API Reference

API Reference#

The API reference guide contains detailed descriptions of the functions and classes of BowshockPy

`bowshockpy.models`#

This module contains the implementation of the momentum conserving bowshock model

class bowshockpy.models.BaseModel(distpc)

Bases: object

Parent Class of Models.

Parameters#

distpcfloat: Distance from the observer to the source in pc

stoyr(value)

Converts seconds to years

Parameters#

valuefloat: Seconds to convert to years

Returns#

float: Years

solMasskm2togcm2(value)

Converts solar masses/km**2 to g/cm**2

Parameters#

valuefloat: Solar masses per km^2 to convert to g/cm^2

Returns#

float: g/cm2

solMasskm3togcm3(value)

Converts solar masses/km**3 to g/cm**3

Parameters#

valuefloat: Solar masses per km^3 to convert to g/cm^3

Returns#

float: g/cm3

km2arcsec(value)

Converts km to arcsec

Parameters#

valuefloat: km to convert to arcsec

Returns#

float: g/cm3

class bowshockpy.models.BowshockModel(L0, zj, vj, va, v0, mass, distpc, rbf_obs=None, rbf_niters=1000)

Bases: BaseModel

Bowshock model for a negligible internal working surface radius.

Parameters#

L0float: Characteristic scale of the bowshock [km]
zjfloat: Distance between the source and the internal working surface [km]
vjfloat: Velocity of the internal working surface [km/s]
vafloat: Velocity of the ambient gas surrounding the jet [km/s]
v0float: Velocity at which the material is ejected sideways from the internal working surface [km/s]
massfloat: Total mass of the bowshock shell [Solar masses]
distpcfloat: Distance between the source and the observer [pc]
rbf_obs: float | None, optional: Final radius of the bowshock [km]. If None, the theoretical final radius is calculated.
rbf_niters: float, optional: Number of iterations to compute the final radius of the bowshock, used only if rbf_obs is None. Default is 1000

Attributes:#

L0float: Characteristic scale of the bowshock [km]
zjfloat: Distance between the source and the internal working surface [km]
vjfloat: Velocity of the internal working surface [km/s]
vafloat: Velocity of the ambient gas surrounding the jet [km/s]
v0float: Velocity at which the material is ejected sideways from the internal working surface [km/s]
massfloat: Total mass of the bowshock shell [Solar masses]
distpcfloat: Distance between the source and the observer [pc]
rbf_obs: float | None: Final radius of the bowshock [km]
rbf_niters: float: Number of iterations to compute the final radius of the bowshock
rbffloat: Final radius of the bowshock [km]
zbffloat: z coordinate at the final radius rbf [km]
tjfloat: Dynamical time defined as zj / vj [s].
tj_yrfloat: Dynamical time in yrs.
rhoafloat: Ambient density [Msun km^3]
rhoa_gcm3float: Ambient density [g cm^-3]
mp0float: Mass rate at which the jet material is ejected sideways from the internal working surface [Msun / s]
mp0_solmassyrfloat: Mass rate at which the jet material is ejected sideways from the internal working surface [Msun / yr]
mpamb_ffloat: Mass rate of ambient material is incorporated into the bowshock shell [Msun / s]
mpamb_f_solmassyrfloat: Mass rate of ambient material is incorporated into the bowshock shell [Msun / yr]
zj_arcsecfloat: Distance from the source to the internal working surface [arcsec]
L0_arcsecfloat: Bowshock characteristic scale [arcsec]
rbf_arcsecfloat: Final radius of the bowshock [arcsec]
zbf_arcsecfloat: z-coordinate at the final radius [arcsec]

References:#

[1] Tabone, B., Raga, A., Cabrit, S. & Pineau des Forêts, G. “Interaction between a pulsating jet and a surrounding disk wind. A hydrodynamical perspective.” Astron. Astrophys. 614, A119 (2018).

[2] Ostriker, E. C., Lee, C.-F., Stone, J. M. & Mundy, L. G. A Ballistic Bow Shock Model for Jet-driven Protostellar Outflow Shells. Astrophys. J. 557, 443–450 (2001).

[3] Blazquez-Calero, G., et al. (under rev.)

gamma()

Computes the gamma parameter, defined as gamma = (vj - va) / v0

Returns#

float: gamma parameter

rb(zb)

Bowshock radius for a given z coordinate of the bowshock

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Bowshock radius at zb [km]

vr(zb)

Computes the transversal component of the velocity (along the r-axis, perpendicular to the symmetry axis of the bowshock)

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Transversal component of the velocity [km/s]

vz(zb)

Computes the longitudinal component of the velocity (along z-axis, the symmetry axis of the bowshock)

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Longitudinal component of the velocity [km/s]

vtot(zb)

Computes the total speed of the velocity

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Speed of the bowshock at zb [km/s]

velangle(zb)

Computes the angle between the bowshock axis and the velocity

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Angle between the bowshock axis and the velocity [radians]

tangent_angle(zb)

Computes the angle between the bowshock axis and the local tangent to the shell surface at the z-coordinate of the bowshock zb. The angle is measured with respect to the symmetry axis of the bowshock towards the negative z-coordinate, so the angle is <90.

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Angle between the bowshock axis and the local tangent to the shell surface at the z-coordinate of the bowshock zb [radians]

tangent_angle_rb(rb)

Computes the angle between the bowshock axis and the local tangent to the shell surface at the z-coordinate of the bowshock zb

Parameters#

rbfloat: r coordinate of the bowshock [km]

Returns#

float: Angle between the bowshock axis and the local tangent to the shell surface at the z-coordinate of the bowshock zb [radians]

theta(zb)

Computes the polar angle of the position vector

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: Polar angle of the position vector in radians

rbf_0(rr)

This is the target function to minimize by rbf_calc() to find the theoretical final radius

Parameters#

rrfloat: r coordinate of the bowshock [km]

Returns#

float: Value to minimize (it will be zero when rr is the final radius of the bowshock)

rbf_calc(ns=None, use_minimize=True)

Computes numerically the bowshock final radius

Parameters#

use_minimizebool: If True, scipy.optimize.minimize_scalar is used. If False, rbf is computed by brute force
nsint: number of iteractions to compute rbf by brute force if use_minimize=False

Returns:#

float: Solution for the final radius of the bowshock [km]

zb_r(rr)

Bowshock z coordinate for a given radius of the bowshock

Parameters#

rrfloat: radius of the bowshock [km]

Returns#

float: z coordinate of the bowshock [km]

surfdens(zb)

Computes the surface density of the bowshock

Parameters#

zbfloat: z coordinate of the bowshock [km]

Returns#

float: surface density at zb [solmass/km^2]

dr_func(zb, dz)

Differential of r given a differential of z

Parameters#

zbfloat: z coordinate of the bowshock [km]
dzfloat: increment in z [km]

Returns#

float: differential of r [km]

dz_func(zb, dr)

Differential of r given a differential of z

Parameters#

zbfloat: z coordinate of the bowshock [km]
drfloat: increment in radius [km]

Returns#

float: differential of r [km]

dsurf_func(zb, dz, dphi)

Differential of surface given a differential in z and phi (azimuthal angle)

Parameters#

zbfloat: z coordinate of the bowshock [km]
dzfloat: increment in radius [km]
dphifloat: increment in azimuthal angle [radians]

Returns#

float: differential of surface [Msun/km^2]

dmass_func(zb, dz, dphi)

Differential of mass given a differential in z and phi (azimuthal angle)

Parameters#

zbfloat: z coordinate of the bowshock [km]
dzfloat: increment in radius [km]
dphifloat: increment in azimuthal angle [radians]

Returns#

float: differential of mass [Msun]

intmass_analytical(rbf)

Computes the total mass of the bowshock shell

Parameters#

rbffloat: final radius of the bowshock [km]

Returns#

float: Total mass of the shell [Msun]

intmass_numerical(r0, rbf, return_residual=False)

Computes numerically the total mass of the bowshock shell in a range of radius from r0 to rbf

Parameters#

r0float: initial radius of the bowshock [km]
rbffloat: final radius of the bowshock [km]

Returns#

float: Total mass of the shell [Msun]

rhoa_fromintmass_analytical(rb, massint)

Computes the ambient density given the integrated mass of the bowshock at rb

Parameters#

rbfloat: radius of the bowshock [km]
massintfloat: integrated mass of the bowshock shell up to rb [Msun]

Returns#

float: Density of the ambient [Msun/km^3]

rhoa_fromintmass_sigma_simple(R0, Rb, massint, return_residual=False)

Computes numerically the ambient density taken into account the integrated mass in a range of radii from R0 to Rb

Parameters#

R0float: initial radius of the bowshock [km]
Rbfloat: radius of the bowshock [km]
massintfloat: integrated mass of the bowshock shell from R0 to Rb [Msun]

Returns#

float: Density of the ambient [Msun/km^3]

mp0_calc(rhoa)

Computes the mass rate at which the jet material is ejected sideways from the internal working surface

Parameters#

rhoafloat: Ambient density

Returns#

float: Mass rate at which the jet material is ejected sideways from the internal working surface [Msun/s]

mpamb_f_calc(rhoa)

