Warning
The text below is flagged to identify cases where files/data are specific to MaNGA or a MaNGA data release. Anything that is not directly tied to the MaNGA-specific execution of the DAP (e.g., the naming convention and directory structure) will be relevant to analysis of non-MaNGA data. If you have questions or find problems, please Submit an issue.
The mask bits for the DAP output files are pulled from last tagged version of IDLUTILS
for SDSS-IV. These are distributed with the DAP and located in $MANGADAP_DIR/mangadap/data/sdss
.
- If you're unfamiliar with maskbits, see the description of SDSS Bitmasks.
- For examples of how to use the mask bits, see
gettingstarted-bitmasks
.
Note
Some mask bits are informational, not necessarily indicating that the pixel should be ignored. Please read and understand the flags listed below to determine if it's reasonable for your science case to simply ignore pixels with a non-zero mask value.
Some mask bits are still placeholders. They're notional bits that are actually never set in the current version of the DAP.
The three bitmask groups for DAP output files are:
metadatamodel-dapqual
: Global quality bitmetadatamodel-dappixmask
: Spaxel-by-spaxel bits for the DAPMAPS
quantitiesmetadatamodel-dapspecmask
:Pixel-by-pixel bits for the DAP modelLOGCUBE
data
These bitmask groups are further described and listed below. For reference, we also list the two DRP bitmask groups that the DAP uses to flag the data it analyzes.
The MaNGA DRP uses a single bit to summarize the quality of the data reduction. The DAP class used to handle these bits and the bit values are below.
The DAP essentially only uses the CRITICAL
flag and only when constructing the MANGA_DAPQUAL
flag value.
The MaNGA DRP flags the datacube data using a small set of bits that are a consolidation of the bits flagged during the data reduction. The DAP currently uses a single class to handle the bitmasks associated with either the 2D RSS files and the 3D datacubes. Below are the bits for the 3D datacubes:
Warning
Because these flags are issued by the MaNGA data-reduction pipeline, they are specific to analysis of the MaNGA data and are not relevant to non-MaNGA applications.
There is a single summary maskbit MANGA_DAPQUAL
included in the headers of both the MAPS
and LOGCUBE
files describing the overall quality of the data. The DAP class used to handle these bits and the bit values are below.
Anything with the CRITICAL
bit set in MANGA_DAPQUAL
should generally not be used for scientific purposes.
MANGA_DAPPIXMASK
is the 2D image bitmask used to describe the quality of individual pixel measurements in the DAP MAPS
file. The DAP class used to handle these bits and the bit values are below.
The most important flags are incorporated into the DONOTUSE
bit, which indicates that a given pixel should not be used for science.
The NEARBOUND
flag is used to signify that a returned parameter is likely biased by an imposed boundary on the allowed parameter space. These are specifically relevant to the pPXF kinematics from ~mangadap.proc.ppxffit.PPXFFit
(stellar) and ~mangdap.proc.sasuke.Sasuke
(gas). We use pPXF with a ± 2000 km/s limit relative to the input guess velocity (set by cz in SCINPVEL
header keyword in the PRIMARY
extension and most often identical to the NSA redshift) on the returned velocity and LOGCUBE
wavelength channel ( ∼ 70 km/s; given by the VSTEP
header keyword in the PRIMARY
extension). The returned velocity is determined to be NEARBOUND
if the "best-fit" value is within 1/100 of the width of the allowed range of either boundary; i.e., NEARBOUND
is triggered if the velocity is − 2000 < v < − 1980 or 1980 < v < 2000. For the velocity dispersion, NEARBOUND
is triggered by the same criterion but geometrically; i.e., if the velocity dispersion is 0.69 < σ < 0.74 or 929.8 < σ < 1000.
The UNRELIABLE
flag is not incorporated into the DONOTUSE
flag. This flag is tripped based on various judgement calls made by the MaNGA data products committee (DPC) and the pipeline development teams. You are strongly encouraged to understand the implications of this flag on the data and how to properly make the distinction between the DONOTUSE
and UNRELIABLE
flags for your science application. The definition of the UNRELIABLE
flag can change with time, in the hope that we eventually converge to a refined set of criteria that allow users to determine when measurements can be trusted carte blanche and when the data should be treated more skeptically. Only spaxels where analysis has been attempted (with non-zero bin IDs) are flagged as UNRELIABLE
if they meet the necessary criteria. Please Submit an issue if you find a set of automated criteria that would be useful to the development team in terms of what you would like to see marked as UNRELIABLE
.
