fantasy_agn package

fantasy_agn.tools module

class fantasy_agn.tools.make_spec(wav, fl, er, ra=None, dec=None, z=None, name='spectrum')[source]

Bases: spectrum

class fantasy_agn.tools.read_gama_fits(filename)[source]

Bases: spectrum

class fantasy_agn.tools.read_sdss(filename)[source]

Bases: spectrum

A class for reading SDSS (Sloan Digital Sky Survey) FITS files and extracting relevant spectral data.

Parameters

filenamestr

The path to the FITS file containing the SDSS spectrum data.

Attributes

zfloat

The redshift of the object from the FITS file.

rafloat

The right ascension of the object from the FITS file header.

decfloat

The declination of the object from the FITS file header.

mjdint

The Modified Julian Date of the observation from the FITS file header.

plateint

The plate ID of the observation from the FITS file header.

fiberint

The fiber ID of the observation from the FITS file header.

namestr

The name of the file (excluding the extension) from which the data was read.

wavenumpy.ndarray

The wavelength values (in Ångstroms) of the spectrum, converted from vacuum to air.

fluxnumpy.ndarray

The flux values of the spectrum.

errnumpy.ndarray

The flux uncertainties derived from the inverse variance.

fwhmnumpy.ndarray

The full-width at half-maximum (FWHM) of the spectral lines, calculated from wavelength dispersion.

velscalefloat

The velocity scale (km/s) derived from the logarithmic dispersion.

Methods

None

This class relies on its parent class spectrum for additional functionality.

Notes

This class handles both lowercase and uppercase column names in the FITS data, ensuring compatibility with variations in SDSS data formats. It also adjusts the inverse variance (ivar) values to avoid division by zero when calculating uncertainties.

References

SDSS FITS file format documentation: https://www.sdss.org/dr16/spectro/spectro_basics/

class fantasy_agn.tools.read_text(filename)[source]

Bases: spectrum

class fantasy_agn.tools.spectrum[source]

Bases: object

CorRed(redshift=0)[source]

The CorRed function corrects the flux for redshift. It takes in a redshift and corrects the wavelength, flux, and error arrays by that given redshift.

Parameters:

  • self – Used to Reference the class object.

  • redshift=0 – Used to Specify the redshift of the object.

Returns:

The wavelength, flux and error arrays for the object at a redshift of z=0.

DeRedden(ebv=0)[source]

Function for dereddening a flux vector using the parametrization given by [Fitzpatrick (1999)](https://iopscience.iop.org/article/10.1086/316293).

Parameters

ebvfloat, optional
Color excess E(B-V). If not given it will be automatically derived from

Dust map data from [Schlegel, Finkbeiner and Davis (1998)](http://adsabs.harvard.edu/abs/1998ApJ…500..525S), by default 0

crop(xmin=4050, xmax=7300)[source]

The crop function crops the spectrum to a specified wavelength range.

Parameters: xmin (float): The minimum wavelength of the crop region. Default is 4050 Angstroms. xmax (float): The maximum wavelength of the crop region. Default is 7300 Angstroms.

Returns: None, but modifies self in place by cropping it to only include wavelengths between xmin and xmax.

Parameters:

  • self – Used to Reference the object itself.

  • xmin=4050 – Used to Set the lower wavelength limit of the cropped spectrum.

  • xmax=7300 – Used to Select the wavelength range of interest.

Returns:

A new spectrum object with the cropped wavelength range.

fit(model, ntrial=1)[source]

The fit function fits a model to the data. It returns a tuple of (model, fit results).

Parameters:

  • self – Used to Reference the class object.

  • model – Used to Define the model that is used in the fit.

  • ntrial=1 – Used to Specify the number of times we want to repeat the fit.

Returns:

The results of the fit.

fit_host(mask_host=False, custom=False, mask_list=[])[source]

The fit_host function fits a host galaxy and an AGN to the observed spectrum. It takes as input: mask_host (bool): If True, it masks the host emission lines using _host_mask function. Default is False. custom (bool): If True, it masks user defined emission lines using _custom_mask function. Default is False. mask_list ([float]): A list of wavelengths in angstroms that will be masked if custom=True .Default is empty list [].