Computes the mass rate of ambient material incorporated into the bowshock shell

Parameters#

rhoafloat: Ambient density

Returns#

float: Mass rate of the ambient incorporated into the bowshock [Msun/s]

get_modelplot(modelname='none', nzs=200, figsize=(16, 3), narrows=10, v_arrow_ref=100, linespacing=0.08, textbox_widthratio=0.7, **kwargs)

Plot a figure including the main parameters of the bowshock model, its morphology and kinematics, and the distribution of the surface density

Parameters#

modelnamestr, optional: Name of the model to include in the plot
nzsint, optional: Number of points used to compute the model solutions
figsizetuple, optional: Tuple passed to matplotib.pyplot.figure to define the dimensions of the figure
narrowsint, optional: Number of arrows to show in order to indicate the velocity at each symmetrical half of the model.
v_arrow_reffloat, optional: Velocity in km/s to use as reference in the reference arrow
linespacingfloat, optional: Spacing between the text lines
textbox_widthratiofloat, optional: Width ratio of the text ax to pass to GridSpec
kwargsoptional: Keyword arguments into ~bowshockpy.plot.BowshockModelPlot

Returns#

modelplot~bowshockpy.plot.BowshockModelPlot class instance: An instance of a class BowshockModelPlot, which contains information on the figure and the model data

class bowshockpy.models.IWSModel(a, z0, zf, vf, vj, sigma_max, distpc)

Bases: BaseModel

Geometrical model of an internal working surface

Parameters#

afloat: Constant that controls the collimation of the paraboloid
z0float: z-coordinate (symmetry axis) of the apex of the paraboloid [km]
zffloat: z-coordinate (symmetry axis) of the edge of the paraboloid [km]
vjfloat: velocity of the jet (z-component of the velocity of the paraboloid at the apex) [km/s]
sigma_maxfloat: Maximum density at the apex
distpcfloat: Distance to the source from the observer in pc

References:#

[1] Tafalla M., Su Y.-N., Shang H., Johnstone D., Zhang Q., Santiago-García J., Lee C.-F., et al., 2017, A&A, 597, A119.

rb(zb)

Radius of the model for a given z coordinate

Parameters#

zbfloat: z-coordinate [km]

Returns#

float: Shell radius at zb [km]

v_tan(zb)

Computes the magnitude of the velocities tangent to the shell surface in the reference frame comoving with the jet

Parameters#

zbfloat: z-coordinate [km]

Returns#

float: Tangent velocity [km/s]

tangent_angle(zb)

Angle between the (z0-z) axis and the tangent to the shell surface

Parameters#

zbfloat: z-coordinate [km]

Returns#

float: Angle of the tangent to the shell surface [radians]

vz(zb)

Computes the longitudinal component of the velocity (along z-axis, the symmetry axis of the model)

Parameters#

zbfloat: z coordinate of the model [km]

Returns#

float: Longitudinal component of the velocity [km/s]

vr(zb)

Computes the radial component of the velocity (along r-axis, perpendicular symmetry axis of the model)

Parameters#

zbfloat: z-coordinate of the model [km]

Returns#

float: Transversal component of the velocity [km/s]

velangle(zb)

Computes the angle between the velocity vector and the z-axis (symmetry axis)

Parameters#

zbfloat: z-coordinate of the model [km]

Returns#

float: Angle between the velocity vector and the z-axis

vtot(zb)

Computes the total speed of the velocity

Parameters#

zbfloat: z-coordinate of the model [km]

Returns#

float: Speed of the model at zb [km/s]

zb_r(rr)

z-coordinate for a given radius of the model shell

Parameters#

rrfloat: radius of the model shell [km]

Returns#

float: z coordinate of the model shell [km]

surfdens(zb)

Surface density of the shell as a function of z-coordinate. The surface density follows a square-root law when r>rf/2, and is constant for r<=rf/2.

Parameters#

zbfloat: z-coordinate [km]

Returns#

float: Surface density of the shell at zb

dz_func(zb, dr)

Differential dz at zb

Parameters#

zbfloat: z-coordinate [km]
drfloat: Differential or radius [km]

Returns#

float: Differential of z [km]

dsurf_func(zb, dz, dphi)

Differential of surface given a differential in z and phi

Parameters#

zbfloat: z coordinate [km]
dzfloat: Differential of z [km]
dphiphi: Differential of azimuthal angle [radians]

Returns#

float: Differential surface density

dmass_func(zb, dz, dphi)

Differential of mass given a differential in z and phi

Parameters#

zbfloat: z coordinate [km]
dzfloat: Differential of z [km]
dphiphi: Differential of azimuthal angle [radians]

Returns#

float: Differential of mass [Msun]

`bowshockpy.modelproj`#

This module contains the class that projects the bowshock model morphology and kinematics

class bowshockpy.modelproj.ObsModel(model, i_deg, pa_deg=0, vsys=0)

Bases: BaseModel

Computes the projected morphology and kinematics of a BowshockModel model

Parameters#

modelclass instance: instance of BowshockModel model to get the attributes
i_degfloat: Inclination angle between the bowshock axis and the line-of-sight [degrees]
pa_degfloat, optional: Position angle, default 0 [degrees]
vsysfloat, optional: Systemic velocity of the source, default 0 [km/s]

vzp(zb, phi)

Calculates the line-of-sight velocity for a point of the bowshock shell with (zb, phi)

Parameters#

zbfloat: z coordinate of the bowshock [km]
phifloat: azimuthal angle [radians]

Returns#

float: Line-of-sight velocity [km/s]

xp(zb, phi)

Calculates the xp coordinate for a point of the bowshock shell with (zb, phi)

Parameters#

zbfloat: z coordinate of the bowshock [km]
phifloat: azimuthal angle [radians]

Returns#

float: xp coordinate in the plane-of-sky [km]

yp(zb, phi)

Calculates the yp coordinate for a point of the bowshock shell with (zb, phi)

Parameters#

zbfloat: z coordinate of the bowshock [km]
phifloat: azimuthal angle [radians]

Returns#

float: yp coordinate in the plane-of-sky [km]

zp(zb, phi)

Calculates the xp coordinate for a point of the bowshock shell with (zb, phi)

Parameters#

zbfloat: z coordinate of the bowshock [km]
phifloat: azimuthal angle [radians]

Returns#

float: zp coordinate, along the line-of-sight direction [km]

get_obsmodelplot(modelname='none', nzs=150, nphis=150, figsize=(12, 6), linespacing=0.09, textbox_widthratio=0.8, cmap='turbo', minpointsize=0.1, maxpointsize=10, **kwargs)

Plot a figure including the main parameters of the bowshock model, its morphology and kinematics, and the distribution of the surface density

Parameters#

modelnamestr, optional: Name of the model to include in the plot
nzsint, optional: Number of z coordinates used to compute the model solutions
nphisint, optional: Number of phi coordinates used to compute the model solutions
figsize: tuple, optional: Tuple passed to matplotib.pyplot.figure to define the dimensions of the figure
linespacingfloat, optional: Spacing between the text lines
textbox_widthratiofloat, optional: Width ratio of the text ax to pass to GridSpec
cmapstr, optional: Colormap label
minpointsizefloat, optional: Minsize of the points to plot
maxpointsizefloat, optional: Minsize of the points to plot
kwargsoptional: Keyword arguments into ~bowshockpy.plot.BowshockObsModelPlot

Returns#

modelplot~bowshockpy.plot.BowshockObsModelPlot class instance: An instance of a class BowshockModelPlot, which contains information on the figure and the model data

`bowshockpy.cubemass`#

This module contains the tools that allows to compute the masses in a spectral cube of a bowshock model

class bowshockpy.cubemass.MassCube(obsmodel, nphis, xpmax, vch0, vchf=None, chanwidth=None, nzs=200, nc=50, nxs=200, nys=200, refpix=[0, 0], cic=True, vt='2xchannel', tolfactor_vt=None, massdiff_tol=0.1, verbose=True)

Bases: ObsModel

Computes the spectral cube of the bowshock model

Parameters#

obsmodelclass instance: Instance of ObsModel
nphisint: Number of azimuthal angles phi to calculate the bowshock solution
xpmaxfloat: Physical size of the channel maps along the x axis [arcsec]
vch0float: Central velocity of the first channel map [km/s]
vchffloat | None: Central velocity of the last channel map [km/s]. If a float is provided, chanwidth input argument should be None, since chanwidth would be computed internally. If vchf is None, you should provide instead the channel width using chanwidth argument. Default is None.
chanwidthfloat | None: Channel width of the spectral cube [km/s]. If a float is provided, vchf input argument should be None, since vchf would be computed internally. If chanwidth>0 then vch0<vchf, if chanwidth<0 then vch0>vchf. If None, you should provide instead the central velocity of the last channel map using vchf argument. Default is None.
nzsint, optional: Number of points used to compute the model solutions
ncint, optional: Number of spectral channel maps
nxsint, optional: Number of pixels in the right ascension axis.
nysint, optional: Number of pixels in the declination axis.
refpixlist | None, optional: Pixel coordinates (zero-based) of the source, i.e., the origin from which the distances are measured. The first index is the R.A. axis, the second is the Dec. axis [[int, int] or None]
cicbolean, optional: Set to True to perform Cloud in Cell interpolation [1].
vtfloat | str, optional: Thermal+turbulent line-of-sight velocity dispersion [km/s]. If thermal+turbulent line-of-sight velocity dispersion is smaller than the instrumental spectral resolution, vt should be the spectral resolution. It can be also set to an integer times the channel width using a string (e.g., “2xchannel”)
tolfactor_vtfloat, optional: The masses corresponding to a channel map are spread along the cube in the velocity axis following a Gaussian distribution, being vt parameter the standard deviation of the Gaussian. tolfactor_vt parameter truncates the Gaussian distribution at vt * tolfactor_vt in order to make the computation substantially faster. A low tolfactor_vt can result in a warning reporting an underestimation of the total mass of the model.
massdiff_tolfloat, optional: Percentage tolerance of the difference between the input and total output mass of the model due to numerical errors.
verbosebolean, optional: Set True to verbose messages about the computation
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plot_channel