Currently, the use of the UNRELIABLE
flag is still rather limited. This is not to say that all measurements are reliable, but reflects our hesitance to set (robust) criteria for isolating unreliable measurements, either because we don't think we're able or because we haven't had sufficient time to do so. Below, we list the condition under which UNRELIABLE
flags are tripped, and the affected masks in the MAPS
file.
Affected mask | Criteria |
---|---|
EMLINE_SFLUX_MASK |
If there are any masked pixels in the three passbands (blue, main, red) used to construct the measurement. |
EMLINE_SEW_MASK |
If there are any masked pixels in the three passbands (blue, main, red) used to construct the measurement. |
SPECINDEX_MASK , SPECINDEX_BF_MASK , SPECINDEX_WGT_MASK |
If there are any masked pixels in the three passbands (blue, main, red) used to construct the measurement. |
MANGA_DAPPIXMASK
is the 3D model cube bitmask used to describe the quality of individual spaxel fits in the DAP model data cube file. The DAP class used to handle these bits and the bit values are below.
Internally, the DAP uses separate bitmasks to flag data resulting from each of its main modules. These bitmasks are written to the module reference files and then consolidated into the bits tabulated above for the main DAP output files (the MAPS
and model LOGCUBE
files). These bits are listed in the description of each analysis module; e.g., ~mangadap.proc.spatiallybinnedspectra.SpatiallyBinnedSpectraBitMask
.
The DAP is configured using an input execution plan file created by the user (when the default plan is not used). There are additional intermediary script files created by the DAP to allow for event handling and cluster coordination.
See execution
for more general information about execution of the DAP; the following is for its survey-level execution.
Warning
Although generic to the DAP, this description of the analysis plan files is specific to the DR17 and earlier version of the DAP. See plan
for the current format and usage of these files.
For a general description the AnalysisPlan
file, see the execution-analysis-plan
.
File root: $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/log/[timestamp]
File name: mpl[MPL]_plan.par
In the file template, [timestamp]
is the time when the rundap
script was executed in the format, e.g., 01Nov2019T16.58.40UTC
and [MPL]
is the MPL number (e.g., 9). This is a single file that lists the ways in which each DRP LOGCUBE
file is to be analyzed for each MPL. This file is created once by the person executing the DAP.
Warning
This file is specific to the survey-level execution of the DAP on MaNGA data.
File root: $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/common
File name: drpcomplete_$MANGADRP_VER.fits
The ~mangadap.survey.drpcomplete.DRPComplete
file is primarily created for the survey-level execution of the DAP. It collates information used to create the input configuration files for each DRP-produced datacube. The ~mangadap.survey.drpcomplete.DRPComplete
database is created/updated at the beginning of each execution-rundap
.
The ~mangadap.survey.drpcomplete.DRPComplete
database is written to a fits file with a primary extension and a binary-table extension; the table extension has the following columns:
Column | Description |
---|---|
|
The plate number of the observation |
|
The IFU used to observe the target |
|
Specifies which DRP files are available on disk: (1) CUBE files only; (2) Both CUBE and RSS files. |
|
String representation of the MaNGA ID |
|
Nominal right ascension of the object center |
|
Nominal declination of the object center |
|
ID number of the parent catalog |
|
0-based index of the row within that parent catalog with the target information |
|
The version of the parent catalog |
|
The ID number of the object in the parent catalog. |
MANGA_TARGET1 |
Targeting bits for main survey galaxies |
MANGA_TARGET3 |
Targeting bits for ancillary programs |
|
Redshift (cz) of the object used as an initial guess redshift. |
|
Characteristic velocity dispersion of the object |
|
Photometric ellipticity |
|
Photometric position angle |
|
Effective (half-light) radius |
Note
- The DAP currently only works with the
LOG
format, and does not search for or analyze theLIN
format. OBJRA
andOBJDEC
are not necessarily located at the center of the IFU field of view. The IFU center coordinates are provided in the DRPall file asIFURA
andIFUDEC
.- The MaNGA ID is defined as
[CATID]-[CATINDX]
- For the main survey galaxies,
TRG_VERSION
andTRG_ID
are drawn from the NASA-Sloan atlas and are identical to 'nsa_nsa_version' and 'nsa_nsaid' in the DRPall file. - The MaNGA targeting bits; see MaNGA Bitmasks.
- The redshifts from the NSA and ancillary-program catalogs are consolidated into the 'z' column in the DRPall file. See discussion of the "redshift fix file" below.
- The characteristic velocity dispersion is virtually always not available and set to -9999. In this case, the DAP will default to a dispersion of 100 km/s.
