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

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

.. _sphx_glr_auto_examples_plot_band_amplitude.py:


Comparing two frequency bands across a cohort
=============================================

A small version of the frequency-amplitude case study on synthetic data. Ten subjects, three
regions: one carries extra slow-4 (0.027–0.073 Hz) power. The pipeline computes each run's
spectrum, ``band_amplitude`` turns it into ALFF per band, and a paired permutation test compares
slow-4 with slow-5 in every region, with family-wise error control.

.. GENERATED FROM PYTHON SOURCE LINES 10-61



.. image-sg:: /auto_examples/images/sphx_glr_plot_band_amplitude_001.png
   :alt: plot band amplitude
   :srcset: /auto_examples/images/sphx_glr_plot_band_amplitude_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    cortex_a  t =   -7.6   FWER p = 0.0020
    cortex_b  t =   -8.9   FWER p = 0.0020
    striatum  t =  +11.0   FWER p = 0.0020






|

.. code-block:: Python


    import tempfile
    from pathlib import Path

    import h5py
    import matplotlib.pyplot as plt
    import numpy as np

    import modewise

    folder = Path(tempfile.mkdtemp())
    rng = np.random.default_rng(1)
    fs = 1.25
    t = np.arange(488) / fs
    for subject in range(1, 11):
        noise = rng.standard_normal((3, t.size)).cumsum(axis=1) * 0.05   # slow, 1/f-like background
        noise[2] += 0.7 * np.sin(2 * np.pi * 0.05 * t + rng.uniform(0, 6))  # the slow-4 region
        with h5py.File(folder / f"sub-{subject:02d}_task-rest_bold.h5", "w") as f:
            f["timeseries"] = noise

    (folder / "labels.txt").write_text("cortex_a\ncortex_b\nstriatum\n")
    dataset = modewise.Dataset.from_toml(f"""
    root = "{folder}"
    [[input]]
    name = "bold"
    pattern = "sub-{{subject}}_task-{{task}}_bold.h5"
    format = "hdf5"
    dataset = "timeseries"
    sampling_rate_hz = {fs}
    labels_file = "labels.txt"
    """)

    pipeline = modewise.Pipeline.from_dict({
        "pipeline": {"name": "amplitude", "inputs": ["bold"]},
        "step": [{"id": "psd", "op": "spectrum", "input": "bold"}],
    })
    batch = pipeline.run_dataset(dataset, folder / "results", progress=False)
    table = batch.results.feature_table("amplitude", "psd", "band_amplitude",
                                        bands={"slow4": (0.027, 0.073), "slow5": (0.01, 0.027)})
    report = modewise.test_paired(table, ("slow4", "slow5"), n_permutations=5000, seed=0)
    for name, t_value, p in zip(report.feature_names, report.t, report.p_fwer):
        print(f"{name:9s} t = {t_value:+6.1f}   FWER p = {p:.4f}")

    slow4 = table.values[[c == "slow4" for c in table.conditions]]
    slow5 = table.values[[c == "slow5" for c in table.conditions]]
    ratio = np.log(slow4 / slow5)
    fig, ax = plt.subplots(figsize=(6, 3.5))
    ax.boxplot(ratio, tick_labels=table.feature_names)
    ax.axhline(0, color="grey", lw=0.8)
    ax.set_ylabel("log(slow-4 / slow-5 ALFF)")
    fig.tight_layout()


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

   **Total running time of the script:** (0 minutes 0.072 seconds)


.. _sphx_glr_download_auto_examples_plot_band_amplitude.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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