Returns:

self.(wave,flux,err) : The wavelength array , flux array and error array after fitting for host galaxy and AGN components respectively.

Parameters:

  • self – Used to Access variables that belongs to the class.

  • mask_host=False – Used to Mask the host.

  • custom=False – Used to Mask the host.

  • mask_list=[] – Used to Mask the data points that are not used in the fit.

Returns:

The host and the agn component.

fit_host_sdss(mask_host=False, custom=False, mask_list=[])[source]

The fit_host_sdss function fits a 5 host galaxy eigenspectra and an 10 AGNs eigenspectra to the observed spectrum. It takes as input: mask_host (bool): If True, it masks the host emission lines using _host_mask function. Default is False. custom (bool): If True, it masks user defined emission lines using _custom_mask function. Default is False. mask_list ([float]): A list of wavelengths in angstroms that will be masked if custom=True .Default is empty list [].

Returns:

self.(wave,flux,err) : The wavelength array , flux array and error array after fitting for host galaxy and AGN components respectively.

Parameters:

  • self – Used to Access variables that belongs to the class.

  • mask_host=False – Used to Mask the host.

  • custom=False – Used to Mask the host.

  • mask_list=[] – Used to Mask the data points that are not used in the fit.

Returns:

The host and the agn component.

monte_carlo(nsample=10, save_files=True)[source]

The monte_carlo function performs Monte Carlo resampling of the data by perturbing the flux based on the input error. It returns a dictionary containing the fit parameters and their uncertainties.

Parameters:

  • self – Used to Reference the class object.

  • model – Used to Define the model that is used in the fit.

  • nsample=100 – Used to Specify the number of Monte Carlo samples to generate.

Returns:

A dictionary containing the fit parameters and their uncertainties.

plot()[source]
plot_spec()[source]

The plot_spec function plots the spectra.

Parameters:

self – Used to Access the class attributes.

Returns:

A tuple containing the x and y values for a plot of the spectrum.

rebin(minw=3900, maxw=6800)[source]

The rebin function rebins the spectrum to a smaller wavelength range. The default is 3900-6800 angstroms, but you can specify your own min and max values.

Parameters:

  • self – Used to Reference the object itself.

  • minw=3900 – Used to Set the minimum wavelength of the new array.

  • maxw=6800 – Used to Define the upper limit of the wavelength range to be used for fitting.

Returns:

The new wavelength and flux values for the spectrum.

restore()[source]

Restore the spectra (wave, flux and error) to the one before host removal

save_json(suffix='pars')[source]

The save_json function saves the parameter values in a JSON file. The filename is constructed from the name of the model and either ‘pars’ or ‘samples’.

Parameters:

  • self – Used to Refer to the object itself.

  • suffix='pars' – Used to Specify the name of the file that is saved.

Returns:

A dictionary of the parameter names and values.

show_range()[source]
vac_to_air()[source]

Convert vacuum to air wavelengths :param lam_vac - Wavelength in Angstroms :return: lam_air - Wavelength in Angstroms

fantasy_agn.models module

fantasy_agn.models.automatic_path(s, path_to_models='/home/docs/checkouts/readthedocs.org/user_builds/fantasy-agn/checkouts/stable/fantasy_agn/input', overwrite=True)[source]

The automatic_path function takes a spectrum object and creates a directory with the name of the spectrum. It then saves all models within the input path that fall within the wavelength range of your data to this directory.

Parameters:

  • s – Used to Define the spectrum object.

  • path_to_models=input_path – Used to Specify the path to the models.

  • overwrite=True – Used to Overwrite a model if it already exists.

Returns:

The path to the directory where the.

fantasy_agn.models.create_feii_model(name='feii', fwhm=2000, min_fwhm=1000, max_fwhm=8000, offset=0, min_offset=-3000, max_offset=3000)[source]

The create_feii_model function creates a FeII model with the specified parameters.

Parameters:

  • name='feii' – Used to Name the component.

  • fwhm=2000 – Used to Set the fwhm of the feii emission line.

  • min_fwhm=1000 – Used to Set the minimum value of the fwhm parameter.

  • max_fwhm=8000 – Used to Set the upper limit of the fwhm range.

  • offset=0 – Used to Set the central wavelength of the feii emission line.

