Emission-Line Measurements

Emission-Line Parameters

The table below provides a compilation of emission line parameters gathered through the development of the DAP. Many of them have not actually been fit by the DAP in any survey-level runs of the software and are simply collected here for reference.

Rest wavelengths are Ritz wavelengths in vacuum, collected from the NIST Atomic Spectra Database.

The “M1” and “E2” values are the Einstein \(A_{ki}\) coefficients for the magnetic dipole and electric quadrapole transitions, respectively. These are collected to fix the expected flux ratio between specific line doublets. The expected flux ratio is:

\[f_1 / f_2 = \lambda_2/\lambda_1\ \cdot\ (M1_1+E2_1)/(M1_2+E2_2)\]

where, e.g., \(\lambda_1\) is the rest wavelength of the first line in the doublet.

Additionally, we have defined some nominal passbands used for calculations of the line equivalent width (EW), including the main passband centered on the line and blue and red sidebands that are used to construct a linear continuum beneath the emission line.

Name Rest \(\lambda\) (Å) M1 E2 EW Passband (Å) Blue Passband (Å) Red Passband (Å)
HeII 3204.038          
NeV 3346.783          
NeV 3426.863          
H25 3670.5154          
H24 3672.5279          
H23 3674.8109          
H22 3677.4160          
H21 3680.4065          
H20 3683.8627          
H19 3687.8870          
H18 3692.6119          
H17 3698.2104          
H16 3704.9133          
H15 3713.0334          
H14 3723.0035     [1] 3706.3 – 3716.3 3738.6 – 3748.6
OII 3727.092     3716.3 – 3738.3 3706.3 – 3716.3 3738.6 – 3748.6
OII 3729.875     [1] 3706.3 – 3716.3 3738.6 – 3748.6
H13 3735.4365     [1] 3706.3 – 3716.3 3738.6 – 3748.6
H12 3751.2243     3746.2 – 3756.2 3738.6 – 3748.6 3756.6 – 3766.6
H11 3771.7080     3761.7 – 3781.7 3756.6 – 3766.6 3779.1 – 3789.1
\({\rm H}\theta\) 3798.9826     3789.0 – 3809.0 3776.5 – 3791.5 3806.5 – 3821.5
\({\rm H}\eta\) 3836.4790     3826.5 – 3846.5 3806.5 – 3826.5 3900.2 – 3920.2
NeIII 3869.86 1.74e-1   3859.9 – 3879.9 3806.5 – 3826.5 3900.2 – 3920.2
HeI 3889.749     [1] 3806.5 – 3826.5 3900.2 – 3920.2
\({\rm H}\zeta\) 3890.1576     3880.2 – 3900.2 3806.5 – 3826.5 3900.2 – 3920.2
NeIII 3968.59 5.40e-2   [1] 3938.6 – 3958.6 3978.6 – 3998.6
\({\rm H}\epsilon\) 3971.2020     3961.2 – 3981.2 3941.2 – 3961.2 3981.2 – 4001.2
HeI 4027.3238     4017.3 – 4037.3 3997.3 – 4017.3 4037.3 – 4057.3
SII 4069.749     4062.7 – 4073.6 4049.7 – 4062.7 4082.0 – 4092.9
SII 4077.500     4073.6 – 4084.5 4049.7 – 4062.7 4082.0 – 4092.9
\({\rm H}\delta\) 4102.8991     4092.9 – 4112.9 4082.0 – 4092.9 4112.9 – 4132.9
\({\rm H}\gamma\) 4341.691     4331.7 – 4351.7 4311.7 – 4331.7 4349.7 – 4358.7
OIII 4364.435     4358.7 – 4374.4 4349.7 – 4358.7 4374.4 – 4384.4
HeI 4472.729     4462.7 – 4482.7 4442.7 – 4462.7 4482.7 – 4502.7
HeII 4687.015     4677.0 – 4697.0 4667.0 – 4677.0 4697.0 – 4707.0
ArIV 4712.58          
HeI 4714.4578     4707.0 – 4722.0 4697.0 – 4707.0 4722.0 – 4732.0
ArIV 4741.45          
\({\rm H}\beta\) 4862.691     4852.7 – 4872.7 4798.9 – 4838.9 4885.6 – 4925.6
