How to use specutils - 10 common examples

date_obs = datetime.now()
        comments = data.meta.get('comments', [])

        for comment in comments:
            if 'date-obs' in comment.lower():
                date_obs = comment.split(':')[1].strip()
            if 'facility' in comment.lower():
                facility_name = comment.split(':')[1].strip()

        facility = get_service_class(facility_name)() if facility_name else None
        wavelength_units = facility.get_wavelength_units() if facility else self.DEFAULT_WAVELENGTH_UNITS
        flux_constant = facility.get_flux_constant() if facility else self.DEFAULT_FLUX_CONSTANT

        spectral_axis = np.array(data['wavelength']) * wavelength_units
        flux = np.array(data['flux']) * flux_constant
        spectrum = Spectrum1D(flux=flux, spectral_axis=spectral_axis)

        return spectrum, Time(date_obs).to_datetime()

header = hdulist[0].header
    meta = {'header': header}
    wcs = WCS(hdulist[1].header)

    data = hdulist[1].data  # spectrum in the first extension
    unit = def_unit('arbitrary units')

    uncertainty = StdDevUncertainty(hdulist[2].data)

    # dispersion from the WCS but convert out of logspace
    dispersion = 10**wcs.all_pix2world(np.arange(data.shape[0]), 0)[0]
    dispersion_unit = Unit('Angstrom')
    hdulist.close()

    return Spectrum1D(data=data * unit,
                      uncertainty=uncertainty,
                      spectral_axis=dispersion * dispersion_unit,
                      meta=meta,
                      wcs=wcs)

Raises
    --------
    NotImplementedError
        If the format can't be read currently
    """
    if dispersion_unit:
        dispersion_unit = u.Unit(dispersion_unit)

    data = fits.getdata(filename)
    header = fits.getheader(filename)

    wcs_info = FITSWCSSpectrum(header)

    if wcs_info.naxis == 1:
        wcs = read_fits_wcs_linear1d(wcs_info, dispersion_unit=dispersion_unit)
        return Spectrum1D(data, wcs=wcs, unit=flux_unit)
    elif wcs_info.naxis == 2 and \
            wcs_info.affine_transform_dict['ctype'] == ["MULTISPE", "MULTISPE"]:
        multi_wcs = multispec_wcs_reader(wcs_info, dispersion_unit=dispersion_unit)
        multispec = []
        for spectrum_data, spectrum_wcs in zip(data, multi_wcs.values()):
            multispec.append(
                Spectrum1D(spectrum_data, wcs=spectrum_wcs, unit=flux_unit))
        return multispec

    elif wcs_info.naxis == 3 and \
            wcs_info.affine_transform_dict['ctype'] == ["LINEAR","LINEAR","LINEAR"]:
        wcs = read_fits_wcs_linear1d(wcs_info, dispersion_unit=dispersion_unit)
        equispec = []
        for i in range(data.shape[0]):
            equispec.append(
                Spectrum1D(data[i][0], wcs=wcs, unit=flux_unit))

header = hdu[0].header
        name = header.get('FILENAME')
        meta = {'header': header}

        unit = Unit("erg/cm**2 Angstrom s")
        disp_unit = Unit('Angstrom')
        data = hdu[1].data['FLUX'].flatten() * unit
        dispersion = hdu[1].data['wavelength'].flatten() * disp_unit
        uncertainty = StdDevUncertainty(hdu[1].data["ERROR"].flatten() * unit)

        sort_idx = dispersion.argsort()
        dispersion = dispersion[sort_idx]
        data = data[sort_idx]
        uncertainty = uncertainty[sort_idx]

    return Spectrum1D(flux=data,
                      spectral_axis=dispersion,
                      uncertainty=uncertainty,
                      meta=meta)

pos : `~astropy.units.Quantity`
            A tuple `~astropy.units.Quantity` with
            (min, max) range of roi.

        Returns
        -------
        None or `~specutils.utils.SpectralRegion`
        """
        if not isinstance(pos, u.Quantity):
            return None
        elif pos.unit == u.Unit("") or \
                pos[0] == pos[1]:
            return None
        elif pos[0] > pos[1]:
            pos = [pos[1], pos[0]] * pos.unit
        return SpectralRegion(*pos)

pos : `~astropy.units.Quantity`
            A tuple `~astropy.units.Quantity` with
            (min, max) range of roi.

