API Reference

This is MUFASA’s class and function reference. In addition to the table below, you can also search with the search bar located on the top right corner of the webpage.

Object	Description
UCubePlus	A subclass of UltraCube that includes directory management for parameter maps and model fits. mufasa.UltraCube
UltraCube	A framework for multi-component spectral cube analysis and model fitting. mufasa.UltraCube
calc_AICc	Calculate the corrected Akaike Information Criterion (AICc) for a spectral cube model. mufasa.UltraCube
calc_AICc_likelihood	Calculate the relative likelihood of two models based on their AICc values. mufasa.UltraCube
calc_chisq	Calculate the chi-squared (χ²) or reduced chi-squared value for a spectral cube model fit. mufasa.UltraCube
calc_rss	Calculate the residual sum of squares (RSS) for a spectral cube model fit. mufasa.UltraCube
convolve_sky_byfactor	Convolve the spatial dimensions of a spectral cube by a specified factor. mufasa.UltraCube
expand_mask	Expand a 3D mask along the spectral axis by a specified buffer size. mufasa.UltraCube
fit_cube	Fit the spectral cube using the specified fitting type. mufasa.UltraCube
get_Tpeak	Calculate the peak value of a model cube at each spatial pixel. mufasa.UltraCube
get_all_lnk_maps	Compute log-likelihood ratio maps for model comparisons up to a specified number of components. mufasa.UltraCube
get_best_2c_parcube	Select the best 2-component parameter cube based on AICc likelihood thresholds. mufasa.UltraCube
get_chisq	Calculate the chi-squared or reduced chi-squared value for a spectral cube. mufasa.UltraCube
get_masked_moment	Calculate a masked moment of a spectral cube. mufasa.UltraCube
get_residual	Calculate the residual between the data cube and the model cube. mufasa.UltraCube
get_rms	Compute a robust estimate of the root mean square (RMS) from the fit residuals. mufasa.UltraCube
get_rss	Calculate the residual sum of squares (RSS) for a spectral cube model fit. mufasa.UltraCube
is_K	Check if a given unit is equivalent to Kelvin (K). mufasa.UltraCube
load_model_fit	Load the spectral fit results from a .fits file. mufasa.UltraCube
save_fit	Save the fitted parameter cube to a .fits file with the appropriate header. mufasa.UltraCube
to_K	Convert the unit of a spectral cube to Kelvin (K). mufasa.UltraCube
AIC	Calculate the Akaike Information Criterion (AIC). mufasa.aic
AICc	Calculate the corrected Akaike Information Criterion (AICc). mufasa.aic
fits_comp_AICc	A wrapper function to calculate corrected Akaike Information Criterion (AICc) values mufasa.aic
fits_comp_chisq	Calculate and save chi-squared values for the given cube and model fits. mufasa.aic
get_comp_AICc	Calculate AICc values for two models over the same samples. mufasa.aic
likelihood	Calculate the log-likelihood of model A relative to model B. mufasa.aic
fit_results	No description available. mufasa.clean_fits
above_ErrV_Thresh	No description available. mufasa.clean_fits
clean_2comp_maps	No description available. mufasa.clean_fits
exclusive_2comp_maps	No description available. mufasa.clean_fits
extremeV_mask	No description available. mufasa.clean_fits
remove_zeros	No description available. mufasa.clean_fits
convolve_sky	No description available. mufasa.convolve_tools
convolve_sky_byfactor	No description available. mufasa.convolve_tools
edge_trim	No description available. mufasa.convolve_tools
get_celestial_hdr	No description available. mufasa.convolve_tools
regrid	No description available. mufasa.convolve_tools
regrid_mask	No description available. mufasa.convolve_tools
snr_mask	No description available. mufasa.convolve_tools
deblend	Deblend hyperfine structures in a cube based on fitted models. mufasa.deblend_cube
FitTypeError	Fitttype provided is not valid. mufasa.exceptions
SNRMaskError	SNR Mask has no valid pixel. mufasa.exceptions
StartFitError	Fitting failed from the beginning mufasa.exceptions
get_celestial_hdr	No description available. mufasa.guess_refine