- For main survey galaxies, photometric measurements are taken from 'nsa_ba', 'nsa_phi' and 'nsa_petro_th50_el' in the DRPall file. If any of these values do not exist or are 'nan', they are set to -9999.0. Importantly, these placeholder values are replaced by
ELL=0; PA=0; REFF=1
when processed by the DAP.
Warning
This file is specific to the survey-level execution of the DAP on MaNGA data.
File root: $MANGADAP_DIR/mangadap/data/fix
File name: redshift_fix.par
The redshift-fix file is an SDSS-style parameter file used to replace any redshift (z) read from the DRPall or plateTargets files. It has a simple format that identifies the plate, ifudesign, and replacement redshift:
typedef struct {
int plate;
int ifudesign;
double z;
} DAPZCORR;
DAPZCORR 9677 6102 0.0
DAPZCORR 9677 6103 0.0
...
This files serves to both provide redshifts for objects that don't have them and replace incorrect redshifts from, e.g., the NASA-Sloan Atlas. The redshift-fix file is updated for each version of the DAP. This file is only used when constructing the metadatamodel-drpcomplete
, which then propagates to the execution-config
and then to the execution-mangadap
.
Warning
This file is specific to the survey-level execution of the DAP on MaNGA data.
File root: $MANGADAP_DIR/mangadap/data/fix
File name: photometry_fix.par
The photometry-fix file is an SDSS-style parameter file used to replace photometric properties from the DRPall or plateTargets files. These properties are the isophotal ellipticity, ϵ ≡ 1 − b/a, the major-axis position angle, ϕ0, and the effective radius,
typedef struct {
int plate;
int ifudesign;
double ell;
double pa;
double reff;
} DAPPHOTCORR;
DAPPHOTCORR 8083 12702 0.265 7.57 28.3
The photometry-fix file is updated for each version of the DAP. This file is only used when constructing the metadatamodel-drpcomplete
, which then propagates to the execution-config
and then to the execution-mangadap
.
Warning
This file is specific to the survey-level execution of the DAP on MaNGA data.
File root: $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/log/[timestamp]/[PLATE]/[IFUDESIGN]
File name: mangadap-[PLATE]-[IFUDESIGN]
In the file template, [timestamp]
is the time when the rundap
script was executed in the format, e.g., 01Nov2019T16.58.40UTC
, [PLATE]
is the plate number and [IFUDESIGN]
is the IFU number. These are the script files that are submitted to the Utah CHPC cluster to execute the DAP, as created by the rundap
script
See execution-rundap
.
Warning
This file is specific to the survey-level execution of the DAP on MaNGA data.
For a general description, see execution-config
.
File root: $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/common/[PLATE]/[IFUDESIGN]
File name: mangadap-[PLATE]-[IFUDESIGN]-LOG[MODE].ini
Symlink root: $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER/[DAPTYPE]/[PLATE]/[IFUDESIGN]/ref
In the file templates, [PLATE]
is the plate number, [IFUDESIGN]
is the IFU number, [MODE]
is the data format (always CUBE
), and [DAPTYPE]
is the keyword for the datamodel-daptype
. These files provide input observational parameters to the DAP and are almost entirely from the NASA-Sloan Atlas.
Warning
This file is specific to the survey-level execution of the DAP on MaNGA data.
