preshanth / Zeeman_modelling

Zeeman_modelling

About

This command line program written in Python aims to standardize and automize the Zeeman anlaysis process in emission line radio astronomy through robust curve fitting and Bayesian-based parameter sampling. We hope to minimize user bias in the study of interstellar magnetic fields through this software solution.

Getting Started

• Clone this repository.
• It is highly to conduct the following installation in a clean environment. Could be conda, mamba, or venv.
• cd into the cloned folder and enter the following command:

pip install .

• cd into the directory where the Stokes I and Stokes V cubes are and call the program by:

zeeman_modeling FILENAME_STOKESI [FILENAME_STOKESV] XPIXEL YPIXEL [OPTIONS]

• see detailed options and examples below
• To verify correct installation, run:

zeeman_modeling -h
# or
zeeman_modeling --help

• Expected output

usage: zeeman_modeling [-h] [--mapping MAPPING [MAPPING ...]] [--output OUTPUT] [--justI] [--vel] [--init] [--trace]
                    [--corner]
                    filename [filename ...] pixel pixel

Zeeman analysis and fitting

positional arguments:
  filename              Filename of the Stoeks I and Stokes V FITS file to be analysed
  pixel                 Pixel coordinates of the region to be analysed

options:
  -h, --help            show this help message and exit
  --mapping MAPPING [MAPPING ...]
                        Number of Gaussian components to fit each visible peak
  --output OUTPUT       Output directory
  --justI               Only fits Stokes I
  --init                Visualize the position of initial guesses
  --trace               Plot trace plots
  --corner              Plot corner plots
  --absorb              Absorption spectrum input
  --sensitivity SENSITIVITY
                        Sensitivity in peak finding

Usage

It is highly encouraged for users to see where the initial guesses by the –init option before proceeding to Stokes I and Stokes V fitting.

filename_I:	filename of the Stokes I cube
filename_V:	filename of the Stokes V cube, optional when using the --justI flag
pixel_x:	x value of the selected pixel
pixel_y:	y value of the selected pixel

-h, --help	show this help message and exit
--mapping	[MAPPING …] Number of Gaussian components to fit each visible peak
--output	Output directory
--justI	Conduct line fitting on just the Stokes I profile
--init	Visualize the position of initial guesses
--trace	Plot trace plots
--corner	Plot corner plots
--absorb	Conduct absorption Zeeman analysis
--sensitivity	Sensitivity in initial peak find

Example

Visualize initial guess:

zeeman_modeling TestI.py TestV.py 64 64 --init

To fit Stokes I and Stokes V FITS cubes named 1720I.FITS and 1720V.FITS at pixel value x = 128, y = 128, one would pass the following line to the terminal. (Assuming there are two visible peaks in Stokes I profile and would like to fit each peak with two Gaussian components)

zeeman_modeling 1720_I.FITS 1720_V.FITS 128 127 --mapping 2 2

To also store the plotting results as well as corner plots and tracing plots to check for MCMC effectiveness, add the following arguments:

zeeman_modeling 1720_I.FITS 1720_V.FITS 128 127 --mapping 2 2 --plot --trace --corner