SÍGAME main module¶

The SÍGAME package features a folder that is imported in python as the main module and contains a number of submodules. The most important submodules are listed below with a short description of the classes and functions that they each contain.

sigame.galaxy submodule¶

Module with classes to set up the main galaxy object, create and load related data products from the simulation itself (particle_data class) and processed outputs (datacube class).

class sigame.galaxy.datacube(gal_ob, **kwargs)¶

Bases: object

An object referring to the datacube constructed for a galaxy (in one of the ISM phases)

Note

Must be added as an attribute to a galaxy object.

add_Z_map(**kwargs)¶: Adds metallicity map as numpy array to datacube object, if not there already.

add_m_map(**kwargs)¶: Adds mass map as numpy array to datacube object, if not there already.

add_moment0_map(**kwargs)¶: Adds moment 0 map as numpy array to datacube object, if not there already.

add_shape()¶: Adds tuple of datacube dimensions (v length, x length, y length) as an attribute to datacube object.

add_vw_disp_map(**kwargs)¶

add_vw_map(**kwargs)¶

create_dc(ISM_dc_phase)¶

Calculates the datacube of a specific ISM_phase

ISM_dc_phase: str: The datacube ISM phase

>>> gal_ob.datacube.create_dc('GMC')

get_dc(**kwargs)¶: Returns one datacube as numpy array.

get_kpc_per_arcsec()¶: Returns physical scale for this galaxy in kpc per arcsec.

get_line_prof(**kwargs)¶

Returns line profile in pixel-integrated Jy as numpy array.

linestr: Line to use for map, default: ‘CII’

get_moment0_map(**kwargs)¶

Returns moment 0 map in Jy*km/s per pixel as numpy array.

linestr: Line to use for map, default: ‘CII’
convolvebool: if True: convolve with beam of FWHM also supplied, default: False
FWHMfloat: FWHM of beam to convolve with, default: None
ISM_dc_phasestr: ISM datacube phase to use for moment 0 map, default: ‘tot’ (all ISM phases)
unitsstr: units for moment0 map, default: ‘Jykms’ for Jy*km/s (other options: ‘Wm2’ for W/m^2)

get_total_sum(**kwargs)¶: Returns total value of datacube for all datacube ISM phases in dictionary.

get_x_axis_arcsec()¶: Returns positional axis (x or y) in arcsec.

class sigame.galaxy.dict_to_attr(dictionary)¶

Bases: object

Essentially turns dictionary into a attributes of an object.

class sigame.galaxy.galaxy(gal_index)¶

Bases: object

An object referring to one particular galaxy.

gal_index: int: Galaxy index, default: 0

>>> import galaxy as gal
>>> gal_ob = gal.galaxy(gal_index=0)

add_attr(attr_name, verbose=False)¶: creates desired attribute and adds it to galaxy.

check_classification()¶: checks if galaxy classification is correct (all galaxies are initialized with a ‘spherical’ classification.)

check_for_attr(attr_name, **kwargs)¶: checks if galaxy has a specific attribute, if not then adds it.

get_radial_axis()¶: returns 1D radius array for galaxy

class sigame.galaxy.interpolate_clouds(gal_index)¶

Bases: sigame.galaxy.galaxy

An object that will interpolate in cloud models of info such as line luminosity for one galaxy.

Child class that inherits from parent class ‘galaxy’.

interpolate_GMCs()¶: Adds info from cloud model runs to GMCs

interpolate_dif()¶: Adds info from cloud model runs to diffuse gas clouds

setup_tasks()¶: Controls tasks to be executed, based on existing files and the overwrite [ow] parameter

class sigame.galaxy.particle_data(gal_ob, **kwargs)¶

Bases: object

An object referring to the particle data (sim or ISM)

Note

Must be added as an attribute to a galaxy object.

gal_obobject: Instance of galaxy class.
silentbool: Parameter telling the code to do (or not) print statements.

