Isis tutorial walkthrough - Revision history

Kreykenbohm: add some more verbatim commands

2026-02-12T16:57:17Z

add some more verbatim commands

Kreykenbohm: Adds hint to switch back to linear scaling before plotting the rmf

2026-02-12T16:41:32Z

Adds hint to switch back to linear scaling before plotting the rmf

Grinberg: Exercise 1 text changed since there is now no previous exercise.

2020-05-27T07:59:14Z

Exercise 1 text changed since there is now no previous exercise.

Grinberg at 07:08, 27 May 2020

2020-05-27T07:08:39Z

Grinberg at 07:06, 27 May 2020

2020-05-27T07:06:22Z

Wilms at 13:57, 19 May 2020

2020-05-19T13:57:48Z

Show changes

Wilms: /* Invoking isis */

2020-05-19T13:40:15Z

Invoking isis

Berger at 09:34, 20 September 2018

2018-09-20T09:34:56Z

Berger at 08:35, 20 September 2018

2018-09-20T08:35:10Z

Kuehnel at 08:55, 31 July 2018

2018-07-31T08:55:37Z

@@ Line 242: / Line 242: @@
 Now let us take a look at what the model looks like
 <pre>
 isis> plot_counts(pca);
 </pre>
@@ Line 299: / Line 301: @@
     Reduced chi-square = 229.1397
 </pre>
 While the reduced chi-square is already much smaller, it is still very much above its ideal value of around unity. Let us take a look what the current best fit looks like by plotting it again:

@@ Line 17: / Line 17: @@
 which then prints out some start up messages before you end with the isis prompt:
 <pre>
-Welcome to ISIS Version 1.6.2-44
+Welcome to ISIS Version 1.6.2-51
 Copyright (C) 1998-2020 Massachusetts Institute of Technology
@@ Line 157: / Line 157: @@
 === Inspecting ARF and RMF ===
 It is always useful in data analysis to have a feeling for the major features introduced by specific properties of the detector used to measure the data. For example, in the spectra above there are drops in detector sensitivity at the K- and L-edges of the detector gas. Usually, the regions around these edges are less well calibrated. Visualizing the ARF and RMF helps in this case (as does reading the user's manual for the satellite you're using...).
 It is easy to produce a plot of the RMF:

@@ Line 86: / Line 86: @@
 '''''Exercise 1'''''
-# Load your data set and check that the information given by ISIS using the above commands is identical to the information that you obtained in the previous exercise.
+# Load your data set and check the information given by ISIS using the above commands.
 === Plotting the Data ===

@@ Line 6: / Line 6: @@
 * <code>standard2f_0134off_top.pha</code> -- the spectrum itself.
 * <code>standard2f_back_SkyVLE_top_good_0134off.pha</code> -- The background spectrum (referred to in the <code>BACKFILE</code> keyword of <code>standard2f_0134off_top.pha</code>; see later for explanations).
-* <code>p2_LR1_2010-07-04.rsp</code> -- The response matrix (referred to in the <code>RESPFILE</code> keyword of <code>standard2f_0134off_top.pha</code>; see later for explanations)
+* <code>p2_LR1_2009-05-06.rsp</code> -- The response matrix (referred to in the <code>RESPFILE</code> keyword of <code>standard2f_0134off_top.pha</code>; see later for explanations)
 The data are in FITS-format, a standard file format that is used in all of astronomy. Right now you can treat these files as a black box, at the end of this document there is some additional information about how to inspect the contents of these files outside of isis.

@@ Line 4: / Line 4: @@
 In the following tutorial, we will be working on a simple data set from an observation of a black hole, Cygnus X-1, that was obtained with NASA's Rossi X-ray Timing Explorer satellite. The test data set can be downloaded from [http://www.sternwarte.uni-erlangen.de/~wilms/isistut/ here]. It consists of the following parts:
-* <code>standard2f_0134off_top.pha</code> -- the spectrum itself. The data are in FITS-format, a standard file format that is used in all of astronomy. Right now you can treat these files as a black box, at the end of this document there is some additional information about how to inspect the contents of these files outside of isis.
+* <code>standard2f_0134off_top.pha</code> -- the spectrum itself.
 === Invoking isis ===

@@ Line 86: / Line 86: @@
 === Invoking isis ===
-Isis is a command-line program and is therefore usually executed from the command line:
+Isis is a command-line program and is therefore usually executed from the command line (the details are explained in the installation instructions):
 <pre>
 wilms@leo:~> isis
@@ Line 92: / Line 92: @@
 which then prints out some start up messages before you end with the isis prompt:
 <pre>
-Welcome to ISIS Version 1.6.2-3
+Welcome to ISIS Version 1.6.2-44
-Copyright (C) 1998-2012 Massachusetts Institute of Technology
+Copyright (C) 1998-2020 Massachusetts Institute of Technology
            Isis web page: http://space.mit.edu/cxc/isis/
@@ Line 105: / Line 105: @@
 In the following we will show you an interactive session with isis. It is the typical approach when working with new data to look at these first by hand, in a way similar to that shown here. In later, more advanced analysis you will probably mainly interact with isis through programs, although it should be emphasized that working interactively with data first is always a good idea. This is the only way how you can get a good feeling for your data, even though automated reductions ''are'' important, especially when working on data sets with many different observations.
 === Loading and Inspecting Your Data Set ===

