kinms_fitter.kinms_fitter

Module Contents

Classes

kinms_fitter

Wrapper for easily kinematically modelling datacubes (typically from ALMA or VLA) using KinMS.
class kinms_fitter.kinms_fitter.kinms_fitter(filename, spatial_trim=None, spectral_trim=None, linefree_chans=[1, 5])

Wrapper for easily kinematically modelling datacubes (typically from ALMA or VLA) using KinMS. …

xc_guessfloat

Guess for Kinematic/morphological centre of the disc. RA, in degrees. [Default = Centre of supplied cube after clipping]

yc_guessfloat

Guess for Kinematic/morphological centre of the disc. Dec, in degrees. [Default = Centre of supplied cube after clipping]

vsys_guessfloat

Guess for Systemic velocity of the gas, in the radio velocity convention. km/s. [Default = Velocity of central channel of supplied cube after clipping]

totflux_guessfloat

Total flux guess. Units the same as those used in the cube (e.g. Jy km/s). [Default = total sum of the input cube] velDisp_guess : float Velocity dispersion guess. km/s. [Default = 8 km/s]

pa_guessfloat

Optional position angle guess, if no warp specified. Degrees. [Default = 0 deg]

inc_guessfloat

Optional Inclination angle guess, if no warp specified. Degrees. [Default = 45 deg]

inc_profilelist of warp_profile objects

Optional variation of the inclination with radius as described by warp_profile objects. [Default = None]

pa_profilelist of warp_profile objects

Optional variation of the inclination with radius as described by warp_profile objects. [Default = None]

sb_profilelist of sb_profs objects

Optional - Define the surface brightness profile with a list of sb_profs objects which will be evaluated in order. [Default = single exponential disc] expscale_guess : float Optional - defines the scalelength of the default single exponential disc used if sb_profile is not set. arcseconds. [Default = a fifth of the total extent of the cube] skySampClouds : ndarray Optional - Input cloud model made with the skySampler tool if you dont want to fit the gas distribution.

vel_profilelist of vel_profs objects

Define the circular velocity profile with a list of vel_profs objects. [Default = tilted rings]

radial_motionlist of radial_motion objects

Optional - Define the radial motion types with radial_motion objects (see base KinMS documentation). [Default: None]

nringsint

Optional - Number of tilted rings to use, spaced a beamwidth apart. [Default = fill the total extent of the cube]

vel_guessfloat

Optional - starting guess for the tilted ring asymptotic velocity. km/s [Default = 28percent of the velocity width coverved by the cube]

xcent_rangetwo element ndarray

Allowed range for fitting of the kinematic centre. RA in degrees [Default: minimum and maximum RA within the input cube]

ycent_rangetwo element ndarray

Allowed range for fitting of the kinematic centre. Dec in degrees [Default: minimum and maximum Dec within the input cube] vsys_range : two element ndarray Allowed range for fitting of the systemic velocity. km/s. [Default: minimum and maximum velocity contained within the input cube]

totflux_rangetwo element ndarray

Allowed range for fitting of the total flux. Units the same as input cube. [Default: Min=0 and Max=3x the total flux in the input cube]

velDisp_rangetwo element ndarray

Allowed range for fitting of the velocity dispersion. km/s. [Default: Min=0 and Max=50 km/s]

pa_rangetwo element ndarray

Optional - Allowed range for fitting of the position angle. Degrees. [Default: Min=0 and Max=360 degrees]

inc_rangetwo element ndarray

Optional - Allowed range for fitting of the inclination angle. Degrees. [Default: Min=0 and Max=89 degrees]

expscale_rangetwo element ndarray

Optional - Allowed range for fitting of the default exponential scale radius. arcseconds. [Default: Min=0 and Max=the size of your input cube]

vel_rangetwo element ndarray

Optional - Allowed range for fitting of the tilted ring velocities. km/s. [Default: Min=0 and Max=half the cube total velocity width]

pa_priorobject

Optional - supply an object defining the PA prior (see GAStimator documentation). [Default = boxcar between range limits]

xc_priorobject

Optional - supply an object defining the RA centre prior (see GAStimator documentation). [Default = boxcar between range limits]