>>> import galaxy as gal
>>> gal_ob = gal.galaxy(gal_index=0)
>>> simgas = gal_ob.particle_data.get_data(data='sim')['gas']

add_Z_map(**kwargs)¶: Adds metallicity map as numpy array to particle data object, if not stored already in sigame/temp/maps/metallicity/.

add_names()¶: Add file location for particle data file (sim_type or ISM_phase)

get_data(**kwargs)¶

Returns rotated particle data as dataframe.

particle_namestr: Name of particles, can be [‘gas’,’star’,’dm’,’GMC’,’dif’], default: ‘GMC’

get_map(**kwargs)¶

Creates map of surface densities (or sum) of some parameters in sim or ISM data.

quanstr: What gets mapped, default: ‘m’
ISM_phasestr: If set, ISM data will be used, default: ‘’
sim_typestr: If set, sim data will be used, default: ‘’
get_sumbool: If True, return map of summed values not divided by area, default: False

get_raw_data(**kwargs)¶: Returns raw not rotated particle data in dictionary.

plot_map(**kwargs)¶: Creates map of surface densities (or sum) of some parameters in sim or ISM data.

class sigame.galaxy.subgrid_galaxy(gal_index)¶

Bases: sigame.galaxy.galaxy

An object that will contain the subgrid information for one galaxy. Child class that inherits from parent class ‘galaxy’.

add_FUV()¶: Adds FUV radiation field to galaxy and stores gas/star sim particle data files again with the new information.

add_GMCs()¶: Generates GMCs and creates new GMC particle data file for a galaxy.

add_P_ext()¶: Adds external pressure to galaxy and stores gas/star sim particle data files again with the new information.

add_dif()¶: Generates diffuse gas clouds and creates new dif particle data file for a galaxy.

setup_tasks()¶: Controls tasks to be executed, based on existing files and the overwrite [ow] parameter

class sigame.galaxy.var(val, err)¶

Bases: object

takes a value and its err and returns strings of printable values with appropriate significant figures for presenting data.

sigame.global_results submodule¶

Module: global_results

class sigame.global_results.global_results(**kwargs)¶

Bases: object

An object referring to the global results of a selection of galaxies, containing global properties of as attributes.

>>> import global_results as glo
>>> GR = glo.global_results()
>>> GR.print_results()

print_galaxy_properties(**kwargs)¶

print_results()¶

sigame.plot submodule¶

Module: plot

sigame.plot.OI_OIII_SFR(plotmodels=True, twopanel=True)¶: Inspect [OI]63micron AND [OIII]88micron emission (called by line_SFR() in analysis.py)

sigame.plot.SFR_Mstar(**kwargs)¶

Plot of SFR vs stellar mass for one or more redshift groups

colorstr: What to color-code the galaxies by, default: age

>>> import sigame as si
>>> si.plot.SFR_Mstar(color='age')

sigame.plot.add_CII_observations_to_plot1(slope_models, intercept_models, mark_reasons=False, mark_uplim=False, mark_det=False, z1='z6', MW=True, ms_scaling=1, alpha=1, line='[CII]')¶: ‘ Purpose ——— Adds observatinos to plot

sigame.plot.add_line_ratio_obs(ratio='CII_NII', zred_sample='lowz')¶

Plots observations of the relevant line ratio against redshift

ratio - str: Options: - ‘CII_NII’: plots the [CII]/[NII]205 line ratio - ‘OIII_NII’: plots the [OIII]88/[NII]122 line ratio
zred_sample - str: Options: - ‘highz’: adds observations at high redshift - ‘lowz’: adds observations at low redshift

sigame.plot.arrow_length(n)¶

sigame.plot.axis_range(x, log=False, **kwargs)¶

Calculates a reasonable axis range

xnp.array(): Must be given, array of values
logbool: If True, takes the log of the values in x, default: False
dexfloat: Dex above and below maximum values in x, effective when log == True, default: max range in x divided by 5
fractionfloat: Fraction of maximum range in x to go above and below on the axis, effective when log == False, default: 1/5.