File root: $MANGA_SPECTRO_ANALYSIS/$MANGADRP_VER/$MANGADAP_VER
File name: dapall-$MANGADRP_VER-$MANGADAP_VER.fits
The DAPall file has an empty primary extension and then one extension for each DAPTYPE
performed by a given analysis plan. The name of the extension is identically the DAPTYPE
and it contains one row per analyzed datacube. For example, in DR17, the list of extensions in the DAPall file are:
Extension | Extension Name |
---|---|
|
PRIMARY |
|
SPX-MILESHC-MASTARSSP |
|
VOR10-MILESHC-MASTARSSP |
|
HYB10-MILESHC-MASTARSSP |
|
HYB10-MILESHC-MASTARHC2 |
The PRIMARY
extension is empty apart from the following header keywords:
Key | Comment |
---|---|
VERSDRP3 |
DRP version |
|
DAP version |
|
Line name for non-parametric (summed) emission-line measurement at vector position n -1 in relevant columns of the database |
|
Line name for Gaussian emission-line measurement at vector position n -1 in relevant columns of the database |
|
Name of spectral index measurement at vector position n -1 in relevant columns of the database |
|
Unit of the spectral index measurement at vector position n -1 in relevant columns of the database |
CHECKSUM |
Used for checking data fidelity |
|
Used for checking data fidelity |
Each subsequent extension, named after the datamodel-daptype
(DAPTYPE), includes a binary table with the following columns:
Key | Type | Units | Comment |
---|---|---|---|
**Basic designation and NSA | information** | ||
|
|
Plate number | |
|
|
IFU design number | |
|
|
String combination of [PLATE]-[IFUDESIGN] to ease searching |
|
|
|
MaNGA ID string | |
|
|
Row index of the observation in the DRPall file | |
|
|
3D mode of the DRP file (CUBE or RSS ) |
|
|
|
Keyword of the analysis approach used (e.g., SPX-MILESHC-MASTARSSP ) |
|
|
|
Flag that MAPS file successfully produced | |
|
|
|
RA of the galaxy center |
|
|
|
Declination of the galaxy center |
|
|
|
RA of the IFU pointing center (generally the same as OBJRA ) |
|
|
|
Declination of the IFU pointing center (generally the same as OBJDEC ) |
|
|
Main survey targeting bit (see MANGA_TARGET1 in MaNGA Bitmasks) |
|
|
|
Non-galaxy targeting bit (see MANGA_TARGET2 in MaNGA Bitmasks) |
|
|
|
Ancillary targeting bit (see MANGA_TARGET3 in MaNGA Bitmasks) |
|
|
|
Redshift used for initial guess velocity (typically identical to NSA_Z ) |
|
|
|
|
Luminosity distance based on Z and a standard cosmology (h = 1; ΩM = 0.3; ΩΛ = 0.7) |
|
|
|
Angular-diameter distance based on Z and a standard cosmology (h = 1; ΩM = 0.3; ΩΛ = 0.7) |
|
|
Redshift from the NASA-Sloan Atlas | |
|
|
NSA distance estimate using pecular velocity model of Willick et al. (1997); multiply by c/H0 for Mpc. | |
|
|
|
Luminosity distance based on NSA_Z and a standard cosmology (h = 1; ΩM = 0.3; ΩΛ = 0.7) |
|
|
|
Angular-diameter distance based on NSA_Z and a standard cosmology (h = 1; ΩM = 0.3; ΩΛ = 0.7) |
|
|
NSA isophotal axial ratio from elliptical Petrosian analysis | |
|
|
|
NSA isophotal position angle from elliptical Petrosian analysis |
|
|
|
NSA elliptical Petrosian effective radius in the r-band; the is the same as Re below. |
|
|
NSA isophotal axial ratio from Sersic fit | |
|
|
|
NSA isophotal position angle from Sersic fit |
|
|
|
NSA effective radius from the Sersic fit |
|
|
NSA Sersic index | |
**Version dependency and qua | lity information** | ||
|
|
Version of DRP used for 2d reductions | |
|
|
Version of DRP used for 3d reductions | |
|
|
Version of mangacore used by the DAP | |
|
|
Version of idlutils used by the DAP | |
|
|
Version of mangadap | |
|
|
DRP 3D quality bit (see metadatamodel-drp3qual ) |
|
|
|
DAP quality bit (see metadatamodel-dapqual ) |
|
|
tion** | ||
|
|
Configuration keyword for the method used to assess the reduced data | |
|
|
Configuration keyword for the spatial binning method | |
|
|
Configuration keyword for the method used to model the stellar-continuum | |
|
|
Configuration keyword that defines the emission-line moment measurement method | |
|
|
Configuration keyword that defines the emission-line modeling method | |
|
|
Configuration keyword that defines the spectral-index measurement method | |
|
|
Type of binning used | |
|
|
Target for bin S/N, if Voronoi binning | |
|
|
The identifier of the template library, e.g., MILES . |
|
|
om DAP fits file h | eaders** | |
|
|
Date the DAP file was created and/or last modified. | |
|
|
The number of "binned" spectra analyzed by the DAP. | |
|
specifically in t | he DAPall file** | |
|
|
|
Semi-major axis radius (R) below which spaxels cover at least 90% of elliptical annuli with width R ± 2.5 arcsec. This should be independent of the DAPTYPE . |