  • min_offset=-3000 – Used to Set the minimum value of the offset parameter.

  • max_offset=3000 – Used to Set the maximum offset velocity of the feii emission line.

Returns:

A feii object.

fantasy_agn.models.create_fixed_model(files=[], name='', amplitude=2, fwhm=3000, offset=0, min_offset=-3000, max_offset=3000, min_amplitude=0, max_amplitude=600, min_fwhm=100, max_fwhm=7000)[source]

The create_fixed_model function creates a model that is fixed fwhm for all lines. The function takes as an argument a list of csv files, which contain the information (name and position) of all lines included in the model. It also takes as arguments: name, amplitude, fwhm (km/s), offset (km/s) and min_offset and max_offset (km/s).

Parameters:

  • files=[] – Used to Pass a list of csv files to the model.

  • name='' – Used to Give the model a name.

  • amplitude=2 – Used to Set the initial value of the amplitude parameter.

  • fwhm=3000 – Used to Set the fwhm of the gaussian profile.

  • offset=0 – Used to Shift the lines to the center of each pixel.

  • min_offset=-3000 – Used to Set the minimum value of the offset.

  • max_offset=3000 – Used to Set the maximum offset of the line from its rest position.

  • min_amplitude=0 – Used to Set the minimum value of the amplitude parameter.

  • max_amplitude=600 – Used to Limit the maximum amplitude of the lines.

  • min_fwhm=100 – Used to Set a lower limit to the fwhm parameter.

  • max_fwhm=7000 – Used to Set the maximum value of the fwhm parameter.

:param : Used to Set the initial value of the amplitude parameter. :return: A fixed_lines class object.

fantasy_agn.models.create_input_folder(xmin=4000, xmax=7000, path_to_folder='', overwrite=True)[source]

The create_input_folder function creates a folder in the specified path. The function takes three arguments:

  1. xmin - the minimum value of the range to be used for creating input files, default is 4000

  2. xmax - the maximum value of the range to be used for creating input files, default is 7000

  3. path_to_folder - The path where you want your new folder created. Default is current directory

Parameters:

  • xmin=4000 – Used to Set the minimum value of the x-axis (position or wavelength).

  • xmax=7000 – Used to Limit the maximum value of the x-axis.

  • path_to_folder='' – Used to Specify the path to the folder where you want to save your file.

  • overwrite=True – Used to Overwrite the files in the input folder.

Returns:

The path to the folder where the input files are stored.

fantasy_agn.models.create_line(name='line', pos=4861, ampl=5, min_ampl=0, max_ampl=500, fwhm=1000, min_fwhm=5, max_fwhm=10000, offset=0, min_offset=-3000, max_offset=3000)[source]

The create_line function creates a line with the specified parameters.

Parameters:

name (str): The name of the emission line.

pos (float): The central wavelength of the emission line in Angstroms.

ampl (float): The amplitude of the emission line in units of flux density at

position x=0, i.e., F(x=0) = ampl * continuum_level + offset . Note that this is not an absolute value but depends on how you normalize your spectrum! Default is 5, which means that if your spectrum has a continuum level equal to 1 then F(x=0)=5 and if it’s 0 then F(x=0)=5+offset . If you want to set an absolute flux density rather than relative values, use hard_min and hard_max instead!

min_ampl (float): A lower limit for amplitude above which no lines will be created by create_line(). This can be useful when creating multiple lines from one input parameter because sometimes there are “bumps” or other features in a single spectrum where it makes sense to have multiple lines with different centroids but similar amplitudes so they don’t overlap each other

Parameters:

  • name='line' – Used to Name the line in the model.

  • pos=4861 – Used to Specify the central wavelength of the line.

  • ampl=5 – Used to Set the amplitude of the emission line.

  • min_ampl=0 – Used to Set the lower limit of the amplitude parameter.

  • max_ampl=500 – Used to Set the maximum value that ampl can take.

  • fwhm=1000 – Used to Set the width of the line.

  • min_fwhm=5 – Used to Set the minimum value of the fwhm.

  • max_fwhm=10000 – Used to Set a hard limit on the fwhm.

  • offset=0 – Used to Shift the line center to a different position.

  • min_offset=-3000 – Used to Set the minimum value of the offset.

