Galaxy kinematics

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr> & Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Fonctions related to kinematical modelling of galaxies.

galaxy.kinematics.apply_mask(mask, image)[source]

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr> & Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

This function applies a mask to an image and puts nan in the masked area.

Parameters

  • mask (ndarray) – array containing the indices of the pixels to be masked

  • image (ndarray) – image to be masked

Returns

the masked image

Return type

ndarray

galaxy.kinematics.clean_galaxy(path, outputpath, name, lsfw, fraction, clean=None, data_mask='snr', thrl=None, thru=None, option='_ssmooth', line='_OII3729')[source]

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr> & Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

This function cleans the maps created by CAMEL for a given galaxy.

Parameters

  • fraction (float) – fraction for a lower threshold on the velocity dispersion map

  • lsfw (float) – spectral resolution in km/s (sigma)

  • name (str) – name of the galaxy

  • ouputpath (str) – path where the ouput data will be stored

  • path (str) – path where the input data are stored

  • clean (str) – (Optional) name of the manually cleaned map. If None, no cleaned map is used to add an additional mask.

  • data_mask (str or list[str]) – (Optional) basename of the map used for the threshold (e.g. ‘snr’ to use the signal to noise ratio map)

  • line (str) – (Optional) line used (suffixe, e.g. ‘_Ha’)

  • option (str) – (Optional) option of CAMEL to find the files to clean (e.g. ‘_ssmooth’)

  • thrl (float or list[float]) – (Optional) lower threshold for cleaning. Is None, the minimum (apart from nan) will be used.

  • thru (float or list[float]) – (Optional) upper threshold for cleaning. Is None, the maximum (apart from nan) will be used.

Returns

None

galaxy.kinematics.clean_setofgalaxies(path, filename='galsList.input', logFile='folderList.list', fraction=1.0, data_mask='snr', thrl=None, thru=None, option='_ssmooth', line='_OII3729', clean=None)[source]

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr> & Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Clean maps created by camel for a list of galaxies.

Note

How to use

Provide:

  • a filename containing two columns: the absolute file name of every galaxy config file (thus ending with .config) and their corresponding spectral resolution in km/s (e.g. /home/wilfried/CGr114_s/o2/CGr114_101_o2.config 30).

  • a keyword for the additional mask (apart from the spectral width criterion), or a list of keywords

  • thresholds if necessary

  • a clean map if there is one. The same name will be used for every galaxy. Best practice would be to use an identical name for all the galaxies (located in different folders), such as ‘clean.fits’.

Parameters

  • filename (str) – name of the input file containing two columns: the list of galaxies and the associated spectral resolution in km/s (sigma)

  • path (str) – path where the input file is stored

  • logFile (str) – name of of the file containing the list of the output folder names

  • clean (str) – (Optional) name of the manually cleaned map.If None, no clean file is used to add an another manual mask.

  • data_mask (str or list[str]) – (Optional) basename of the map used for threshold (e.g. ‘snr’ for signal to noise ratio map)

  • fraction (float) – (Optional) fraction for a lower threshold on the velocity dispersion map

  • thrl (float) – (Optional) lower threshold for cleaning. Is None, the minimum (apart from nan) will be used.

  • thru (float) – (Optional) upper threshold for cleaning. If None, the maximum (apart from nan) will be used.

  • option (str) – (Optional) option from camel to find the files to clean (e.g. ‘_ssmooth’)

  • line (str) – (Optional) line used (suffixe, e.g. ‘_Ha’)

Returns

None

galaxy.kinematics.compute_velres(z: float, lbda0: float, a2: float = 5.835e-08, a1: float = - 0.000908, a0: float = 5.983) → Tuple[float][source]

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr>

Compute the spectral resolution in terms of velocity sigma from the line restframe wavelength, the redshift of the source and from MUSE LSF model

\[{\rm{FWHM}}(\lambda) = a2 \times \lambda^2 + a1 \times \lambda + a0\]
Parameters

  • lbda0 (float) – rest frame wavelength of the line used to infer kinematics in Angstroms

  • z (float) – redshift of the galaxy

  • a0 (float) – (Optional) lambda ** 0 coefficient of the variation of LSF FWHM with respect to lambda

  • a1 (float) – (Optional) lambda ** 1 coefficient of the variation of LSF FWHM with respect to lambda

  • a2 (float) – (Optional) lambda ** 2 coefficient of the variation of LSF FWHM with respect to lambda

Returns

the observed (redshifted) wavelength, the LSF FWHM in Angstroms and the LSF dispersion in km/s, assuming a Gaussian shape for the LSF profile.

Return type

float, float and float

galaxy.kinematics.correct_redshift(z: Union[float, numpy.ndarray], Vsys: Union[float, numpy.ndarray, astropy.units.quantity.Quantity]) → Union[float, numpy.ndarray][source]

Correct the given redshifts using the systemic velocity due to the galaxies proper motion.

Parameters

  • z (float or ndarray) – cosmological redshift

  • Vsys (float, ndarray or Astropy Quantity) – systemic velocity in km/s if not an Astropy Quantity

Returns

corrected redshifts

Return type

float or ndarray

galaxy.kinematics.create_mask(image, thrl=None, thru=None)[source]

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr> & Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

This function creates a mask from an image using a lower and an upper threshold.

Parameters

  • image (ndarray) – image used to create the mask

  • thrl (float) – (Optional) lower threshold

  • thru (float) – (Optional) upper threshold

Returns

boolean mask (True everywhere thrl<=image<=thru)

Return type

ndarray(bool)

galaxy.kinematics.velocityAtR(radius, Vt, Rt, Rlast, verbose=True)[source]

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Assuming a linear ramp model, try to compute the velocity at a single radius

\[V(R) = V_t \times R/r_t \ \ \rm{if}\ \ R \leq r_t \ \ \rm{else} \ \ V_t.\]
Parameters

  • radius (int or float) – position where the velocity must be computed (in the same units as Rt and Rlast)

  • Vt (float) – plateau velocity

  • Rt (float) – radius of transition between the inner linear slope and the outer plateau

  • Rlast (float) – distance from the centre of the furthest pixel used in the fit

  • verbose (bool) – (Optional) whether print error messages or not

Returns

the computed velocity in units of Vt and a boolean value indicating whether the computed value is reliable or not

Return type

int or float and bool

galaxy.kinematics.velres_setofgalaxies(inname, outname, lbda0, a2=5.835e-08, a1=- 0.000908, a0=5.983)[source]

Code author: Epinat Benoit - LAM <benoit.epinat@lam.fr> & Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Compute the resolution in velocity for a list of galaxies and write it into an output file along the corresponding file name.

Note

How to use

Provide an input and output file names and the line rest-frame wavelength in Angstroms. The input file shoudl contain the following columns:

  • galaxy file names

  • redshift of the galaxies

Parameters

  • inname (str) – input file name containing the list of galaxies and their redshift. In this version, the redshift is in the name itself, as well as the line used.

  • outname (str) – output file name containing the list of galaxies and the spectral resolution

  • a0 (float) – (Optional) lambda ** 0 coefficient of the variation of LSF FWHM with respect to lambda

  • a1 (float) – (Optional) lambda ** 1 coefficient of the variation of LSF FWHM with respect to lambda

  • a2 (float) – (Optional) lambda ** 2 coefficient of the variation of LSF FWHM with respect to lambda

Returns

None