Data Model¶
The DAP data model consists of a number of input files and two main
output files, the DAP MAPS file and DAP Model LOGCUBE file files,
one for each unique observation (PLATEIFU
) and DAPTYPE
combination.
The MAPS
file contains the 2D maps with the DAP-derived properites,
whereas the model LOGCUBE
file contains the best-fitting model
spectra.
DAP Directory Structure¶
The root output directory is codified in the environmental variable
$MANGA_SPECTRO_ANALYSIS
. On the (internal) SAS, the root directory
is here
The results of each run of the DAP tied to the DRP version used to
produce the analyzed datacubes and version of the DAP used to do the
analysis, such that the top-level directory for the DAP output is:
$MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER
.
The top level within a given DAP version contains the following subdirectories:
[DAPTYPE]
: User-level directory containing the results from a primary analysis method orDAPTYPE
.log
: Survey-level log files for how the DAP was executedcommon
: Survey-level directory containing files common to multipleDAPTYPE
methods.
Most users will only interact with the [DAPTYPE]
directories. For
the MPL-9, these are:
SPX-MILESHC-MASTARHC/
: Analysis of each individual spaxel; spaxels must have a valid continuum fit for an emission-line model to be fitVOR10-MILESHC-MASTARHC/
: Analysis of spectra binned to \({\rm S/N}\sim 10\) using the Voronoi binning algorithm (Cappellari & Copin 2003).HYB10-MILESHC-MASTARHC/
: Stellar-continuum analysis of spectra binned to \({\rm S/N}\sim 10\) for the stellar kinematics (same asVOR10
approach); however, the emission-line measurements are performed on the individual spaxels. See a description of the HYB binning scheme.
See the advice for DAPTYPE selection appropriate for your science.
Within each [DAPTYPE]
directory, you’ll find the following:
[PLATE]
: Top-level directory for analysis of the observations on each plate.qa
: Quality assessment plots based on data from the DAPall file specifically for this[DAPTYPE]]
Within each [PLATE]
directory, you’ll find the following:
[IFUDESIGN]
: Subdirectory with the main analysis products for eachPLATEIFU
combination for the relevant[DAPTYPE]
. The DAP maps and logcube output files are here.qa
: Quality assessment plots consolidated for all the observations on this plate.
Within each [IFUDESIGN]
directory, you’ll find the following subdirectories:
qa
: Contains PNG plots for quick QA of the DAP analysis of this observation.ref
: A reference directory with intermediate files written during the analysis.
HDUCLASS¶
As with the DRP output data (internal; see here)
the DAP output files follow the HDUCLASS
header group convention;
see also here.
All headers specify HDUCLASS=SDSS
. The HDUCLASS
header block
in, e.g., the EMLINE_GFLUX
extension in the MAPS
files looks
like this:
HDUCLASS= 'SDSS ' / SDSS format class
HDUCLAS1= 'CUBE '
HDUCLAS2= 'DATA '
ERRDATA = 'EMLINE_GFLUX_IVAR' / Associated inv. variance extension
QUALDATA= 'EMLINE_GFLUX_MASK' / Associated quality extension
The ERRDATA
and QUALDATA
keywords provide the names of the
extensions with the associated uncertainty and quality flags,
respectively, for the data. In the headers of the EMLINE_GFLUX_IVAR
and EMLINE_GFLUX_MASK
extensions, the SCIDATA
keyword provides
the extension with the associated science data (EMLINE_GFLUX
in this
case).
The QUALDATA
extensions provide bit masks of each property value. It is important
that you use these :ref:`metadatamodel-maskbits` when using the data.
DAP MAPS file¶
File template:
$MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/[DAPTYPE]/[PLATE]/[IFUDESIGN]/manga-[PLATE]-[IFUDESIGN]-MAPS-[DAPTYPE].fits.gz
The MAPS
files are the primary output file from the DAP and provide
2D “maps” (i.e., images) of DAP measured properties. The shape and WCS
of these images identically match that of a single wavelength channel in
the corresponding DRP LOGCUBE
file. Most properties are provided in
groups of three fits extensions:
[property]
: the measurement value,[property]_IVAR
: the measurement uncertainty stored as the inverse variance, and[property]_MASK
: a corresponding bit mask for each spaxel.
Extensions can either be a single 2D image (HDUCLAS1= 'IMAGE'
) or
they can have a series of images that are organized along the third
dimension (HDUCLAS1= 'CUBE'
). For the latter, each image is said to
be in a specific “channel”. For example, each Gaussian-fitted
emission-line flux is provided in a single channel in the
EMLINE_GFLUX
extension. The header of extensions with multiple
channels provide the names of the quantities in each channel using
header keyword C[n]
, where [n]
is the 1-indexed number of the
channel.
It’s best to select the extension and channel based on its name, not its extension or channel number; see our Usage example. The ordering of, e.g., the emission lines in the relevant extensions has changed between different DRs/MPLs and may change again.
Note
Internally, the DAP performs all spectral fitting on the binned
spectra (termed as such even if a bin only contains a single spaxel)
after they have been corrected for Galactic extinction.
Therefore, the output emission-line fluxes have been corrected for
Galactic extinction. However, the models and binned spectra in the
output DAP model LOGCUBE
file are reverted to their reddened
values for direct comparison with the DRP LOGCUBE
file.
