spectrAOD 0.0.1

SpectrAOD

spectrAOD is a package for measuring the apparent optical depth, and thus, the apparent column density for spectral absorption features as outlined by Savage and Sembach in their 1991 paper. Many researchers have their own code for performing these measurements but we set out to create an open-source, well-maintained python package for people who didn't want to reinvent the wheel. Currently, the package has a limited use case scenario for Cosmic Origins Spectrograph data at a redshift of zero, but we hope to expand the capabilities of the package in terms of what missions are supported, the computation abilities, and visualization for these calculations. Stay tuned!

Installation

This package will soon be registered on PyPI and complete with its own environment file specifications, but until then you'll have to install it the old fashioned way. You will need a working, and preferably current version of Anaconda.

Make a new environment

conda create --name <environment_name> python=3.5 <other packages>

Activate the new environment with:

conda activate <environment_name>

We recommend a short and simple name for the environment such as spectraod.

Clone the repository and install it

This repository has a button near the top where you can click for the link to clone or download. Choose the https version unless you have set up an ssh token for Github. Move into the directory that you would like this package to live in, then:

git clone https://github.com/cmagness/spectrAOD.git
cd spectrAOD
pip install .

Alternately, if you are having issues installing with pip, you can also use python setup.py install.

Using spectrAOD

Configuring Settings

In this repository you will see a file called sample_settings.yaml. You will need a settings file to use this package that is of the same format. Copy the settings file and rename it as you please. For spectrAOD to find this file, you have two options:

Set an environment variable (Recommended)

We recommend creating an environment variable in your .bashrc or .bash_profile to point to this file. To do so, open your .bashrc or .bash_profile in a text editor (this will be a hidden file in your home directory if you are unfamiliar) and then add the line:

export SPECTRAOD_SETTINGS="/path/to/your/settings/file"

Save and close your .bash_profile and then activate these changes with:

source .bash_profile

Now spectrAOD will know where to look for your file. If you decide to move it, just update the path.

Move your copy (Slightly faster)

If you don't want to mess with setting an environment variable, that is just fine. You can move your settings file to the directory you plan to run the package from and spectrAOD will look for a .yaml file if no environment variable is set. Just be warned that it will look for any .yaml file.

Running the package

Once you've told spectrAOD where to find your settings file, be sure to actually populate it. Each parameter in the sample file has a comment with information about what should go into that file. Remove that comment and replace it with the default entries you want to use--don't worry, you can change the value in each run from the command line.

Setting a Target List

In the settings file you will notice one of the parameters asks for the path to your target list file. To perform the LSR correction spectrAOD needs a target list that has the RA and DEC. The target name needs to match the name that is used in the file header if you are processing fits files. You can see the format for this file (it must also be a csv at this time) in sample_targets.csv. Feel free to use that file to build your target list.

Command line arguments

To run the default measurements you've put in that file, from the command line, in any directory, enter:

measure <ion>

or, from within the package level:

python measure_aod.py <ion>

Where the ion is the name of the ion you wish to measure. Currently, you may use any of the ions in the mini_ions.csv list, or add your own in the same format to that file.

To see the full list of parameter options, run:

measure --help

This will give you information about all the parameters you can change from the command line. By default, spectrAOD will use the values in your settings file but you can alter any of them from the default by adding the correct flag at the command line.

Say you perform a measurement of NV in the region from -100 to 100 km/s but then decide it may be advantageous to perform the measurement in the window from -100 to 150 km/s. You can do this without making changes to your settings file by running:

measure NV --vel_max 150