block:: Python


    if 0:
        meso_exp_reference = mesoframe.MesocircuitExperiment(
            'reference', load=True)
        meso_exp_upscaled = mesoframe.MesocircuitExperiment(
            'upscaled_1mm2', load=True)
        figures.parameters(
            output_dir,
            meso_exp_reference.circuits[0], meso_exp_upscaled.circuits[0])


.. GENERATED FROM PYTHON SOURCE LINES 33-34

Reference vs. upscaled (1mm2 sampled): spike raster and statistics overview.

.. GENERATED FROM PYTHON SOURCE LINES 34-45

.. code-block:: Python


    if 0:
        meso_exp_reference = mesoframe.MesocircuitExperiment(
            'reference', load=True)
        meso_exp_upscaled_1mm2 = mesoframe.MesocircuitExperiment(
            'upscaled_1mm2', load=True)
        figures.reference_vs_upscaled(
            output_dir,
            meso_exp_reference.circuits[0], meso_exp_upscaled_1mm2.circuits[0],
            plot_rasters=True, plot_statistics=True)


.. GENERATED FROM PYTHON SOURCE LINES 46-47

Upscaled (1mm2 sampled): correlation.

.. GENERATED FROM PYTHON SOURCE LINES 47-55

.. code-block:: Python

    if 1:
        meso_exp_upscaled_1mm2 = mesoframe.MesocircuitExperiment(
            'upscaled_1mm2', load=True)
        figures.correlation(
            output_dir,
            meso_exp_upscaled_1mm2.circuits[0])



.. GENERATED FROM PYTHON SOURCE LINES 56-57

Evoked activity.

.. GENERATED FROM PYTHON SOURCE LINES 57-62

.. code-block:: Python


    if 0:
        meso_exp_evoked = mesoframe.MesocircuitExperiment(
            'evoked', load=True)
        figures.evoked_activity(output_dir, meso_exp_evoked.circuits[0])


.. _sphx_glr_download_auto_examples_ms_figures_plotting.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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