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rbcodes

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.

Installation:

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.

Contents:

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...

DOI

DOI