Loving ISIS - Confessions of a Former XSPEC User

Five Basics

The ISIS manual gives an overview of its commands and syntax, as well as an introduction to S-lang syntax in general. Once you've installed ISIS, starting it and running a script is as simple as:

   unix%> isis -g
   Welcome to ISIS Version 1.6.0-3
   Copyright (C) 1998-2010 Massachusetts Institute of Technology

   isis> () = evalfile("/path/my_script.sl");
   isis> () = evalfile("/path/.isisrc")        % Happens automatically if .isisrc
                                               % is placed in home directory
   isis> () = evalfile("./analysis_script.sl") % Run the analysis on these web pages

In the above, the -g option gives extra debugging information when running a script. Note the presence of ()= before evalfile. The evalfile returns a success/fail flag which otherwise would be "placed on the stack", and then "popped off the stack" and printed to screen, (The S- in S-lang stands for "stack".) The ()= captures and discards this value. For the case of multiple return values, let's say a, b, c, first a is placed on the stack, then b, then c. The "popping off the stack" happens in the reverse order: c, b, then a. This is the order they will print to the screen. Thus we would have:

   isis> returns_abc(); % Dump the output to screen
   c
   b
   a
   isis> (a,b,c) = returns_abc();  % Capture the output to variables
   isis> (,,) = returns_abc();     % Discard the output

Once you've gotten used to that basic syntax, there are five other useful things to remember that will help you during an analysis session:

The who; command will give you a list of the variables that you have defined on the command line during the session (but won't list the global variables loaded from scripts).
The .apropos command (which doesn't require an ending semi-colon!) will give you a list of commands (including globally defined functions imported from scripts) that contain a given substring.
The .help command (which also doesn't require the semi-colon) will give you a help file for most ISIS intrinsic commands.
Many commands (including most of the functions defined by my .isisrc file) will give you a usage message if they are invoked without any arguments.
Any command name that you don't like you can alias to a name that you do like. Commonly used aliases and custom defined S-lang functions can be stored in your home directory in an .isisrc file, which will be loaded every time you start ISIS. (Invoking ISIS as: unix%> isis -n will run ISIS without loading your .isisrc)

With the five basics above you can find a good deal of information during an analysis session, and you can make life more familiar for yourself. Below is an example (where my .isisrc file has been loaded on startup):

   Welcome to ISIS Version 1.6.0-3
   Copyright (C) 1998-2010 Massachusetts Institute of Technology

   isis> a = [0:10]; b = 3.5; c = "pizza";
   isis> who;
   a: Integer_Type[11]
   b: 3.5
   c: pizza
   isis> .apropos load

   Found 26 function matches in namespace Global:
   add_to_isis_load_path      append_to_isis_load_path   autoload
   get_isis_load_path         get_slang_load_path        load_alt_ioniz
   load_arf                   load_buf                   load_conf
   load_data                  load_dataset               load_fit_method
   load_fit_statistic         load_kernel                load_line_profile_function
   load_model                 load_par                   load_radio
   load_rmf                   load_xspec_fun             load_xspec_local_models
   load_xspec_symbol          mt_load_model              prepend_to_isis_load_path
   set_isis_load_path         set_slang_load_path

   isis> .help load_arf
   Searched: /usr/local/isis/doc/local_help.txt
   Searched: /usr/local/isis/doc/cfitsio.hlp
   load_arf

    SYNOPSIS
       Load an effective area (ARF) file

    USAGE
       status = load_arf ("filename")

    DESCRIPTION
       This function loads either a FITS Type I or Type II ARF file;
       the updated list of currently loaded ARFs is automatically
       displayed. On return, status is equal to the integer index of
       the ARF just loaded ( status > 0); a return value of status =
       -1 is used to indicate failure.  (For Type II ARF input, a
       return value of zero indicates success).


    SEE ALSO
       load_dataset, list_arf, delete_arf, assign_arf, unassign_arf

   isis> load_radio;

    radio_id = load_radio(radio_struct);

       Takes the structure output from `read_radio();' and loads
       it up for fitting.  Also ignores all the zero count
       channels.  (Note: Those could come back if any further filters
       are applied.)

   isis> alias("load_arf","arf");
   isis> alias("fit_fun","model");

Next up: Loading the Data.

This page was last updated Sep 16, 2013 by Michael Nowak. To comment on it or the material presented here, send email to mnowak@space.mit.edu.