mangadap.datacube.manga module

Implement the derived class for MaNGA datacubes.

Todo

  • Further optimize calculation of transfer matrix/

  • Make DRP file class flexible to linear or log-linear wavelength sampling? Incorporate into MODE?

  • Reconstructed broad-band images and PSFs are not restructured in the CUBE files!

  • Image reconstruction has transpose sense wrt DRP output!

  • Add logging

  • Need to be clear about which functions use the RSS spectra to create CUBE related data, like the covariance matrix and instrumental dispersion calculations.

  • Computing the approximate covariance cube is currently not possible with only the CUBE on disk. There’s a logic problem that needs to be fixed.

License

Copyright © 2019, SDSS-IV/MaNGA Pipeline Group

class mangadap.datacube.manga.MaNGADataCube(ifile, z=None, vdisp=None, ell=None, pa=None, reff=None, sres_ext=None, sres_fill=True, covar_ext=None)[source]

Bases: MaNGAConfig, DataCube

Container class for a MaNGA datacube.

For additional description and attributes, see the two base classes.

See from_plateifu() to instantiate using the plate and ifu numbers. See from_config() to instantiate from a configuration file.

Note that z, vdisp, ell, pa, and reff are saved to the meta dictionary.

Parameters:

  • ifile (str, Path) – The file with the MaNGA datacube. The name is expected to follow the nominal naming convention, which is used to parse the plate, ifudesign, and whether or not the datacube has been binned logarithmically in wavelength.

  • z (float, optional) – Estimated bulk redshift. If None, some of the DAP analysis modules will fault.

  • vdisp (float, optional) – Estimated velocity dispersion. If None, some of the DAP analysis modules will assume an initial guess of 100 km/s.

  • ell (float, optional) – Characteristic isophotal ellipticity (1-b/a). If None, some of the DAP modules will issue a warning and continue by assuming ell=0.

  • pa (float, optional) – Characteristic isophotal position angle (through E from N). If None, some of the DAP modules will issue a warning and continue by assuming pa=0.

  • reff (float, optional) – Effective (half-light) radius in arcsec. If None, some of the DAP modules will issue a warning and continue by assuming reff=1.

  • sres_ext (str, optional) – The extension to use when constructing the spectral resolution vectors. See spectral_resolution().

  • sres_fill (bool, optional) – Fill masked values by interpolation. Default is to leave masked pixels in returned array.

  • covar_ext (str, optional) – Extension to use as the single spatial correlation matrix for all wavelength channels, read from the DRP file. For generating the covariance matrix directly for an arbitrary wavelength channel using the RSS file, see mangadap.datacube.datacube.DataCube.covariance_matrix().

approximate_correlation_matrix(sigma_rho=1.92, rlim=None, rho_tol=None, redo=False)[source]

Construct an approximate correlation matrix for the datacube.

This is a simple wrapper for mangadap.datacube.datacube.DataCube.approximate_correlation_matrix() that defaults to the expected values for a MaNGA datacube. See that method for a description of the arguments. The default sigma_rho is from Westfall et al. (2019, AJ, 158, 231). The default rlim is provided by mangadap.config.manga.MaNGAConfig.regrid_rlim().

approximate_covariance_cube(channels=None, sigma_rho=1.92, rlim=None, rho_tol=None, csr=False, quiet=False)[source]

Construct approximate covariance matrices for multiple channels.

This is a simple wrapper for mangadap.datacube.datacube.DataCube.approximate_covariance_cube() that defaults to the expected values for a MaNGA datacube. See that method for a description of the arguments. The default sigma_rho is from Westfall et al. (2019, AJ, 158, 231). The default rlim is provided by mangadap.config.manga.MaNGAConfig.regrid_rlim().

approximate_covariance_matrix(channel, sigma_rho=1.92, rlim=None, rho_tol=None, csr=False, quiet=False)[source]

Construct an approximate covariance matrix.

This is a simple wrapper for mangadap.datacube.datacube.DataCube.approximate_covariance_matrix() that defaults to the expected values for a MaNGA datacube. See that method for a description of the arguments. The default sigma_rho is from Westfall et al. (2019, AJ, 158, 231). The default rlim is provided by regrid_rlim().

classmethod from_config(cfgfile)[source]

Construct a mangadap.datacube.manga.MaNGADataCube or mangadap.spectra.manga.MaNGARSS object from a configuration file.

Using the data read from the configuration file, the method instantiates the class using mangadap.spectra.manga.MaNGARSS.from_plateifu() or mangadap.datacube.manga.MaNGADataCube.from_plateifu(). This method will therefore fault for this base class!

The format of the configuration file is:

Todo

Fill this in.

Parameters:

  • cfgfile (str) – Configuration file

  • drpver (str, optional) – DRP version, which is used to define the default DRP redux path. Overrides any value in the configuration file.

  • redux_path (str, optional) – The path to the top level directory containing the DRP output files for a given DRP version. Overrides any value in the configuration file.

  • directory_path (str, optional) – The exact path to the DRP file. Providing this ignores anything provided for drpver or redux_path. Overrides any value in the configuration file.

classmethod from_plateifu(plate, ifudesign, log=True, drpver=None, redux_path=None, chart_path=None, directory_path=None, **kwargs)[source]

Construct a mangadap.datacube.manga.MaNGADataCube object based on its plate-ifu designation.

This is a simple wrapper function that calls default_paths() to construct the file names, and then calls the class instantiation method.

Parameters:
load_rss(force=False)[source]

Try to load the source row-stacked spectra for this datacube.

If rss is not None, this method does not attempt to reload it, unless force is True.

The method first looks for the relevant file in the same directory with the datacube. If the file is not there, it uses the DRP version in the header of the datacube file and the paths defined by the keyword arguments to construct the nominal path to the RSS file. If the file is also not there, the method faults.

Nothing is returned. If successful, the method initializes the row-stacked spectra object (mangadap.spectra.manga.MaNGARSS) to rss.

Parameters:

force (bool, optional) – Reload the row-stacked spectra if rss is not None.

mean_sky_coordinates(center_coo=None, offset='OBJ')[source]

Calculate the sky coordinates for each spaxel.

This is a simple wrapper for mangadap.datacube.datacube.DataCube.mean_sky_coordinates() that passes the relevant set of center coordinates; see that function for the default behavior. Any provided coordinates (see center_coo) take precedence.

Parameters:

  • center_coo (tuple, optional) – A two-tuple with the coordinates in right-ascension and declination for the coordinate-frame origin. If None, no offset is performed.

  • offset (str, optional) – The offset coordinates to use from the primary header. Must be either ‘obj’ or ‘ifu’. If None, no header coordinates are used.

Returns:

Two numpy.ndarray objects with the RA and declination of each pixel in degrees, or its offset from the center in arcseconds. In both cases the shape of the returned arrays matches the spatial shape of the datacube.

Return type:

tuple