  • max_offset=3000 – Used to Set the maximum offset of the line.

Returns:

An instance of the emission_line class.

fantasy_agn.models.create_model(files=[], prefix='', default_limits=True, amplitude=2, fwhm=3000, offset=0, min_offset=-3000, max_offset=3000, min_amplitude=0, max_amplitude=600, min_fwhm=100, max_fwhm=7000)[source]

The create_broad_model function creates a model for the broad lines in the data. It takes as input:

filename - The name of the file containing all of your line names and positions.

This should be a csv file with columns named ‘line’, ‘position’. The first row should contain column headers.

prefix - A string that will be added to each component name in your model, e.g., if you give it “broad_”, all components will have names like “broad_[LINE NAME]”.

default_limits - If True, limits on amplitudes, fwhms, offsets are set automatically based on what is reasonable for this dataset (see below). If False, no limits are set except such that min(amplitude) > 0 and max(amplitude) < 100 (this is because some models may not have any amplitude parameters at all).

amplitude - Initial value for amplitudes; see above documentation about how this value might change depending on whether default_limits=True or False.. Default = 2.0 .

fwhm - Initial value for FWHMs; see above documentation about how this value might change depending on whether default_limits=

Parameters:

  • filename='' – Used to Specify the name of the file that contains all of the lines.

  • prefix='' – Used to Give each line a unique name.

  • default_limits=True – Used to Set the limits of the parameters to a default value.

  • amplitude=2 – Used to Set the default amplitude of the lines to 2.

  • fwhm=3000 – Used to Set the default value for the fwhm of each line.

  • offset=0 – Used to Indicate that the offset is not fixed.

  • min_offset=-3000 – Used to Set the minimum value for the offset.

  • max_offset=3000 – Used to Set the upper limit of the offset parameter.

  • min_amplitude=0 – Used to Remove the baseline from the fit.

  • max_amplitude=100 – Used to Set the upper limit of the amplitude to 100.

  • min_fwhm=100 – Used to Remove the noise lines in the spectra.

  • max_fwhm=7000 – Used to Avoid the model to go out of the data range.

Returns:

A model, which is a list of line objects.

fantasy_agn.models.create_tied_model(name='OIII5007', files=[], prefix='', fix_oiii_ratio=True, position=5006.803341, amplitude=2, fwhm=10, offset=0, min_offset=-3000, max_offset=1000, min_amplitude=0, max_amplitude=1000, min_fwhm=0, max_fwhm=10000, included=False)[source]

The create_tied_model function creates a model that is tied to another parameter. It takes the following arguments:

name - The name of the line (e.g., OIII5007) files - A list of csv files containing data for this line (optional) prefix - The prefix used in defining parameters in other functions (default = “”)

If included == True and fix_oiii_ratio==True, then it creates an instance of the OIII_NII class with a reference emission line defined by ref_line.

If included == True and fix_oiii_ratio==False, then it creates an instance of EmissionLine with a reference emission line defined by ref_line.

If included == False and fix_oiii_ratio==True, then it creates an instance of OIII5007 only.

Parameters:

  • name='OIII5007' – Used to Name the emission line.

  • files=[] – Used to Pass a list of csv files to the model.

  • prefix="" – Used to Give a name to the model.

  • fix_oiii_ratio=True – Used to Fix the ratio of oiii5007 to nii6583.

  • position=0 – Used to Define the position of the reference line.

  • amplitude=2 – Used to Set the amplitude of the emission line to 2.

  • fwhm=10 – Used to Set the fwhm of the reference line.

  • offset=0 – Used to Indicate that the line should be fixed to 0.

  • min_offset=-3000 – Used to Set the minimum offset of the line.

  • max_offset=1000 – Used to Set the maximum offset of a line to 1000 km/s.

  • min_amplitude=0 – Used to Avoid the model to go below 0.

  • max_amplitude=1000 – Used to Set a maximum value for the amplitude of the emission line.

  • min_fwhm=0 – Used to Avoid the fwhm of lines to be set to 0.

  • max_fwhm=10000 – Used to Avoid errors when the fwhm is very high.

  • included=False – Used to Create a model without the emission line of interest.

Returns:

A model that is tied to the parameters of a reference line.