The MAPS
files contain the following extensions:
HDU | Name | Channels | Units | Description |
---|---|---|---|---|
0 | PRIMARY | 0 | Empty extension with primary header information. | |
Coordinate and binning extensions | ||||
1 | SPX_SKYCOO | 2 | arcsec | Sky-right offsets – +x toward +RA and +y toward +DEC – of each spaxel from the galaxy center |
2 | SPX_ELLCOO | 4 | rcsec,unitless, \(h^{-1} {\rm kpc}\), deg | Elliptical polar coordinates of each spaxel from the galaxy center; \(R\) in arcsec, \(R/R_e\), \(R\) in \(h^{-1} {\rm kpc}\), and azimuthal angle \(\theta\). In the limit of tilted thin disk, these are the in-plane disk radius and azimuth. |
3 | SPX_MFLUX | 1 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\A/spaxel}\) | g-band-weighted mean flux, not corrected for Galactic extinction or internal attenuation. |
4 | SPX_MFLUX_IVAR | 1 | Inverse variance of g-band-weighted mean flux. | |
5 | SPX_SNR | 1 | Mean g-band weighted signal-to-noise ratio per pixel. | |
6 | BINID | 5 | Numerical ID for spatial bins for the binned spectra, stellar-continuum results, emission-line moment results, emission-line model results, and spectral-index results; see DAP BINIDs and usage. | |
7 | BIN_LWSKYCOO | 2 | arcsec | Light-weighted sky-right offsets – +x toward +RA and +y toward +DEC – of each bin from the galaxy center. |
8 | BIN_LWELLCOO | 4 | arcsec,unitless,:math:h^{-1} {rm kpc},deg | Light-weighted elliptical polar coordinates of each bin from the galaxy center; \(R\) in arcsec, \(R/R_e\), \(R\) in \(h^{-1} {\rm kpc}\), and azimuthal angle \(\theta\). In the limit of tilted thin disk, these are the in-plane disk radius and azimuth. |
9 | BIN_AREA | 1 | \({\rm arcsec}^2\) | Area of each bin. |
10 | BIN_FAREA | 1 | Fractional area that the bin covers for the expected bin shape (only relevant for radial binning). | |
11 | BIN_MFLUX | 1 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | g-band-weighted mean flux for the binned spectra, not corrected for Galactic extinction or internal attenuation. |
12 | BIN_MFLUX_IVAR | 1 | Inverse variance of g-band-weighted mean flux for the binned spectra. | |
13 | BIN_MFLUX_MASK | 1 | Bit mask for the g-band-weighted mean flux per bin. | |
14 | BIN_SNR | 1 | Mean g-band-weighted signal-to-noise ratio per pixel in the binned spectra. | |
Stellar (absorption-line) kinematics | ||||
15 | STELLAR_VEL | 1 | km/s | Line-of-sight stellar velocity, relative to the input guess
redshift (given as \(cz\) by the keyword SCINPVEL in the
header of the PRIMARY extension, and most often identical to
the NSA redshift). |
16 | STELLAR_VEL_IVAR | 1 | Inverse variance of stellar velocity measurements. | |
17 | STELLAR_VEL_MASK | 1 | Data quality mask for stellar velocity measurements. | |
18 | STELLAR_SIGMA | 1 | km/s | Raw line-of-sight stellar velocity dispersion; see
MAPS Corrections for how to use the STELLAR_SIGMACORR to
obtain the astrophysical stellar velocity dispersion. |
19 | STELLAR_SIGMA_IVAR | 1 | Inverse variance of raw stellar velocity dispersion. | |
20 | STELLAR_SIGMA_MASK | 1 | Data quality mask for stellar velocity dispersion. | |
21 | STELLAR_SIGMACORR | 1 | km/s | Quadrature correction for STELLAR_SIGMA to obtain the
astrophysical velocity dispersion; see MAPS Corrections for how
to use this extension with the STELLAR_SIGMA extension to
obtain the astrophysical stellar velocity dispersion. |
22 | STELLAR_FOM | 9 | Figures-of-merit for the stellar-continuum fit in 9 channels: (1) RMS of residuals (in \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\)), (2) RMS of fractional residuals, (3) reduced \(\chi^2\), (4-6) 68th and 99th percentile and maximum value of fractional residuals, and (7-9) 68th and 99th percentile and maximum value of error-normalized residual (\(\chi\)). | |
Emission-line measurements | ||||
23 | EMLINE_SFLUX | 35 | \(10^{-17} {\rm erg/s/cm}^2{\rm /spaxel}\) | Non-parametric summed flux after subtracting the
stellar-continuum model. The emission-line fluxes account for
Galactic reddening using the E(B-V) value (copied to the DAP
primary headers, see the EBVGAL header keyword) provided by
the DRP header and assuming an O’Donnell (1994, ApJ, 422, 158)
reddening law; however, no attenuation correction is applied due
to dust internal to the galaxy. |
24 | EMLINE_SFLUX_IVAR | 35 | Inverse variance for summed flux measurements. | |
25 | EMLINE_SFLUX_MASK | 35 | Data quality mask for summed flux measurements. | |
