API

dysmalpy.galaxy Module

Classes

Galaxy([z, cosmo, Om0, Tcmb0, Neff, m_nu, ...])

Container for simulating or modelling a galaxy

dysmalpy.models Package

Functions

surf_dens_exp_disk(r, mass, rd)	Radial surface density function for an infinitely thin exponential disk
menc_exp_disk(r, mass, rd)	Enclosed mass function for exponential disk
vcirc_exp_disk(r, mass, rd)	Rotation curve function for exponential disk
sersic_mr(r, mass, n, r_eff)	Radial surface mass density function for a generic sersic model
sersic_menc_2D_proj(r, mass, n, r_eff)	Enclosed mass as a function of r for a generic sersic model
v_circular(mass_enc, r)	Circular velocity given an enclosed mass and radius
menc_from_vcirc(vcirc, r)	Enclosed mass given a circular velocity and radius

Classes

ModelSet()	Object that contains all model components, parameters, and settings
Sersic([invq, noord_flat, baryon_type])	Mass distribution following a Sersic profile
DiskBulge([invq_disk, invq_bulge, ...])	Mass distribution with a disk and bulge
LinearDiskBulge([invq_disk, invq_bulge, ...])	Mass distribution with a disk and bulge
ExpDisk([baryon_type])	Infinitely thin exponential disk (i.e. Freeman disk).
BlackHole(**kwargs)	Central black hole.
GaussianRing([baryon_type])	Mass distribution following an infinitely thin Gaussian ring profile.
NFW([z, cosmo, Om0, Tcmb0, Neff, m_nu, Ob0])	Dark matter halo following an NFW profile
LinearNFW([z, cosmo, Om0, Tcmb0, Neff, ...])	Same as NFW except with the virial mass in linear units
TwoPowerHalo([z, cosmo, Om0, Tcmb0, Neff, ...])	Two power law density model for a dark matter halo
Burkert([z, cosmo, Om0, Tcmb0, Neff, m_nu, Ob0])	Dark matter halo following a Burkert profile
Einasto([z, cosmo, Om0, Tcmb0, Neff, m_nu, ...])	Dark matter halo following an Einasto profile
DekelZhao([z, cosmo, Om0, Tcmb0, Neff, ...])	Dekel-Zhao halo profile (Dekel et al. 2017, Freundlich et al. 2020).
BiconicalOutflow([profile_type])	Model for a biconical outflow
UnresolvedOutflow([vcenter, fwhm, amplitude])	Model for an unresolved outflow component described by a Gaussian
UniformRadialFlow(**kwargs)	Model for a uniform radial flow.
PlanarUniformRadialFlow(**kwargs)	Model for a planar uniform radial flow, with radial flow only in the plane of the galaxy.
AzimuthalPlanarRadialFlow([vr])	Model for a planar radial flow, with radial flow only in the plane of the galaxy,
UniformBarFlow(**kwargs)	Model for a uniform flow along a bar, along some axis in the galaxy midplane.
VariableXBarFlow([vbar])	Model for flow along a bar, along some axis in the galaxy midplane,
UniformWedgeFlow(**kwargs)	Model for a uniform planar radial flow (only in the plane of the galaxy),
SpiralDensityWave([Vrot, rho0, f, k, dVrot_dR])	Model for a spiral density wave, assumed in the galaxy midplane.
LightTruncateSersic([tracer])	Light distribution following a Sersic profile.
LightGaussianRing([tracer])	Light distribution following a Gaussian ring profile.
LightClump([tracer])	Light distribution for a clump following a Sersic profile, at a given galaxy midplane R and azimuthal angle phi.
LightGaussianRingAzimuthal([tracer])	Light distribution following a Gaussian ring profile, with azimuthal brightness variation.
DispersionConst([sigma0])	Model for a constant dispersion
ThinCentralPlaneDustExtinction([inc, pa, ...])	Model for extinction due to a thin plane of dust
ForegroundConstantExtinction([Alam])	Model for extinction due to a foreground plane of dust
ForegroundExponentialExtinction([Alam0, rd])	Model for extinction due to a foreground plane of dust
ConstantDimming([amp_lumtoflux])	Model for constant dimming.
CosmologicalDimming([z, cosmo, Om0, Tcmb0, ...])	Model for constant cosmological dimming.
Geometry([obs_name])	Model component defining the transformation from galaxy to sky coordinates
KinematicOptions([adiabatic_contract, ...])	Object for storing and applying kinematic corrections
ZHeightGauss(**kwargs)	Gaussian flux distribution in the z-direction
ZHeightExp(**kwargs)	Exponential flux distribution in the z-direction
NoordFlat([n, invq])	Class to handle circular velocities / enclosed mass profiles for a thick Sersic component.
InfThinMassiveGaussianRing([invh])	Class to handle circular velocities / enclosed mass profiles for an infinitely thin, massive Gaussian ring.

dysmalpy.instrument Module

Classes

Instrument([beam, beam_type, lsf, pixscale, ...])	Base class to define an instrument to observe a model galaxy.
GaussianBeam([major, minor, pa, area, ...])	Re-definition of radio_beam.Beam to allow it to work with copy.deepcopy and copy.copy.
DoubleBeam([major1, minor1, pa1, scale1, ...])	Beam object that is the superposition of two Gaussian Beams
Moffat([major_fwhm, minor_fwhm, pa, beta, ...])	Object describing a Moffat PSF
LSF([dispersion, default_unit, meta])	An object to handle line spread functions.

dysmalpy.data_classes Module

Classes

Data([data, error, weight, ndim, mask, ...])
Data1D(r, velocity[, vel_err, vel_disp, ...])	Convention:
Data2D(pixscale, velocity[, vel_err, ...])
Data3D(cube, pixscale, spec_type, spec_arr)

dysmalpy.aperture_classes Module

Functions

setup_aperture_types([obs, profile1d_type, ...])