guess_from_cnvpara	No description available. mufasa.guess_refine
mask_cleaning	No description available. mufasa.guess_refine
mask_swap_2comp	No description available. mufasa.guess_refine
master_mask	No description available. mufasa.guess_refine
quick_2comp_sort	No description available. mufasa.guess_refine
refine_2c_guess	No description available. mufasa.guess_refine
refine_each_comp	No description available. mufasa.guess_refine
refine_guess	No description available. mufasa.guess_refine
regrid	No description available. mufasa.guess_refine
save_guesses	No description available. mufasa.guess_refine
simple_para_clean	No description available. mufasa.guess_refine
tautex_renorm	No description available. mufasa.guess_refine
Region	A class to represent the observed spectral cube to perform the model fits. mufasa.master_fitter
expand_fits	Expand fits in a region by incrementally fitting pixels beyond a defined mufasa.master_fitter
fit_best_2comp_residual_cnv	Fit the convolved residual of the best-fit two-component spectral model mufasa.master_fitter
fit_surroundings	Expand fits around a region based on model log-likelihood thresholds and mufasa.master_fitter
get_2comp_wide_guesses	Generate initial guesses for fitting a two-component spectral model with mufasa.master_fitter
get_best_2comp_model	Retrieve the best-fit model cube for the given Region object. mufasa.master_fitter
get_best_2comp_residual	Calculate the residual cube for the best-fit two-component model. mufasa.master_fitter
get_best_2comp_residual_SpectralCube	Generate the residual spectral cube for the best-fit two-component mufasa.master_fitter
get_best_2comp_residual_cnv	Generate a convolved residual cube for the best-fit two-component mufasa.master_fitter
get_best_2comp_snr_mod	Calculate the signal-to-noise ratio (SNR) map for the best-fit two- mufasa.master_fitter
get_convolved_cube	Generate and save a convolved version of the spectral cube for a given mufasa.master_fitter
get_convolved_fits	Fit a model to the convolved cube and save the results. mufasa.master_fitter
get_fits	Fit a model to the original spectral cube and save the results. mufasa.master_fitter
get_local_bad	Identify local pixels with significantly lower relative log-likelihood mufasa.master_fitter
get_marginal_pix	Return pixels at the edge of structures with values greater than mufasa.master_fitter
get_refit_guesses	Generate initial guesses for refitting based on neighboring pixels or mufasa.master_fitter
get_skyheader	Generate a 2D sky projection header from a 3D spectral cube header. mufasa.master_fitter
iter_2comp_fit	Perform a two-component fit iterantively through two steps. The first mufasa.master_fitter
master_2comp_fit	Perform a two-component fit on the data cube within a Region object. mufasa.master_fitter
refit_2comp_wide	Refit pixels to recover compoents with wide velocity separation for mufasa.master_fitter
refit_bad_2comp	Refit pixels with poor 2-component fits, as determined by the log- mufasa.master_fitter
refit_marginal	Refit pixels with fits that appears marginally okay, as deterined by the mufasa.master_fitter
refit_swap_2comp	Refit the cube by using the previous fit result as guesses, but with the mufasa.master_fitter
replace_bad_pix	Refit pixels marked by the mask as “bad” and adopt the new model if it mufasa.master_fitter
replace_para	Replace parameter values in a parameter cube with those from a reference mufasa.master_fitter
replace_rss	Replace RSS-related maps in a `UltraCube` object for specific mufasa.master_fitter
save_best_2comp_fit	Save the best two-component fit results for the specified region. mufasa.master_fitter
save_map	Save a 2D map as a FITS file. mufasa.master_fitter
save_updated_paramaps	Save the updated parameter maps for specified components. mufasa.master_fitter
standard_2comp_fit	Perform a two-component fit for the cube using default moment map mufasa.master_fitter
LineSetup	No description available. mufasa.moment_guess
adaptive_moment_maps	No description available. mufasa.moment_guess