26 | EMLINE_SEW | 35 | angstrom | Non-parametric equivalent widths measurements (based on
the non-parametric fluxes in EMLINE_SFLUX ). |
27 | EMLINE_SEW_CNT | 35 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | New in MPL-9: Continuum value used to compute the emission-line equivalent width |
28 | EMLINE_SEW_IVAR | 35 | Inverse variance for non-parametric equivalent width measurements. | |
29 | EMLINE_SEW_MASK | 35 | Data quality mask for non-parametric equivalent width measurements | |
30 | EMLINE_GFLUX | 35 | \(10^{-17} {\rm erg/s/cm}^2{\rm /spaxel}\) | Gaussian profile integrated flux from a combined
continuum+emission-line fit. The flux ratio of the [OIII],
[OI], and [NII] lines are fixed and cannot be treated as
independent measurements. The emission-line fluxes account for
Galactic reddening using the E(B-V) (copied to the DAP primary
headers, see the EBVGAL header keyword) value provided by the
DRP header and assuming an O’Donnell (1994, ApJ, 422, 158)
reddening law; however, no attenuation correction is applied due
to dust internal to the galaxy. |
31 | EMLINE_GFLUX_IVAR | 35 | Inverse variance for Gaussian flux measurements | |
32 | EMLINE_GFLUX_MASK | 35 | Data quality mask for Gaussian flux measurements | |
33 | EMLINE_GEW | 35 | angstrom | Gaussian-fitted equivalent widths measurements (based on the
parametric fluxes in EMLINE_GFLUX ). |
34 | EMLINE_GEW_CNT | 35 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | New in MPL-9: Continuum value used to compute the emission-line equivalent width |
35 | EMLINE_GEW_IVAR | 35 | Inverse variance of the above. | |
36 | EMLINE_GEW_MASK | 35 | Data quality mask of the above. | |
37 | EMLINE_GVEL | 35 | km/s | Line-of-sight emission-line velocity, relative to the input guess
redshift (given as \(cz\) by the keyword SCINPVEL in the
header of the PRIMARY extension, and most often identical to
the NSA redshift). A velocity is provided for each line,
but the velocities are identical for all lines because the
parameters are tied during the fitting process. |
38 | EMLINE_GVEL_IVAR | 35 | Inverse variance for Gaussian-fitted velocity measurements, which are the same for all lines and should not be combined as if independent measurements. | |
39 | EMLINE_GVEL_MASK | 35 | Data quality mask for Gaussian-fitted velocity measurements. | |
40 | EMLINE_GSIGMA | 35 | km/s | Gaussian profile velocity dispersion as would be measured from a
direct Gaussian fit; see MAPS Corrections for how
to use the EMLINE_INSTSIGMA extension with these data to
obtain the astrophysical gas velocity dispersion. Tied velocity
dispersions ([OII], [OIII], [OI], [NII], [NI] and H-zeta+HeI 3889)
cannot be treated as independent measurements. |
41 | EMLINE_GSIGMA_IVAR | 35 | Inverse variance for Gaussian profile velocity dispersion. | |
42 | EMLINE_GSIGMA_MASK | 35 | Data quality mask for Gaussian profile velocity dispersion. | |
43 | EMLINE_INSTSIGMA | 35 | km/s | The instrumental dispersion at the fitted center of each emission line. |
44 | EMLINE_TPLSIGMA | 35 | km/s | The dispersion of each emission line used in the template spectra; see Emission-line template resolution. |
45 | EMLINE_GA | 35 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | The amplitude of the model Gaussian fit to each emission line. |
46 | EMLINE_GANR | 35 | The amplitude of the model Gaussian fit relative to the median noise in two sidebands near the line; the sidebands are identical to those used in the equivalent width measurement. | |
47 | EMLINE_FOM | 9 | Figures-of-merit for the continuum+emission-line model fit in 9 channels: (1) RMS of residuals (in \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\)), (2) RMS of fractional residuals, (3) reduced \(\chi^2\), (4-6) 68th and 99th percentile and maximum value of fractional residuals, and (7-9) 68th and 99th percentile and maximum value of error-normalized residual (\(\chi\)). | |
48 | EMLINE_LFOM | 35 | The reduced \(\chi^2\) of the fit to each line calculated in 15-pixel windows centered on each line. | |
Spectral index measurements | ||||
49 | SPECINDEX | 46 | ang,mag | Spectral-index measurements. |
50 | SPECINDEX_IVAR | 46 | Inverse variance for spectral index maps. | |
51 | SPECINDEX_MASK | 46 | Data quality mask for spectral index maps. | |
52 | SPECINDEX_CORR | 46 | mag | Corrections to apply to account for the velocity dispersion and effectively determine the index without Doppler broadening; see MAPS Corrections. |
