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Michael Mayer
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doc/source/user_manual/iact_analysis/analysis.rst
doc/source/user_manual/iact_analysis/high_level.rst
doc/source/user_manual/iact_analysis/tipps.rst
@@ -109,8 +109,6 @@ model XML file will then contain both, the background model and the input sky mo
  
   $ csiactobs inmodel="mymodel.xml"
  
-A list of available sky models can be found here: `models <http://gammalib.sourceforge.net/user_manual/modules/model.html>`_
-
 Alternatively, models can be merged at any times using the simple tool :ref:`csmodelmerge`:
  
 .. code-block:: bash
@@ -120,7 +118,100 @@ Alternatively, models can be merged at any times using the simple tool :ref:`csm
   Output model file [crab_models.xml]
  
 Note that the number of files to merge is not limited to two. Detailled options how the input model XML file can
-be passed is given on the reference page of :ref:`csmodelmerge`.
+be passed is given on the reference page of :ref:`csmodelmerge`. It is also important to know that each model in the container
+must have a unique name. This implies, for instance, merging the same XML model twice will result in an exception.
+
+A list of available sky models can be found here: `models <http://gammalib.sourceforge.net/user_manual/modules/model.html>`_.
+Of particular help to create sky models for your dataset is the section about :ref:`modelling CTA data <models>`.
+
+
+Example XML files
+-----------------
+To get familiar with the XML syntax and format example files for an observation container and a model container
+are shown in the following.
+
+Observation XML file
+^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: xml
+
+	<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+	<observation_list title="observation list">
+	  <observation name="Crab Nebula" id="11111" instrument="HESS">
+	    <parameter name="EventList" file="/path/to/fits/file/events_11111.fits.gz" />
+	    <parameter name="EffectiveArea" file="/path/to/fits/file/aeff_11111.fits.gz" />
+	    <parameter name="PointSpreadFunction" file="/path/to/fits/file/psf_11111.fits.gz" />
+	    <parameter name="EnergyDispersion" file="/path/to/fits/file/edisp_11111.fits.gz" />
+	    <parameter name="Background" file="/path/to/fits/file/bgmodel_11111.fits.gz" />
+	  </observation>
+	  <observation name="Crab Nebula" id="11112" instrument="HESS">
+	    <parameter name="EventList" file="/path/to/fits/file/events_11112.fits.gz" />
+	    <parameter name="EffectiveArea" file="/path/to/fits/file/aeff_11112.fits.gz" />
+	    <parameter name="PointSpreadFunction" file="/path/to/fits/file/psf_11112.fits.gz" />
+	    <parameter name="EnergyDispersion" file="/path/to/fits/file/edisp_11112.fits.gz" />
+	    <parameter name="Background" file="/path/to/fits/file/bgmodel_11112.fits.gz" />
+	  </observation>
+	  <observation name="Crab Nebula" id="11113" instrument="HESS">
+	    <parameter name="EventList" file="/path/to/fits/file/events_11113.fits.gz" />
+	    <parameter name="EffectiveArea" file="/path/to/fits/file/aeff_11113.fits.gz" />
+	    <parameter name="PointSpreadFunction" file="/path/to/fits/file/psf_11113.fits.gz" />
+	    <parameter name="EnergyDispersion" file="/path/to/fits/file/edisp_11113.fits.gz" />
+	    <parameter name="Background" file="/path/to/fits/file/bgmodel_11113.fits.gz" />
+	  </observation>
+	  <observation name="Crab Nebula" id="11114" instrument="HESS">
+	    <parameter name="EventList" file="/path/to/fits/file/events_11114.fits.gz" />
+	    <parameter name="EffectiveArea" file="/path/to/fits/file/aeff_11114.fits.gz" />
+	    <parameter name="PointSpreadFunction" file="/path/to/fits/file/psf_11114.fits.gz" />
+	    <parameter name="EnergyDispersion" file="/path/to/fits/file/edisp_11114.fits.gz" />
+	    <parameter name="Background" file="/path/to/fits/file/bgmodel_11114.fits.gz" />
+	  </observation>
+	</observation_list>
+
+Model XML file
+^^^^^^^^^^^^^^
+
+.. code-block:: xml
+
+	<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+	<source_library title="source library">
+	  <source name="bkg_11111" type="CTAIrfBackground" instrument="HESS" id="11111">
+	    <spectrum type="ConstantValue">
+	      <parameter name="Value" value="1" error="0" scale="1" min="0.01" max="100" free="1" />
+	    </spectrum>
+	  </source>
+	  <source name="bkg_11112" type="CTAIrfBackground" instrument="HESS" id="11112">
+	    <spectrum type="ConstantValue">
+	      <parameter name="Value" value="1" error="0" scale="1" min="0.01" max="100" free="1" />
+	    </spectrum>
+	  </source>
+	  <source name="bkg_11113" type="CTAIrfBackground" instrument="HESS" id="11113">
+	    <spectrum type="ConstantValue">
+	      <parameter name="Value" value="1" error="0" scale="1" min="0.01" max="100" free="1" />
+	    </spectrum>
+	  </source>
+	  <source name="bkg_11114" type="CTAIrfBackground" instrument="HESS" id="11114">
+	    <spectrum type="ConstantValue">
+	      <parameter name="Value" value="1" error="0" scale="1" min="0.01" max="100" free="1" />
+	    </spectrum>
+	  </source>
+	    <source name="Crab" type="PointSource">
+	    <spectrum type="PowerLaw">
+	       <parameter name="Prefactor" scale="1e-17" value="3.0"  min="1e-07" max="1000.0" free="1"/>
+	       <parameter name="Index"     scale="-1"    value="2.5" min="0.0"   max="+5.0"   free="1"/>
+	       <parameter name="Scale"     scale="1e6"   value="1.0"  min="0.01"  max="1000.0" free="0"/>
+	    </spectrum>
+	    <spatialModel type="SkyDirFunction">
+	      <parameter name="RA"  scale="1.0" value="83.6331" min="-360" max="360" free="1"/>
+	      <parameter name="DEC" scale="1.0" value="22.0145" min="-90"  max="90"  free="1"/>
+	    </spatialModel>
+	  </source>
+	</source_library>
+
+.. note::
+
+   It is important to ensure background models are properly linked to their respective observation.
+   Therefore it is required to keep the attributes ``instrument`` and ``id`` the same for the observation
+   and the corresponding background model. The tool :ref:`csiactobs` makes sure this is the case.
  
