GoFish

Fishing for molecular line detections in protoplanetary disks.
For more information, read the documentation.

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Installation

The quickest way to install is using PyPI:

> pip install gofish

which will install all the necessary dependancies.

Example Usage

For a thorough introduction on how to use GoFish, see the extensive documentation.

In brief, the user will attach an image cube to GoFish which will read the necessary header information:

# Attach an image cube.
from gofish import imagecube
cube = imagecube('path/to/cube.fits')

Once attached, you can extract the average spectrum over a user-specified region using the known geometrical properties of the disk and priors about the velocity profile of the disk:

# Return the averaged spectrum between 0.0" and 1.0".
x, y, dy = cube.average_spectrum(r_min=0.0, r_max=1.0, inc=5.0,
                                 PA=152., mstar=0.88, dist=59.5)

where x is the velocity axis, y is the spectrum and dy is the uncertainty. Alternatively the integrated spectrum can be extracted in a similar manner,

# Return the integrated spectrum between 0.0" and 1.0".
x, y, dy = cube.integrated_spectrum(r_min=0.0, r_max=1.0, inc=5.0,
                                    PA=152., mstar=0.88, dist=59.5)

where y is now the integrated flux in units of Jy.

Citation

If you use GoFish as part of your research, please cite the JOSS article:

@article{GoFish,
    doi = {10.21105/joss.01632},
    url = {https://doi.org/10.21105/joss.01632},
    year = {2019},
    month = {sep},
    publisher = {The Open Journal},
    volume = {4},
    number = {41},
    pages = {1632},
    author = {Richard Teague},
    title = {GoFish: Fishing for Line Observations in Protoplanetary Disks},
    journal = {The Journal of Open Source Software}
}

A list of works using GoFish can be found here.