HeI 4923.3051     4913.3 – 4933.3 4898.3 – 4913.3 4933.3 – 4948.3
OIII 4960.295 6.21e-3 4.57e-6 4950.3 – 4970.3 4930.3 – 4950.3 4970.3 – 4990.3
OIII 5008.240 1.81e-2 3.52e-5 4998.2 – 5018.2 4978.2 – 4998.2 5028.2 – 5048.2
HeI 5017.0769     [1] 4988.2 – 4983.2 5028.2 – 5048.2
NI 5199.3490     5189.3 – 5209.3 5169.4 – 5189.3 5211.7 – 5231.7
NI 5201.7055     [1] 5169.4 – 5189.4 5211.7 – 5231.7
NII 5756.19          
HeI 5877.243     5867.2 – 5887.2 5847.2 – 5867.2 5887.2 – 5907.2
NaI 5891.583          
NaI 5897.558          
OI 6302.046 5.63e-3 2.11e-5 6292.0 – 6312.0 6272.0 – 6292.0 6312.0 – 6332.0
OI 6365.535 1.82e-3 3.39e-6 6355.5 – 6375.5 6335.5 – 6355.5 6375.5 – 6395.5
NII 6549.86 9.84e-4 9.22e-7 6542.9 – 6556.9 6483.0 – 6513.0 6623.0 – 6653.0
\({\rm H}\alpha\) 6564.632     6557.6 – 6571.6 6483.0 – 6513.0 6623.0 – 6653.0
NII 6585.271 2.91e-3 8.65e-6 6575.3 – 6595.3 6483.0 – 6513.0 6623.0 – 6653.0
HeI 6679.9956     6670.0 – 6690.0 6652.0 – 6670.0 6690.0 – 6708.0
SII 6718.294     6711.3 – 6725.3 6690.0 – 6708.0 6748.0 – 6768.0
SII 6732.674     6725.7 – 6739.7 6690.0 – 6708.0 6748.0 – 6768.0
HeI 7067.1252     7057.1 – 7077.1 7037.1 – 7057.1 7077.1 – 7097.1
ArIII 7137.76 3.21e-1 1.4e-3 7127.8 – 7147.8 7107.8 – 7127.8 7147.8 – 7167.8
ArIV 7172.68          
ArIV 7239.76          
ArIV 7265.33          
OII 7321.003   5.19e-2 [1] 7291.0 – 7311.0 7342.8 – 7362.8
OII 7322.01 8.37e-3 9.07e-2 7313.8 – 7326.8 7291.0 – 7311.0 7342.8 – 7362.8
OII 7331.68 9.32e-3 7.74e-2 7326.8 – 7339.8 7291.0 – 7311.0 7342.8 – 7362.8
OII 7332.75 1.49e-2 3.85e-2 [1] 7291.0 – 7311.0 7342.8 – 7362.8
ArIV 7334.17          
ArIII 7753.24 8.3e-2 1.3e-4 7743.2 – 7763.2 7703.2 – 7743.2 7763.2 – 7803.2
P20 8394.703          
P19 8415.630          
P18 8440.274          
P17 8469.581          
P16 8504.819     8494.8 – 8514.8 8474.8 – 8494.8 8514.8 – 8534.8
P15 8547.731     8534.8 – 8557.7 8514.8 – 8534.8 8557.7 – 8587.7
P14 8600.754     8587.7 – 8610.8 8557.7 – 8587.7 8610.8 – 8650.8
P13 8667.398     8657.4 – 8677.4 8617.4 – 8657.4 8677.4 – 8717.4
P12 8752.876     8742.9 – 8762.9 8702.9 – 8742.9 8762.9 – 8802.9
\({\rm P}\theta\) 8865.216     8855.2 – 8875.2 8815.2 – 8855.2 8875.2 – 8915.2
SIII 8831.8          
\({\rm P}\eta\) 9017.384     9007.4 – 9027.4 8977.4 – 9007.4 9027.4 – 9057.4
SIII 9071.1 1.85e-2 3.94e-5 9061.1 – 9081.1 9026.1 – 9061.1 9081.1 – 9116.1
\({\rm P}\zeta\) 9231.546     9221.5 – 9241.5 9181.5 – 9221.5 9241.5 – 9281.5
SIII 9533.2 4.78e-2 2.09e-4 9525.5 – 9540.9 9483.2 – 9523.2 9558.6 – 9598.6
\({\rm P}\epsilon\) 9548.588     9540.9 – 9556.3 9483.2 – 9523.2 9558.6 – 9598.6
\({\rm P}\delta\) 10052.123     10042.1 – 10062.1 10002.1 – 10042.1 10062.1 – 10102.1

Non-parametric Emission-Line Measurements

The DAP performs non-parametric measurements of the emission lines using a simple moment analysis. See mangadap.proc.emissionlinemoments and Emission-line Moments. In survey-level runs of the DAP, we have typically paired the set of moment measurements and Gaussian models; however, the number of emission-line moment measurements need not be matched to the number of emission-line Gaussian models and vice versa.

