Metadata-Version: 2.1
Name: spectrAOD
Version: 0.0.3
Summary: This package is for measuring the apparent optical depth of spectra
Home-page: https://github.com/cmagness/spectrAOD
Author: Camellia Magness
Author-email: cmagness@stsci.edu
License: UNKNOWN
Description: SpectrAOD
        ------------
        ![spectraod_technique](spectraod_ddrf_final.png)
        
        `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.
        
        > N.B.: If you are having any issues with installation, please consult the 
        [Common Issues](#common-issues) section.
        
        ##### 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==0.0.3
        ```
        
        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 [COS]
          instrument:
          # string: filetype [X1DSUM, BART]
          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, must match header keyword
          grating:
          # float: redshift of interest. use 0.0 if not specified
          redshift:
        
        defaults:
          continuum_left: [-450, -300]
          continuum_right: [300, 450]
          # string: path to ions file
          all_ions: "mini_ions.csv"
        ```
        You should leave the `all_ions` field as is to use the list of "mini_ions.csv" 
        included with the package, unless you wish to provide the path to your own
        list. If you choose to use your own ions list, you may either copy the mini 
        list from the repository and add to it in the same format, or you may create 
        an entirely new ions file with four columns, a header column, and the values 
        space separated as follows:
         
         ```
        ion wavelength f(oscillating strength) damping
        <STR:ION> <FLOAT:WAVELENGTH> <FLOAT:f> <FLOAT:damping>
        ```
        > N.B.: the column names don't particularly matter as long as you have a 
        header column.
        
        ###### Setting a Target List
        
        **If you are working with `X1DSUM` data you do not need a target list and
        can skip this section. The RA and DEC used to calculate the LSR correction
        will be retrieved from the file header. Just make sure to set `targets: ""`.**
        
        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. 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.
        
        For `spectrAOD` to find the `settings.yaml` 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.
        
        #### 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
        ```
        
        #### Common Issues
        
        The following are issues encountered by people during the use of this 
        package. These are usually due to machine level installation problems but 
        they are being documented here in case someone else runs into a similar issue.
        
        * *Problem*: If you encounter an issue, error message, or traceback 
        referencing or relating to `setuptools`, you may have a corrupt version of the 
        package. 
        *Solution*: You may need to uninstall your version before installing 
        `spectrAOD`. You can do this with `pip uninstall setuptools` and then you 
        should be able to proceed with `spectrAOD` installation as usual. `spectrAOD` 
        will install a new version of `setuptools` for you.
        
        Should you encounter any other issues with the use of this package, please 
        open a new issue on the repository [here](https://github.com/cmagness/spectrAOD/issues).
        
        <!---
        
        Contributing Code, Documentation, or Feedback
        ---------------------------------------------
        
        
        3rd Party Libraries this package requires
        -----------------------------------------
        
        
        License
        -------
        
        ---> 
Keywords: astronomy
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Astronomy
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.5
Description-Content-Type: text/markdown
