mangadap.dapfits module¶

Defines a class used to interface with the final maps files produced by the MaNGA Data Analysis Pipeline (DAP).

Todo

Allow DAPFits to read/access both the MAPS and the LOGCUBE files, not just the former.

class mangadap.dapfits.DAPCubeBitMask[source]¶

Bases: mangadap.util.dapbitmask.DAPBitMask

Class used to flag/interpret bits in DAP model LOGCUBE files.

The defined bits are listed at MANGA_DAPSPECMASK.

Todo

Force read IDLUTILS version as opposed to internal one?

cfg_root = 'dap_cube_bits'¶

class mangadap.dapfits.DAPMapsBitMask[source]¶

Bases: mangadap.util.dapbitmask.DAPBitMask

Class used to flag/interpret bits in DAP MAPS files.

The defined bits are listed at MANGA_DAPPIXMASK.

Todo

Force read IDLUTILS version as opposed to internal one?

cfg_root = 'dap_maps_bits'¶

class mangadap.dapfits.DAPQualityBitMask[source]¶

Bases: mangadap.util.dapbitmask.DAPBitMask

Class used to flag/interpret global quality bit.

The defined bits are listed at MANGA_DAPQUAL.

Todo

Force read IDLUTILS version as opposed to internal one?

cfg_root = 'dap_quality_bits'¶

mangadap.dapfits.add_snr_metrics_to_header(hdr, cube, r_re)[source]¶

For all valid spaxels within 1 Re < R < 1.5 Re calculate the median S/N and combined S/N (including covariance) in the griz bands.

Adds the following keywords (8) to the header:

SNR?MED: Median S/N within 1-1.5 Re in each of the griz bands.
SNR?RING: The combined S/N of all spaxels within 1-1.5 Re in the griz bands, incuding covariance

The inclusion of covariance is based on the exact calculation of the correlation matrix at the flux-weighted center of each band, and assuming no change in the correlation between the response-weighted correlation within the broad band.

Parameters

hdr (astropy.io.fits.Header) – Header object to edit
cube (mangadap.datacube.datacube.DataCube) – Datacube
r_re (numpy.ndarray) – Flattened array with the semi-major axis radius in units of the effective radius for all spaxels in the datacube. Shape should be (Nx*Ny,), where the shape of the datacube is (Nx,Ny,Nwave).

Returns

The edited header object.

Return type

astropy.io.fits.Header

Raises

FileNotFoundError – Raised if any of the response function files cannot be found.

mangadap.dapfits.combine_binid_extensions(cube, binned_spectra, stellar_continuum, emission_line_moments, emission_line_model, spectral_indices, dtype=None)[source]¶: Combine the bin IDs from the different analysis steps into a single multichannel extension.

mangadap.dapfits.confirm_dap_types(cube, rdxqa, binned_spectra, stellar_continuum, emission_line_moments, emission_line_model, spectral_indices)[source]¶

class mangadap.dapfits.construct_cube_file(cube, metadata, binned_spectra=None, stellar_continuum=None, emission_line_model=None, dapver=None, analysis_path=None, directory_path=None, output_file=None, clobber=True, loggers=None, quiet=False, single_precision=False)[source]¶

Bases: object

Construct a DAP cube file based on the input data.

Set as a class for coherency reasons, but should not be used as an object!

Should force all intermediate objects to be provided.

_get_data_mask(binned_spectra, binned_spectra_3d_hdu)[source]¶

For the binned spectra:

consolidate ANY flag except NO_STDDEV from binned_spectra into IGNORED; done use SpatiallyBinnedSpectra.do_not_fit_flags
propagate NONE_IN_STACK from binned_spectra into FLUXINVALID
propagate IVARINVALID and FORESTAR

_get_emission_line_model_mask(emission_line_model, emission_line_model_3d_hdu)[source]¶

For the emission-line models:

propagate FORESTAR
propagate ARTIFACT
consolidate DIDNOTUSE, FORESTAR, LOW_SNR, ARTIFACT, OUTSIDE_RANGE, TPL_PIXELS, TRUNCATED, PPXF_REJECT, INVALID_ERROR into FITIGNORED