Classes

Aperture([aper_center, nx, ny, ...])	Base Aperture class, containting a single aperture from which to extract a 1D spectrum and flux, velocity, and dispersion.
EllipAperture([slit_PA, pix_perp, ...])	Elliptical Aperture
RectAperture([slit_PA, pix_perp, ...])	Rectangular aperture.
Apertures([apertures, slit_PA, rotate_cube])	Base Aperture class, continaing a list/array of Aperture objects defining the full set of apertures for a kinematic observation.
EllipApertures([rarr, slit_PA, pix_perp, ...])	Set of elliptical apertures.
CircApertures([rarr, slit_PA, rpix, nx, ny, ...])	Set of circular apertures.
RectApertures([rarr, slit_PA, pix_perp, ...])	Set of rectangular apertures.

dysmalpy.fitting Package

Functions

reload_all_fitting([filename_galmodel, ...])	Utility to reload the Galaxy and Results object from a previous fit.
chisq_red(gal)	Evaluate reduced chi square of model, relative to the data.
chisq_eval(gal)	Evaluate chi square of model, relative to the data.
chisq_red_per_type(obs, nparams_free[, type])	Evaluate reduced chi square of the model velocity/dispersion/flux map/profile
setup_oversampled_chisq(gal)

Classes

MCMCFitter(**kwargs)	Class to hold the MCMC fitter attributes + methods
NestedFitter(**kwargs)	Class to hold the Nested sampling fitter attributes + methods
MPFITFitter(**kwargs)	Class to hold the MPFIT fitter attributes + methods
MCMCResults([model, sampler_results, ...])	Class to hold results of MCMC fitting to DYSMALPY models.
NestedResults([model, sampler_results, ...])	Class to hold results of nested sampling fitting to DYSMALPY models.
MPFITResults([model, blob_name])	Class to hold results of using MPFIT to fit to DYSMALPY models.

dysmalpy.plotting Module

Functions

plot_trace(bayesianResults[, fileout, overwrite])	Plot trace of Bayesian samples
plot_corner(bayesianResults[, gal, fileout, ...])	Plot corner plot of Bayesian result posterior distributions.
plot_bestfit(mcmcResults, gal[, ...])	Plot data, bestfit model, and residuals from the MCMC fitting.

dysmalpy.fitting_wrappers Package

dysmalpy.lensing Module

This is a Python code to implement lensing tranformation in DysmalPy. This code uses the C++ library libLensingTransformer.so.

Classes

LensingTransformer(mesh_file, mesh_ra, mesh_dec)

docstring for LensingTransformer

dysmalpy.parameters Module

Classes

DysmalParameter([name, description, ...])	New parameter class for dysmalpy based on Parameter
Prior()	Base class for priors
UniformPrior()	Object for flat priors
GaussianPrior([center, stddev])	Object for gaussian priors
BoundedGaussianPrior([center, stddev])	Object for Gaussian priors that only extend to a minimum and maximum value
BoundedGaussianLinearPrior([center, stddev])
BoundedSineGaussianPrior([center, stddev])	Object for priors described by a bounded sine Gaussian distribution
UniformLinearPrior()
ConditionalUniformPrior([f_bounds, f_cond])	Object for flat priors, but with boundaries that are conditional on other model parameters.
ConditionalEmpiricalUniformPrior([f_cond, ...])	Object for flat priors, but with boundaries that are conditional on other model parameters.

dysmalpy.utils Module

Functions

rebin(arr, new_2dshape)
calc_pixel_distance(nx, ny, center_coord)	Function to calculate the distance of each pixel from a specific pixel as well as the position angle
create_aperture_mask(nx, ny, center_coord, dr)	Function to create an aperture mask.
determine_aperture_centers(nx, ny, ...)	Determine the centers of the apertures that span an image/cube along a line with position angle pa and goes through center_coord.
calc_pix_position(r, pa, xcenter, ycenter)	Simple function to determine the pixel that is r away from (xcenter, ycenter) along a line with position angle (pa)
measure_1d_profile_apertures(cube, rap, pa, ...)	Measure the 1D rotation curve using equally spaced apertures along a defined axis
apply_smoothing_2D(vel, disp[, ...])
apply_smoothing_3D(cube[, smoothing_type, ...])
symmetrize_velfield(xbin, ybin, velBin, errBin)	This routine generates a bi-symmetric ('axisymmetric') version of a given set of kinematical measurements.
symmetrize_1D_profile(rin, vin, errin[, sym])
fit_truncated_gaussian(trace, truncate_value)	Find the best fitting mean and standard deviation of a sample assuming the distribution is a truncated Gaussian with the truncation occurring at low values.
lnlike_truncnorm(params, x)
fit_uncertainty_ellipse(chain_x, chain_y[, bins])	Get the uncertainty ellipse of the sample for each photocenter.
gaus_fit_sp_opt_leastsq(x, y, flux_guess, ...)
gaus_fit_apy_mod_fitter(x, y, flux_guess, ...)
get_cin_cout(shape[, asint])
citations()	Return the papers that should be cited when using DYSMALPY

dysmalpy.config Module

Classes

OutputOptions([outdir, save_model, ...])

Class to hold all options for file output during and after fitting