Attributes:#

nrsint: Number of model points to which the solution has been computed.
rsnumpy.ndarray: Array of the radii of the model.
drfloat: Increment of radii between the points, which is constant.
zsnumpy.ndarray: Array of the z-coordinates of the model.
dzsnumpy.ndarray: Increment of z-coordinates between the points.
phisnumpy.ndarray: Array of the azimuthal angles of the model.
dphifloat: Increment in azimuthal angle of the points of the model.
vsnumpy.ndarray: Array with the velocities of the points of the model.
velchansnumpy.ndarray: Array with the line-of-sight velocities of the channels of the spectral cube.
cubenumpy.ndarray: Spectral cube of the masses of the bowshock model.
cube_samplingnumpy.ndarray: Cube where the values are the number of model points used to sample each pixel at each channel.

References:#

[1] Fehske, H., Schneider, R., & Weiße, A. (2008), Computational Many-Particle Physics, Vol. 739 (Springer), doi: 10.1007/978-3-540-74686-7.

makecube(fromcube=None)

Makes the spectral cube of the model

Parameters#

fromcubenumpy.ndarray, optional: Cube that will be populated with the model data. If None, and empty cube will be considered.

plot_channel(chan, vmax=None, vmin=None, cmap='inferno', interpolation='bilinear', savefig=None, return_fig_axs=False)

Plots a channel map of a cube

Parameters#

chanint: Channel map to plot
vmaxfloat, optional: Maximum value of the colormap. If None (default), the maximum value of the channel is chosen.
vminfloat, optional: Minimum value of the colormap. If None (default), the minimum value of the channel is chosen.
cmapstr, optional: Label of the colormap, by default “inferno”.
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
savefigstr, optional String of the full path to save the figure. If: None, no figure is saved. By default, None.
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

plot_channels(savefig=None, return_fig_axs=False, **kwargs)

Plots several channel map of a spectral cube.

Parameters#

ncolint, optional: Number of columns in the figure, by default 4
nrowint, optional: Number of rows of the figure, by default 4
figsizetuple, optional: Size of the figure. If None, an optimal size will be computed. By default None.
wspacefloat, optional: Width space between the channel plots, by default 0.05
hspacefloat, optional: Height space between the cannel plots, by default 0.0
vmaxfloat, optional: Maximum value of the colormap. If None (default), the maximum value of the channel is chosen.
vcenter_type_, optional: _description_, by default None
vminfloat, optional: Minimum value of the colormap. If None (default), the minimum value of the channel is chosen.
cmapstr, optional: Label of the colormap, by default “inferno”.
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
unitsstr, optional: Units of the values of the cube, by default “Mass [Msun]”
xmajor_locatorfloat, optional: Major locator in x-axis, by default 1
xminor_locatorfloat, optional: Minor locator in x-axis, by default 0.2
ymajor_locatorfloat, optional: Major locator in y-axis, by default 1
yminor_locatorfloat, optional: Minor locator in y-axis, by default 0.2
refpixlist, optional: Pixel of reference, by default [0,0]
savefigstr, optional String of the full path to save the figure. If: None, no figure is saved. By default, None.

`bowshockpy.cubeproc`#

This module contains the tools that allows to compute the column densities, opacities, and intensities of the bowshock model spectral cubes

class bowshockpy.cubeproc.CubeProcessing(modelcubes, modelname='none', J=3, nu=<Quantity 345.7959899 GHz>, abund=8.5e-05, meanmolmass=2.8, mu=<Quantity 0.112 D>, Tex=<Quantity 100. K>, Tbg=<Quantity 2.7 K>, tau_custom_function=None, Inu_custom_function=None, coordcube='offset', ra_source_deg=None, dec_source_deg=None, bmin=None, bmaj=None, pabeam=0, papv=0.0, sigma_beforeconv=None, maxcube2noise=None, verbose=True, **kwargs)

Bases: MassCube

Process a MassCube instance

Parameters#

modelcubesclass instance: Instance of MassCube
modelnamestr, optional: Name of the folder in /models where the outputs will be saved
Jint, optional: Upper level of the rotational transition (e.g. 3 for transition “3-2”)
nufloat | astropy.units.Quantity, optional: Frequency of the transition. If float, the units of nu should be GHz
abundfloat, optional: Abundance relative to the molecular hydrogen
meanmolmassfloat, optional: Mean mass per H molecule.
mufloat | astropy.unit.Quantity, optional: Permanent dipole moment of the molecule. If float, the units of mu should be Debye.
Texfloat | astropy.unit.Quantity, optional: Excitation temperature. If float, the units of Tex should be Kelvin.
Tbgfloat | astropy.unit.Quantity, optional: Excitation temperature. If float, the units of Tex should be Kelvin.
tau_custom_functioncallable, optional: By default, BowshockPy will compute the opacities from a rotational transition of a linear molecule (neglecting vibrational excited states and centrifugal distortion of the molecule). You can provide a custom function to compute the opacities from the column densities per velocity bin. This function should accept only the column densities per velocity bin, and return the opacities.
Inu_custom_functioncallable, optional: Custom function to compute the intensities from the opacities
coordcubestr, optional: Set to “sky” if you would like to set the cube headers in sky coordinates, or “offset” if you prefer them in offsets relative to the origin (the source).
ra_source_degfloat, optional: Source right ascension [deg]
dec_source_degfloat, optional: Source declination [deg]
bminfloat | None, optional: Beam minor axis [arcsec]
bmajfloat | None, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
papvfloat: Position angle used to calculate the PV [degrees]
sigma_beforeconvfloat: Standard deviation of the noise of the map, before convolution. Set to None if maxcube2noise is used.
maxcube2noisefloat: Standard deviation of the noise of the map, before convolution, relative to the maximum pixel in the cube. The actual noise will be computed after convolving. This parameter would not be used if sigma_beforeconve is not None.
verbosebolean, optional: Set True to verbose messages about the computation
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plot_channel

Attributes#

cubesdict: Dictionary of the processed cubes. Keys are abbreviations of the quantity of the cube and the operations performed to it
refpixsdict: Dictionary of the reference pixel of the cubes. Keys are abbreviations of the quantity of the cube and the operations performed to it
hdrsdict: Dictionary of the headers astropy.io.fits.header.Header of each cube. The headers are generated when savecube method is used.
areapix_cmfloat: Area of a pixel in cm.
x_FWHMfloat | None: Full width half maximum of the Gaussian beam for the x direction [pixel]
y_FWHMfloat | None: Full width half maximum of the Gaussian beam for the y direction [pixel]
beamareafloat | None: Area of the beam [pixel^2]
beamarea_srastropy.units.Quantity | None: Area of the beam in stereoradians. If no beam is provided, beamarea_sr will be None, and all the intensities will be expressed in Jy/arcsec^2
listmompvslist: List of cubes to which the moments and the position velocity diagrams are going to performed when the method self.momentsandpv_and_params_all is called

combine_cubes(modelcubes)

Combines (sums) a list of cubes

Parameters#

modelcubeslist: List of cubes to combine

calc_Ntot(): Computes the total (molecular hydrogen + heavier components) column densities of the model cube

calc_Nmol(): Computes the emitting molecule column densities of the model cube

calc_tau(): Computes the opacities of the model cube

calc_I(): Calculates the intensity [Jy/beam] of the model cube.

add_source(ck='m', value=None)

Adds a source to the cube in the reference pixel

Parameters#

ckstr, optional: Key of the cube to add the source
valuefloat, optional: Pixel value of the source. If None, the maximum of the cube will be considered

add_noise(ck='m')

Adds Gaussian noise to the cube.

Parameters#

ckstr, optional: Key of the cube to rotate

convolve(ck='m')

Convolves the cube with the defined Gaussian kernel (self.bmaj, self.bmin, self.pabeam)

Parameters#

ckstr, optional: Key of the cube to convolve

calc(userdic)

Computes the quantities and the operations to the cubes.

Parameters#

userdicdict

Dictionary indicating the desired output spectral cubes and the operations performed over them. The keys of the dictionary are strings indicating the quantities of the desired cubes. These are the available quantities of the spectral cubes:

“mass”: Total mass of molecular hydrogen in solar mass.
“mol_column_density”: Column density of the emitting molecule in cm-2.
“intensity”: Intensity in Jy/beam.
“tau”: Opacities.