53 | SPECINDEX_BCEN | 46 | angstrom | New in MPL-9: Luminosity-weighted center of the blue sideband used during the absorption-line index measurment. |
54 | SPECINDEX_BCNT | 46 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | New in MPL-9: Continuum in the blue sideband used to compute linear continuum in the absorption-line index measurment. |
55 | SPECINDEX_RCEN | 46 | angstrom | New in MPL-9: Luminosity-weighted center of the red sideband used during the absorption-line index measurment. |
56 | SPECINDEX_RCNT | 46 | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | New in MPL-9: Continuum in the red sideband used to compute linear continuum in the absorption-line index measurment. |
57 | SPECINDEX_MODEL | 46 | ang,mag | New in MPL-9: Spectral-index measurements for the best-fitting model spectrum. |
The emission-line measurements for MPL-9 are:
C01 = 'OII-3727' / Data in channel 1
C02 = 'OII-3729' / Data in channel 2
C03 = 'H12-3751' / Data in channel 3
C04 = 'H11-3771' / Data in channel 4
C05 = 'Hthe-3798' / Data in channel 5
C06 = 'Heta-3836' / Data in channel 6
C07 = 'NeIII-3869' / Data in channel 7
C08 = 'HeI-3889' / Data in channel 8
C09 = 'Hzet-3890' / Data in channel 9
C10 = 'NeIII-3968' / Data in channel 10
C11 = 'Heps-3971' / Data in channel 11
C12 = 'Hdel-4102' / Data in channel 12
C13 = 'Hgam-4341' / Data in channel 13
C14 = 'HeII-4687' / Data in channel 14
C15 = 'Hb-4862 ' / Data in channel 15
C16 = 'OIII-4960' / Data in channel 16
C17 = 'OIII-5008' / Data in channel 17
C18 = 'NI-5199 ' / Data in channel 18
C19 = 'NI-5201 ' / Data in channel 19
C20 = 'HeI-5877' / Data in channel 20
C21 = 'OI-6302 ' / Data in channel 21
C22 = 'OI-6365 ' / Data in channel 22
C23 = 'NII-6549' / Data in channel 23
C24 = 'Ha-6564 ' / Data in channel 24
C25 = 'NII-6585' / Data in channel 25
C26 = 'SII-6718' / Data in channel 26
C27 = 'SII-6732' / Data in channel 27
C28 = 'HeI-7067' / Data in channel 28
C29 = 'ArIII-7137' / Data in channel 29
C30 = 'ArIII-7753' / Data in channel 30
C31 = 'Peta-9017' / Data in channel 31
C32 = 'SIII-9071' / Data in channel 32
C33 = 'Pzet-9231' / Data in channel 33
C34 = 'SIII-9533' / Data in channel 34
C35 = 'Peps-9548' / Data in channel 35
Note
- The order of the emission-line channels has changed since MPL-8!
- For the emission-line moments:
- Channels 2 (‘OII-3729’), 8 (‘HeI-3889’), 10 (‘NeIII-3968’), and 19 (‘NI-5201’) are empty because the line falls in the passband of another line: ‘OII-3729’ in ‘OIId-3728’, ‘HeI-3889’ in ‘Hzet-3890’, ‘NeIII-3968’ in ‘Heps-3971’, and ‘NI-5201’ in ‘NI-5199’. To compare these fluxes with the Gaussian-fitted values, you should sum the Gaussian-fitted fluxes first.
- OIId is contaminated by H14 and H13
- Hzet is contaminated by HeI
- Heps is contaminated by NeIII
- Red sideband of Hbeta is contaminated by HeI
- Unknown line at 4990 and may contaminate red sideband of OIII 4960 and the blue sideband of OIII 5008
- OIII 5008 contaminated by HeI 5017
The spectral-index measurements for MPL-9 are:
Because the spectral index measurements can be either angstroms,
magnitudes, or unitless, the header of the spectral-index extensions
also include the units using header keywords U[n]
. The index and
unit in each channel is:
C01 = 'CN1 ' / Data in channel 1
U01 = 'mag ' / Units of data in channel 1
C02 = 'CN2 ' / Data in channel 2
U02 = 'mag ' / Units of data in channel 2
C03 = 'Ca4227 ' / Data in channel 3
U03 = 'ang ' / Units of data in channel 3
C04 = 'G4300 ' / Data in channel 4
U04 = 'ang ' / Units of data in channel 4
C05 = 'Fe4383 ' / Data in channel 5
U05 = 'ang ' / Units of data in channel 5
C06 = 'Ca4455 ' / Data in channel 6
U06 = 'ang ' / Units of data in channel 6
C07 = 'Fe4531 ' / Data in channel 7
U07 = 'ang ' / Units of data in channel 7
C08 = 'C24668 ' / Data in channel 8
U08 = 'ang ' / Units of data in channel 8
C09 = 'Hb ' / Data in channel 9
U09 = 'ang ' / Units of data in channel 9
C10 = 'Fe5015 ' / Data in channel 10
U10 = 'ang ' / Units of data in channel 10
C11 = 'Mg1 ' / Data in channel 11
U11 = 'mag ' / Units of data in channel 11
C12 = 'Mg2 ' / Data in channel 12
U12 = 'mag ' / Units of data in channel 12
C13 = 'Mgb ' / Data in channel 13
U13 = 'ang ' / Units of data in channel 13
C14 = 'Fe5270 ' / Data in channel 14
U14 = 'ang ' / Units of data in channel 14
C15 = 'Fe5335 ' / Data in channel 15
U15 = 'ang ' / Units of data in channel 15
C16 = 'Fe5406 ' / Data in channel 16