@@ Line 400: / Line 400: @@
 Note the following:
-* instead of using <code>plot_counts</code> we have used <code>plot_data</code> (which is in reality an alias for the <code>plot_data_counts</code> function. <code>plot_counts</code> displays the counts and the model in terms of counts per keV, while previously we used counts per PHA bin. This is the preferred way to plot X-ray data, since it is slightly closer to showing the proper spectrum than <code>plot_counts</code>.
+* instead of using <code>plot_counts</code> we have used <code>plot_data</code> (which is in reality an alias for the <code>plot_data_counts</code> function). <code>plot_data</code> displays the counts and the model in terms of counts per keV, while previously we used counts per PHA bin. This is the preferred way to plot X-ray data, since it is slightly closer to showing the proper spectrum than <code>plot_counts</code>.
 * Secondly, in addition to plotting the data we are also plotting the residuals, by using the "qualifier" <code>res=1</code>. In Slang/isis, qualifiers are special switches in functions. They all have names (<code>res</code> in the above example), i.e., the order in which they are listed after the initial semicolon does not matter. The most important ways of displaying residuals are
 ** <code>res=1</code>: Display the residual in terms of chi, i.e., display the value of <latex>(data-model)/\sigma</latex> where <latex>\sigma</latex> is the statistical uncertainty of the bin.

@@ Line 261: / Line 261: @@
 === Performing a First Spectral Fit ===
-We are now ready to perform a first spectral fit. We first need to define the spectral model that we want to describe our data with. In general, one first tries to get a rough description of the data, which is for example based on earlier observations of the object, and then refines this spectral model by adding further spectral components if an initial fit was successful. Isis includes a large number of spectral models. Since the models are derived from XSPEC, a good overview is given by the exhaustive list of the models in the [http://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecModels.html XSPEC manual].
+We are now ready to perform a first spectral fit. We first need to define the spectral model that we want to describe our data with. In general, one first tries to get a rough description of the data, which is for example based on earlier observations of the object, and then refines this spectral model by adding further spectral components if an initial fit was successful. Isis includes a large number of spectral models. Since the models are derived from XSPEC, a good overview is given by the exhaustive list of the models in the [https://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecManual.html XSPEC manual].
 What model to use depends on the object one looks at. In most cases, one tries either a power law or a black body first and only later works with more CPU-intensive, physics-based models. Since all X-ray sources are absorbed by the interstellar medium in our Galaxy, one ''always'' includes Galactic absorption.
@@ Line 282: / Line 282: @@
 Amongst other information, which we will be discussing in a later tutorial, the table contains the following information:
 * <code>idx</code>: The index of the parameter (see below)
-* <code>param</code>: The name of the parameter. For example, <code>tbabs(1).nH</code> is the absorption column (in units of 10^22 cm<sup>-2</sup>. The physical meaning of the parameters is explained in the [http://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecModels.html XSPEC manual].
+* <code>param</code>: The name of the parameter. For example, <code>tbabs(1).nH</code> is the absorption column (in units of 10^22 cm<sup>-2</sup>. The physical meaning of the parameters is explained in the [https://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecManual.html XSPEC manual].
 * <code>tie-to</code> and <code>freeze</code>: see later
 * <code>value</code>: the current value of the parameter
@@ Line 421: / Line 421: @@
    - there is a "soft excess" at low energies, which might be indicative of an accretion disk.
-Looking at the [http://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecModels.html XSPEC] manual tells us that accretion disk spectra are modeled with the <code>diskbb</code> model while emission lines are modeled using the <code>gauss</code> model. However, reading the isis manual tells us that the ''only'' model that has a different name in isis and in XSPEC is <code>gauss</code> where we will have to use <code>egauss</code> instead.
+Looking at the [https://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XspecManual.html XSPEC] manual tells us that accretion disk spectra are modeled with the <code>diskbb</code> model while emission lines are modeled using the <code>gauss</code> model. However, reading the isis manual tells us that the ''only'' model that has a different name in isis and in XSPEC is <code>gauss</code> where we will have to use <code>egauss</code> instead.
 Based with this information we setup the new fit function as follows

@@ Line 102: / Line 102: @@
 isis>
 </pre>
-As part of its startup, isis executes a file called <code>~/.isisrc</code> (i.e., the file named <code>.isisrc</code> which is located in your home directory). This file is useful for setting up a standard environment. We recommend this file to be short and to include only the most important commands. We will later show you how to load powerful additional libraries of command into isis, which avoids cluttering <code>~/.isisrc</code> with lots of setup commands.
+As part of its startup, isis executes a file called [[ISIS auto start (.isisrc)|.isisrc]], which is useful for setting up a standard environment.
 In the following we will show you an interactive session with isis. It is the typical approach when working with new data to look at these first by hand, in a way similar to that shown here. In later, more advanced analysis you will probably mainly interact with isis through programs, although it should be emphasized that working interactively with data first is always a good idea. This is the only way how you can get a good feeling for your data, even though automated reductions ''are'' important, especially when working on data sets with many different observations.