This is a public release of python codes commonly used for astrophysical reserach by Rongmon Bordoloi. This package is constantly under development and will be periodically updated.
Add this folder to your pythonpath and you are good to go. To make sure the GUIs function properly we recommend that you create a new environemnt as shown in requirements_simple.txt
Dependencies: astropy, lmfit, scipy, numpy, matplotlib, linetools
Partial Dependencies: PysimpleGUI for some GUIs.
The GUIs folder contains several graphical user interfaces for astrophysics.
1) rb_cont.py : A simple interactive continuum fitter.
2) rb_spec.py : An absorption line analysis pipeline. Allowing to create an object from an 1D
spectrum do continuum fitting, measure equivalenth widths/column densities and
save the final data and measurements. Also allows the fitting of a simple Voigt profile.
NOTE: Major overhaul to calling sequence since April 2022. See example in the file.
3) rb_interactive_vpfit_singlet.py : Interactive simple Voigt profile fitter [used with rb_spec.py]
[ Look for rbvfit github repository for an interactive Voigt
profile fitter, suited for any complex profiles.]
4) rb_plot_spec.py: To plot 1D spectrum, smooth, pan, zoom and explore spectrum. Allows to plot
absorption lines at any redshifts, and do simple equivalent width and Gaussian
fitting. My version of x_specplot routine. Now updated to plot multiple absorbers
and load previously identified absorbers.
5) abstools: A complex absorption line analysis GUI to simultaneously continuum fit and
measure EW/logN of several absorption lines. This is under GUIs/abstools.
Look up readme file in that folder for a working example.
6) rb_specgui: Wrapper for a complex 1d spectrum viwer and line identifier [Plotspec_integrated.py].
This is the upgraded pyqt5 version of rb_plot_spec package.
7) zgui/main.py : This is a new GUI to measure redshifts of galaxies using 1d or 2d spectrum.
Can be used in batch mode and is optimized for JWST NIRCam/Grism spectroscopy.
The IGM folder contains several python routines for intergalactic medium and circumgalactic medium calculations.
1) compute_EW.py : Compute equivalent width and column densities of any absorption/emission lines.
2) rb_setline.py : For any given rest frame wavelength find corresponding atomic transition and
the fvalues. [Can find any line nearest to the input wavelength].
3) rb_iter_contfit.py : Iteratively fit [with sigma clipping] continuum to a small slice of 1D
spectrum using Legendre polynomials.
4) rb_specbin.py : Rebin 1D spectrum to increase S/N
5) ransac_contfit.py : Powerful hybrid continuum fitter. Initial fit is done by an automated ransac
algorithm, then allows user to tweak the fit using linetools.fit_continuum
routine. Saves the fitted continuum and the 1D spectrum as a xspectrum1D object
Very helpful to fit a full quasar continuum.
6) lens_sep_to_kpc.py :Function to compute physical separation between sightlines in a lensed quasar system under the thin lens approximation.
The halo folder contains modules to compute NFW halo profiles
1) rb_nfw.py : Compute NFW halo profile
2) mstar2mhalo.py : Convert stellar mass to Halo mass using Moster et al. 2010.
The stat folder contains several statistical codes:
1) rb_wilsonscore.py : Wilsonscore confidence intervals.
2) rb_boot.py : Bootstrap function
The lensing folder contains code to ray trace positions to source plane for a given deflection matrix.
1) lens_ang_sep.py : Inititate the delensing object to load the required deflection matrices
The utils folder contains several utility modules:
1) rb_utility.py : Several utility functions
2) rb_x1d_id.py : This function will read all HST/COS x1d fits files in a folder and print out
the header info for raw spectra. It will print filename, exposure type,
and object type entries from the header.
3) readmultispec.py : Read IRAF (echelle) spectrum in multispec format from a FITS file. Can read
most multispec formats including linear, log, cubic spline, Chebyshev or
Legendre dispersion spectra. I got this code from https://github.com/kgullikson88/General.
The catalog folder contains codes for catalog search:
1)rb_search.py. : Function to do a cone search around any (ra,dec) pointing with respect to a list of ra,dec entries.
2) convert_FIRE_coordinates.py: Custom code only to take Magellan 1D FIRE spectrum and use the header information
to transform the co-ordinates to J2000 epoch.
We are constantly developing...