The values of the dictionary are lists of strings indicating the operations to be performed over the cube. These are the available operations:

“add_source”: Add a point source at the reference pixel.
“add_noise”: Add Gaussian noise, defined by maxcube2noise parameter.
“convolve”: Convolve with a Gaussian defined by the parameters bmaj, bmin, and pabeam.
“moments_and_pv”: Computes the moments 0, 1, and 2, the maximum intensity and the PV-diagram.

The operations will be performed folowing the order of the strings in the list (from left to right). The list can be left empty if no operations are desired.

Example:#

>>> cp = CubeProcessing(...)
>>> outcubes = {
>>>    "intensity": ["add_noise", "convolve", "moments_and_pv"],
>>>    "opacity": [],
>>>    "mol_column_density": ["convolve"],
>>>    "mass": [],
>>> }
>>> cp.calc(outcubes)

will save 4 spectral cubes in fits format. The first one are the intensities with Gaussian noise added, it will be convolved, and the moments and PV-diagrams will be computed; the second cube will be the opacity; the third will be the mol_column_density, which will be convolved; and the forth cube will be the masses. The first spectral cube will be named I_nc.fits, the second tau.fits, the third Nmol_c.fits, and the fourth m.fits.

savecube(ck, fitsname=None)

Saves the cube in fits format

Parameters#

ckstr: Key of the cube to convolve
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}.fits. If the path does not exist, it will be created.

savecubes(cks=None)

Saves the cubes specified by userdic

Parameters#

ckslist: List of keys of the cube to save. Default is None. If None, all calculated cubes will be saved.

plot_channel(ck, chan, vmax=None, vmin=None, cmap='inferno', savefig=None, add_beam=False, return_fig_axs=False)

Plots a channel map of a cube

Parameters#

ckstr: Key of the cube to plot (see keys of self.cubes dictionary)
chanint: Channel map to plot
vmaxfloat, optional: Maximum value of the colormap. If None (default), the maximum value of the channel is chosen.
vminfloat, optional: Minimum value of the colormap. If None (default), the minimum value of the channel is chosen.
cmapstr, optional: Label of the colormap, by default “inferno”.
savefigstr, optional String of the full path to save the figure. If: None, no figure is saved. By default, None.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
return_fig_axsbool, optional: If True, returns a tuple of the ax of the channel map and the colorbar. If False, does not return anything.

Returns#

(fig, ax, cbax)tuple of matplotlib.axes.Axes Axes of the channel map: and the colorbar, only returns if return_fig_axs=True.

plot_channels(ck, savefig=None, add_beam=False, return_fig_axs=False, **kwargs)

Plots several channel map of a spectral cube.

Parameters#

ckstr: Key of the cube to plot (see keys of self.cubes dictionary)
ncolint, optional: Number of columns in the figure, by default 4
nrowint, optional: Number of rows of the figure, by default 4
figsizetuple, optional: Size of the figure. If None, an optimal size will be computed. By default None.
wspacefloat, optional: Width space between the channel plots, by default 0.05
hspacefloat, optional: Height space between the cannel plots, by default 0.0
vmaxfloat, optional: Maximum value of the colormap. If None (default), the maximum value of the channel is chosen.
vcenter_type_, optional: _description_, by default None
vminfloat, optional: Minimum value of the colormap. If None (default), the minimum value of the channel is chosen.
cmapstr, optional: Label of the colormap, by default “inferno”.
unitsstr, optional: Units of the values of the cube, by default “Mass [Msun]”
xmajor_locatorfloat, optional: Major locator in x-axis, by default 1
xminor_locatorfloat, optional: Minor locator in x-axis, by default 0.2
ymajor_locatorfloat, optional: Major locator in y-axis, by default 1
yminor_locatorfloat, optional: Minor locator in y-axis, by default 0.2
refpixlist, optional: Pixel of reference, by default [0,0]
savefigstr, optional String of the full path to save the figure. If: None, no figure is saved. By default, None.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

pvalongz(ck, halfwidth=0, savefits=False, fitsname=None)

Performs the position velocity diagram along the self.papv direction

Parameters#

ckstr: Key of the cube to perform the PV-diagram.
halfwidthint, optional: Number of pixels around xpv that will be taking into account to compute the PV-diagram.
savefitsboolean: If True, save the PV-diagram in fits format.
fitsnamestr: Full path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_pv.fits. If the path does not exist, it will be created.

Returns#

pvimagenumpy.ndarray: Position velocity diagram

sumint(ck, chan_range=None, savefits=False, fitsname=None)

Computes the image of the summation of pixels of the cube along the velocity axis

Parameters#

ckstr: Key of the cube to perfomr the PV-diagram.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
savefitsboolean: If True, save the PV-diagram in fits format.
fitsnamestr: Full path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_sumint.fits. If the path does not exist, it will be created.

Returns#

sumintnumpy.ndarray: Image of the summation of the pixels of the cube along the velocty axis

mom0(ck, chan_range=None, savefits=False, fitsname=None)

Computes the 0th order moment along the velocity axis

Parameters#

ckstr: Key of the cube to perfomr the PV-diagram.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
savefitsboolean: If True, save the PV-diagram in fits format.
fitsnamestr: Full path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_mom0.fits. If the path does not exist, it will be created.

Returns#

mom0numpy.ndarray: Moment 0 image of the cube

mom1(ck, chan_range=None, clipping=0, savefits=False, fitsname=None)

Computes the 1th order moment along the velocity axis

Parameters#

ckstr: Key of the cube to perfomr the PV-diagram.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
clippingfloat, optional: Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
savefitsboolean, optional: If True, save the PV-diagram in fits format.
fitsnamestr: Full path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_mom1.fits. If the path does not exist, it will be created.

Returns#

mom1numpy.ndarray: Moment 1 image of the cube

mom2(ck, chan_range=None, clipping=0, savefits=False, fitsname=None)

Computes the 2th order moment along the velocity axis

Parameters#

ckstr: Key of the cube to perfomr the PV-diagram.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
clippingfloat, optional: Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
savefitsboolean, optional: If True, save the PV-diagram in fits format.
fitsnamestr, optional: Full path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_mom2.fits. If the path does not exist, it will be created.

Returns#

mom2numpy.ndarray: Moment 2 image of the cube

maxintens(ck, chan_range=None, clipping=0, savefits=False, fitsname=None)

Computes the maximum value of the cube along the velocity axis

Parameters#

ckstr: Key of the cube to perfomr the moment.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
clippingfloat, optional: Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
savefitsboolean, optional: If True, save the moment in fits format.
fitsnamestr, optional: Full path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_maxintens.fits. If the path does not exist, it will be created.

Returns#

maxintensnumpy.ndarray: Maximum value of the pixels of the cubes along the velocity axis

plotpv(ck, halfwidth, ax=None, cbax=None, savefits=False, fitsname=None, savefig=None, return_fig_axs_im=False, **kwargs)

Plots the position velocity diagram.

Parameters#

ckstr: Key of the cube to which the PV-diagram will be computed.
halfwidthint, optional: Number of pixels around xpv that will be taking into account to compute the PV-diagram.
axmatplotlib.axes.Axes, optional The matplotlib.axes.Axes` instance: in which the position velodity diagram is drawn. If None, it will create one. By default, None
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn. If None, it will create one. By default, None
savefitsbool: If True, the position velocity diagram will be saved in fits format
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_pv.fits. If the path does not exist, it will be created.
savefigstr, optional: String of the full path to save the figure. If None, no figure is saved. By default, None.
return_fig_axs_imbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the image. If False, does not return anything.
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plotpv

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_im=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_im=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_im=True.
pvimagenumpy.ndarray: Position velocity diagram

plotsumint(ck, chan_range=None, ax=None, cbax=None, add_beam=False, savefits=False, fitsname=False, savefig=None, return_fig_axs_im=False, **kwargs)

Plots the sum of the pixels of the cubes along the velocity axis.

Parameters#

ckstr: Key of the cube to which the moment will be computed.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes` instance in which the position velodity diagram is drawn. If None, it will create one. By default, None
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn. If None, it will create one. By default, None
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
savefitsbool: If True, the moment will be saved in fits format
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_sumint.fits. If the path does not exist, it will be created.
savefigstr, optional: String of the full path to save the figure. If None, no figure is saved. By default, None.
return_fig_axs_imbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the image. If False, does not return anything.
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plotsumint

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_im=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_im=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_im=True.
sumintnumpy.ndarray: Sum of all the pixels along the velocity axis.

plotmom0(ck, chan_range=None, ax=None, cbax=None, add_beam=False, savefits=False, fitsname=None, savefig=None, return_fig_axs_im=False, **kwargs)

Plots the moment 0 (integrated intensity).