|
double (vector) | Median S/N per pixel in the ''griz'' bands within 1.0-1.5 Re. This should be independent of the DAPTYPE . |
|
|
double (vector) | S/N in the ''griz'' bands when binning all spaxels within 1.0-1.5 Re. This should be independent of the DAPTYPE . |
|
|
|
|
Mean g-band surface brightness of valid spaxels within 1 Re. This should be independent of the DAPTYPE . |
|
|
|
Maximum g-band luminosity-weighted semi-major radius of any "valid" binned spectrum. |
|
double (vector) | Number of binned spectra with g-band luminosity-weighted centers within 0-1, 0.5-1.5, and 1.5-2.5 Re. | |
|
double (vector) | Median g-band S/N of all binned spectra with luminosity-weighted centers within 0-1, 0.5-1.5, and 1.5-2.5 Re. | |
|
|
Flux-weighted mean redshift of the stellar component within a 2.5 arcsec aperture at the galaxy center. | |
|
|
|
Stellar velocity at 2.5% growth of all valid spaxels. |
|
|
|
Stellar velocity at 97.5% growth of all valid spaxels. |
|
|
|
Stellar velocity at 2.5% growth after iteratively clipping 3σ outliers. |
|
|
|
Stellar velocity at 97.5% growth after iteratively clipping 3σ outliers. |
|
|
|
Flux-weighted mean stellar velocity dispersion of all spaxels within 1 Re. |
STELLAR_RCHI2_1RE |
|
Median reduced chi2 of the stellar-continuum fit within 1 Re. | |
|
|
Flux-weighted mean redshift of the Hα line within a 2.5 arcsec aperture at the galaxy center. | |
|
|
|
Gaussian-fitted velocity of the |
|
|
|
Gaussian-fitted velocity of the |
|
|
|
Gaussian-fitted velocity of the |
|
|
|
Gaussian-fitted velocity of the |
|
|
|
Flux-weighted |
|
|
|
|
|
|
|
|
|
|
Median reduced χ2 of the continuum+emission-line fit within 1 Re. | |
|
double (vector) |
|
Summed emission-line flux integrated within a 2.5 arcsec aperture at the galaxy center. |
|
double (vector) |
|
Summed emission-line flux integrated within a 1 Re aperture at the galaxy. |
|
double (vector) |
|
Total integrated flux of each summed emission measurement within the full MaNGA field-of-view. |
|
double (vector) |
|
Mean emission-line surface-brightness from the summed flux measurements within 1 Re. |
|
double (vector) |
|
Peak summed-flux emission-line surface brightness. |
|
double (vector) |
|
Mean emission-line equivalent width from the summed flux measurements within 1 Re. |
|
double (vector) |
|
Peak emission-line equivalent width from the summed flux measurements. |
|
double (vector) |
|
Gaussian-fitted emission-line flux integrated within a 2.5 arcsec aperture at the galaxy center. |
|
double (vector) |
|
Gaussian-fitted emission-line flux integrated within a 1-Re aperture at the galaxy. |
|
double (vector) |
|
Total integrated flux of the Gaussian fit to each emission line within the full MaNGA field-of-view. |
|
double (vector) |
|
Mean emission-line surface-brightness from the Gaussian-fitted flux measurements within 1 Re. |
|
double (vector) |
|
Peak Gaussian-fitted emission-line surface brightness. |
|
double (vector) |
|
Mean emission-line equivalent width from the Gaussian-fitted flux measurements within 1 Re. |
|
double (vector) |
|
Peak emission-line equivalent width from the Gaussian-fitted flux measurements. |
|
double (vector) |
|
Spectral index at 2.5% growth of all valid spaxels. |
|
double (vector) |
|
Spectral index at 97.5% growth of all valid spaxels. |
|
double (vector) |
|
Spectral index at 2.5% growth after iteratively clipping 3σ outliers. |
|
double (vector) |
|
Spectral index at 97.5% growth after iteratively clipping 3σ outliers. |
|
double (vector) |
|
Median spectral index within 1 Re. |
|
|
|
Simple estimate of the star-formation rate within 1 Re based on the Gaussian-fitted |
|
|
|
Simple estimate of the star-formation rate within the IFU field-of-view based on the Gaussian-fitted Hα flux; |
Note
- Distance estimates do not include an estimate of the peculiar motions.
- Volume weights are included in the DRPall file.
RCOV90
is calculated for theCUBE
files; however, a more sophisticated calculation would use theRSS
files to account for the significant overlap of the fiber "beams."- All radially averaged or summed properties are calculated within ''elliptical'' apertures defined using the NSA ellipticity and position angle.
- Possible future additions:
- Add
nsa_sersic_mass
from the DRPall file. - Balmer decrement extinction corrections for SFR
- Provide default set of cross matching: SDSS I/II, Galaxy Zoo?
- Include initial radial profiles of the emission-line, spectral-index, and other derived properties?
- Add