"""
This is a module for XPS analysis. It is modelled after the Galore package (https://github.com/SMTG-UCL/galore), but
with some modifications for easier analysis from pymatgen itself. Please cite the following original work if you use
this:

    Adam J. Jackson, Alex M. Ganose, Anna Regoutz, Russell G. Egdell, David O. Scanlon (2018). Galore: Broadening and
    weighting for simulation of photoelectron spectroscopy. Journal of Open Source Software, 3(26), 773,
    doi: 10.21105/joss.007733

You may wish to look at the optional dependency galore for more functionality such as plotting and other cross-sections.
Note that the atomic_subshell_photoionization_cross_sections.csv has been reparsed from the original compilation:

    Yeh, J. J.; Lindau, I. Atomic Subshell Photoionization Cross Sections and Asymmetry Parameters: 1 ⩽ Z ⩽ 103.
    Atomic Data and Nuclear Data Tables 1985, 32 (1), 1-155. https://doi.org/10.1016/0092-640X(85)90016-6.

This version contains all detailed information for all orbitals.
"""

from __future__ import annotations

import warnings
from collections import defaultdict
from pathlib import Path
from typing import TYPE_CHECKING

import numpy as np
import pandas as pd

from pymatgen.core import Element
from pymatgen.core.spectrum import Spectrum
from pymatgen.util.due import Doi, due

if TYPE_CHECKING:
    from typing_extensions import Self

    from pymatgen.electronic_structure.dos import CompleteDos


due.cite(
    Doi("10.21105/joss.007733"),
    description="Galore: Broadening and weighting for simulation of photoelectron spectroscopy.",
)
due.cite(
    Doi("10.1016/0092-640X(85)90016-6"),
    description="Atomic Subshell Photoionization Cross Sections and Asymmetry Parameters: 1 ⩽ Z ⩽ 103.",
)


def _load_cross_sections(fname):
    data = pd.read_csv(fname)

    dct = defaultdict(dict)
    for row in data.itertuples():
        sym = row.element
        el = Element(sym)
        if el.Z > 92:
            continue
        orb = row.orbital
        outer_shell = int(orb[0])
        orb_type = orb[1]
        n_elect = None
        for shell, orb, n_ele in el.full_electronic_structure:
            if shell == outer_shell and orb == orb_type:
                n_elect = n_ele
                break
        if n_elect is not None:
            dct[sym][orb_type] = row.weight / n_elect
    return dct


CROSS_SECTIONS = _load_cross_sections(Path(__file__).parent / "atomic_subshell_photoionization_cross_sections.csv")


class XPS(Spectrum):
    """An X-ray photoelectron spectra."""

    XLABEL = "Binding Energy (eV)"
    YLABEL = "Intensity"

    @classmethod
    def from_dos(cls, dos: CompleteDos) -> Self:
        """
        Args:
            dos: CompleteDos object with project element-orbital DOS.
            Can be obtained from Vasprun.get_complete_dos.
            sigma: Smearing for Gaussian.

        Returns:
            XPS: X-ray photoelectron spectrum.
        """
        total = np.zeros(dos.energies.shape)
        for el in dos.structure.composition:
            spd_dos = dos.get_element_spd_dos(el)
            for orb, pdos in spd_dos.items():
                weight = CROSS_SECTIONS[el.symbol].get(str(orb))
                if weight is not None:
                    total += pdos.get_densities() * weight
                else:
                    warnings.warn(f"No cross-section for {el}{orb}", stacklevel=2)
        return XPS(-dos.energies, total / np.max(total))