Parameters#

ckstr: Key of the cube to which the moment will be computed.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes` instance in which the position velodity diagram is drawn. If None, it will create one. By default, None
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn. If None, it will create one. By default, None
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
savefitsbool: If True, the moment will be saved in fits format
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_mom0.fits. If the path does not exist, it will be created.
savefigstr, optional: String of the full path to save the figure. If None, no figure is saved. By default, None.
return_fig_axs_imbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the image. If False, does not return anything.
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plotmom0

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_im=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_im=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_im=True.
mom0numpy.ndarray: Integrated intensity

plotmom1(ck, chan_range=None, mom1clipping=0, ax=None, cbax=None, add_beam=False, savefits=False, fitsname=None, savefig=None, return_fig_axs_im=False, **kwargs)

Plots the moment 1 (Intensity weighted mean velocity field).

Parameters#

ckstr: Key of the cube to which the moment will be computed.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
mom1clippingfloat: Clipping to in order to compute the moment 1. Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes` instance in which the position velodity diagram is drawn. If None, it will create one. By default, None
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn. If None, it will create one. By default, None
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
savefitsbool: If True, the moment will be saved in fits format.
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_mom1.fits. If the path does not exist, it will be created.
savefigstr, optional: String of the full path to save the figure. If None, no figure is saved. By default, None.
return_fig_axs_imbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the image. If False, does not return anything.
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plotmom1

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_im=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_im=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_im=True.
mom1numpy.ndarray: Intensity weighted velocity field.

plotmom2(ck, chan_range=None, mom2clipping=0, ax=None, cbax=None, add_beam=False, savefits=False, fitsname=None, savefig=None, return_fig_axs_im=False, **kwargs)

Plots the moment 2 (velocity dispersion).

Parameters#

ckstr: Key of the cube to which the moment will be computed.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
mom2clippingfloat: Clipping to in order to compute the moment 2. Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
axmatplotlib.axes.Axes, optional The matplotlib.axes.Axes` instance: in which the position velodity diagram is drawn. If None, it will create one. By default, None
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn. If None, it will create one. By default, None
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
savefitsbool: If True, the moment will be saved in fits format
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_mom2.fits. If the path does not exist, it will be created.
savefigstr, optional: String of the full path to save the figure. If None, no figure is saved. By default, None.
return_fig_axs_imbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the image. If False, does not return anything.
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plotmom2

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_im=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_im=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_im=True.
mom2numpy.ndarray: Velocity dispersion

plotmaxintens(ck, chan_range=None, ax=None, cbax=None, add_beam=False, savefits=False, fitsname=None, savefig=None, return_fig_axs_im=False, **kwargs)

Plots the moment 8 (peak intensity).

Parameters#

ckstr: Key of the cube to which the moment diagram will be computed.
chan_rangelist, optional: Two element list with the last and first channels used to compute the moment. If None, the whole cube will be considered.
axmatplotlib.axes.Axes, optional The matplotlib.axes.Axes` instance: in which the position velodity diagram is drawn. If None, it will create one. By default, None
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn. If None, it will create one. By default, None
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
savefitsbool: If True, the moments and the position velocity diagram will be saved in fits format
fitsnamestr: Relative path name of the fits file. If None, it will be saved as models/{self.modelname}/fits/{ck}_maxintens.fits. If the path does not exist, it will be created.
savefigstr, optional: String of the full path to save the figure. If None, no figure is saved. By default, None.
return_fig_axs_imbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the image. If False, does not return anything.
kwargsoptional: Keyword arguments into ~bowshockpy.plot.plotmaxintens

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_im=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_im=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_im=True.
maxintensnumpy.ndarray: Peak intensity

momentsandpv_and_params(ck, savefits=False, saveplot=False, mom1clipping=0, mom2clipping=0, verbose=True, chan_range=None, halfwidth_pv=0, add_beam=False, mom0values={'vcenter': None, 'vmax': None, 'vmin': None}, mom1values={'vcenter': None, 'vmax': None, 'vmin': None}, mom2values={'vcenter': None, 'vmax': None, 'vmin': None}, maxintensvalues={'vcenter': None, 'vmax': None, 'vmin': None}, pvvalues={'vcenter': None, 'vmax': None, 'vmin': None}, custom_showtext=None)

Computes the moments and position velocity diagram including also the main parameters of the model listed in the first ax

Parameters#

ckstr: Key of the cube to which the moments and the position velocity diagram will be computed.
savefitsbool: If True, the moments and the position velocity diagram will be saved in fits format
saveplotbool: If True, a plot of the moments and position velocity diagrams will be saved
mom1clippingfloat: Clipping to in order to compute the moment 1. Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
mom2clippingfloat: Clipping to in order to compute the moment 2. Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
maxintensclippingfloat: Clipping to in order to compute the maximum value of the pixels along the velocity axis. Pixels with values smaller than the one given by clipping parameter will be masked with 0 values.
mom0valuesdict or None: Dictionary with the maximum, central, and minimum value to show in the plot of the moment 0. If the dictionary value is None for vmax, vcenter, or vmin, then the maximum, central, or the minimum value of the moment image will be considered, respectively. Example: mom0values = {“vmax”: None, “vcenter”: None, “vmin”: 0,}.
mom1valuesdict or None: Dictionary with the maximum, central, and minimum value to show in the plot of the moment 1. If the dictionary value is None for vmax, vcenter, or vmin, then the maximum, central, or the minimum value of the moment image will be considered, respectively. Example: mom1values = {“vmax”: None, “vcenter”: None, “vmin”: 0,}.
mom2valuesdict or None: Dictionary with the maximum, central, and minimum value to show in the plot of the moment 2. If the dictionary value is None for vmax, vcenter, or vmin, then the maximum, central, or the minimum value of the moment image will be considered, respectively. Example: mom1values = {“vmax”: None, “vcenter”: None, “vmin”: 0,}.
maxintensvaluesdict or None: Dictionary with the maximum, central, and minimum value to show in the plot of the maximum value along the velocity axis. If the dictionary value is None for vmax, vcenter, or vmin, then the maximum, central, or the minimum value of the moment image will be considered, respectively. Example: maxintensvalues = {“vmax”: None, “vcenter”: None, “vmin”: None,}.

momentsandpv_and_params_all(**kwargs)

Computes all the moments and pv to the cubes listed in self.listmompvs, including a list of values of the main parameters of the model in the first ax

kwargsoptional: Keyword arguments into ~bowshockpy.cubeproc.CubeProcessing.momentsandpv_and_params

`bowshockpy.radtrans`#

This module contains the general equations that allows to compute the column densities and opacities, and to perform the radiative transfer

bowshockpy.radtrans.column_density_tot(m, area, meanmolmass)

Computes the total (H2 + heavier components) column density given the mass and the projected area

Parameters#

mfloat | astropy.units.Quantity: Mass. If float, units should be Solar Masses.
areafloat | astropy.units.Quantity: Projected area. If float, the area should be in cm**2.
meanmolmassfloat: Mean molecular mass per hydrogen molecule

Returns#

astropy.units.Quantity: Total column density (H2 + heavier components)

bowshockpy.radtrans.column_density_mol(Ntot, abund)

Computes the column density of a molecule given its abundance with respect to the H2

Parameters#

Ntotfloat | astropy.units.Quantity: Total column density (H2 + heavier components). If float, the column density should be given in particles per cm**2
abundfloat: Abundance relative to molecular hydrogen

Returns#

astropy.units.Quantity: Column density of the molecule

bowshockpy.radtrans.Qpart(Tex, Ei, gi, Ei_args=(), gi_args=(), tol=1e-15)

Computes the partition function.

Parameters#

Texfloat | astropy.units.quntity: Excitation temperature. If float, it should be in Kelvin
Eicallable: Function Ei(i, *Ei_args) to compute the energy at level i
gicallable: Function gi(i, *gi_args) to compute the degeneracy at level i
Ei_argstuple, optional: Extra arguments passed to Ei function
gi_argstuple, optional: Extra arguments passed to gi
tolfloat, optional: Tolerance at which the summation is stopped, by default 10**(-15)

Returns#

float: Partition function

bowshockpy.radtrans.column_density_mol_i(Nmol, Tex, i, Ei, gi, Ei_args=(), gi_args=())

Computes the column density of a molecule at energy level i.

