kinms.KinMS2

Legacy version 2 version of Kinematic modelling code KinMS.

Copyright (C) 2019, Timothy A. Davis, Nikki Zabel, James M. Dawson E-mail: DavisT -at- cardiff.ac.uk, zabelnj -at- cardiff.ac.uk, dawsonj5 -at- cardiff.ac.uk Updated versions of the software are available through github: https://github.com/TimothyADavis/KinMSpy

If you have found this software useful for your research, I would appreciate an acknowledgment to the use of the “KINematic Molecular Simulation (KinMS) routines of Davis et al., (2013)”. [MNRAS, Volume 429, Issue 1, p.534-555]

This software is provided as is without any warranty whatsoever. For details of permissions granted please see LICENCE.md

Module Contents

Classes

KinMS

class KinMS
exception kinms.KinMS2.KinMSError

Bases: Exception

Generates errors under the flag ‘KinMSError’.

Class KinMSError

Instantiates the Exception error ‘KinMSError’, for warning the user of faults and exceptions.

class kinms.KinMS2.KinMS(xs, ys, vs, cellSize, dv, beamSize, inc, posAng, gasSigma=0, diskThick=0, flux_clouds=None, sbProf=[], sbRad=[], velRad=[], velProf=[], inClouds=[], vLOS_clouds=[], massDist=[], radial_motion_func=None, ra=None, dec=None, nSamps=None, seed=None, intFlux=None, vSys=None, phaseCent=[0, 0], vOffset=0, vPosAng=[], vPhaseCent=[0, 0], restFreq=None, fileName='', fixSeed=False, cleanOut=False, returnClouds=False, huge_beam=False, verbose=False, skySampler=False, bunit='Jy/beam')
Class KinMS

Main workhorse of KinMSpy, used to generate spectral cubes.

print_variables()

If “verbose”, prints a summary of parameters for the user’s convenience.

Returns

(string) formatted display of all parameters used in KinMS() initialisation

makebeam(xpixels, ypixels, beamSize, cellSize=1, cent=None)

Creates a psf with which one can convolve their cube based on the beam provided.

Parameters

  • xpixels – (float or int) Number of pixels in the x-axis

  • ypixels – (float or int) Number of pixels in the y-axis

  • beamSize – (float or int, or list or array of float or int) Scalar or three element list for size of convolving beam (in arcseconds). If a scalar then beam is assumed to be circular. If a list/array of length two. these are the sizes of the major and minor axes, and the position angle is assumed to be 0. If a list/array of length 3, the first 2 elements are the major and minor beam sizes, and the last the position angle (i.e. [bmaj, bmin, bpa]).

  • cellSize – (float or int) Pixel size required (arcsec/pixel)

  • cent –

    (array or list of float or int) Optional, default value is [xpixels / 2, ypixels / 2].

    Central location of the beam in units of pixels.

Return psf or trimmed_psf

(float array) psf required for convlution in self.model_cube(). trimmed_psf returned if self.huge_beam=False, otherwise default return is the untrimmed psf.

kinms_sampleFromArbDist_oneSided(sbRad, sbProf, nSamps, diskThick, fixSeed=None)

Samples cloudlets from radial profiles provided given that inClouds is not provided in the __init__.

Parameters

  • sbRad – (numpy array) Radius vector for surface brightness profile (units of arcseconds).

  • sbProf – (numpy array) Surface brightness profile (arbitrarily scaled) as a function of ‘sbrad’.

  • nSamps – (int) Number of cloudlets to use to create the model. Large numbers will reduce numerical noise (especially in large cubes), at the cost of increasing runtime.

  • diskThick – (numpy array) The disc scaleheight in arcseconds. If a single value then this is used at all radii. If an array/list then it should have the same length as ‘sbrad’, and will be the disc thickness as a function of that.

  • fixSeed – (bool) Whether to use a fixed (or random) seed (list of four integers).

Return inClouds

(numpy array) 3 dimensional array of cloudlet positions within the cube initialised by KinMS().

kinms_create_velField_oneSided(velRad, posAng_rad=None, inc_rad=None)

Creates an array of line-of-sight velocities, accounting for velocity dispersion and projection.

Parameters

  • velRad – (numpy array) Radius vector for velocity profile (units of arcseconds).

  • posAng_rad – (float or int, or array of float or int) Optional, default value is None. Position angle (PA) of the disc (a PA of zero means that the redshifted part of the cube is aligned with the positive y-axis). If single valued then the disc major axis is straight. If an array is passed then it should describe how the position angle changes as a function of velrad (so this can be used to create position angle warps).

  • inc_rad – (float or int, or array of float or int) Optional, default value is None. Inclination angle of the gas disc on the sky (degrees). Can input a constant or a vector, giving the inclination as a function of the radius vector ‘velrad’ (in order to model warps etc).