_get_stellar_continuum_mask(stellar_continuum, stellar_continuum_3d_hdu)[source]¶

For the stellar continuum models:

propagate FORESTAR
propagate INVALID_ERROR into IVARINVALID
propagate ARTIFACTs
consolidate DIDNOTUSE, FORESTAR, LOW_SNR, ARTIFACT, OUTSIDE_RANGE, EML_REGION, TPL_PIXELS, TRUNCATED, PPXF_REJECT, INVALID_ERROR, NO_FIT into FITIGNORED
consolidate FIT_FAILED into FITFAILED

_include_no_model_mask(mask)[source]¶

Assign the NOMODEL bit to spectral regions outside of the fitted spectral range.

Modeled off of StellarContiuumModel.reset_continuum_mask_window.

_set_no_model(mask)[source]¶

_set_paths(directory_path, dapver, analysis_path, output_file, binned_spectra, stellar_continuum, emission_line_model)[source]¶: Set the paths relevant to the map file.

binned_data_cube(prihdr, binned_spectra, binned_spectra_3d_hdu)[source]¶

Constructs the ‘FLUX’, ‘IVAR’, ‘MASK’, ‘LSF’, ‘WAVE’, and ‘REDCORR’ model cube extensions, and begins the construction of the ‘MASK’.

Returns the primary header, a list of ImageHDUs, and the mask array.

model_cubes(prihdr, binned_spectra, stellar_continuum, stellar_continuum_3d_hdu, emission_line_model, emission_line_model_3d_hdu)[source]¶: Constructs the ‘MODEL’, ‘MODEL_MASK’, ‘EMLINE’, ‘STELLAR’, and ‘STELLAR_MASK’ model cube extensions, adds the model information to the header, and appends data to the mask.

class mangadap.dapfits.construct_maps_file(cube, metadata, rdxqa=None, binned_spectra=None, stellar_continuum=None, emission_line_moments=None, emission_line_model=None, spectral_indices=None, redshift=None, dapver=None, analysis_path=None, directory_path=None, output_file=None, clobber=True, loggers=None, quiet=False, single_precision=False)[source]¶

Bases: object

Construct a DAP MAPS file.

Set as a class to enforce a namespace. Should not be used as an object!

Should force all intermediate objects to be provided.

_build_binning_mask(binned_spectra)[source]¶: Consolidate the map mask values into NOVALUE.

_consolidate_donotuse(mask)[source]¶

_emission_line_model_mask_to_map_mask(emission_line_model, elf_mask, for_dispersion=False)[source]¶

Propagate and consolidate the emission-line moment masks to the map pixel mask.

INSUFFICIENT_DATA propagated to NOVALUE

FIT_FAILED, UNDEFINED_COVAR propagated to FITFAILED

NEAR_BOUND copied to NEARBOUND

UNDEFINED_SIGMA propagated to UNRELIABLE

_emission_line_moment_mask_to_map_mask(emission_line_moments, elm_mask)[source]¶

Propagate and consolidate the emission-line moment masks to the map pixel mask.

DIDNOTUSE, FORESTAR propagated from already existing mask (self.bin_mask)

MAIN_EMPTY, BLUE_EMPTY, RED_EMPTY, UNDEFINED_BANDS propagated to NOVALUE

MAIN_JUMP, BLUE_JUMP, RED_JUMP, JUMP_BTWN_SIDEBANDS propagated to FITFAILED

MAIN_INCOMP, BLUE_INCOMP, RED_INCOMP propagated to UNRELIABLE

NO_ABSORPTION_CORRECTION propagated to NOCORRECTION

DIVBYZERO propagated to MATHERROR

Second moments not provided so no need to include UNDEFINED_MOM2

static _get_kpc_per_arcsec(z)[source]¶

static _join_maps(a)[source]¶

_set_paths(directory_path, dapver, analysis_path, output_file, binned_spectra, stellar_continuum, emission_line_model)[source]¶: Set the paths relevant to the map file.

_spectral_index_mask_to_map_mask(spectral_indices, si_mask)[source]¶

Propagate and consolidate the spectral index masks to the map pixel mask.