Parameters#

Nmolfloat | astropy.units.Quantity: Column density of the emitting molecule. If float, should be in cm**(-2)
Texfloat | astropy.units.Quantity: Excitation temperature. If float, should be in Kelvin.
Eicallable: Function Ei(i, *Ei_args) to compute the energy at level i
gicallable: Function gi(i, *gi_args) to compute the degeneracy at level i
Ei_argstuple, optional: Extra arguments passed to Ei function
gi_argstuple, optional: Extra arguments passed to gi

Returns#

astropy.units.Quantity: Column density of the molecule at energy level i

bowshockpy.radtrans.A_ul(nu, mu_ul)

Calculates the spontaneous emission coeffitient for the u -> l level transition

Parameters#

nufloat | astropy.units.Quantity: Frequency of the transition. If float, it should be in GHz.
mu_ulfloat | astropy.units.Quantity: Dipole moment matrix element u,l. If float, it should be in Debye.

bowshockpy.radtrans.tau_func(dNmoldv, nu, Tex, i, Ei, gi, mu_ul, Ei_args=(), gi_args=())

Computes the opacity as a function of the column density per channel width

Parameters#

dNmoldvfloat | astropy.units.Quantity: Column density per velocity bin. If float, it should be given in cm**(-2) * s * km**(-1)
nufloat | astropy.units.Quantity: Frequency. If float, it should be in GHz.
Texastropy.units.Quantity: Excitation temperature. If float, it should be in Kelvin.
iint: Level
mu_ulfloat | astropy.units.Quantity: Dipole moment matrix element i, i-1. If float should be in Debye.
Eicallable: Function Ei(i, *Ei_args) to compute the energy at level i
gicallable: Function gi(i, *gi_args) to compute the degeneracy at level i
Ei_argstuple, optional: Extra arguments passed to Ei function
gi_argstuple, optional: Extra arguments passed to gi

Returns#

float: Opacity

bowshockpy.radtrans.exp_hnkt(nu, T)

Computes exp(h nu / k_B/T)

Parameters#

nufloat | astropy.units.Quantity: Frequency. If float, it should be in GHz
Tfloat | astropy.units.Quantity: Temperature. If float, should be in Kelvin

Returns#

float: exp(h nu / k_B/T)

bowshockpy.radtrans.Bnu_func(nu, T)

Computes the spectral radiance or specific intensity of a Planckian (energy per unit of area, time, frequency, and solid angle)

Parameters#

nufloat | astropy.units.Quantity: Frequency. If float, it should be in GHz.
Tfloat | astropy.units.Quantity: Temperature. If float, it should be in Kelvin.

Returns#

Bnuastropy.units.Quantity: Spectral radiance in u.Jy / u.sr

bowshockpy.radtrans.Inu_func(tau, nu, Tex, Tbg)

Computes the intensity through the radiative transfer equation.

Parameters#

taufloat: Opacity.
nufloat | astropy.units.Quantity: Frequency of the transition. If float, it should be in GHz
Texfloat | astropy.units.quntity: Excitation temperature. If float, it should be in Kelvin.
Tbg: float | astropy.units.Quantity: Background temperature. If float, it should be in Kelvin

Returns#

astropy.units.Quantity: Intensity (energy per unit of area, time, frequency and solid angle)

`bowshockpy.rotlinearmol`#

This module contains the implementation of the model of a rotational transition of a linear molecule. The assumptions are: Local Thermodynamical Equilibrium, negligible population of vibrational excited states, negligible centrifugal distortions

bowshockpy.rotlinearmol.gJ(J)

Degeneracy of the level J at which the measurement was made. For a linear molecule, g = 2J + 1

Parameters#

Jint: Rotational level

Returns#

int: Degeneracy of the level J

bowshockpy.rotlinearmol.B0J(J, nu)

Rigid rotor rotation constant, being nu the frequency for the transition J-> J-1. For high J an aditional term is needed

Parameters#

Jint: Rotational level
nufloat | astropy.units.Quantity: Frequency of the transition. If float, it should be in GHz

Returns#

float: Rigid rotor rotation constant.

bowshockpy.rotlinearmol.EJ(J, B0)

Energy state of a rigid rotor, neglecting centrifugal distortions

Parameters#

Jint: Rotational level
B0float | astropy.units.Quantity: Rotation constant. If float, it should be in GHz

Returns#

astropy.units.Quantity: Energy state of a rotator

bowshockpy.rotlinearmol.muJ_Jm1(J, mu)

Computes the dipole moment matrix element squared for rotational transition J->J-1

Parameters#

Jint: Rotational level
mufloat | astropy.units.Quantity: Permanent dipole moment of the molecule. If float, it should be in Debye

bowshockpy.rotlinearmol.tau_linearmol(dNmoldv, J, nu, Tex, mu)

Computes the opacity as a function of the column density per channel width for a rotational transition of a linear molecule

Parameters#

dNmoldvfloat | astropy.units.Quantity: Column density per velocity bin dv. If float, it should be in s / km / cm**2
Jint: Rotational level
nufloat | astropy.units.Quantity: Frequency. If float, it should be in GHz.
Texfloat | astropy.units.Quantity: Excitation temperature. If float, it should be in Kelvin
mufloat | astropy.units.Quantity: Permanent dipole moment of the molecule. If float, it should be in Debye

Returns#

float: Opacity

`bowshockpy.moments`#

This module contains the functions that perform the statistical moments to the spectral cubes

bowshockpy.moments.sumint(cube, chan_range)

Sums all pixels of a cube along the 0 axis.

Parameters#

cubenumpy.ndarray: Input 3 dimensional array.
chan_rangelist: Two element list with the last and first channels used to compute the summation.

Returns#

sumint_imnp.ndarray: 2 dimensional array

bowshockpy.moments.mom0(cube, chan_vels, chan_range)

Computes the moment of order 0 of a cube along the 0 axis.

Parameters#

cubenumpy.ndarray: Input 3 dimensional array.
chan_vels: list or numpy.ndarray: 1-dimensional array of the velocity corresponding to the channels.
chan_rangelist: Two element list with the last and first channels used to compute the moment.

Return:#

mom0_imnumpy.ndarray: Moment of order 0

References:#

https://www.aoc.nrao.edu/~kgolap/casa_trunk_docs/CasaRef/image.moments.html

bowshockpy.moments.summixvi(cube, chan_vels, chan_range, exp=1)

Computes the summation: sum (m_i * v_i)**exp

Parameters#

cubenumpy.array: Input 3 dimensional array
chan_velslist or numpy.array: 1-dimensional array of the velocity corresponding to the channels.
chan_rangelist: Two element list with the last and first channels used to compute the moment.
expint, optional: Exponent, by default 1

Returns#

_type_: _description_

bowshockpy.moments.mom1(cube, chan_vels, chan_range)

Computes the moment of order 1 (intensity weighted mean velocity field) of a cube along the 0 axis.

Parameters#

cubenumpy.ndarray: Input 3 dimensional array.
chan_vels: list or numpy.ndarray: 1-dimensional array of the velocity corresponding to the channels.
chan_rangelist: Two element list with the last and first channels used to compute the moment.

Return:#

mom1_imnumpy.ndarray: Moment of 1 order

References:#

https://www.aoc.nrao.edu/~kgolap/casa_trunk_docs/CasaRef/image.moments.html

But note that the equation for the moment 1 is wrong in this reference (units should be km/s, and not an adimensional value). The moment1 is the intensity intensity weighted mean velocity = Sigma m_i v_i/Sigma m_i

bowshockpy.moments.mom2(cube, chan_vels, chan_range)

Computes the moment 2 (the intensity weighted dispersion) of a cube along the 0 axis

Parameters#

cubenumpy.ndarray: Input 3 dimensional array.
chan_vels: list or numpy.ndarray: 1-dimensional array of the velocity corresponding to the channels.
chan_rangelist: Two element list with the last and first channels used to compute moment.

Return:#

dispnumpy.ndarray: Moment of 2 order

References:#

https://www.aoc.nrao.edu/~kgolap/casa_trunk_docs/CasaRef/image.moments.html

But note that the equation for the moment 2 is wrong in this reference (units should be km/s, no sqrt(km/s)). The moment2 is intensity weighted dispersion = [Sigma m_i v^2_i/Sigma m_i]**(1/2)

bowshockpy.moments.maxintens(cube, chan_range)

Computes the moment the maximum value of a cube along the along the 0 axis

Parameters#

cubenumpy.ndarray: Input 3 dimensional array
chan_rangelist: Two element list with the last and first channels used to compute the moment

Return:#

maxintens_imnumpy.ndarray: Moment 8 (maximum value along the 0 axis)

References:#

https://www.aoc.nrao.edu/~kgolap/casa_trunk_docs/CasaRef/image.moments.html

bowshockpy.moments.pv(cube, xpv, halfwidth, axis=1)

Computes the Position-Velocity diagram of a cube

Parameters#

cubenumpy.ndarray: Input 3 dimensional array.
xpvint: Pixel along which the PV-diagram is computed.
halfwidthint: Number of pixels around xpv that will be taking into account to compute the PV-diagram.

Return:#

pv_imnumpy.ndarray: PV-diagram.