sigame.plot.comp_ISM_phases(**kwargs)¶: Plotting function for comparing fractions of mass or line luminosity vs. SFR of Z. Called by ISM_line_contributions and ISM_line_efficiency() and ISM_mass_contributions() in analysis.py

sigame.plot.delete_old_plots()¶

sigame.plot.getlabel(foo)¶: Gets axis labels for plots

sigame.plot.grid_parameters(histo_color='teal', FUV=0.1, ISM_phase='GMC', figsize=(10, 7))¶

Make histograms of galaxies with grid points on top What this function does ——— 1) Makes 4-panel figure with histograms of [Mgmc, G0, Z, P_ext] in GMCs 2) OR makes 4-panel figure with histograms of [nH, R, Z, Tk] in diffuse clouds Arguments ——— ISM_phase: ISM phase in cloudy models, can be either ‘GMC’ or ‘dif’ - str default: ‘GMC’ histo_color: color selection for histograms - str options:

‘<a specific color>’: all histograms will have this color

‘colsel’: each galaxy will have a different color, using colsel from param_module.read_params

sigame.plot.grid_parameters_checkParam(histo_color='teal', FUV=0.002, ISM_phase='GMC', figsize=(10, 7))¶

Make histograms of galaxies to check what parameters to be used for dif_cloud_grid.py and GMC_cloud_grid.py to make cloudy grids.

ISM_phase: str

if ‘GMC’: make 4-panel figure with histograms of [Mgmc, G0, Z, P_ext] in GMCs if ‘dif’: make 4-panel figure with histograms of [nH, R, Z, Tk] in diffuse clouds

histo_color: str

color selection for histograms options:

‘<a specific color>’: all histograms will have this color

‘colsel’: each galaxy will have a different color, using colsel from param_module.read_params

sigame.plot.histos(**kwargs)¶

Makes histograms of all (particles in all) galaxies in the sample on the same plot.

binsint/float: Number of bins, default: 100
addbool: If True, add to an existing plot, default: False
one_colorbool: If True, use only one color for all lines, default: True
fs_labelsint/float: Fontsize, default: 15

sigame.plot.line_SFR(**kwargs)¶

Plots line luminosity against SFR (together with observations)

line: str: Line to look at, default: ‘CII’

sigame.plot.line_prof(**kwargs)¶

Plots line luminosity against SFR (together with observations)

line: str: Line to look at, default: ‘CII’

sigame.plot.make_contour(i, fontsize, kwargs)¶

Makes contour plot (called by simple_plot)

contour_type: str: Method used to create contour map (see simple_plot)

sigame.plot.map_line(**kwargs)¶

Makes moment0 map of line using datacubes.

gal_index: int: Galaxy index, default: 0
linestr: Line to use for map, default: ‘CII’
R_maxfloat: Maximum radius for moment0 map in kpc, default: 15
ISM_dc_phasestr: ISM phase(s) to map, default: ‘tot’ (sum of all)
unitsstr: Units; ‘Wm2’ for W/m^2, ‘Jykms’ for Jy*km/s, default: ‘Jykms’
convolvebool: Whether moment0 map should be convolved by corresponding Herschel beam, default: True
min_fractionfloat: Fraction of maximum in image used as lower limit for colorbar, default: 1/1e6

sigame.plot.set_mpl_params()¶

sigame.plot.simple_plot(**kwargs)¶

A function to standardize all plots

Plots that can be created this way:

1. errorbar plot (with x and/or y errorbars)
1. line
1. histogram
1. markers
1. bar
1. hexbin
1. contour plot
1. scatter plot
1. hatched/filled region

The ‘1’ below can be replaced by ‘2’, ‘3’, ‘4’ etc for several plotting options in the same figure.