yc_priorobject

Optional - supply an object defining the Dec centre prior (see GAStimator documentation). [Default = boxcar between range limits]

vsys_priorobject

Optional - supply an object defining the Vsys prior (see GAStimator documentation). [Default = boxcar between range limits]

inc_priorobject

Optional - supply an object defining the inc prior (see GAStimator documentation). [Default = boxcar between range limits]

totflux_priorobject

Optional - supply an object defining the totflux prior (see GAStimator documentation). [Default = boxcar between range limits]

velDisp_priorobject

Optional - supply an object defining the velocity dispersion prior (see GAStimator documentation). [Default = boxcar between range limits] initial_guesses : ndarray Override the initial guesses used for the fit. [Default = No override]

objname : string Name of the object you are fitting. [Default = read from FITS header OBJECT entry, or ‘object’] nprocesses : int Number of processors to use for MCMC fitting. [Default = fall back on GAStimator default choices]

nitersint

Number of iterations to use when fitting. [Default=3000]

output_initial_modelbool

Save the initially generated model as a FITS file. [Default=False]

pdfbool

Make PDF outputs. [Default = True]

silentbool

Fit silently. [Default = False]

show_cornerbool

Show corner plots if MCMC fitting. [Default = True]

nSampsint

Number of samples to use for KinMS model. [Default = 5e5] chi2_var_correct : bool Use chi-sqr variance correction. [Default = True] text_output : bool Save output text files. [Default = True]

save_all_acceptedbool

Save all the accepted guesses (allowing you to recreate corner plots etc). [Default = True]

interactivebool

Use interactive mode for plots. [Default = True]

show_plotsbool

Show the diagnotic plots. [Default = True]

output_cube_filerootstring

File root for output best fit datacube. [Default = False] lnlike_func : object Override the default likelihood function. [Default =. Dont override] tolerance : float Tolerance for simple fit. Smaller numbers are more stringent (longer runtime) [Default=0.1]

bunit : string Unit of datacube fluxes

cellsizefloat

Cube cellsize in arcsec timetaken : float Time taken for the fit in seconds.

chi2_correct_facfloat

chi2 correction factor applied.

mask_sum0

Number of detected pixels in the data mask.

labelsndarray of strings

Label for each fitted quantity

colorbar(mappable, ticks=None)

Add a colorbar to a given plot

param mappablematplotlib figure

Figure which to add the colorbar too

param ticksndarray

Ticks to show on the colourbar. [Default = None]

read_in_a_cube(path)

Reads in the datacube.

get_header_coord_arrays(hdr)

Get coordinate arrays from a FITS header

rms_estimate(cube, chanstart, chanend)

Estimate the RMS in the inner quarter of the datacube in a given channel range.

from_fits_history(hdr)

Get beam parameters if they happen to be in history keywords.

Stolen from radio_beam, with thanks!

read_primary_cube(cube)

Wrapper method for reading in datacube.

setup_params()

Setup the fit guesses, minima, maxima etc from the inputs.

clip_cube()

Clip the input datacube to size.

model_simple(param, fileName='')

Function to create a model from the given input parameters.

mcmc_fit(initial_guesses, labels, minimums, maximums, fixed, priors, precision)

Function to run the MCMC fit.

simple_chi2(theargs, info)

Likelihood function for the simple fit mode.

Returns the KinMS logo.

simple_fit(initial_guesses, labels, minimums, maximums, fixed)

Runs the simple fit.

plot(block=True, overcube=None, savepath=None, **kwargs)

Makes the plots.

write_text(bestvals, errup, errdown, units, fixed, runtime, mode, errors_warnings='None', fname='KinMS_fitter_output.txt')

Write output text files.

run(method='mcmc', justplot=False, savepath='./', **kwargs)

Run the fit.

Parameters

  • method (string - choice of 'mcmc', 'simple' or 'both'.) – Type of fit to run.

  • justplot (bool) – Just show the initial model plot without fitting. Helpful for setting initial guesses.

  • savepath (string) – Path to append to saved files.

  • **kwargs –

    any additional keywords to pass to other methods.