<commit_before>"""
Specific intensity for a variety of atomic transitions, assuming ionization equilibrium.
"""
import os
import sys
import logging
import pickle

import numpy as np
from scipy.interpolate import splrep, splev
from scipy.ndimage import map_coordinates
import astropy.units as u
import h5py
from ChiantiPy.tools.io import elvlcRead, wgfaRead, scupsRead, splupsRead

from synthesizAR.atomic import ChIon


class ModelIon(object):
    """
    Top-level ion object to be used by emission model.
    """

    def __init__(self, chianti_ion, resolved_wavelengths, temperature_mesh, density_mesh):
        self.chianti_ion = chianti_ion
        self.resolved_wavelengths = np.sort(resolved_wavelengths)
        self.temperature_mesh = temperature_mesh
        self.density_mesh = density_mesh

    @property
    def fractional_ionization(self):
        return np.reshape(self.chianti_ion.equilibrium_fractional_ionization, self.temperature_mesh)

    @property
    def wavelength(self):
        if hasattr(self, 'emissivity_savefile'):
            with h5py.File(self.emissivity_savefile, 'r') as hf:
                dset = hf['/'.join(['{}_{}'.format(self.chianti_ion.meta['Element'],
                                                   self.chianti_ion.meta['Ion']), 'wavelength'])]
                wavelength = np.array(dset)*u.Unit(dset.attrs['units'])
        else:
            if hasattr(self, '_wavelength'):
                wavelength = self._wavelength
            else:
                wavelength = None

        return wavelength

    @property
    def emissivity(self):
        if hasattr(self, 'emissivity_savefile'):
            with h5py.File(self.emissivity_savefile, 'r') as hf:
                dset = hf['/'.join(['{}_{}'.format(self.chianti_ion.meta['Element'],
                                                   self.chianti_ion.meta['Ion']), 'emissivity'])]<commit_msg>bug fix in ioneq reshape<commit_after>"""
Specific intensity for a variety of atomic transitions, assuming ionization equilibrium.
"""
import os
import sys
import logging
import pickle

import numpy as np
from scipy.interpolate import splrep, splev
from scipy.ndimage import map_coordinates
import astropy.units as u
import h5py
from ChiantiPy.tools.io import elvlcRead, wgfaRead, scupsRead, splupsRead

from synthesizAR.atomic import ChIon


class ModelIon(object):
    """
    Top-level ion object to be used by emission model.
    """

    def __init__(self, chianti_ion, resolved_wavelengths, temperature_mesh, density_mesh):
        self.chianti_ion = chianti_ion
        self.resolved_wavelengths = np.sort(resolved_wavelengths)
        self.temperature_mesh = temperature_mesh
        self.density_mesh = density_mesh

    @property
    def fractional_ionization(self):
        return np.reshape(self.chianti_ion.equilibrium_fractional_ionization, self.temperature_mesh.shape)

    @property
    def wavelength(self):
        if hasattr(self, 'emissivity_savefile'):
            with h5py.File(self.emissivity_savefile, 'r') as hf:
                dset = hf['/'.join(['{}_{}'.format(self.chianti_ion.meta['Element'],
                                                   self.chianti_ion.meta['Ion']), 'wavelength'])]
                wavelength = np.array(dset)*u.Unit(dset.attrs['units'])
        else:
            if hasattr(self, '_wavelength'):
                wavelength = self._wavelength
            else:
                wavelength = None

        return wavelength

    @property
    def emissivity(self):
        if hasattr(self, 'emissivity_savefile'):
            with h5py.File(self.emissivity_savefile, 'r') as hf:
                dset = hf['/'.join(['{}_{}'.format(self.chianti_ion.meta['Element'],
                                                   self.chianti_ion.meta['Ion']), 'emissivity'])]
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