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https://github.com/deshima-dev/galspec

GalSpec package
https://github.com/deshima-dev/galspec

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GalSpec package

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README 

        
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# GalSpec package

This package is intended to quickly and easily generate a galaxy spectrum with a blackbody continuum emission and emission lines. The lines in this package are:

* CO lines 

* SIII

* SiII

* OIII, OI 

* NIII, NII 

* CII, CI



*Code by Tom Bakx, packaging and addition of molecular lines and rescaling by Stefanie Brackenhoff*



## Functionalities & Usage

* A spectrum can be generated using the ```spectrum()``` function. 



It takes the following inputs:

* **luminosity** in units of log(L_fir [L_sol])

* **redshift** z

* **fLow, fHigh** minimum and maximum frequency that will be in the spectrum in units of GHz

* **numFreqBins** amount of linearly spaced frequency bins at which the spectrum should be evaluated

* **linewidth** width of spectral lines in units of km/s

* **COlines** 'Kamenetzky' [1] or 'Rosenberg' [2] determines the amplitude of the CO lines, default is Kamenetzky. 

* **lines** 'Bonato' [3] or 'Spinoglio' [4] determines the amplitude of the remaining spectral lines, default is Bonato

* **mollines** 'True' or 'False'. Toggles whether molecularlines are shown. Values estimated using [5]. Defaults as 'True'

* **variance** adds uncertainty to the amplitude of the atomic lines. Defaults to 0. Variation in molecular lines not implemented in the current version.

* **manualrescale** sets whether the lines should be default ratios by Kamenetzky/Rosenberg and Bonato/Spinoglio, or set by user. Options: 

	- **'False'** default line amplitudes used

    - **'Absolute'** numpy array of 37 line amplitudes in Jy additive to blackbody emission can be set in rescaleArray. Additional entries ignored if mollines is set to 'False'.

    - **'Relative'** numpy array of 37 scalars can be set in rescaleArray. The default ratios from Kamenetzky/Rosenberg are multiplied by these scalars prior to addition to the blackbody spectrum. Additional entries ignored if mollines is set to 'False'.

* **rescaleArray** rescales the emission lines according to setting in 'manualrescale'. Order of the lines can be found using ```linenames()```



And creates as output:

* **freqArray** array frequencies in units of GHz

* **spectrum** array of the flux densities in the spectrum in units of Jy



[1]: http://dx.doi.org/10.3847/0004-637X/829/2/93

[2]: https://ui.adsabs.harvard.edu/link_gateway/2015ApJ...801...72R/doi:10.1088/0004-637X/801/2/72

[3]: https://ui.adsabs.harvard.edu/link_gateway/2014MNRAS.438.2547B/doi:10.1093/mnras/stt2375

[4]: https://ui.adsabs.harvard.edu/link_gateway/2012ApJ...745..171S/doi:10.1088/0004-637X/745/2/171

[5]: https://arxiv.org/pdf/1106.5054.pdf



* The spectrum can quickly be plotted using the ```plotspectrum()``` function



This function takes the outputs of ```spectrum()``` as an input and creates a plot with axis labels



* The names of the spectral lines and their order for the ```rescaleArray``` in ```spectrum()``` are outputted in a numpy array. Whether the names of molecular lines are shown can be toggled by setting the keyword mollines to 'False'.



## Examples

* Simple example

```

import galspec



luminosity = 13.7

z = 4.43

fLow = 90 #GHz

fHigh = 910 #GHz

numFreqBins = 1500

linewidth = 600

gal_freq, gal_flux = galspec.spectrum(luminosity, z, fLow, fHigh, numFreqBins, linewidth, mollines = 'False')



galspec.plotspectrum(gal_freq, gal_flux)

```



![Example](/example_spectrum.png)



* Using the ratios by Rosenberg and Spinoglio

```

import galspec



luminosity = 13.7

z = 4.43

fLow = 90 #GHz

fHigh = 910 #GHz

numFreqBins = 1500

linewidth = 600

gal_freq, gal_flux = galspec.spectrum(luminosity, z, fLow, fHigh, numFreqBins, linewidth, 'Rosenberg', 'Spinoglio', mollines = 'False')



galspec.plotspectrum(gal_freq, gal_flux)

```

![Example2](/example_spectrum_RosSpin.png)



* Using manual ratios to only show CO lines

```

import galspec

import numpy as np



luminosity = 13.7

z = 4.43

fLow = 90 #GHz

fHigh = 910 #GHz

numFreqBins = 1500

linewidth = 600



names = galspec.linenames()

lines = np.zeros(len(names))

for i in range(len(names)):

    if names[i].startswith('CO'): lines[i]=1



gal_freq, gal_flux = galspec.spectrum(luminosity, z, fLow, fHigh, numFreqBins, linewidth, manualrescale = 'Relative', rescaleArray = lines, mollines = 'False')



galspec.plotspectrum(gal_freq, gal_flux)

```

![Example3](/example_spectrum_CO_only.png)



* Including molecular lines

```

import galspec

import numpy as np



luminosity = 13.7

z = 4.43

fLow = 90 #GHz

fHigh = 910 #GHz

numFreqBins = 1500

linewidth = 600



gal_freq, gal_flux = galspec.spectrum(luminosity, z, fLow, fHigh, numFreqBins, linewidth)



galspec.plotspectrum(gal_freq, gal_flux)

```

![Example4](/example_spectrum_with_mols.png)



## Installation

```pip install galspec```



## Required packages

* ```Numpy```

* ```astropy```

* ```matplotlib```

* ```scipy```