U16 = 'ang ' / Units of data in channel 16
C17 = 'Fe5709 ' / Data in channel 17
U17 = 'ang ' / Units of data in channel 17
C18 = 'Fe5782 ' / Data in channel 18
U18 = 'ang ' / Units of data in channel 18
C19 = 'NaD ' / Data in channel 19
U19 = 'ang ' / Units of data in channel 19
C20 = 'TiO1 ' / Data in channel 20
U20 = 'mag ' / Units of data in channel 20
C21 = 'TiO2 ' / Data in channel 21
U21 = 'mag ' / Units of data in channel 21
C22 = 'HDeltaA ' / Data in channel 22
U22 = 'ang ' / Units of data in channel 22
C23 = 'HGammaA ' / Data in channel 23
U23 = 'ang ' / Units of data in channel 23
C24 = 'HDeltaF ' / Data in channel 24
U24 = 'ang ' / Units of data in channel 24
C25 = 'HGammaF ' / Data in channel 25
U25 = 'ang ' / Units of data in channel 25
C26 = 'CaHK ' / Data in channel 26
U26 = 'ang ' / Units of data in channel 26
C27 = 'CaII1 ' / Data in channel 27
U27 = 'ang ' / Units of data in channel 27
C28 = 'CaII2 ' / Data in channel 28
U28 = 'ang ' / Units of data in channel 28
C29 = 'CaII3 ' / Data in channel 29
U29 = 'ang ' / Units of data in channel 29
C30 = 'Pa17 ' / Data in channel 30
U30 = 'ang ' / Units of data in channel 30
C31 = 'Pa14 ' / Data in channel 31
U31 = 'ang ' / Units of data in channel 31
C32 = 'Pa12 ' / Data in channel 32
U32 = 'ang ' / Units of data in channel 32
C33 = 'MgICvD ' / Data in channel 33
U33 = 'ang ' / Units of data in channel 33
C34 = 'NaICvD ' / Data in channel 34
U34 = 'ang ' / Units of data in channel 34
C35 = 'MgIIR ' / Data in channel 35
U35 = 'ang ' / Units of data in channel 35
C36 = 'FeHCvD ' / Data in channel 36
U36 = 'ang ' / Units of data in channel 36
C37 = 'NaI ' / Data in channel 37
U37 = 'ang ' / Units of data in channel 37
C38 = 'bTiO ' / Data in channel 38
U38 = 'mag ' / Units of data in channel 38
C39 = 'aTiO ' / Data in channel 39
U39 = 'mag ' / Units of data in channel 39
C40 = 'CaH1 ' / Data in channel 40
U40 = 'mag ' / Units of data in channel 40
C41 = 'CaH2 ' / Data in channel 41
U41 = 'mag ' / Units of data in channel 41
C42 = 'NaISDSS ' / Data in channel 42
U42 = 'ang ' / Units of data in channel 42
C43 = 'TiO2SDSS' / Data in channel 43
U43 = 'mag ' / Units of data in channel 43
C44 = 'D4000 ' / Data in channel 44
U44 = '' / Units of data in channel 44
C45 = 'Dn4000 ' / Data in channel 45
U45 = '' / Units of data in channel 45
C46 = 'TiOCvD ' / Data in channel 46
U46 = '' / Units of data in channel 46
DAP Model LOGCUBE file¶
File template:
$MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/[DAPTYPE]/[PLATE]/[IFUDESIGN]/manga-[PLATE]-[IFUDESIGN]-LOGCUBE-[DAPTYPE].fits.gz
The LOGCUBE
files provide the binned spectra and the best-fitting
model spectrum for each spectrum that was successfully fit. These files
are useful for detailed assessments of the model parameters because they
allow you to return to the spectra and compare the model against the
data. As described by the DAP Overview paper, the
DAP fits the spectra in two stages, one to get the stellar kinematics
and the second to determine the emission-line properties. The
emission-line module (used for all binning schemes) fits both the
stellar continuum and the emission lines at the same time, where the
stellar kinematics are fixed by the first fit. The stellar-continuum
models from the first fit are provided in the STELLAR
extension; to
get the stellar continuum determined during the emission-line modeling,
you have to subtract the emission-line model (in the EMLINE
extension) from the full model (in the MODEL
extension). Our
Usage example shows how how to plot the model
LOGCUBE data.
Warning
In the HYB binning case the binned spectra provided in the
LOGCUBE
files are from the Voronoi binning step. However, the
emission-line models are fit to the individual spaxels. So:
- The stellar continuum fits from the first iteration, in the
STELLAR
extension, should be compared to the Voronoi binned spectra in the file, but- the best-fitting model spectra in the
MODEL
extension should be compared to the individual spectra from the DRPLOGCUBE
file!
Note
Internally, the DAP performs all spectral fitting on the binned
spectra (termed as such even if a bin only contains a single spaxel)
after they have been corrected for Galactic extinction.
Therefore, the output emission-line fluxes have been corrected for
Galactic extinction. However, the models and binned spectra in the
output DAP model LOGCUBE
file are reverted to their reddened
values for direct comparison with the DRP LOGCUBE
file.
