tardis.visualization.tools.sdec_plot module

Spectral element DEComposition (SDEC) Plot for TARDIS simulation models.

This plot is a spectral diagnostics plot similar to those originally proposed by M. Kromer (see, for example, Kromer et al. 2013, figure 4).

class tardis.visualization.tools.sdec_plot.SDECData(last_interaction_type, last_line_interaction_in_id, last_line_interaction_out_id, last_line_interaction_in_nu, lines_df, packet_nus, packet_energies, r_inner, spectrum_delta_frequency, spectrum_frequency_bins, spectrum_luminosity_density_lambda, spectrum_wavelength, t_inner, time_of_simulation)

Bases: object

The data of simulation model used by Spectral element DEComposition (SDEC) Plot.

This preprocesses the data required by SDECPlotter class for doing calculations and plotting.

Initialize the SDECData with required properties of simulation model.

Parameters

last_interaction_typenp.array

Interaction type (no-interaction: -1, e-scattering: 1 and line interaction: 2) values of emitted packets

last_line_interaction_in_idnp.array

IDs of atomic lines with which emitted packet had their last absorption (interaction in)

last_line_interaction_out_idnp.array

IDs of atomic lines with which emitted packet had their last emission (interaction out)

last_line_interaction_in_nunp.array

Frequency values of the last absorption of emitted packets

lines_dfpd.DataFrame

Data about the atomic lines present in simulation model’s plasma

packet_nusastropy.Quantity

Frequency values of the last emission of emitted packets, having unit of Hz

packet_energiesastropy.Quantity

Energy values of emitted packets, having unit of erg

r_innerastropy.Quantity

Radius of innermost shell, having unit of cm

spectrum_delta_frequencyastropy.Quantity

Frequency bin width of spectrum, having unit of Hz

spectrum_frequency_binsastropy.Quantity

Frequency bin edges of spectrum, having unit of Hz

spectrum_wavelengthastropy.Quantity

Wavelength values of spectrum, having unit of Angstrom

t_innerastropy.Quantity

Temperature of innermost shell, having unit of K

time_of_simulationastropy.Quantity

Time of simulation, having unit of s (second)

classmethod from_hdf(hdf_fpath, packets_mode)

Create an instance of SDECData from a simulation HDF file.

Parameters

hdf_fpathstr

Valid path to the HDF file where simulation is saved

packets_mode{‘virtual’, ‘real’}

Mode of packets to be considered, either real or virtual

Returns

SDECData

classmethod from_simulation(sim, packets_mode)

Create an instance of SDECData from a TARDIS simulation object.

Parameters

simtardis.simulation.Simulation

TARDIS Simulation object produced by running a simulation

packets_mode{‘virtual’, ‘real’}

Mode of packets to be considered, either real or virtual

Returns

SDECData

class tardis.visualization.tools.sdec_plot.SDECPlotter(data)

Bases: object

Plotting interface for Spectral element DEComposition (SDEC) Plot.

It performs necessary calculations to generate SDEC Plot for a simulation model, and allows to plot it in matplotlib and plotly.

Initialize the SDECPlotter with required data of simulation model.

Parameters

datadict of SDECData

Dictionary to store data required for SDEC plot, for both packet modes i.e. real and virtual

classmethod from_hdf(hdf_fpath, packets_mode=None)

Create an instance of SDECPlotter from a simulation HDF file.

Parameters

hdf_fpathstr

Valid path to the HDF file where simulation is saved

packets_mode{‘virtual’, ‘real’}, optional

Mode of packets to be considered, either real or virtual. If not specified, both modes are returned

Returns

SDECPlotter

classmethod from_simulation(sim)

Create an instance of SDECPlotter from a TARDIS simulation object.

Parameters

simtardis.simulation.Simulation

TARDIS Simulation object produced by running a simulation

Returns

SDECPlotter

generate_plot_mpl(packets_mode='virtual', packet_wvl_range=None, distance=None, observed_spectrum=None, show_modeled_spectrum=True, ax=None, figsize=(12, 7), cmapname='jet', nelements=None, species_list=None, blackbody_photosphere=True)

Generate Spectral element DEComposition (SDEC) Plot using matplotlib.