        Returns
        -------
        None or `~specutils.utils.SpectralRegion`
        """
        if not isinstance(pos, u.Quantity):
            return None
        elif pos.unit == u.Unit("") or \
                pos[0] == pos[1]:
            return None
        elif pos[0] > pos[1]:
            pos = [pos[1], pos[0]] * pos.unit
        return SpectralRegion(*pos)

def wrapper(data, spectral_axis, *args, **kwargs):
                    spec = Spectrum1D(flux=u.Quantity(data),
                                      spectral_axis=spectral_axis)
                    return func(spec, *args, **kwargs).flux.value
                return wrapper

elif wcs_info.naxis == 2 and \
            wcs_info.affine_transform_dict['ctype'] == ["MULTISPE", "MULTISPE"]:
        multi_wcs = multispec_wcs_reader(wcs_info, dispersion_unit=dispersion_unit)
        multispec = []
        for spectrum_data, spectrum_wcs in zip(data, multi_wcs.values()):
            multispec.append(
                Spectrum1D(spectrum_data, wcs=spectrum_wcs, unit=flux_unit))
        return multispec

    elif wcs_info.naxis == 3 and \
            wcs_info.affine_transform_dict['ctype'] == ["LINEAR","LINEAR","LINEAR"]:
        wcs = read_fits_wcs_linear1d(wcs_info, dispersion_unit=dispersion_unit)
        equispec = []
        for i in range(data.shape[0]):
            equispec.append(
                Spectrum1D(data[i][0], wcs=wcs, unit=flux_unit))
        return equispec
        
    elif wcs_info.naxis == 3 and \
            wcs_info.affine_transform_dict['ctype'] == ["MULTISPE", "MULTISPE","LINEAR"]:
        multi_wcs = multispec_wcs_reader(wcs_info, dispersion_unit=dispersion_unit)
        multispec = []
        for j in range(data.shape[1]):
            equispec = []
            for i in range(data.shape[0]):
                equispec.append(
                    Spectrum1D(data[i][j], wcs=list(multi_wcs.values())[j], unit=flux_unit))
            multispec.append(equispec)
        return multispec

    else:
        raise NotImplementedError("Either the FITS file does not represent a 1D"

A ``region`` defined as ``SpectralRegion(0.2*u.um, 0.5*u.um)``

        And we calculate ``sub_spectrum = extract_region(spectrum, region)``, then the ``sub_spectrum``
        spectral axis will be ``[0.2, 0.3, 0.4, 0.5] * u.um``.

    If the ``region`` does not overlap with the ``spectrum`` then an empty Spectrum1D object
    will be returned.

    """
    extracted_spectrum = []
    for subregion in region._subregions:
        left_index, right_index = _to_edge_pixel(subregion, spectrum)

        # If both indices are out of bounds then return None
        if left_index is None and right_index is None:
            empty_spectrum = Spectrum1D(spectral_axis=[]*spectrum.spectral_axis.unit,
                                        flux=[]*spectrum.flux.unit)
            extracted_spectrum.append(empty_spectrum)
        else:

            # If only one index is out of bounds then set it to
            # the lower or upper extent
            if left_index is None:
                left_index = 0

            if right_index is None:
                right_index = len(spectrum.spectral_axis)

            if left_index > right_index:
                left_index, right_index = right_index, left_index

            extracted_spectrum.append(spectrum[left_index:right_index])

resampled_spectrum = resampler(spectrum, wave_array)
    resampled_template = resampler(template, wave_array)

    # Resampler leaves Nans on flux bins that aren't touched by it.
    # We replace with zeros. This has the net effect of zero-padding
    # the spectrum and/or template so they exactly match each other,
    # wavelengthwise.
    clean_spectrum_flux = np.nan_to_num(resampled_spectrum.flux.value) * resampled_spectrum.flux.unit
    clean_template_flux = np.nan_to_num(resampled_template.flux.value) * resampled_template.flux.unit

    clean_spectrum = Spectrum1D(spectral_axis=resampled_spectrum.spectral_axis,
                        flux=clean_spectrum_flux,
                        uncertainty=resampled_spectrum.uncertainty,
                        velocity_convention='optical',
                        rest_value=spectrum.rest_value)
    clean_template = Spectrum1D(spectral_axis=resampled_template.spectral_axis,
                        flux=clean_template_flux,
                        uncertainty=resampled_template.uncertainty,
                        velocity_convention='optical',
                        rest_value=template.rest_value)

    return clean_spectrum, clean_template