API Reference

Image

Line

class pymcfost.line.Line(dir=None, line_file=None, **kwargs)

Bases: object

A class to handle MCFOST spectral line data.

This class reads and processes MCFOST line radiative transfer outputs, providing methods to plot channel maps, spectra, and calculate moment maps.

Variables:

• dir (str) – Directory containing MCFOST output files

• lines (numpy.ndarray) – The line data cube

• P (Params) – MCFOST parameter object

• pixelscale (float) – Image pixel scale in arcsec

• unit (str) – Unit of the line data

• nx (int) – Number of pixels in x direction

• ny (int) – Number of pixels in y direction

• nv (int) – Number of velocity channels

• velocity (numpy.ndarray) – Velocity array in km/s

• freq (numpy.ndarray) – Frequency array in Hz

• is_casa (bool) – Whether the data is in CASA format

• star_positions (numpy.ndarray) – Array of stellar positions

• extent (list) – Image extent for plotting [xmin, xmax, ymin, ymax]

Example

>>> line = Line(dir="path/to/mcfost/data")
>>> line.plot_map(i=0, iaz=0, iTrans=0, iv=10)

__init__(dir=None, line_file=None, **kwargs)

Initialize a Line object.

Parameters:

• dir (str) – Path to directory containing MCFOST output

• line_file (str, optional) – Name of line data file

• **kwargs – Additional arguments passed to _read()

get_moment_map(i=0, iaz=0, iTrans=0, moment=0, i_convolve=False, beam=None, conv_method=None, subtract_cont=False, M0_threshold=None, iv_support=None, v_minmax=None)

Calculate a moment map from the line cube.

Parameters:

• moment (int) – Moment to compute: - 0: Integrated intensity - 1: Intensity-weighted velocity - 2: Velocity dispersion - 8: Peak intensity - 9: Velocity at peak intensity

• iTrans (int) – Transition index

• iv_support (array-like, optional) – Velocity channels to include

• **kwargs – Additional arguments for convolution

Returns:

The computed moment map

Return type:

numpy.ndarray

plot_line(i=0, iaz=0, iTrans=0, psf_FWHM=None, bmaj=None, bmin=None, bpa=None, plot_beam=False, plot_cont=True, subtract_cont=False)

Plot the line spectrum.

Parameters:

• i (int) – Inclination index

• iaz (int) – Azimuth angle index

• iTrans (int) – Transition index

• plot_cont (bool) – Whether to plot the continuum level

• **kwargs – Additional arguments passed to plotting function

plot_map(i=0, iaz=0, iTrans=0, v=None, iv=None, insert=False, subtract_cont=False, moment=None, psf_FWHM=None, bmaj=None, bmin=None, bpa=None, plot_beam=None, beam_position=(0.125, 0.125), axes_unit='arcsec', conv_method=None, fmax=None, fmin=None, fpeak=None, dynamic_range=1000.0, color_scale=None, colorbar=True, colorbar_size=10, colorbar_label=True, cmap=None, ax=None, no_xlabel=False, no_ylabel=False, no_vlabel=False, no_xticks=False, no_yticks=False, vlabel_position=(0.5, 0.1), vlabel_size=8, title=None, title_size=14, limit=None, limits=None, Tb=False, Jy=False, mJy=False, per_arcsec2=False, per_beam=False, Delta_v=None, shift_dx=0, shift_dy=0, plot_stars=False, sink_particle_size=6, sink_particle_color='cyan', M0_threshold=None, iv_support=None, v_minmax=None, rms=0, interpolation=None, plot_type='imshow', alpha=1.0, linewidths=None, zorder=None, origin='lower', levels=None, colors=None, colorbar_side='right')

Plot a channel map or moment map.

Parameters:

• i (int) – Inclination index

• iaz (int) – Azimuth angle index

• iTrans (int) – Transition index

• v (float, optional) – Velocity in km/s (alternative to iv)

• iv (int, optional) – Velocity channel index

• moment (int, optional) – Moment to plot (0=integrated intensity, 1=velocity, 2=dispersion)

• **kwargs – Additional arguments passed to plotting function

Returns:

The plotted image

Return type:

matplotlib.image.AxesImage

plot_wake(i=0, i_planet=1, HonR=0.1, q=0.25, ax=None, rmax=None, rmin=None, **kwargs)

SED

class pymcfost.SED.SED(dir=None, **kwargs)

Bases: object

A class to handle MCFOST spectral energy distributions and temperature structures.