Input Data Format

The parameters that define the emission-line moments to calculate are provided via the mangadap.par.emissionmomentsdb.EmissionMomentsDB object, which is built using an SDSS-style parameter file.

The columns of the parameter file are:

Parameter Format Description
index int Unique integer identifier of the emission line. Must be unique.
name str Name of the transition.
lambda float Rest frame wavelength of the emission line to analyze.
waveref str The reference frame of the wavelengths; must be either ‘air’ for air or ‘vac’ for vacuum.
primary float[2] A two-element vector with the starting and ending wavelength for the primary passband surrounding the emission line(s).
blueside float[2] A two-element vector with the starting and ending wavelength for a passband to the blue of the primary band.
redside float[2] A two-element vector with the starting and ending wavelength for a passband to the red of the primary band.

and an example file might look like this:

typedef struct {
    int index;
    char name[6];
    double lambda;
    char waveref[3];
    double primary[2];
    double blueside[2];
    double redside[2];
} DAPELB;

DAPELB   2  OIId    3728.4835  vac  { 3716.3  3738.3 } { 3706.3  3716.3 } { 3738.6  3748.6 }
DAPELB   3  OII     3729.875   vac  {   -1      -1   } {   -1      -1   } {   -1      -1   }

Note in the above example that the second set of parameters set the passbands to have nonsensical limits of {-1 -1}. This is used to signify that the moment parameters are “dummy” or placeholder parameters. This is used to create an empty channel in the output MAPS file and is used just to synchronize the channel indices between the non-parametric and Gaussian-fit results. That is, it’s used to ensure that, e.g., the \({\rm H}\alpha\) measurements are in the same channel for both the EMLINE_SFLUX and EMLINE_GFLUX extensions.

Changing the moment parameters

The moment measurements are performed by mangadap.proc.emissionlinemoments.EmissionLineMoments; see Emission-line Moments. A set of parameter files that define a list of emission-line moment sets are provided with the DAP source distribution and located at $MANGADAP_DIR/data/emission_bandpass_filters. There are a few methods that you can use to change the set of emission-line parameters used by mangadap.proc.emissionlinemoments.EmissionLineMoments:

  1. To use one of the existing parameter databases, you can change the emission_passbands keyword in the mangadap.proc.emissionlinemoments.EmissionLineMoments configuration file. The keyword should be the capitalized root of the parameter filename. E.g., to use $MANGADAP_DIR/data/emission_bandpass_filters/elbmpl9.par, set the keyword to ELBMPL9.
  2. To use a new parameter database, write the file and save it in the $MANGADAP_DIR/data/emission_bandpass_filters/ directory, and then change the relevant configuration file in the same way as described above.

Gaussian Emission-Line Modeling

The DAP models the emission lines using single component Gaussian functions. See mangadap.proc.emissionlinemoments and Emission-line Modeling. In survey-level runs of the DAP, we have typically paired the set of moment measurements and Gaussian models; however, the number of emission-line moment measurements need not be matched to the number of emission-line Gaussian models and vice versa.

Input Data Format

The parameters that define the emission-line models to fit are provided via the mangadap.par.emissionlinedb.EmissionLineDB object, which is built using an SDSS-style parameter file.

