spectrAOD 0.0.2

This package is for measuring the apparent optical depth of spectra

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 is registered on PyPI and available via pip. pip installations will provide the latest version released to PyPI, and is sufficient for installing the package. However, in case you would like the latest version, between published releases, we also offer instructions on how to install by cloning the repository. 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>

<other packages> simply denotes any other packages you may wish to install in this environment, such as stsci or notebook. All required packages for spectrAOD will be installed as a dependency automatically.

Activate the new environment with:

conda activate <environment_name>

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

Install with pip (Latest published release, recommended)

From the command line, in your new environment:

pip install spectrAOD==0.0.2

You can drop the version number and just use the name of the package if you would like the version most recently published. pip will also give you instructions on how to upgrade your version if there is a newer published one available.

Clone the repository and install it (Latest version, recommended for developers only)

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, but retain the .yaml extension. If you've installed via pip, you will not be easily able to find this file. Create a .yaml file and make sure it has the following information in it:

inputs:
  # string: path to data
  datadir:
  # string: path to output directory
  outdir:
  # string: path to target list
  targets:

parameters:
  # string: instrument
  instrument:
  # string: filetype
  filetype:
  # int: minimum number for velocity window in km/s
  vel_min:
  # int: maximum number for velocity window in km/s
  vel_max:
  # string: grating
  grating:

defaults:
  continuum_left: [-450, -300]
  continuum_right: [300, 450]
  all_ions: 

You should leave the all_ions field blank to use the list of "mini_ions .csv" included with the package, unless you wish to provide the path to your own list.

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.

Populating the settings

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. These settings provide a default for spectrAOD 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. Explicitly, this needs to be a path to a target list and NOT a list of targets. 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.

Running the package

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