Parameters

packets_mode{‘virtual’, ‘real’}, optional

Mode of packets to be considered, either real or virtual. Default value is ‘virtual’

packet_wvl_rangeastropy.Quantity or None, optional

Wavelength range to restrict the analysis of escaped packets. It should be a quantity having units of Angstrom, containing two values - lower lambda and upper lambda i.e. [lower_lambda, upper_lambda] * u.AA. Default value is None

distanceastropy.Quantity or None, optional

Distance used to calculate flux instead of luminosity in the plot. It should have a length unit like m, Mpc, etc. Default value is None

observed_spectrumtuple or list of astropy.Quantity, optional

Option to plot an observed spectrum in the SDEC plot. If given, the first element should be the wavelength and the second element should be flux, i.e. (wavelength, flux). The assumed units for wavelength and flux are angstroms and erg/(angstroms * s * cm^2), respectively. Default value is None.

show_modeled_spectrumbool, optional

Whether to show modeled spectrum in SDEC Plot. Default value is True

axmatplotlib.axes._subplots.AxesSubplot or None, optional

Axis on which to create plot. Default value is None which will create plot on a new figure’s axis.

figsizetuple, optional

Size of the matplotlib figure to display. Default value is (12, 7)

cmapnamestr, optional

Name of matplotlib colormap to be used for showing elements. Default value is “jet”

nelements: int

Number of elements to include in plot. Determined by the largest contribution to total luminosity absorbed and emitted. Other elements are shown in silver. Default value is None, which displays all elements

species_list: list of strings or None

list of strings containing the names of species that should be included in the SDEC plots. Must be given in Roman numeral format. Can include specific ions, a range of ions, individual elements, or any combination of these: e.g. [‘Si II’, ‘Ca II’, ‘C’, ‘Fe I-V’]

blackbody_photosphere: bool

Whether to include the blackbody photosphere in the plot. Default value is True

Returns

matplotlib.axes._subplots.AxesSubplot

Axis on which SDEC Plot is created

generate_plot_ply(packets_mode='virtual', packet_wvl_range=None, distance=None, observed_spectrum=None, show_modeled_spectrum=True, fig=None, graph_height=600, cmapname='jet', nelements=None, species_list=None, blackbody_photosphere=True)

Generate interactive Spectral element DEComposition (SDEC) Plot using plotly.

Parameters

packets_mode{‘virtual’, ‘real’}, optional

Mode of packets to be considered, either real or virtual. Default value is ‘virtual’

packet_wvl_rangeastropy.Quantity or None, optional

Wavelength range to restrict the analysis of escaped packets. It should be a quantity having units of Angstrom, containing two values - lower lambda and upper lambda i.e. [lower_lambda, upper_lambda] * u.AA. Default value is None

distanceastropy.Quantity or None, optional

Distance used to calculate flux instead of luminosity in the plot. It should have a length unit like m, Mpc, etc. Default value is None

observed_spectrumtuple or list of astropy.Quantity, optional

Option to plot an observed spectrum in the SDEC plot. If given, the first element should be the wavelength and the second element should be flux, i.e. (wavelength, flux). The assumed units for wavelength and flux are angstroms and erg/(angstroms * s * cm^2), respectively. Default value is None.

show_modeled_spectrumbool, optional

Whether to show modeled spectrum in SDEC Plot. Default value is True

figplotly.graph_objs._figure.Figure or None, optional

Figure object on which to create plot. Default value is None which will create plot on a new Figure object.

graph_heightint, optional

Height (in px) of the plotly graph to display. Default value is 600

cmapnamestr, optional

Name of the colormap to be used for showing elements. Default value is “jet”

nelements: int

Number of elements to include in plot. Determined by the largest contribution to total luminosity absorbed and emitted. Other elements are shown in silver. Default value is None, which displays all elements

species_list: list of strings or None

list of strings containing the names of species that should be included in the SDEC plots. Must be given in Roman numeral format. Can include specific ions, a range of ions, individual elements, or any combination of these: e.g. [‘Si II’, ‘Ca II’, ‘C’, ‘Fe I-V’]

blackbody_photosphere: bool

Whether to include the blackbody photosphere in the plot. Default value is True

Returns

plotly.graph_objs._figure.Figure

Figure object on which SDEC Plot is created

static to_rgb255_string(color_tuple)

Convert a matplotlib RGBA tuple to a generic RGB 255 string.

Parameters

color_tupletuple

Matplotlib RGBA tuple of float values in closed interval [0, 1]

Returns

str

RGB string of format rgb(r,g,b) where r,g,b are integers between 0 and 255 (both inclusive)