`bowshockpy.plots`#

This module contains the tools to plot the bowshock model, the spectral cubes, moments maps and position-velocity diagrams

class bowshockpy.plots.BowshockModelPlot(bsm, modelname='none', nzs=200, figsize=(16, 3), narrows=10, v_arrow_ref=100, linespacing=0.08, textbox_widthratio=0.7, gs_wspace=0.2, gs_hspace=0.4)

Bases: object

Figure including the main parameters of the bowshock model, its morphology and kinematics, and the distribution of the surface density

Parameters:#

bsm~bowshockpy.models.BowshockModel class instance: Instance of the model to plot
modelnamestr, optional: Name of the model to include in the plot
nzsint, optional: Number of points used to compute the model solutions
figsizetuple, optional: Tuple passed to matplotib.pyplot.figure to define the dimensions of the figure
narrowsint, optional: Number of arrows to show in order to indicate the velocity at each symmetrical half of the model.
v_arrow_reffloat, optional: Velocity in km/s to use as reference in the reference arrow
linespacingfloat, optional: Spacing between the text lines
textbox_widthratiofloat, optional: Width ratio of the text ax to pass to GridSpec
gs_wspacefloat, optional: wspace passed to GridSpec
gs_hspacefloat, optional: hspace passed to GridSpec

Attributes:#

nzsint: Number of points used to compute the model solutions
zsnumpy.ndarray: Array of the z-coordinates of the model.
dzsnumpy.ndarray: Increment of z-coordinates between the points.
rsnumpy.ndarray: Array with the radii of the model at each z-coordinate [km].
thetasnumpy.ndarray: Array of the polar angle of the position vector at each point of the model [radians].
vsnumpy.ndarray: Array of the total velocity for each point of the model [km/s].
vrsnumpy.ndarray: Array of the radial component of the velocity at each point of the model [km/s].
vzsnumpy.ndarray: Array of the z-coordinate component of the velocity at each point of the model [km/s].
surfdenssnumpy.ndarray: Array of the surfance density of the shell at each z-coordinate [Msun km-2]
surfdenss_gcm2numpy.ndarray: Array of the surfance density of the shell at each z-coordinate [g cm-2]
axsdict: Dictionary of matplotlib.axes.Axes in the figure
cbaxsdict: Dictionary of matplotlib.axes.Axes of the colorbars in the figure

plot(custom_showtext=None, min_plotvel=None, max_plotvel=None, min_plotdens=None, max_plotdens=None, normdens='log'): Plots the 2D bowshock model

savefig(figname=None, **kwargs)

Saves the plot of the bowhsock model.

Parameters#

fignamestr, optional: Full path name of the figure. If None, the the full path name will be models/{self.modelname}/bowshock_model.pdf. If the folder tree does not exist, it will be created.
kwargsoptional: Keyword arguments into ~matplotlib.pyplot.savefig

class bowshockpy.plots.BowshockObsModelPlot(bsmobs, modelname='none', nzs=150, nphis=150, figsize=(12, 6), linespacing=0.09, textbox_widthratio=0.8, cmap='turbo', minpointsize=0.1, maxpointsize=10, x_obs_arrow=0.98, y_obs_arrow=0.95)

Bases: object

Figure including the main parameters of the bowshock model, its projected morphology, kinematics, and a PV diagram along the symmetry axis with the distribution of the surface density in color code.

Parameters:#

bsm~bowshockpy.models.BowshockModel class instance: Instance of the model to plot
modelnamestr, optional: Name of the model to include in the plot
nzsint, optional: Number of z coordinates used to compute the model solutions
nphisint, optional: Number of phi coordinates used to compute the model solutions
figsize: tuple, optional: Tuple passed to matplotib.pyplot.figure to define the dimensions of the figure
linespacingfloat, optional: Spacing between the text lines
textbox_widthratiofloat, optional: Width ratio of the text ax to pass to GridSpec
cmapstr, optional: Colormap label
minpointsizefloat, optional: Minsize of the points to plot
maxpointsizefloat, optional: Minsize of the points to plot
x_obs_arrowfloat, optional: x-axis coordinate of the reference observer arrow
y_obs_arrowfloat, optional: y-axis coordinate of the reference observer arrow

Attributes:#

nrsint: Number of r coordinates used to compute the model solutions
zsnumpy.ndarray: Array of the z-coordinates of the model.
dzsnumpy.ndarray: Increment of z-coordinates between the points.
rsnumpy.ndarray: Array with the radii of the model at each z-coordinate [km].
thetasnumpy.ndarray: Array of the polar angle of the position vector at each point of the model [radians].
vsnumpy.ndarray: Array of the total velocity for each point of the model [km/s].
vrsnumpy.ndarray: Array of the radial component of the velocity at each point of the model [km/s].
vzsnumpy.ndarray: Array of the z-coordinate component of the velocity at each point of the model [km/s].
surfdenssnumpy.ndarray: Array of the surfance density of the shell at each z-coordinate [Msun km-2]
surfdenss_gcm2numpy.ndarray: Array of the surfance density of the shell at each z-coordinate [g cm-2]
axsdict: Dictionary of matplotlib.axes.Axes in the figure
cbaxsdict: Dictionary of matplotlib.axes.Axes of the colorbars in the figure

plot(custom_showtext=None): Plots the 2D bowshock model

savefig(figname=None, **kwargs)

Saves the plot of the bowhsock model.

Parameters#

fignamestr, optional: Full path name of the figure. If None, the the full path name will be models/{self.modelname}/bowshock_projected.pdf. If the folder tree does not exist, it will be created.
kwargsoptional: Keyword arguments into ~matplotlib.pyplot.savefig

bowshockpy.plots.plot_channel(cube, chan, arcsecpix, velchans, vmax=None, vmin=None, cmap='inferno', interpolation='bilinear', units='Mass [Msun]', refpix=None, markorigin=True, add_beam=False, bmin=None, bmaj=None, pabeam=None, return_fig_axs=False)

Plots a channel map of a spectral cube

Parameters#

cubenumpy.ndarray(): Spectral cube from which the channel is plotted
chanint: Index of the channel to plot
arcsecpixfloat: Arcseconds per pixel
velchanslist or numpy.ndarray(): Array with the velocities of each channel
vmaxfloat, optional: Maximum value of the colormap. If None (default), the maximum value of the channel is chosen.
vminfloat, optional: Minimum value of the colormap. If None (default), the minimum value of the channel is chosen.
cmapstr, optional: Label of the colormap, by default “inferno”.
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
unitsstr, optional: Units of the values of the cube, by default “Mass [Msun]”
refpixlist, optional: Pixel of reference, by default [0,0]
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

bowshockpy.plots.plot_channels(cube, arcsecpix, velchans, ncol=4, nrow=4, figsize=None, wspace=0.05, hspace=0.0, vmax=None, vcenter=None, vmin=None, cmap='inferno', interpolation='bilinear', units='Mass [Msun]', xmajor_locator=1, xminor_locator=0.2, ymajor_locator=1, yminor_locator=0.2, refpix=None, markorigin=True, add_beam=False, bmin=None, bmaj=None, pabeam=None, return_fig_axs=False)

Plots several channel map of a spectral cube.

Parameters#

cubenumpy.ndarray(): Spectral cube from which the channel is plotted
arcsecpixfloat: Arcseconds per pixel
velchanslist or numpy.ndarray(): Array with the velocities of each channel
ncolint, optional: Number of columns in the figure, by default 4
nrowint, optional: Number of rows of the figure, by default 4
figsizetuple, optional: Size of the figure. If None, an optimal size will be computed. By default None.
wspacefloat, optional: Width space between the channel plots, by default 0.05
hspacefloat, optional: Height space between the cannel plots, by default 0.0
vmaxfloat, optional: Maximum value of the colormap. If None (default), the maximum value of the channel is chosen.
vcenterfloat, optional: Center value of the colormap. If None (default), the middle vale will be chosen.
vminfloat, optional: Minimum value of the colormap. If None (default), the minimum value of the channel is chosen.
cmapstr, optional: Label of the colormap, by default “inferno”.
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
unitsstr, optional: Units of the values of the cube, by default “Mass [Msun]”
xmajor_locatorfloat, optional: Major locator in x-axis, by default 1
xminor_locatorfloat, optional: Minor locator in x-axis, by default 0.2
ymajor_locatorfloat, optional: Major locator in y-axis, by default 1
yminor_locatorfloat, optional: Minor locator in y-axis, by default 0.2
refpixlist, optional: Pixel of reference, by default [0,0]
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

bowshockpy.plots.plotpv(pvimage, rangex, chan_vels, ax=None, cbax=None, vmax=None, vcenter=None, vmin=None, cmap='nipy_spectral', interpolation='bilinear', cbarlabel='Intensity [Jy/beam]', return_fig_axs=False)

Plots the Position-Velocity diagram

Parameters#

pvimagenumpy.ndarray: Position velocity diagram to plot.
rangexlist or numpy.ndarray: 2 element list or numpy.ndarray corresponding to the physical coordinates of the boundaries of the image in the spatial direction.
chan_velslist or numpy.ndarray: list or numpy.ndarray with the velocities corresponding to the channels
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes` instance in which the position velodity diagram is drawn.
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn.
vmaxfloat, optional: Maximum value of the colorbar
vcenterfloat, optional: Center value of the colorbar
vminfloat, optional: Minimum value of the colorbar
cmapstr, optional: Label of the colorbar
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
cbarlabelstr, optional: String with information on the quantity represented in the Position Velocity diagram
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

bowshockpy.plots.plotsumint(sumint, ax=None, cbax=None, extent=None, vmax=None, vcenter=None, vmin=None, cmap='inferno', interpolation='bilinear', cbarlabel='Intensity', add_beam=False, bmin=None, bmaj=None, pabeam=None, markorigin=True, return_fig_axs=False)

Plots the sumation of all the pixels along the velocity axis

Parameters#

sumintnumpy.ndarray: Image of the sumation of all the pixels along the velocty axis.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the position velodity diagram is drawn.
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn.
extentlist: Physical coordinates of the boundaries of the image.
vmaxfloat, optional: Maximum value of the colorbar
vcenterfloat, optional: Center value of the colorbar
vminfloat, optional: Minimum value of the colorbar
cmapstr, optional: Label of the colorbar
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
cbarlabelstr, optional: String with information on the quantity represented in the plot
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

bowshockpy.plots.plotmom0(mom0, ax=None, cbax=None, extent=None, vmax=None, vcenter=None, vmin=None, cmap='inferno', interpolation='bilinear', cbarlabel='Moment 0 [Jy/beam km/s]', add_beam=False, bmin=None, bmaj=None, pabeam=None, markorigin=True, return_fig_axs=False)