The columns of the parameter file are:

Parameter Format Description
index int Unique integer identifier of the emission line. Must be unique. Specifically used when tying line parameters.
name str Name of the transition.
lambda float Rest frame wavelength of the emission line to analyze.
waveref str The reference frame of the wavelengths; must be either ‘air’ for air or ‘vac’ for vacuum.
action str A single character setting how the line should be treated. See Emission-Line “Actions”.
relative_flux float Relative flux of the emission lines. This should most often be unity when the flux is not tied to another line; see Emission-Line “Modes”.
mode str Fitting mode for the line. See Emission-Line “Modes”.
profile str The name of the class used to construct the line profile. The available options are any of the classes in mangadap.util.lineprofiles. This functionality will likely be deprecated because the lineprofile should essentially always be mangadap.util.lineprofiles.FFTGaussianLSF; selected by setting this parameter to “FFTGaussianLSF”.
ncomp int The number of components to fit. NOT TYPICALLY USED!
output_model int Flag to include the best-fitting model of the line in the emission-line model spectrum. NOT TYPICALLY USED!
par float[3] A list of the initial guess for the line profile parameters. NOT TYPICALLY USED! The number of parameters must match the struct declaration at the top of the file. The initial parameters are automatically adjusted to provide any designated flux ratios, and the center is automatically adjusted to the provided redshift for the spectrum. For example, for a GaussianLineProfile, this is typically set to “{1.0 0.0 100.0}”.
fix int[3] A list of flags for fixing the input guess parameters during the fit. NOT TYPICALLY USED! Use 0 for a free parameter, 1 for a fixed parameter. The parameter value is only fixed AFTER adjusted in the flux and or center based on the redshift and the implied tied parameters. For a free set of parameters using a GaussianLineProfile, this is set to “{ 0 0 0 }”.
lower_bound str[3] A list of lower bounds for the parameters. NOT TYPICALLY USED! For each parameter, use None to indicate no lower bound. For a GaussianLineProfile with positive flux and standard deviation, this is set to ‘{ 0.0 None 0.0 }’.
upper_bound str[3] A list of upper bounds for the parameters. NOT TYPICALLY USED! For each parameter, use None to indicate no upper bound. For a GaussianLineProfile with maximum standard deviation of 800 km/s, this is set to ‘{ None None 800.0 }’.
log_bounded int[3] A list of flags used when determining if a fit parameter is near the imposed boundary. NOT TYPICALLY USED! If true, the fraction of the boundary range used is done in logarithmic, not linear, separation. Use 0 for False, 1 for True.
blueside float[2] A two-element vector with the starting and ending wavelength for a passband to the blue of the primary band.
redside float[2] A two-element vector with the starting and ending wavelength for a passband to the red of the primary band.

and an example file might look like this:

typedef struct {
    int index;
    char name[6];
    double lambda;
    char waveref[3];
    char action;
    double relative_flux;
    char mode[6];
    char profile[30];
    int ncomp;
    int output_model;
    double par[3];
    int fix[3];
    char lower_bound[3][10];
    char upper_bound[3][10];
    int log_bounded[3];
    double blueside[2];
    double redside[2];
} DAPEML;

DAPEML   2  OII     3727.092   vac  f   1.00  v34  FFTGaussianLSF  1  1  { 1.0 0.0 100.0 }  { 0 0 0 }  {  0.0 None 30.0 }  { None None 400. }  { 0 0 1 }  { 3706.3  3716.3 } { 3738.6  3748.6 }
DAPEML   3  OII     3729.875   vac  f   1.00   k2  FFTGaussianLSF  1  1  { 1.0 0.0 100.0 }  { 0 0 0 }  {  0.0 None 30.0 }  { None None 400. }  { 0 0 1 }  { 3706.3  3716.3 } { 3738.6  3748.6 }
DAPEML  33  NII     6549.86    vac  f   0.34  a35  FFTGaussianLSF  1  1  { 1.0 0.0 100.0 }  { 0 0 0 }  {  0.0 None 30.0 }  { None None 400. }  { 0 0 1 }  { 6483.0  6513.0 } { 6623.0  6653.0 }
DAPEML  34  Ha      6564.632   vac  f   1.00    f  FFTGaussianLSF  1  1  { 1.0 0.0 100.0 }  { 0 0 0 }  {  0.0 None 30.0 }  { None None 400. }  { 0 0 1 }  { 6483.0  6513.0 } { 6623.0  6653.0 }
DAPEML  35  NII     6585.271   vac  f   1.00  v34  FFTGaussianLSF  1  1  { 1.0 0.0 100.0 }  { 0 0 0 }  {  0.0 None 30.0 }  { None None 400. }  { 0 0 1 }  { 6483.0  6513.0 } { 6623.0  6653.0 }

Note

  • Both the emission-line moments database and the emission-line modeling database define the sidebands used for the equivalent width calculations. Nominally, these should be the same, but it’s up to the person that writes the two parameter files to make sure that’s true.
  • Many of the current parameters in the emission line modeling parameter file are hold-overs from when mangadap.proc.elric.Elric was the standard class used for the emission-line fitting. Anything marked as “NOT TYPICALLY USED” hasn’t been adapted for use with the currently preferred module, mangadap.proc.sasuke.Sasuke.

