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.
Revision history¶
08 Jun 2016: Original Implementation by K. Westfall (KBW)Feb 2017: (KBW) Merged construct maps and cube functions here and removed dapmaps.py and dapcube.py.** 3 May 2017**: (KBW) Allow output maps and cube types to be single-precision (float32) floats, and changed BINID from int (defaults to 64-bit) to int32.24 Aug 2017: (KBW) Added BADGEOM DAPQUAL bit; signifies invalid photometric geometry parameters used when instantiating themangadap.par.obsinput.ObsInputPar
object.29 Aug 2017: (KBW) Add S/N metrics to the MAPS primary header30 Aug 2017: (KBW) Convert some changes from Xihan Ji.19 Mar 2018: (KBW) Mask spectral indices with incomplete band coverage as unreliable.
Copyright © 2019, SDSS-IV/MaNGA Pipeline Group
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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?
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cfg_root
= 'dap_cube_bits'¶
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class
mangadap.dapfits.
DAPFits
(plate, ifudesign, method, drpver=None, dapver=None, analysis_path=None, directory_path=None, reference_path=None, par_file=None, read=True, checksum=False)[source]¶ Bases:
object
Object used to hold properties of and read data from a DAP-produced file.
- Parameters
plate (
int
) – Plate numberifudesign (
int
) – IFU designmethod (
str
) – Method type (e.g.,'SPX-GAU-MILESTHIN'
)drpver (
str
, optional) – DRP version, which is used to define the default DAP analysis path. Default is defined bymangadap.config.defaults.drp_version()
.dapver (
str
, optional) – DAP version, which is used to define the default DAP analysis path. Default is defined bymangadap.config.defaults.dap_version()
.analysis_path (
str
, optional) – The path to the top level directory containing the DAP output files for a given DRP and DAP version. Default is defined bymangadap.config.defaults.dap_analysis_path()
.directory_path (
str
, optional) – The exact path to the DAP file. Default is defined bymangadap.config.defaults.dap_method_path()
.reference_path (
str
, optional) – The exact path of the DAP reference directory. Default is defined bymangadap.config.defaults.dap_method_path()
.par_file (
str
, optional) – SDSS parameter file used to provide input parameters for the DAP. Default is defined bymangadap.config.defaults.dap_par_file()
.read (
bool
, optional) – Read the DAP file upon instantiation of the object.checksum (
bool
, optional) – Flag for astropy.io.fits.open checksum operation.
-
plate
¶ Plate number
- Type
int
-
ifudesign
¶ IFU design
- Type
int
-
method
¶ Method type
- Type
str
-
drpver
¶ DRP version
- Type
str
-
dapver
¶ DAP version
- Type
str
-
analysis_path
¶ The path to the top level directory containing the DAP output files for a given DRP and DAP version.
- Type
str
-
directory_path
¶ The exact path to the DAP file.
- Type
str
-
reference_path
¶ The exact path of the DAP reference directory.
- Type
str
-
par_file
¶ SDSS parameter file used to provide input parameters for the DAP.
- Type
str
-
dapqual
¶ Global quality bit
- Type
mangadap.dapmaps.DAPQualityBitMask
-
bitmask
¶ Map mask bits
- Type
mangadap.dapmaps.DAPMapsBitMask
-
hdu
¶ HDUList read from the DRP file
-
par
¶ List of parameters used by the DAP.
- Type
mangadap.par.ObsInputPar
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checksum
¶ Boolean to use for checksum in astropy.io.fits.open.
- Type
bool
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channel_map
(ext, channel=None, flag=None)[source]¶ Return a 2D array with the map for the specified channel.
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guess_inclination
(q0=None)[source]¶ Return a guess inclination based on the isophotal ellipticity from the input parameter file using the equation:
\[\cos^2 i = \frac{ q^2 - q_0^2 }{ 1 - q_0^2 },\]where \(q\) is the observed oblateness (the semi-minor to semi-major axis ratio, \(q = 1-\epsilon = b/a\)) and \(q_0\) is the intrinsic oblateness.
If \(q < q_0\), the function returns a 90 degree inclination.
- Parameters
q0 (float) – (Optional) The intrinsic oblateness of the system. If not provided, the system is assumed to be infinitely thin.
- Raises
Exception – Raised if the input intrinsic oblatenss is not less than one and greater than 0.
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guess_position_angle
(flip=False)[source]¶ Return the guess position angle from the parameter file.
- Parameters
flip (bool) – (Optional) Offset the provided position angle by 180 deg.
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open_hdu
(permissions='readonly', checksum=False, quiet=True)[source]¶ Open the fits file and save it to
hdu
; ifhdu
is not None, the function returns without re-reading the data.- Parameters
permissions (
str
, optional) – Open the fits file with these read/write permissions.checksum (
bool
, optional) – Flag for astropy.io.fits.open checksum operation. This overrides the internalchecksum
attribute for the current operation only.quiet (
bool
, optional) – Suppress terminal output
- Raises
FileNotFoundError – Raised if the DAP file doesn’t exist.
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thin_disk_polar_coo
(xc=None, yc=None, rot=None, pa=None, inc=None, flip=False)[source]¶ Calculate the disk-plane coordinates for all the binned spectra using
mangadap.util.geometry.SemiMajorAxisCoo
. See the documentation their for further information regarding the calculations.If not provided, the default position angle and inclination will be taken from the input parameter file, if available. If the parameter file cannot be read, the default values for the position angle and ellipticity in
mangadap.util.geometry.SemiMajorAxisCoo
are used.- Parameters
xc,yc (float,float) – (Optional) a reference on-sky position relative to the center of the projected plane (galaxy center).
rot (float) – (Optional) Cartesian rotation of the focal-plane relative to the sky-plane (+x toward East; +y toward North).
pa (float) – (Optional) On-sky position angle of the major axis of the ellipse traced on the sky by a circle in the projected plane, defined as the angle from North through East.
inc (float) – (Optional) Inclination of the plane, angle between the disk normal and the normal of the sky plane (inc=0 is a face-on plane).
flip (bool) – (Optional) Offset the provided position angle by 180 deg; e.g., to set the position angle will be defined along the receding major axis.
- Returns
- Two numpy arrays with the projected polar
coordinates: \(R, \theta\).
- Return type
numpy.ndarray
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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'¶
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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'¶
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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.
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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.
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mangadap.dapfits.
confirm_dap_types
(cube, rdxqa, binned_spectra, stellar_continuum, emission_line_moments, emission_line_model, spectral_indices)[source]¶
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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.
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_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
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_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
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_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
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_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.
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_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.
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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.
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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.
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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.
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_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
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_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
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_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.
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_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).
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_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
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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.
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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.
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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.
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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.
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