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

.. only:: html

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

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

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

.. _sphx_glr_followup_examples_PyFstat_example_semi_coherent_directed_follow_up.py:


Follow up example
=================

Multi-stage MCMC follow up of a CW signal produced by an isolated
source using a ladder of coherent times.

.. GENERATED FROM PYTHON SOURCE LINES 8-112

.. code-block:: Python
   :lineno-start: 9


    import os

    import matplotlib.pyplot as plt
    import numpy as np

    import pyfstat

    label = "PyFstatExampleSemiCoherentDirectedFollowup"
    outdir = os.path.join("PyFstat_example_data", label)
    logger = pyfstat.set_up_logger(label=label, outdir=outdir)

    # Properties of the GW data
    data_parameters = {
        "sqrtSX": 1e-23,
        "tstart": 1000000000,
        "duration": 100 * 86400,
        "detectors": "H1",
    }
    tend = data_parameters["tstart"] + data_parameters["duration"]
    mid_time = 0.5 * (data_parameters["tstart"] + tend)

    # Properties of the signal
    depth = 40
    signal_parameters = {
        "F0": 30.0,
        "F1": -1e-10,
        "F2": 0,
        "Alpha": np.radians(83.6292),
        "Delta": np.radians(22.0144),
        "tref": mid_time,
        "h0": data_parameters["sqrtSX"] / depth,
        "cosi": 1.0,
    }

    data = pyfstat.Writer(
        label=label, outdir=outdir, **data_parameters, **signal_parameters
    )
    data.make_data()

    # The predicted twoF (expectation over noise realizations) can be accessed by
    twoF = data.predict_fstat()
    logger.info("Predicted twoF value: {}\n".format(twoF))

    # Search
    VF0 = VF1 = 1e5
    DeltaF0 = np.sqrt(VF0) * np.sqrt(3) / (np.pi * data_parameters["duration"])
    DeltaF1 = np.sqrt(VF1) * np.sqrt(180) / (np.pi * data_parameters["duration"] ** 2)
    theta_prior = {
        "F0": {
            "type": "unif",
            "lower": signal_parameters["F0"] - DeltaF0 / 2.0,
            "upper": signal_parameters["F0"] + DeltaF0 / 2,
        },
        "F1": {
            "type": "unif",
            "lower": signal_parameters["F1"] - DeltaF1 / 2.0,
            "upper": signal_parameters["F1"] + DeltaF1 / 2,
        },
    }
    for key in "F2", "Alpha", "Delta":
        theta_prior[key] = signal_parameters[key]


    ntemps = 3
    log10beta_min = -0.5
    nwalkers = 100
    nsteps = [100, 100]

    mcmc = pyfstat.MCMCFollowUpSearch(
        label=label,
        outdir=outdir,
        sftfilepattern=data.sftfilepath,
        theta_prior=theta_prior,
        tref=mid_time,
        minStartTime=data_parameters["tstart"],
        maxStartTime=tend,
        nwalkers=nwalkers,
        nsteps=nsteps,
        ntemps=ntemps,
        log10beta_min=log10beta_min,
    )

    NstarMax = 1000
    Nsegs0 = 100
    walkers_fig, walkers_axes = plt.subplots(nrows=2, figsize=(3.4, 3.5))
    mcmc.run(
        NstarMax=NstarMax,
        Nsegs0=Nsegs0,
        plot_walkers=True,
        walker_plot_args={
            "labelpad": 0.01,
            "plot_det_stat": False,
            "fig": walkers_fig,
            "axes": walkers_axes,
            "injection_parameters": signal_parameters,
        },
    )
    walkers_fig.savefig(os.path.join(outdir, label + "_walkers.png"))
    plt.close(walkers_fig)

    mcmc.print_summary()
    mcmc.plot_corner(add_prior=True, truths=signal_parameters)
    mcmc.plot_prior_posterior(injection_parameters=signal_parameters)


.. _sphx_glr_download_followup_examples_PyFstat_example_semi_coherent_directed_follow_up.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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