This class reads and processes MCFOST SED outputs, providing methods to plot SEDs and temperature distributions.

Variables:

• dir (str) – Directory containing MCFOST output files

• basedir (str) – Base directory without data_th suffix

• P (Params) – MCFOST parameter object

• sed (numpy.ndarray) – SED data from ray-tracing

• wl (numpy.ndarray) – Wavelength array in microns

• T (numpy.ndarray) – Temperature structure

Example

>>> sed = SED(dir="path/to/mcfost/data")
>>> sed.plot(i=0)  # Plot SED for first inclination

__init__(dir=None, **kwargs)

Initialize an SED object.

Parameters:

• dir (str) – Path to directory containing MCFOST output

• **kwargs – Additional arguments passed to _read()

convert_to_text(sed_text_path, i=0, iaz=0)

Convert MCFOST SED fits file to text format. The created file can be used as a sample file for chi² calculation.

Parameters:

• sed_text_path (str) – Path where the text file will be saved

• i (int, optional) – Inclination index. Defaults to 0.

• iaz (int, optional) – Azimuth angle index. Defaults to 0.

Returns:

Path to the created text file, or None if conversion failed

Return type:

str or None

plot(i, iaz=0, MC=False, contrib=False, Av=0, Rv=3.1, color='black', **kwargs)

Plot the spectral energy distribution.

Parameters:

• i (int) – Inclination index

• iaz (int) – Azimuth angle index

• MC (bool) – Whether to plot Monte Carlo results

• contrib (bool) – Whether to plot individual contributions

• Av (float) – Extinction in V band

• Rv (float) – Total to selective extinction ratio

• color (str) – Line color

• **kwargs – Additional arguments passed to plotting function

plot_T(iaz=0, log=False, Tmin=None, Tmax=None)

Plot the temperature structure.

Parameters:

• iaz (int) – Azimuth angle index

• log (bool) – Whether to use logarithmic scale

• Tmin (float, optional) – Minimum temperature to plot

• Tmax (float, optional) – Maximum temperature to plot

plot_Tr(h_r=0.05, iaz=0, log=True, **kwargs)

Plot radial temperature profile at specified height.

Parameters:

• h_r (float) – Height above midplane in scale heights

• iaz (int) – Azimuth angle index

• log (bool) – Whether to use logarithmic scale

• **kwargs – Additional arguments passed to plotting function

Returns:

(radius array, temperature array)

Return type:

tuple

plot_Tz(r=100.0, dr=5.0, log=False, **kwargs)

Plot vertical temperature profile at specified radius.

Parameters:

• r (float) – Radius in AU

• dr (float) – Radial range to average over in AU

• log (bool) – Whether to use logarithmic scale

• **kwargs – Additional arguments passed to plotting function

spectral_index(wl1, wl2, i=0, iaz=0)

Calculate spectral index between two wavelengths.

Parameters:

• wl1 (float) – First wavelength in microns

• wl2 (float) – Second wavelength in microns

• i (int) – Inclination index

• iaz (int) – Azimuth angle index

Returns:

Spectral index

Return type:

float

verif()

Compare SEDs from step 1 and 2 to verify energy conservation.

Disc Structure

class pymcfost.disc_structure.Disc(dir=None, **kwargs)

Bases: object

A class to handle MCFOST disc structure data.

This class reads and processes MCFOST disc structure outputs, providing methods to access the spatial grid, gas density, and add geometric features.

Variables:

• dir (str) – Directory containing MCFOST output files

• P (Params) – MCFOST parameter object

• grid (numpy.ndarray) – Spatial grid structure

• gas_density (numpy.ndarray) – Gas density distribution

• volume (numpy.ndarray) – Cell volumes

Example

>>> disc = Disc(dir="path/to/mcfost/data")
>>> r = disc.r()  # Get radial coordinates

__init__(dir=None, **kwargs)

Initialize a Disc object.