Plots the moment 0

Parameters#

mom0numpy.ndarray: Image of the moment 0.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the position velodity diagram is drawn.
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn.
extentlist: Physical coordinates of the boundaries of the image.
vmaxfloat, optional: Maximum value of the colorbar
vcenterfloat, optional: Center value of the colorbar
vminfloat, optional: Minimum value of the colorbar
cmapstr, optional: Label of the colorbar
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
cbarlabelstr, optional: String with information on the quantity represented in the plot
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
return_fig_axsbool, optional: If True, returns the figure, axes of the channel map, and the axes the colorbar. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

bowshockpy.plots.plotmom1(mom1, ax=None, cbax=None, extent=None, vmin=None, vmax=None, vcenter=None, extend_cbar='max', bg='black', cmap_ref='jet_r', interpolation='bilinear', cbarlabel='Moment 1 [km/s]', add_beam=False, bmin=None, bmaj=None, pabeam=None, markorigin=True, return_fig_axs_velcmap=False)

Plots the moment 1

Parameters#

mom1numpy.ndarray: Image of the moment 1.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the position velodity diagram is drawn.
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn.
extentlist: Physical coordinates of the boundaries of the image.
vmaxfloat, optional: Maximum value of the colorbar
vcenterfloat, optional: Center value of the colorbar
vminfloat, optional: Minimum value of the colorbar
extend_cbarstr,: Extremum to extend the colorbar: “max” or “min”
bgstr: Color of the background image.
cmap_refstr, optional: Label of the colorbar used for reference.
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
cbarlabelstr, optional: String with information on the quantity represented in the plot
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
return_fig_axs_velcmapbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the colormap created to plot the moment 1. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_velcmap=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_velcmap=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_velcmap=True.
velcmapmatplotlib.colors.ListedColormap: Colormap created to plot the moment 1

bowshockpy.plots.plotmom2(mom2, ax=None, cbax=None, extent=None, vmin=None, vmax=None, vcenter=None, extend_cbar='max', bg='black', cmap_ref='jet_r', cbarlabel='Moment 2 [km/s]', interpolation=None, add_beam=False, bmin=None, bmaj=None, pabeam=None, markorigin=True, return_fig_axs_velcmap=False)

Plots the moment 2

Parameters#

mom2numpy.ndarray: Image of the moment 2.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the position velodity diagram is drawn.
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn.
extentlist: Physical coordinates of the boundaries of the image.
vmaxfloat, optional: Maximum value of the colorbar
vcenterfloat, optional: Center value of the colorbar
vminfloat, optional: Minimum value of the colorbar
extend_cbarstr,: Extremum to extend the colorbar: “max” or “min”
bgstr: Color of the background image.
cmap_refstr, optional: Label of the colorbar used for reference.
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
cbarlabelstr, optional: String with information on the quantity represented in the plot
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]
return_fig_axs_velcmapbool, optional: If True, returns the figure, axes of the channel map, the axes the colorbar, and the colormap created to plot the moment 2. If False, does not return anything.

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs_velcmap=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs_velcmap=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs_velcmap=True.
velcmapmatplotlib.colors.ListedColormap: Colormap created to plot the moment 2

bowshockpy.plots.plotmaxintens(maxintens, ax=None, cbax=None, extent=None, vmax=None, vcenter=None, vmin=None, cmap='inferno', interpolation='bilinear', cbarlabel='Moment 8', add_beam=False, bmin=None, bmaj=None, pabeam=None, markorigin=True, return_fig_axs=False)

Plots the maximum value of the pixels along the velocity axis

Parameters#

maxintensnumpy.ndarray: Image of the maximum pixel along the velocty axis.
axmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the position velodity diagram is drawn.
cbaxmatplotlib.axes.Axes, optional: The matplotlib.axes.Axes instance in which the color bar is drawn.
extentlist: Physical coordinates of the boundaries of the image.
vmaxfloat, optional: Maximum value of the colorbar
vcenterfloat, optional: Center value of the colorbar
vminfloat, optional: Minimum value of the colorbar
cmapstr, optional: Label of the colorbar
interpolationstr, optional: Interpolation to pass to matplotlib.pyplot.imshow
cbarlabelstr, optional: String with information on the quantity represented in the plot
markoriginboolean, optional: If True, a marker will be plot at [0,0]. Default True.
add_beambolean, optional: If True, plots a ellipse of the beam size in the left bottom corner.
bminfloat, optional: Beam minor axis [arcsec]
bmajfloat, optional: Beam major axis [arcsec]
pabeamfloat: Beam position angle [degrees]

Returns:#

figmatplotlib.figure.Figure: Figure instance, only return_fig_axs=True
axmatplotlib.axes.Axes: Axes of the channel map, only return_fig_axs=True
cbaxtuple of matplotlib.axes.Axes: Axes of the channel map and the colorbar, only returns if return_fig_axs=True.

`bowshockpy.utils`#

This module contains the definition of useful tools used in the rest of BowshockPy modules

bowshockpy.utils.formatwarning(message, category, filename, lineno, line): Custom format of warning compatible with the progress bar

exception bowshockpy.utils.UserError

Bases: Warning

Warning category to interrupt the program

bowshockpy.utils.print_example(example)

Prints one of the available examples of input file to run bowshockpy.

Parameters:#

nexamplestr or int

Number of the example to print. There are 4 examples:

Example 1: A redshfted bowshock
Example 2: A blueshifted bowshock
Example 3: A side-on bowshock
Example 4: Several bowshocks in one cube
Example 5: Custom computation of opacities and intensities

bowshockpy.utils.list2str(a, precision=2)

Converts a list to a str

Parameters#

alist: List to convert as string
precisionint: Number of decimals to display

bowshockpy.utils.progressbar_bowshock(iteration, total, timelapsed, intervaltime, decimals=1, length=100, fill='─', printend='\r')

Bowshock-like progress bar

Parameters#

iterationint: Current iteraction
totalint: Total iteractions
timelapsedfloat: Current time elapsed
intervaltimefloat: Duration of an iteraction
decimalsint: Number of decimals to show
lengthfloat: Length of the progress bar
fillstr: String to define the filled part of the progress bar
printendstr: End of the progress bar

bowshockpy.utils.make_folder(foldername)

Makes a folder of the model

Parameters#

foldernamestr: Name of the folder of the model

bowshockpy.utils.mb_sa_gaussian_f(maja, mina)

Computes the solid angle of a Gaussian main beam

Parameters:#

majaastropy.units.Quantity: Beam major axis (FWHM)
minaastropy.units.Quantity: Beam minor axis (FWHM)

Returns:#

omega_mastropy.units.sr: Beam solid angle in stereoradians

bowshockpy.utils.gaussconvolve(data, x_FWHM, y_FWHM, pa, return_kernel=False)

Convolves data with a Gaussian kernel

Parameters:#

datanumpy.ndarray: Data to convolve
x_FWHMfloat: Full width half maximum of the Gaussian kernel for the x direction
y_FWHMfloat: Full width half maximum of the Gaussian kernel for the y direction
pafloat: Position angle in degrees
return_kerneloptional, bool: Whether to return the kernel or not

Returns:#

data_convnumpy.ndarray: Convolved data
kernelnumpy.ndarray: Image of the Gaussian kernel. Is returned only if return_kernel = True

bowshockpy.utils.get_color(vel_range, vel, cmap, norm='linear', customnorm=None)

Gets the color that corresponds in a colormap linearly interpolated taking into account the values at the limits.

Parameters:#

vel_rangelist: List with 2 elements defining the range of values to be represented by the colors
velfloat: Value to get the corresponding color from
cmapstr: Colormap label
normoptional, str: Set “linear” for a linear scale, “log” for log scale.
customnormoptional, str: Custom norm from matplotlib.colors

class bowshockpy.utils.VarsInParamFile(params)

Bases: object

This class takes as attributes the keys and values of a dictionary

Parameters#

paramsdict: Input dictionary

bowshockpy.utils.allequal(inputlist)

Checks if all elements of a list or a np.array are equal

Parameters#

inputlistlist: List object to check that all its elements are equal

Returns#

boolean: True if all elements are equal, False if they are not

bowshockpy.utils.make_astropy_units(quantity, astropy_unit)

Transform to astropy.units.Quantity unless it is already an astropy.units.Quantity

Parameters:#

quantityfloat | astropy.units.Quantity: Value to transform to astropy.units.Quantity
astropy_unitastropy.units.Quantity: Unit

Returns:#

astropy.units.Quantity: Input quantity as an astropy.units.Quantity type

API Reference

Contents

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`bowshockpy.models`#

`bowshockpy.modelproj`#

`bowshockpy.cubemass`#

`bowshockpy.cubeproc`#

`bowshockpy.radtrans`#