Emission-Line “Actions”

The action parameter allows the emission-line database to be used both in masking during the stellar-continuum modeling (see mangadap.util.pixelmask.SpectralPixelMask) and during the emission-line modeling itself.

The valid actions are:

  • i: ignore the line, as if the line were commented out.
  • f: fit the line and mask the line when fitting the stellar continuum.
  • m: mask the line when fitting the stellar continuum but do not fit the line itself
  • s: defines a sky line that should be masked. When masked, the wavelength of the line is not adjusted for the redshift of the object spectrum.

I.e., when using the emission-line database for the emission-line modeling, lines with the action set to f are fit, whereas all other lines are ignored.

Emission-Line “Modes”

The mode parameter sets how the emission line should be treated with respect of the rest of the lines being modeled.

The valid modes are:

  • f: Fit the line independently of all others.
  • wN: Used by mangadap.proc.elric.Elric only. Fit the line with untied parameters, but use a window that includes both this line and the line with index N.
  • xN: Used by mangadap.proc.elric.Elric only. Fit the line with its flux tied to the line with index N.
  • vN: Fit the line with the velocity tied to the line with index N.
  • sN: Fit the line with the velocity dispersion tied to the line with index N.
  • kN: Fit the line with the velocity and velocity dispersion tied to the line with index N.
  • aN: Fit the line with the flux, velocity, and velocity dispersion tied to the line with index N.

As noted in the mode description, many of the modes are only available when using the mangadap.proc.elric.Elric module. For the w mode, this is simply because the preferred module, mangadap.proc.sasuke.Sasuke, fits the full spectrum instead of fitting the lines within small spectral windows. The other limitation are because mangadap.proc.sasuke.Sasuke is based on the use of template spectra to fit the emission lines (see mangadap.proc.emissionelinetemplates.EmissionLineTemplates): To tie line fluxes, the lines to be tied are included in the same template spectrum, meaning that their kinematics are also automatically tied. That means that, for mangadap.proc.sasuke.Sasuke, the x and a modes are identical.

In the Input Data Format example, the modes set the \({\rm H}\alpha\) line as the “reference” line. I.e., there should always be one line whose mode is f. This requirement is simply practical in setting up the tied parameter structure; there is no more weight given to the fit of the reference line than any other line. The blue [OII] and red [NII] lines have their velocities tied to the \({\rm H}\alpha\) line, all kinematics of the red [OII] line are tied to the blue [OII] line, and all parameters of the blue [NII] line are tied to the red [NII] line with a fixed flux ratio of NII-6550/NII-6585 == 0.34. By virtue of being tied to lines that have their velocites tied to the \({\rm H}\alpha\) line, the velocities of the red [OII] and blue [NII] lines are also tied to the \({\rm H}\alpha\) line. Again, this doesn’t mean that the fit to the \({\rm H}\alpha\) line is given any more weight than any other line, it just means that there is one model parameter that defines the velocity of all lines.

Changing the modeling parameters

The emission-line modeling is performed by mangadap.proc.emissionlinemodel.EmissionLineModel; see Emission-line Modeling. A set of files that define a list of emission-line model parameter sets are provided with the DAP source distribution and located at $MANGADAP_DIR/data/emission_lines. There are a few methods that you can use to change the set of emission-line parameters used by mangadap.proc.emissionlinemodel.EmissionLineModel:

  1. To use one of the existing parameter databases, you can change the emission_lines keyword in the mangadap.proc.emissionlinemodel.EmissionLineModel configuration file. The keyword should be the capitalized root of the parameter filename. E.g., to use $MANGADAP_DIR/data/emission_lines/elpmpl9.par, set the keyword to ELPMPL9.
  2. To use a new parameter database, write the file and save it in the $MANGADAP_DIR/data/emission_lines/ directory, and then change the relevant configuration file in the same way as described above.
[1](1, 2, 3, 4, 5, 6, 7, 8, 9) No primary band defined because it overlaps with another line.