mangadap.spectra.manga module

Implement the derived class for MaNGA row-stacked spectra.

class mangadap.spectra.manga.MaNGARSS(ifile, sres_ext=None, sres_fill=True)[source]

Bases: mangadap.config.manga.MaNGAConfig, mangadap.spectra.rowstackedspectra.RowStackedSpectra

Container class for MaNGA row-stacked spectra.

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.

Parameters

ifile (str) – The file with the MaNGA row-stacked spectra. The name is expected to follow the nominal naming convention, which is used to parse the plate, ifudesign, and whether or not the spectra are binned logarithmically in wavelength.
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.

static _parse_rectification_parameters(pixelscale, rlim, sigma, recenter, width_buffer)[source]

Parse the datacube rectification parameters.

Values that are None are set to their defaults as set by MaNGAConfig.

Returns: The default or input values of arguments, in the same order.
Return type: tuple

binned_on_sky_area(bin_indx, offset=True, **kwargs)[source]

Compute the on-sky area of a set of binned spectra.

This is a simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.binned_on_sky_area() and mean_sky_coordinates().

The arguments are passed directly to mean_sky_coordinates(), and the results are then passed to the base class function. The area of the fibers “beams” are all renormalized to \(\pi {\rm arcsec}^2\) by the DRP.

Parameters

bin_indx (array-like) – An array with size \(N_{\rm spec}\) that gives which spaxels were included in each bin. Valid bins have indices of \(\geq 0\).
offset (bool, optional) – Offset the coordinates in xpos and ypos by the difference between the IFU and OBJ coordinates in the header (see pointing_offset()). The coordinates are nominally defined with respect to the IFU pointing center, such that this offsets the coordinates to be centered on the galaxy.
**kwargs – Passed directly to mean_sky_coordinates().

Returns

Two numpy.ndarray objects are returned. The first has the unique (non-negative) bin indices, and the second provides the on-sky area of that bin.

Return type

tuple

covariance_cube(channels=None, pixelscale=None, rlim=None, sigma=None, recenter=None, width_buffer=None, csr=False, quiet=False, rej_flag='3DREJECT')[source]

Construct the covariance matrices for many wavelength channels.

A simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.covariance_cube() that defaults to the nominal rectification parameters for MaNGA datacubes. See this base class function for the argument descriptions.

covariance_matrix(channel, pixelscale=None, rlim=None, sigma=None, recenter=None, width_buffer=None, csr=False, quiet=False, rej_flag='3DREJECT')[source]

Construct the covariance matrix for a given wavelength channel.

A simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.covariance_matrix() that defaults to the nominal rectification parameters for MaNGA datacubes. See this base class function for the argument descriptions.

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.MaNGARSS 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

plate (int) – Plate number
ifudesign (int) – IFU design
log (bool, optional) – Use the spectra that are logarithmically binned in wavelength.
drpver (str, optional) – DRP version, which is used to define the default DRP redux path. Default is defined by mangadap.config.manga.drp_version()
redux_path (str, optional) – The path to the top level directory containing the DRP output files for a given DRP version. Default is defined by mangadap.config.manga.drp_redux_path().
chart_path (str, optional) – The path to the directory containing the finding chart images for this plate. Default is defined by mangadap.config.manga.drp_finding_chart_path().
directory_path (str, optional) – The exact path to the DRP file. Default is defined by mangadap.config.manga.drp_directory_path(). Providing this ignores anything provided for drpver or redux_path.
**kwargs – Keyword arguments passed directly to the primary instantiation method; see mangadap.spectra.manga.MaNGARSS.

instrumental_dispersion_plane(channel, dispersion_factor=None, pixelscale=None, rlim=None, sigma=None, recenter=None, width_buffer=None, quiet=False, rej_flag='3DREJECT')[source]

Construct the instrumental dispersion for a given wavelength channel.

A simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.instrumental_dispersion_plane() that defaults to the nominal rectification parameters for MaNGA datacubes. See this base class function for the argument descriptions.

mean_sky_coordinates(offset=True, **kwargs)[source]

Compute the weighted or unweighted mean sky coordinates for each spectrum.

This is a simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.mean_sky_coordinates(); see that method for additional keyword arguments.

Warning

Flux-weighting the coordinates can produce spurious results in low-flux regimes.

Parameters

offset (bool, optional) – Offset the coordinates in xpos and ypos by the difference between the IFU and OBJ coordinates in the header (see pointing_offset()). The coordinates are nominally defined with respect to the IFU pointing center, such that this offsets the coordinates to be centered on the galaxy.
**kwargs – Passed directly to mangadap.spectra.rowstackedspectra.RowStackedSpectra.mean_sky_coordinates();

Returns

Two numpy.ndarray objects with the fiducial x and y on-sky positions of each spectrum in arcseconds relative to a given center. The shape of the two arrays is \((N_{\rm spec},)\).

Return type

tuple

pointing_offset()[source]

Return the offsets in RA and DEC between the pointing coordinates (IFURA, IFUDEC) and the designated object center coordinates (OBJRA, OBJDEC), drawn from the primary header of the DRP fits file.

Returns: Sky-right arcsecond offsets in RA and DEC.
Return type: float

rectification_transfer_matrix(channel, pixelscale=None, rlim=None, sigma=None, recenter=None, width_buffer=None, quiet=False, rej_flag='3DREJECT')[source]

Construct the rectification transfer matrix.

A simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.rectification_transfer_matrix() that defaults to the nominal rectification parameters for MaNGA datacubes. See this base class function for the argument descriptions.

rectify_wavelength_plane(channel, pixelscale=None, rlim=None, sigma=None, recenter=None, width_buffer=None, quiet=False, rej_flag='3DREJECT', return_ivar=False, return_covar=False)[source]

Rectify a wavelength channel into a monochromatic flux map.

A simple wrapper for mangadap.spectra.rowstackedspectra.RowStackedSpectra.rectify_wavelength_plane() that defaults to the nominal rectification parameters for MaNGA datacubes. See this base class function for the argument descriptions.