Introduction

What is IFSCube?

IFSCube is a python package designed to perform analysis tasks in data cubes of integral field spectroscopy. It was originally intended to be used as part of your own scripts, hopefully making them a lot more concise, and saving you a lot of time. However, since everything you can do in a Python script can also be done using an interactive interpreter such as ipython, you can choose to perform your analysis on the fly.

During development I found out that some tasks work better as executable programs that the user could call directly from the command line, with options being set by an ASCII configuration file. These tasks are the fitting of spectral features in 1D spectra and data cubes, the fitting of rotation models to velocity fields and the inspection of fit results, which are accomplished by the programs specfit, ifscube, fit_rotation and fit_scrutinizer respectively.

The preferred data format for IFSCube is the Flexible Image Transport System (FITS) standard. However, if you wish to use other formats or perform some preliminary processing of your data, it is enough to subclass the ifscube.datacube.Cube or ifscube.onedspec.Spectrum classes, substituting the __init__() and _load() methods.

Installation instructions

The preferred method for the installation of IFSCube is to use pip. Pip can install directly from the git repository using the following command:

pip install git+https://github.com/danielrd6/ifscube.git

IFSCube uses third party programs that are not distributed with the package, namely pPXF and Voronoi Binning, written by Michelle Cappellari. If you wish to use IFSCube in conjunction with these programs you will have to install them first, by downloading and following the instructions at the following address: http://www-astro.physics.ox.ac.uk/~mxc/software/

Requirements

Apart from the Python modules listed in the requirements.txt file, IFSCube also requires that some Fortran compiler be present in the system. If you are using Ubuntu you can install one using the following command:

sudo apt-get update && sudo apt-get install gfortran

Upgrade

If you want to upgrade an existing installation of IFSCube use

pip install --upgrade git+https://github.com/danielrd6/ifscube.git

If you are having trouble with the Fortran compiler you can force one with pip’s install options, which are exemplified below.

To force a specific compiler:

pip install --install-option=build --install-option='--fcompiler=gnu95' git+https://github.com/danielrd6/ifscube.git

IFSCube has been extensively tested with the astroconda [1] distribution, therefore it is highly recommended that you install it within the astroconda’s Python 3 environment.

If you want to be able to change the package to suit your needs, or contribute with your own code to the project, it is recommended to clone the git repository and install the package as an editable package.

git clone https://github.com/danielrd6/ifscube.git
cd ifscube
pip install -e .

If you are using Conda you can substitute the last line by

conda develop -b .

Remember to switch to the desired Conda environment prior to running this command.

Footnotes

[1]	https://astroconda.readthedocs.io/en/latest/