The LOGCUBE
files contain the following extensions:
HDU | Name | Units | Description |
---|---|---|---|
0 | PRIMARY | Empty extension with primary header information. | |
1 | FLUX | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | Flux of the ‘’binned’’ spectra |
2 | IVAR | Inverse variance in the binned spectra | |
3 | MASK | Bitmask for the binned spectra. Note that this mask only applies to the binned spectra. | |
4 | WAVE | angstrom | Vacuum-wavelength vector |
5 | REDCORR | Reddening correction applied during the fitting procedures. | |
6 | MODEL | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | The best-fitting model spectra (sum of the fitted continuum and emission-line models) |
7 | MODEL_MASK | The mask from the combined continuum+emission-line model fit | |
8 | EMLINE | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | The model spectrum with only the emission lines |
9 | STELLAR | \(10^{-17} {\rm erg/s/cm}^2{\rm /\AA/spaxel}\) | The best-fitting model spectra fit from the stellar-continuum-only fit (used to model the stellar kinematics) |
10 | STELLAR_MASK | The mask for the best-fitting model spectra fit from the stellar-continuum-only fit (used to model the stellar kinematics) | |
11 | BINID | Numerical ID for spatial bins in 5 channels: (1) binned spectra,
(2) stellar-continuum results, (3) empty, (4) emission-line model
results, and (5) empty; i.e., channels 1, 2, and 4 are the same as
the BINID extension in the MAPS files and channels 3 and 5 are
empty. |
Note
The shape and WCS of all extensions with datacubes identically match that of the corresponding DRP
LOGCUBE
file.To calculate the dereddened flux:
dereddened_flux = FLUX * REDCORR
Special considerations¶
Importantly, please consult the DAP papers (see Citation) for for usage guidelines and limitations of the data.
DAP BINIDs and usage¶
It’s important to understand that, for all but the SPX
binning type,
not all of the data in the MAPS
and model LOGCUBE
files are
independent. Putting aside the issue of Spatial Covariance, we
repeat measurements for a given binned spectrum in all the spaxels
associated with that bin for consistency between the DAP and DRP data
formats. Therefore, if you are, e.g., fitting a model the the MAPS
data or calculating azimuthal averages, you should pull out the binned
quantities that are unique before proceeding. In addition to any
associated mask values, you should use the BINID extension (and,
indeed, its main purpose is) to extract the unique (but still
correlated) data to use in such an analysis.
The BINID extension has one channel for each of the five main processing steps: binning, stellar-continuum and -kinematics fitting, emission-line moment measurements, emission-line Gaussian modeling, and spectral indices.
- Keep in mind the following:
BINID == -1
means that the spaxel was not included in the analysis. For example, BINID values of -1 in the first BINID channel means that either the spaxel had insufficiently good/unmasked pixels or too low S/N to be included in the binning procedure. Any spaxel with BINID = -1 should also be masked as DONOTUSE in the respective property map.- A BINID may be \(> -1\) in one channel and \(= -1\) in a different channel. For example, a spaxel in the binning BINID map may be \(> -1\) but -1 in the stellar-continuum BINID. This likely means that the spaxels were successfully binned, but the bin had \({\rm S/N} < 1\) meaning it was not analyzed by the stellar-continuum fitting module.
- Currently, the only difference in BINIDs is the -1 vs. non-negative distinction described in the last point, except for the HYB binning scheme. For the HYB binning case, the emission-line moments, emission-line modeling, and spectral-index measurements are done on a spaxel-by-spaxel basis, meaning that the BINIDs are redetermined and is just a running number (not, e.g., ordered by S/N) for the spaxels that were analyzed.
See Using the BINID extension for usage examples that extracts both
the unique and unmasked data from a MAPS
file to produce the g-band
and H-alpha surface brightness profiles.
HYB binning scheme¶
In all cases except the HYB binning approach, each analysis module only works with the “binned” spectra after the binning is performed. (I’ve put “binned” in quotes here because all spectra are treated the same after the binning step, even if the “bin” only includes a single spaxel.) In the HYB case, the emission-line modeling is done by first fitting the continuum+emission-line data simultaneously, distributing those results as a starting point for fitting the spaxels within the bin, and then redoing the simultaneous fit for each spaxel. By fitting the data as a hybrid between the VOR10 and SPX binning schemes, there are a few things to keep in mind:
Because the stellar kinematics are held fixed to the binned results during the spaxel-by-spaxel continuum+emission-line fit, there will be (subtle) spatial covariance issues between spaxels associated with a single bin, beyond the Spatial Covariance from the [wiki:MANGA/Projects/Covariance_cube datacube construction] alone.
The binned spectra provided in the HYB model
LOGCUBE
files are from the Voronoi binning step; however, the emission-line models are fit to the individual spaxels. When using the modelLOGCUBE
files for this binning scheme:
- The stellar-continuum fits (in the
STELLAR
extension) should be compared to the Voronoi binned spectra in the file;- however, the best-fitting model spectra (stellar continuum + gas emission) in the
MODEL
extension should be compared to the individual spectra from the DRP LOGCUBE file!Because the emission-line modeling is done on the individual spaxels, the emission-line moments are recalculated after the emission-line modeling to ensure the stellar continuum used for both the Gaussian model and the moment calculation is identical. In the HYB case, this means the emission-line moments are also provided for the individual spaxels.
The spectral indices are measured on the individual spaxels because the emission-line model is first subtracted from the data before the index measurements.
