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.
Copyright © 2019, SDSS-IV/MaNGA Pipeline Group
- class mangadap.dapfits.DAPCubeBitMask[source]
Bases:
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:
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:
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
) – Datacuber_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
- 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, method=None, rdxqa=None, binned_spectra=None, stellar_continuum=None, emission_line_moments=None, emission_line_model=None, spectral_indices=None, output_path=None, output_file=None, overwrite=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.
- 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, method=None, rdxqa=None, binned_spectra=None, stellar_continuum=None, emission_line_moments=None, emission_line_model=None, spectral_indices=None, redshift=None, output_path=None, output_file=None, overwrite=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.
- _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
- _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.
- mangadap.dapfits.default_paths(cube, file_type='MAPS', rdxqa_method=None, binning_method=None, stelcont_method=None, elmom_method=None, elmodel_method=None, sindex_method=None, method=None, output_path=None, output_file=None)[source]
Set the default directory and file name for the output file.
- Parameters
cube (
mangadap.datacube.datacube.DataCube
) – Datacube to analyze.file_type (
str
, optional) – The DAP output file type. Should be ‘MAPS’ or ‘LOGCUBE’.rdxqa_method (
str
, optional) – The method key for the basic assessments of the datacube.binning_method (
str
, optional) – The method key for the spatial binning.stelcont_method (
str
, optional) – The method key for the stellar-continuum fitting method. If None, not included in output file name.elmom_method (
str
, optional) – The method key for the emission-line moments method. If None, not included in the output file name.elmodel_method (
str
, optional) – The method key for the emission-line modeling method. If None, not included in the output file name.sindex_method (
str
, optional) – The method key for the spectral index measurements. If None, not included in the output file name.method (
str
, optional) – The method to use instead of the default. The default method is to simply concatenate the list of methods used by eadch module. The order of the keys is the order of operations (rdxqa, binning, stellar continuum, emission-line model, spectral indices).output_path (
str
, Path, optional) – The path for the output file. If None, the current working directory is used.output_file (
str
, optional) – The name of the output file. The full path of the output file will bedirectory_path
/output_file
. If None, the default is to combinecube.output_root
and the method (seemethod
).
- Returns
Returns a Path with the output directory and a
str
with the output file name.- Return type
tuple