Parameters:

• dir (str) – Path to directory containing MCFOST output

• **kwargs – Additional arguments passed to _read()

add_banana(r0=None, phi0=None, f=1, delta_r=None, delta_phi=None, n_az=None, sigma=None)

Add a geometrical banana on a 2D (or 3D) mcfost density grid and return a 3D array which can be directly written as a fits file for mcfost to read

surface density is mutiply by (1+f) at the crest of the banana the banana has a Gaussian profile in (r,phi) with sigma given in au, degrees

Parameters:

• r0 (float) – Radial position of enhancement in AU

• phi0 (float) – Azimuthal position in degrees

• f (float) – Density enhancement factor

• delta_r (float) – Radial width in AU

• delta_phi (float) – Azimuthal width in degrees

• n_az (int, optional) – Number of azimuthal points

• sigma (str) – Path to sigma data file

Returns:

Modified density structure with banana feature

Return type:

numpy.ndarray

add_spiral(a=30, sigma=10, f=1, theta0=0, rmin=None, rmax=None, n_az=None)

Add a geometrical spiral on a 2D (or 3D) mcfost density grid and return a 3D array which can be directly written as a fits file for mcfost to read

geometrical spiral r = a (theta - theta0) surface density is mutiply by f at the crest of the spiral the spiral has a Gaussian profil in (x,y) with sigma given in au

Parameters:

• a (float) – Spiral parameter, r = a(θ - θ₀)

• sigma (float) – Width of the spiral in AU

• f (float) – Density enhancement factor at spiral crest

• theta0 (float) – Initial angle in radians

• rmin (float, optional) – Inner radius in AU

• rmax (float, optional) – Outer radius in AU

• n_az (int, optional) – Number of azimuthal points

Returns:

Modified density structure with spiral

Return type:

numpy.ndarray

r()

Get radial coordinates of the grid.

Returns:

Radial coordinates in AU

Return type:

numpy.ndarray

sigma(dust=False)

Compute the surface density of a model

Returns:

surface density in g/cm2

Return type:

numpy.ndarray

z()

Get vertical coordinates of the grid.

Returns:

Vertical coordinates in AU

Return type:

numpy.ndarray

Dust Model

class pymcfost.dust.Dust_model(dir=None, **kwargs)

Bases: object

A class to handle MCFOST dust opacity models.

This class reads and processes MCFOST dust opacity data, providing methods to plot and analyze various dust properties.

Variables:

• dir (str) – Directory containing MCFOST output files

• P (Params) – MCFOST parameter object

• wl (numpy.ndarray) – Wavelength grid in microns

• kappa (numpy.ndarray) – Total opacity in cm²/g

• albedo (numpy.ndarray) – Dust albedo

• kappa_abs (numpy.ndarray) – Absorption opacity in cm²/g

• kappa_sca (numpy.ndarray) – Scattering opacity in cm²/g

• phase_function (numpy.ndarray) – Scattering phase function

• polarisability (numpy.ndarray) – Dust polarisability

Example

>>> dust = Dust_model(dir="path/to/mcfost/data")
>>> dust.plot_kappa()  # Plot opacity

__init__(dir=None, **kwargs)

Initialize a Dust_model object.

Parameters:

• dir (str) – Path to directory containing MCFOST output

• **kwargs – Additional arguments passed to _read()

plot_albedo(linewidth=1, **kwargs)

Plot dust albedo as function of wavelength.

Parameters:

• linewidth (float) – Line width for plotting

• **kwargs – Additional arguments passed to plotting function

plot_kappa(abs=True, scatt=True, linewidth=1, **kwargs)

Plot dust opacity coefficients.

Parameters:

• abs (bool) – Whether to plot absorption opacity

• scatt (bool) – Whether to plot scattering opacity

• linewidth (float) – Line width for plotting

• **kwargs – Additional arguments passed to plotting function

plot_phase_function(k=0, linewidth=1, **kwargs)

Plot scattering phase function.

Parameters:

• k (int) – Wavelength index

• linewidth (float) – Line width for plotting

• **kwargs – Additional arguments passed to plotting function

plot_polarisability(k=0, linewidth=1, **kwargs)

Plot dust polarisability.

Parameters:

• k (int) – Wavelength index

• linewidth (float) – Line width for plotting

• **kwargs – Additional arguments passed to plotting function

print_kappa(file='opacities.txt')

Save opacity data to a text file.

Parameters:

file (str) – Output filename

Running MCFOST

Utilities

CASA Simulations