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 quadrupole 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 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 define nonsensical passbands with 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 in the DAP MAPS file.

Changing the moment parameters

The moment measurements are performed by 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/mangadap/data/emission_bandpass_filters. There are a few methods that you can use to change the set of emission-line parameters used by EmissionLineMoments:

1. To use one of the existing parameter databases, you can change the emission_passbands keyword in the EmissionLineMoments configuration file. The keyword should be the capitalized root of the parameter filename. E.g., to use $MANGADAP_DIR/mangadap/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/mangadap/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 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 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 is true.

• Many of the current parameters in the emission-line modeling parameter file are hold-overs from when 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, 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 to 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 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/mangadap/data/emission_lines. There are a few methods that you can use to change the set of emission-line parameters used by EmissionLineModel:

1. To use one of the existing parameter databases, you can change the emission_lines keyword in the EmissionLineModel configuration file. The keyword should be the capitalized root of the parameter filename. E.g., to use $MANGADAP_DIR/mangadap/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/mangadap/data/emission_lines/ directory, and then change the relevant configuration file in the same way as described above.

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1(1,2,3,4,5,6,7,8,9)

No primary band defined because it overlaps with another line.