Usage Guidlines¶
Stellar velocity dispersions¶
Measurement of stellar (and gas!) velocity dispersions in MaNGA is complicated by the spectral resolution, particularly at low S/N and low \(\sigma\). Please tread carefully! In particular, please consult Section 7.7 of the DAP Overview paper <https://ui.adsabs.harvard.edu/abs/2019AJ….158..231W/abstract>_ for a detailed discussion of best practices for the stellar velocity dispersion data.
In summary, there is no hard and fast rule along the f lines of, “Only use measurements when the S/N is above X”. (In fact, having measurements at the lower S/N level is useful for understanding the affects of the error distribution.) However, here are some rough guidelines to consider when handling the velocity dispersion data:
- Kinematics should smoothly vary between adjacent spaxels
- All velocities are statistically well behaved, except possibly at \({\rm S/N} < 5\) for \(\sigma \sim \sigma_{\rm inst}/2\)
- Be aware of the ‘’distribution’’ of \(\sigma\) at a given radius or surface brightness when assessing the data.
- Don’t trust single \(\sigma\) measurements at \({\rm S/N}<5\), only use them to understand the error distribution.
- Systematic errors in individual \(\sigma\) become appreciable at:
- \({\rm S/N} < 20\) for \(\sigma \sim \sigma_{\rm inst}/2\) (\(\sim 35\) km/s)
- \({\rm S/N} < 10\) for \(\sigma \sim \sigma_{\rm inst}\) (\(\sim 70\) km/s)
Emission-line template resolution¶
When using the new emission line module
(mangadap.proc.sasuke.Sasuke
), the emission lines are fit in a
very similar way to the stellar continuum using a set of emission-line
templates. Given the varying spectral resolution of the MaNGA data, we
setup these templates to have a non-zero “instrumental dispersion” that
is the same as the MaNGA data up to some quadrature offset. The value
of the “template instrumental dispersion” at the location of each
emission line is provided in the EMLINE_TPLSIGMA
extension of the
MAPS
files. The velocity dispersion actually measured by this
emission-line module (using pPXF) is the quadrature difference between
the template dispersion and the directly observed sigma of the
emission-line (as fit by a Gaussian).
To keep things consistent between MPLs and provide what people expect,
the EMLINE_GSIGMA
data provide the sigma of the line as it would be if
measured by a direct fit of a Gaussian to the line; i.e., we add back
the template instrumental dispersion in quadrature to the pPXF-fitted
sigma and propagate the error as follows:
- \(\sigma^2 = \sigma_{\rm ppxf}^2 + \sigma_{\rm tpl}^2\)
- \(\epsilon[\sigma] = \sigma_{\rm ppxf} \epsilon[\sigma_{\rm ppxf}]/\sigma\)
The EMLINE_TPLSIGMA
(\(\sigma_{\rm tpl}\)) extension is provided
so that one can recover the exact output from pPXF following the
equations above, where \(\sigma\) and
\((\epsilon[\sigma])^{-2}\) are provided in EMLINE_GSIGMA
and
EMLINE_GSIGMA_IVAR
, respectively. One does not need to consider
EMLINE_TPLSIGMA
when calculating the astrophysical Doppler
broadening of each line; see MAPS Corrections.
DAP global header data¶
The first extension of each of the main DAP output files (the MAPS
and model LOGCUBE
) is empty apart from the header data. The header
data is an exact copy of the primary header for the DRP LOGCUBE files
(internal)
file except that the BSCALE, BZERO, and BUNIT keywords
are removed and the AUTHOR and MASKNAME keywords are
changed.
The following keywords are also added, any keyword enclose in () are only written under certain conditions:
Keyword | Description |
---|---|
VERSPY | Python version |
VERSNP | Numpy version |
VERSSCI | Scipy version |
VERSAST | Astropy version |
VERSPYDL | pydl version |
VERSDAP | MaNGA DAP version |
DAPTYPE | The analysis method identifier for the DAP analysis (HYB10-MILESHC-MASTARHC ) |
DAPFRMT | The format of this output file, either MAPS or LOGCUBE |
RDXQAKEY | Configuration keyword for the method used to assess the reduced data |
ECOOPA | Position angle used for the semi-major axis polar coordinate calculations |
ECOOELL | Ellipticity (1-b/a) used for the semi-major axis polar coordinate calculations |
BBWAVE | Wavelength of the LOGCUBE channel used for calculating the covariance used in
the per spaxel S/N calculation |
BBINDX | Index of the channel |
REFF | Effective radius |
BINKEY | Configuration keyword for the spatial binning method |
BINMINSN | Minimum S/N of spectrum to include in the binning |
FSPCOV | Minimum allowed fraction of good pixels across the full spectral range |
NBINS | Number of unique spatial bins |
(EMPTYBIN) | List of empty bins, if any exist |
BINTYPE | Spatial binning method |
(BINCX) | If radial binning, on-sky X center for all bins |
(BINCY) | If radial binning, on-sky Y center for all bins |
(BINPA) | If radial binning, position angle used for all bins |
(BINELL) | If radial binning, ellipticity (1-b/a) used for all bins |
(BINSCL) | If radial binning, the radius has been scaled by this value (arcsec) |
(BINRAD) | If radial binning, provides the start, end, and number of radial bins |
(BINLGR) | If radial binning, the geometric step used to set the radial bins |