addbool: If True add to existing axis object, otherwise new figure+axes will be created, default: False
figint: Figure number, default: 0
figsizetuple: Figure size, default: (8,6)
fignamestr: If defined, a figure will be saved with this path+name, default = not defined (no figure saved)
figtypestr: Format of figure, default: ‘png’
figresfloat: The dpi of the saved figure, default: 1000
fontsizefloat: Fontsize of tick labels, default: 15
x1list or numpy array: x values
y1list or numpy array: y values
xrlist: x range
yrlist: y range
xlogbool: If True: x-axis will be in log units
ylogbool: If True: y-axis will be in log units
fill1str: If defined, markers will be used (‘y’ for filled markers, ‘n’ for open markers), default: ‘y’
ls1str: Linestyle, default: ‘None’ (markers by default)
ds1str: Drawstyle, default: ‘None’ (solid line by default)
ma1str: Marker type, default: ‘x’
ms1int/float: Marker size, default: 5
mew1int/float: Marker edge width, default: 2
col1str: Color of markers/lines, default: ‘k’
ecol1str: Edgecolor, default: ‘k’
lab1str: Label for x1,y1 points, default: ‘’
alpha1float: Transparency fraction, default: 1.1
dashes1str: Custom-made dashes/dots, default = ‘’
legendbool: Whether to plot legend or not, default: False
leg_fsfloat: Legend fontsize, default: not defined (same as fontsize for labels/tick marks)
leglocstr or list of coordinates: Legend location, default: ‘best’
cmap1str: Colormap for contour plots, default: ‘viridis’
xlabstr: x axis label, default: no label
ylabstr: y axis label, default: no label
titlestr: Plot title, default: no title
xticks: bool: Whether to put x ticks or not, default: True
yticks: bool: Whether to put y ticks or not, default: True
lab_to_tickint/float: If axis labels should be larger than tick marks, say how much here, default: 1.0
lex1,uex1: list or numpy array: Lower and upper errorbars on x1, default: None, options: If an element in uex1 is 0 that element will be plotted as upper limit in x
ley1,uey1: list or numpy array: lower and upper errorbars on y1, default: None, options: If an element in uey1 is 0 that element will be plotted as upper limit in y
histo1bool: Whether to make a histogram of x1 values, default: False
histo_real1bool: Whether to use real values for histogram or percentages on y axis, default: False
bins1int: Number of bins in histogram, default: 100
weights1list or numpy array: weights to histogram, default: np.ones(len(x1))
hexbin1bool: If True, will make hexbin contour plot, default: False
contour_type1str: If defined, will make contour plot, default: not defined, options: plain: use contourf on colors alone, optionally with contour levels only (no filling), hexbin: use hexbin on colors alone, median: use contourf on median of colors, mean: use contourf on mean of colors, sum: use contourf on sum of colors
barwidth1float: If defined, will make bar plot with this barwidth
scatter_color1list or numpy array: If defined, will make scatter plot with this color, default: not defined (will not do scatter plot)
colormin1float: Minimum value for colorbar in scatter plot, default: not defined (will use all values in scatter_color1)
lab_colorbarstr: Label for colorbar un scatter plot, default: not defined (will not make colorbar)
hatchstyle1str: If defined, make hatched filled region, default: not defined (will not make hatched region), options: if set to ‘’, fill with one color, otherwise, use ‘/’ ‘//’ ‘///’’ etc.
textstr: If defined, add text to figure with this string, default: not defined (no text added)
textloclist: Must be specified in normalized axis units, default: [0.1,0.9]
textboxbool: If True, put a box around text, default: False
fontsize_textint/float: Fontsize of text on plot, default: 0/7 * fontsize
gridbool: Turn on grid lines, default: False
SC_returnbool: Return scatter plot object or not, default = False

sigame.plot.trim_df(file, skip, maxcol)¶: Comment columns to trim a dataframe

sigame.param submodule¶

Submodule: param

sigame.param.add_default_args()¶: Make custom namespace for specific method

sigame.param.read_params(params_file, params)¶: Extracts parameters from parameter file set in sigame/__init__.py

sigame.param.update_params_file(new_params, verbose=False)¶