get_rms_prefit	No description available. mufasa.moment_guess
get_tau	No description available. mufasa.moment_guess
get_tex	No description available. mufasa.moment_guess
get_window_slab	No description available. mufasa.moment_guess
master_guess	No description available. mufasa.moment_guess
mom_guess_wide_sep	No description available. mufasa.moment_guess
moment_guesses	Generate reasonable initial guesses for multiple component fits based on moment maps. mufasa.moment_guess
moment_guesses_1c	No description available. mufasa.moment_guess
noisemask_moment	No description available. mufasa.moment_guess
peakT	No description available. mufasa.moment_guess
vmask_cube	No description available. mufasa.moment_guess
vmask_moments	No description available. mufasa.moment_guess
window_mask_pcube	No description available. mufasa.moment_guess
window_moments	Calculate the zeroth, first, and second moments of a spectrum or cube mufasa.moment_guess
cubefit_gen	No description available. mufasa.multi_v_fit
cubefit_simp	No description available. mufasa.multi_v_fit
default_masking	No description available. mufasa.multi_v_fit
get_chisq	No description available. mufasa.multi_v_fit
get_start_point	No description available. mufasa.multi_v_fit
get_vstats	No description available. mufasa.multi_v_fit
handle_snr	No description available. mufasa.multi_v_fit
make_header	No description available. mufasa.multi_v_fit
match_pcube_mask	No description available. mufasa.multi_v_fit
register_pcube	No description available. mufasa.multi_v_fit
retry_fit	No description available. mufasa.multi_v_fit
save_guesses	No description available. mufasa.multi_v_fit
save_pcube	No description available. mufasa.multi_v_fit
set_pyspeckit_verbosity	No description available. mufasa.multi_v_fit
snr_estimate	No description available. mufasa.multi_v_fit
estimate_mode	Estimate the mode of the data using a histogram. mufasa.signals
get_moments	Calculate moments of the signals in a cube. mufasa.signals
get_rms_robust	Make a robust RMS estimate. mufasa.signals
get_signal_mask	Provide a 3D mask indicating signal regions based on RMS and SNR threshold. mufasa.signals
get_snr	Calculate the peak signal-to-noise ratio of the cube. mufasa.signals
get_v_at_peak	Find the velocity corresponding to the peak emission. mufasa.signals
get_v_mask	Return a mask centered on a reference velocity with a spectral window. mufasa.signals
refine_rms	Refine the RMS estimate by masking out signal regions. mufasa.signals
refine_signal_mask	Refine a signal mask by removing noisy features and expanding the mask. mufasa.signals
trim_cube_edge	Remove spatial edges from a cube. mufasa.signals
trim_edge	Trim edges using a 2D mask. mufasa.signals
v_estimate	Estimate the velocity centroid based on peak emission. mufasa.signals
distance_metric	No description available. mufasa.slab_sort
mask_swap_2comp	No description available. mufasa.slab_sort
quick_2comp_sort	No description available. mufasa.slab_sort
refmap_2c_mask	No description available. mufasa.slab_sort
sort_2comp	No description available. mufasa.slab_sort
BaseModel	Generalized base class for multi-component spectral models. mufasa.spec_models.BaseModel
HyperfineModel	Spectral model for multi-component fitting with hyperfine structure. mufasa.spec_models.HyperfineModel
AmmoniaModel	Ammonia (NH₃) spectral model for multi-component fitting. mufasa.spec_models.SpecModels
N2HplusModel	N₂H⁺ (Diazenylium) spectral model for multi-component fitting. mufasa.spec_models.SpecModels
T_antenna	No description available. mufasa.spec_models.ammonia_multiv
ammonia_multi_v	No description available. mufasa.spec_models.ammonia_multiv
nh3_multi_v_model_generator	No description available. mufasa.spec_models.ammonia_multiv
MetaModel	A class to store spectral model-specific information relevant to spectral modeling tasks, such as fitting. mufasa.spec_models.meta_model
n2hp_vtau_singlemodel_deblended	No description available. mufasa.spec_models.n2hp_deblended
