specex.specex module

SPECEX - SPECtra EXtractor.

Extract spectra from spectral data cubes.

specex.cubex.get_spplate_fits(cube_header, spec_header, obj_ids, spec_data, var_data=None, and_mask_data=None, or_mask_data=None, wdisp_data=None, sky_data=None)[source]

Generate a plate fits file similar to the ones used in SDSS.

Parameters

cube_headerTYPE: DESCRIPTION.
spec_headerTYPE: DESCRIPTION.
obj_idsTYPE: DESCRIPTION.
spec_dataTYPE: DESCRIPTION.
var_dataTYPE, optional: DESCRIPTION. The default is None.
and_mask_dataTYPE, optional: DESCRIPTION. The default is None.
or_mask_dataTYPE, optional: DESCRIPTION. The default is None.
wdisp_dataTYPE, optional: DESCRIPTION. The default is None.
sky_dataTYPE, optional: DESCRIPTION. The default is None.

Returns

hdulTYPE: DESCRIPTION.

specex.cubex.get_spsingle_fits(main_header, spec_wcs_header, obj_spectrum, spec_hdu_header, obj_spectrum_var=None, no_nans=False)[source]

Generate a fits containing the spectral data.

Parameters

main_headerdict: Dictionary containing the base information of the spectrum extraction. The keys of the dictionaries are the names of the fits CARDS that will be written, while the values can be either strings or tuples in the form of (cadr value, card comment).
spec_wcs_headerastropy.io.fits.Header object: Header containing the WCS information of the spectrum.
obj_spectrumnumpy.ndarray: The actual spectral data.
spec_hdu_headerastropy.io.fits.Header object: Header of the HDU of the original cube containing the spectral data.
obj_spectrum_varnumpy.ndarray (default=None): The variance of the spectral data.
no_nansbool, optional: If true, nan values in the spectrum are replaced by a linear interpolation. In this case an additional extension is added to the fits file, containing a mask for identifying the previously bax pixels.

Returns

hdulastropy.io.fits.HDUList object: The fits HDUL containing the extracted spectra.

specex.cubex.load_specex_file(filename, spec_hdu_index=None, var_hdu_index=None, wd_hdu_index=None, mask_hdu_index=None, smoothing=0)[source]

Load a spectrum file generated by specex (or any compatible file).

Parameters

filenamestr: The path of the fits file containing the spectrum.
spec_hdu_indexint or str, optional: The index or name of the HDU containing the flux. The default is None.
var_hdu_indexint or str, optional: The index or name of the HDU containing the variance. The default is None.
wd_hdu_indexint or str, optional: The index or name of the HDU containing the resolution curve. The default is None.
mask_hdu_indexint or str, optional: The index or name of the HDU containing the flux nan mask. The default is None.
smoothingint, optional: If greather than zero, the the spectrum is smoothed with a window of this size. The default is 0.

Raises

ValueError: When flux and variance have different shape.

Returns

dict

A dict containing the following keys:

‘id’: the ID of the spectrum,
‘main_header’: the FITS header of the primary HDU,
‘wavelength’: the wavelengths of the dispersion grid,
‘flux’: the fluxes,
‘variance’: the variance of the fluxes,
‘r_curve’: the resolution curve,
‘nan_mask’: a mask indicating invalid fluxes,
‘flux_units’: the units of the fluxes,
‘wavelength_units’: the units of the wavelengths

specex.cubex.specex(options=None)[source]: Run the main program.

Returns

None.

specex.cubex.speclist2ez(spec_files, spec_hdu_name='SPECTRUM', var_hdu_name='VARIANCE')[source]

Generate a list of spectra that can be imported into pandora EZ.

Parameters

spec_fileslist of str: List of file paths.
spec_hdu_namestr, optional: The name of the HDU containing the spectral data. The default is ‘SPECTRUM’.
var_hdu_namestr, optional: The name of the HDU containing the variance data. The default is ‘VARIANCE’.

Returns

txt_dataTYPE: DESCRIPTION.