DIDNOTUSE, FORESTAR propagated from already existing mask (self.bin_mask)

MAIN_EMPTY, BLUE_EMPTY, RED_EMPTY, UNDEFINED_BANDS propagated to NOVALUE

MAIN_INCOMP, BLUE_INCOMP, RED_INCOMP propagated to UNRELIABLE

NO_DISPERSION_CORRECTION propagated to NOCORRECTION

DIVBYZERO propagated to MATHERROR

Need to further assess *_INCOMP to see if these lead to bad values (BADVALUE).

_stellar_continuum_mask_to_map_mask(stellar_continuum, sc_mask, for_dispersion=False)[source]¶

sc_mask constains the reconstructed map of the masks in each stellar continuum fit (using the stellar continuum bitmask).

Propagate and consolidate the stellar-continuum masks to the map pixel mask.

DIDNOTUSE, FORESTAR propagated from already existing mask: (self.bin_mask)

LOW_SNR, NO_FIT, INSUFFICIENT_DATA propagated to NOVALUE

FIT_FAILED, NEAR_BOUND propagated to FITFAILED and NEARBOUND

NEGATIVE_WEIGHTS consolidated into UNRELIABLE; if: dispersion=True, include BAD_SIGMA in this

binned_spectra_maps(prihdr, binned_spectra)[source]¶: Constructs the ‘BIN_LWSKYCOO’, ‘BIN_LWELLCOO’, ‘BIN_AREA’, ‘BIN_FAREA’, ‘BIN_MFLUX’, ‘BIN_MFLUX_IVAR’, ‘BIN_MFLUX_MASK’, and ‘BIN_SNR’ map extensions.

emission_line_model_maps(prihdr, emission_line_model)[source]¶: Construct the ‘EMLINE_GFLUX’, ‘EMLINE_GFLUX_IVAR’, ‘EMLINE_GFLUX_MASK’, ‘EMLINE_GEW’, ‘EMLINE_GEW_CNT’, ‘EMLINE_GEW_IVAR’, ‘EMLINE_GEW_MASK’, ‘EMLINE_GVEL’, ‘EMLINE_GVEL_IVAR’, ‘EMLINE_GVEL_MASK’, ‘EMLINE_GSIGMA’, ‘EMLINE_GSIGMA_IVAR’, ‘EMLINE_GSIGMA_MASK’, ‘EMLINE_INSTSIGMA’, ‘EMLINE_TPLSIGMA’, ‘EMLINE_GA’, ‘EMLINE_GANR’, ‘EMLINE_FOM’, ‘EMLINE_LFOM’ map extensions.

emission_line_moment_maps(prihdr, emission_line_moments)[source]¶: Construct the ‘EMLINE_SFLUX’, ‘EMLINE_SFLUX_IVAR’, ‘EMLINE_SFLUX_MASK’, ‘EMLINE_SEW’, ‘EMLINE_SEW_IVAR’, and ‘EMLINE_SEW_MASK’ maps extensions.

reduction_assessment_maps(prihdr, rdxqa)[source]¶: Constructs the ‘SPX_SKYCOO’, ‘SPX_ELLCOO’, ‘SPX_MFLUX’, ‘SPX_MFLUX_IVAR’, and ‘SPX_SNR’ map extensions.

Todo

Add the spaxel correlation data.

spectral_index_maps(prihdr, spectral_indices)[source]¶: Construct the ‘SPECINDEX’, ‘SPECINDEX_IVAR’, ‘SPECINDEX_MASK’, and ‘SPECINDEX_CORR’.

stellar_continuum_maps(prihdr, stellar_continuum)[source]¶: Construct the ‘STELLAR_VEL’, ‘STELLAR_VEL_IVAR’, ‘STELLAR_VEL_MASK’, ‘STELLAR_SIGMA’, ‘STELLAR_SIGMA_IVAR’, ‘STELLAR_SIGMA_MASK’, ‘STELLAR_SIGMACORR’, ‘STELLAR_FOM’ maps extensions.

mangadap.dapfits.finalize_dap_primary_header(prihdr, cube, metadata, binned_spectra, stellar_continuum, loggers=None, quiet=False)[source]¶