T_antenna	No description available. mufasa.spec_models.n2hp_multiv
n2hp_multi_v	No description available. mufasa.spec_models.n2hp_multiv
n2hp_multi_v_model_generator	No description available. mufasa.spec_models.n2hp_multiv
nh3_vtau_singlemodel_deblended	No description available. mufasa.spec_models.nh3_deblended
assign_to_dataframe	Assign values from a new data array to an existing DataFrame based on spatial coordinates and component index. mufasa.utils.dataframe
make_dataframe	Create a DataFrame from a 3D parameter array, applying optional velocity and error thresholds. mufasa.utils.dataframe
read	Read a FITS file and convert the data to a pandas DataFrame, optionally including the header. mufasa.utils.dataframe
deprecated	Mark a function or class as deprecated. mufasa.utils.decorators
downsample_header	Downsample a FITS header along a specified axis. mufasa.utils.fits_utils
get_pixel_mapping	Compute the pixel mapping between two FITS headers or WCS objects. mufasa.utils.fits_utils
expand_interpolate	No description available. mufasa.utils.interpolate
iter_expand	No description available. mufasa.utils.interpolate
dist_divide	No description available. mufasa.utils.map_divide
watershed_divide	No description available. mufasa.utils.map_divide
calculate_dask_memory_limit	Mimic Dask’s default memory limit setting. mufasa.utils.memory
calculate_target_memory	Calculate target memory per core for chunked computations. mufasa.utils.memory
get_size_mb	No description available. mufasa.utils.memory
get_system_free_memory	No description available. mufasa.utils.memory
monitor_peak_memory	Decorator to monitor and record the peak memory usage of a function. mufasa.utils.memory
peak_memory	Decorator to monitor and display the peak memory usage of a function, mufasa.utils.memory
tmp_save_gauge	Return whether or not it’s worth DaskSpectralCube results temporary mufasa.utils.memory
OriginContextFilter	No description available. mufasa.utils.mufasa_log
WarningContextFilter	No description available. mufasa.utils.mufasa_log
get_logger	No description available. mufasa.utils.mufasa_log
init_logging	:param logfile: file to save to (default mufasa.log) mufasa.utils.mufasa_log
reset_logger	No description available. mufasa.utils.mufasa_log
validate_n_cores	No description available. mufasa.utils.multicore
disk_neighbour	No description available. mufasa.utils.neighbours
footprint_rectangle	Generate a rectangular or hyper-rectangular footprint. mufasa.utils.neighbours
get_neighbor_coord	No description available. mufasa.utils.neighbours
get_valid_neighbors	No description available. mufasa.utils.neighbours
maxref_neighbor_coords	No description available. mufasa.utils.neighbours
square_neighbour	No description available. mufasa.utils.neighbours
ScatterPPV	A class to plot the fitted parameters in 3D scatter plots. Most of the data is stored in a pandas DataFrame. mufasa.visualization.scatter_3D
scatter_3D	Plot a 3D scatter plot with optional opacity scaling for point ranges. mufasa.visualization.scatter_3D
scatter_3D_df	A wrapper for scatter_3D to quickly plot a pandas DataFrame in 3D. mufasa.visualization.scatter_3D
Plotter	No description available. mufasa.visualization.spec_viz
ensure_units_compatible	Ensure the limits have compatible units with the data, converting if needed. mufasa.visualization.spec_viz
get_cube_slab	Extract a spectral slab from the cube over the specified velocity range. mufasa.visualization.spec_viz
get_spec_grid	Create a grid of subplots for spectra. mufasa.visualization.spec_viz
plot_fits_grid	Plot a grid of model fits from the cube centered at (x, y). mufasa.visualization.spec_viz
plot_model	Plot a model fit for a spectrum. mufasa.visualization.spec_viz
plot_spec	Plot a spectrum. mufasa.visualization.spec_viz
plot_spec_grid	Plot a grid of spectra from the cube centered at (x, y). mufasa.visualization.spec_viz
strip_units	Helper function to strip units from a limit tuple if it contains Quantity. mufasa.visualization.spec_viz