(BINSNR) | If Voronoi binning, the target S/N for each bin |
(BINCOV) | If Voronoi binning, the method used to incorporate covariance into the S/N calculation |
(NCALIB) | If Voronoi binning and using a calibration of the noise vector that incorporates covariance, the noise calibration coefficient |
(STCKOP) | If binning spectra, the operation used for stacking spectra |
(STCKVREG) | If binning spectra, a boolean flag that the spectra were shifted in velocity before stacked |
(STCKCRMD) | If binning spectra, the approach used to account for covariance in the resulting inverse variance of the binned spectrum |
(STCKCRPR) | If binning spectra, the method-specific parameters used to incorporate covariance in the stacking procedure |
(STCKRES) | Stacking operation performs a stack of the individual spaxel resolution vectors (DISP) as opposed to the single median vector (SPECRES) |
(STCKPRE) | Stacking operation uses the pre-pixelized spectral resolution instead of the post-pixelized version |
GEXTLAW | Galactic extinction law used to deredden the data |
RVGAL | Ratio of total to selective extinction, \(R_V\) |
VSTEP | Velocity step per spectral channel |
SCKEY | Configuration keyword for the method used to model the stellar-continuum |
SCMINSN | Minimum S/N of spectrum to include in stellar-continuum fits |
SCINPVEL | Initial guess stellar velocity |
SCINPSIG | Initial guess stellar velocity dispersion |
NSCMOD | Number of unique stellar-continuum models |
(EMPTYSC) | List of bins without a stellar-continuum model, if any exist |
SCTYPE | Type of spectral fitting method used for the stellar-continuum fits |
SCMETH | Algorithm used for the stellar-continuum fits |
PPXFTPLK | Configuration keyword for the template library key used with pPXF |
PPXFBIAS | pPXF bias value |
PPXFMOM | Number of fitted LOSVD moments in pPXF |
PPXFAO | Order of additive polynomial in pPXF |
PPXFMO | Order of multiplicative polynomial in pPXF |
PPXFRBOX | Size of the boxcar filter used during rejection iterations |
ELMKEY | Configuration keyword that defines the emission-line moment measurement method |
ELMMINSN | Minimum S/N of spectrum to include in emission-line moment measurements |
ARTDB | Artifact database keyword |
MOMDB | Emission-line moments database keyword |
ELFKEY | Configuration keyword that defines the emission-line modeling method |
ELFMINSN | Minimum S/N of spectrum to include in emission-line modeling |
EMLDB | Emission-line database keyword |
NELMOD | Number of unique emission-line models |
ELTYPE | Type of spectral fitting method used for the emission-line fits |
ELMETH | Algorithm used for the emission-line modeling |
SIKEY | Configuration keyword that defines the spectral-index measurement method |
SIMINSN | Minimum S/N of spectrum to include in spectral-index measurements |
SIFWHM | FWHM of index system resolution (ang) to which the galaxy spectra were matched |
ABSDB | Absorption-line index database keyword |
BHDDB | Bandhead-index database keyword |
SICORR | Flag that indices have been corrected for velocity dispersion |
SNRGMED | Median g-band signal-to-noise of spaxels within 1-1.5 \(R_e\) |
SNRGRING | Total g-band signal-to-noise of a binned spectrum using spaxels within 1-1.5 \(R_e\) bin |
SNRRMED | Median r-band signal-to-noise of spaxels within 1-1.5 \(R_e\) |
SNRRRING | Total r-band signal-to-noise of a binned spectrum using spaxels within 1-1.5 \(R_e\) bin |
SNRIMED | Median i-band signal-to-noise of spaxels within 1-1.5 \(R_e\) |
SNRIRING | Total i-band signal-to-noise of a binned spectrum using spaxels within 1-1.5 \(R_e\) bin |
SNRZMED | Median z-band signal-to-noise of spaxels within 1-1.5 \(R_e\) |
SNRZRING | Total z-band signal-to-noise of a binned spectrum using spaxels within 1-1.5 \(R_e\) bin |
DAPQUAL | Global DAP quality bit mask: MANGA_DAPQUAL |
- The headers of the data extensions are more minimal. They include:
- the WCS information,
- the HDUCLASS keyword block,
- the channel description for the DAP MAPS file files,
- the units for any single image or datacube extensions (BUNIT), and
- the DATASUM and CHECKSUM values.
Reference Files¶
For storage of many more fitting products (so far not deemed useful for
the MAPS
files) and rerunning the code, intermediate reference files
are written after each main analysis step. The naming convention is
essentially to append the necessary analysis keyword to the file name.
These are identically the keys used in the
The DAP AnalysisPlan file: drpqa_key
, bin_key
,
continuum_key
, elmom_key
, elfit_key
, spindex_key
.
The DAPTYPE is constructed based on these keys and must be unique.
Currently, the DAPTYPE is [bin_key]-[sctpl]-[emltpl]
, where
[sctpl]
and [emltpl]
are the keywords for the continuum
templates used during the stellar-continuum and emission-line modules,
respectively.
The reference files are primarily for developer use, but may contain information that you want. A bare-bones description of the content of these files is forthcoming. If you’re interested in using something in these files, it’s probably best to Submit an issue.