IMPORTANT WARNING

The FITS headers produced by CUBEGEN are adequate for HSIM3 simulations. However the magnitude and spectral normalization of the sources might not be as expected.

Input data cube generator

Written by Simon Zieleniewski & Nicholas Zieleniewski

Last Edited: 23-09-21

PURPOSE:

This package produces simple input data cubes for simulations using the HSIM pipeline for the ELT/HARMONI IFU. It can produce simple point or extended sources with template spectra or simple emission line profiles. The output FITS files are formatted to run through the pipelines.

FILES:

The pipeline currently runs using the main python file:

cubegen.py

which requires several routines in the Modules/ subdirectory:

main.py

spectra.py
spaxelfunc.py
plotdata.py
mag_rescale.py
intensityprofiles.py
header_format.py
datacube_init.py
SimpleNumericalCalculus.py

There are also several data files:

Simul_spectra/pickles_spectra/ - contains stellar spectra for use as input templates Simul_spectra/lyman_alpha_spectra/ - contains Lyman-alpha emission line template spectra

DEPENDENCIES:

The following Python modules are essential to run the pipeline: numpy - http://www.scipy.org/scipylib/download.html scipy - http://www.scipy.org/scipylib/download.html astropy - http://www.astropy.org/

The following is strongly recommended for optimum running: wxPython - This is used to load the GUI. It can be downloaded from: http://www.wxpython.org/download.php

Make sure the modules can by found by your Python implementation. E.g. in a Python environment try:

        >>> import numpy
        >>> import astropy
        >>> import scipy
        >>> import wx

there should be no errors!

HOW TO USE:

The code can be run in two ways:

1. Running the GUI: $ python cubegen.py This opens the graphical interface from which you can enter the various parameters and start the simulation.

2. From the command line: $ python cubegen.py -c arg1 arg2 arg3 etc…

Use: $ python cubegen.py -c to display arguments list

The commands must be entered in the following order:

1. cubename: Output data cube file name
2. userspec: Path to input spectrum datafile (wavelength[A], flux[erg/s/cm2/A]) - enter None if not using
3. userres: Resolution element of user spectrum [A] - enter 0 if not using
4. start_lambda: Start wavelength value [A] - enter anything if uploading spectrum
5. end_lambda: End wavelength value [A] - enter anything if uploading spectrum
6. R: Spectral resolving power - enter anything if uploading spectrum
7. ABmag: AB magnitude - enter anything if uploading spectrum
8. band: AB magnitude normalisation band [V, R, I, J, H, K, L, M] - enter anything if uploading spectrum
9. z: Redshift - enter anything if uploading spectrum'
10. spectype: Spectrum type [Flat, Emission, O5V, O9V, B0V, B3V, B9V, A0V, A3V, A5V, F0V, F2V, F5V, G0V, G2V, G5V, K0V, K2V, K5V, K7V, M0V, M2V, M3V, M4V, M5V, M6V, lyaem1, lyaem2, lyaem3, lyaem4]
11. spaxel_scale: Spaxel box size [mas]
12. fov: Field of view: [spaxels]
13. source_type: Source type [Point, Galaxy(=Sersic)]
14. num_sources: No. of sources [1,2]
15. source_sep: Separation of sources (if two) [spaxels] - enter value regardless!
16. sersic_k: Sersic k parameter - enter value regardless!
17. sersic_n: Sersic n parameter - enter value regardless!
18. brightness_ratio: Brightness ratio between two sources - enter value regardless!
19. linewave: Emission line central wavelength [A] - enter value regardless!
20. linewidth: Emission line width [km/s] - enter value regardless!
21. lineflux: Emission line total flux [erg/s/cm2] - enter value regardless!

Use -h or --help to display help message and exit Use -c or --cline option to use command line. Use -o or --odir when using command line to specify output file directory. Default is /hsim/Output_cubes/

An example command line entry:

$ python2 cubegen.py -c -o Generated_Cubes New_datacube None 0 6000 7000 200 20 V 0 Flat 1 500 Galaxy 2 100 1 4 1.5 0 0 0