Return los_vel

(numpy array) Line-of-sight velocities for projected particles positioned by velRad.

save_fits(cube, cent)

Outputs a .fits file containing the datacube and relevant header information.

Parameters

  • cube – (numpy array) 3 dimensional spectral cube required for saving to .fits file

  • cent – (numpy array of intigers) Location of the central x and y positions (in units of pixels), and index of the central velocity channel.

Returns

None

gasGravity_velocity(x_pos, y_pos, z_pos, massDist, velRad)

Calculates an array of line-of-sight velocity alterations, accounting for the effects of the mass of gas in the disk (in this case assuming spherical symmetry).

Parameters

  • x_pos – (numpy array) X position of each cloudlet. Units of arcseconds.

  • y_pos – (numpy array) Y position of each cloudlet. Units of arcseconds.

  • z_pos – (numpy array) Z position of each cloudlet. Units of arcseconds.

  • massDist – (numpy array) Array of ([gasmass,distance]) - total gas mass in solar masses, total distance in Mpc.

  • velRad – (numpy array) Radius vector for cloudlets (in units of pixels).

Return add_to_circ_vel

(numpy array) Additions to the circular velocity due to the internal mass of the gas, in units of km/s.

generate_cloudlets()

A helper function for generating cloudlets by running kinms_sampleFromArbDist_oneSided. Raises a KinMSError if generate_cloudlets is called but sbRad and sbProf are not set.

Returns

None

set_cloud_positions()

Calculate and return the positions and velocities of the cloudlets in inClouds, and the radial distance in the x and y plane.

Returns

None

create_warp(array, r_flat)

If the array provided has a length > 1, create a warp. If it’s a single value, create a flat profile.

Parameters

  • array – (ndarray) array containing the radial profile

  • r_flat – (ndarray) Radius of each cloudlet from the kinematic centre in the plane of the disc (units of pixels)

Returns

ndarray with the radial profile of the disc

inclination_projection(ang, x1, y1, z1)

Apply the projection as a result of inclination to the cloudlets.

Parameters

  • ang – (float) inclination angle (in degrees)

  • x1 – (ndarray) x-positions of the cloudlets

  • y1 – (ndarray) y-positions of the cloudlets

  • z1 – (ndarray) z-positions of the cloudlets

Returns

x-, y-, and z-positions of the projected cloudlets

position_angle_rotation(ang, x2, y2, z2)

Apply the projection as a result of the position angle to the cloudlets.

Parameters

  • ang – (float) position angle (in degrees)

  • x2 – (ndarray) x-positions of the cloudlets

  • y2 – (ndarray) y-positions of the cloudlets

  • z2 – (ndarray) z-positions of the cloudlets

Returns

x-, y-, and z-positions of the projected cloudlets

set_cloud_velocities()

Find the los velocity and cube position of the clouds. If los velocity specified, assume that the clouds have already been projected correctly.

Returns

arrays with the x-, y-, and z- positions of the cloudlets, and their los velocities

find_clouds_in_cube(los_vel, cent, x2, y2, x_size, y_size, v_size)

Returns the clouds that lie inside the cube.

Parameters

  • los_vel – (ndarray) contains the line of sight velocities of each cloudlet, in km/s.

  • cent – (ndarray of length 2) contains the x and y coordinates of the centre of the object within the cube

  • x2 – (ndarray) x-positions of the cloudlets within the cube

  • y2 – (ndarray) y-positions of the cloudlets within the cube

  • x_size – (int) size of the cube in the x-direction

  • y_size – (int) size of the cube in the y-direction

  • v_size – (int) size of the cube in the z-direction

Returns

arrays with the positions of the cloudlets within the cube, and the indices of these positions

add_fluxes(clouds2do, subs, x_size, y_size, v_size)

If there are clouds to use, and we know the flux of each cloud, add them to the cube. If not, bin each position to get a relative flux.

Parameters

  • clouds2do – (ndarray) contains the x-, y-, and v-positions of the cloudslets in the cube

  • subs – (ndarray) the indices of the cloudlets in the cube

  • x_size – (int) size of the cube in the x-direction

  • y_size – (int) size of the cube in the y-direction

  • v_size – (int) size of the cube in the v-direction

Returns

spectral cube with fluxes added to the cloudlets

normalise_cube(cube, psf)

Normalise cube by the known integrated flux.

Parameters

  • cube – (3D array) unnormalised spectral cube

  • psf – (2D array) psf of the mock observations, to convolve the cube with

model_cube(toplot=False, **kwargs)

Do the actual modelling of the spectral cube

Returns

~~the cube~~