Plotting Separate X-ray Absorption Spectroscopy Measurements
============================================================

This example demonstrates how to process and visualize multiple X-ray absorption
spectroscopy (XAS) scans from different ranges, including normalization and plotting for
comparison.

.. literalinclude:: ../../examples/xas_separate_measurements.py
    :language: python

Detailed Explanations
---------------------

First, we import the necessary modules and we set up logging.

.. code-block:: python

    import logging
    import sys

    import matplotlib.pyplot as plt

    from daxs.measurements import Xas
    from daxs.sources import Hdf5Source
    from daxs.utils import resources

    # Create a logger to track the processing steps.
    logging.basicConfig(level=logging.INFO, stream=sys.stdout)
    # The default level for the *daxs* logger is set to INFO.
    # Increase to DEBUG to get more detailed output.
    logging.getLogger("daxs").setLevel(logging.INFO)

Next, we define the data mappings that specify which datasets in the HDF5 file
correspond to the x-axis (incident energy), signal, and monitor for normalization.

.. code-block:: python

    data_mappings = {
        "x": ".1/measurement/hdh_energy",
        "signal": [".1/measurement/det_dtc_apd"],
        "monitor": ".1/measurement/I02",
    }

We then load the HDF5 file and process measurements for two scan ranges (`"1-4"` and
`"5-6"`). For each range, we create a data source and a measurement object, set a common
x-axis across scans, normalize by area, and collect the measurements.

.. code-block:: python

    hdf5_filename = resources.getfile("CuCO3_Ka_XANES.h5")
    measurements = []
    for selection in ("1-4", "5-6"):
        source = Hdf5Source(hdf5_filename, selection, data_mappings=data_mappings)
        measurement = Xas(source)
        measurement.x = measurement.scans.get_common_axis("x", "intersection")
        measurement.normalize(mode="area")
        measurements.append(measurement)

Finally, we create a plot to visualize the normalized spectra from both scan ranges on
the same axis for comparison.

.. code-block:: python

    fig, ax = plt.subplots(figsize=(6, 3.7))
    for i, measurement in enumerate(measurements):
        ax.plot(measurement.x, measurement.signal)
    ax.set_title("X-ray Absorption Spectroscopy Measurements from Separate Scan Ranges")
    ax.set_xlabel("Energy (keV)")
    ax.set_ylabel("Intensity (a.u.)")
    ax.set_xlim(8.97, 9.05)
    plt.tight_layout()
    plt.show()

The resulting plot shows the processed XAS data, allowing comparison between different
measurement sets.

.. image:: ../_static/images/xas_separate_measurements.png
    :alt: X-ray Absorption Spectroscopy measurements from separate scan ranges
    :align: center
    :width: 80%