 Run ctselect
 ------------
@@ -173,9 +264,11 @@ On default, energy dispersion is not considered in the fit. To switch on the usa
 the hidden parameter ``edisp=yes`` can be provided. Note that this will cause a significant reduction of the computing
 speed.
  
-Binned analysis
----------------
-For binned analysis, some intermediated data products have to be produced. The products are a binned data cube,
+Stacked (binned) analysis
+-------------------------
+The stacked analysis mode is using a binned analysis where all observations are included and stacked into one event cube.
+This analysis mode is much faster than unbinned analysis when having a large dataset (e.g. > 100 hours).
+For this type of binned analysis, some intermediate data products have to be produced. The products are a binned data cube,
 an exposure cube, a psf cube, and a background cube. 
  
 Bin events
@@ -10,15 +10,108 @@ High level analysis tools for IACT data
  
 Inspecting observation definition files
 ---------------------------------------
+After having created an observation definition file, the user might want to know a summary of its content.
+Important quantities usually are the number of observations, the total livetime, or the mean zenith angle.
+For this purpose, :ref:`csobsinfo` inspects an observation XML container for its content.
+
+.. code-block:: bash
+
+  $ csobsinfo
+  Event list, counts cube, or observation definition file [obs.xml] selected_obs.xml 
+  
+This dumps general information of the observation container in a logfile ``csobsinfo.log``.
+For a direct output on the screen, pass the hidden parameter ``debug=yes`` on the command line:
+
+.. code-block:: bash
+
+  $ csobsinfo debug=yes
+  Event list, counts cube, or observation definition file [obs.xml] selected_obs.xml 
+  ...
+  2016-02-19T15:43:08: +=========+
+  2016-02-19T15:43:08: | Summary |
+  2016-02-19T15:43:08: +=========+
+  2016-02-19T15:43:08:  Unbinned observations .....: 4
+  2016-02-19T15:43:08:  Number of events ..........: 6085
+  2016-02-19T15:43:08:  Binned observations .......: 0
+  2016-02-19T15:43:08:  Number of bins ............: 0
+  2016-02-19T15:43:08: 
+  2016-02-19T15:43:08: === Pointings ===
+  2016-02-19T15:43:08:  Mean zenith angle .........: 46.89
+  2016-02-19T15:43:08:  Mean azimuth angle ........: 13.63
+  2016-02-19T15:43:08: 
+  2016-02-19T15:43:08: === Energy range ===
+  2016-02-19T15:43:08:  Emin ......................: 461.48 GeV
+  2016-02-19T15:43:08:  Emax ......................: 37.8832 TeV
+  2016-02-19T15:43:08: 
+  2016-02-19T15:43:08: === Time range ===
+  2016-02-19T15:43:08:  Start [MJD] ...............: 53343.9212153
+  2016-02-19T15:43:08:  Stop [MJD] ................: 53347.9321065
+  2016-02-19T15:43:08:  Total ontime ..............: 6877.00 s = 114.62 min = 1.91 h
+  2016-02-19T15:43:08:  Total livetime ............: 6427.52 s = 107.13 min = 1.79 h
+  ... 
+
+Further options are described on the reference page :ref:`csobsinfo`. 
  
 Inspecting model XML files
 --------------------------
+Similar to the observation containers, model XML file can be inspected, too.
+The tool :ref:`csmodelinfo` gives a summary of the model container. In particular,
+the number of free parameters, number of sky and background models and also number of
+parameters that are at their limits might be of interest.
+
+.. code-block:: bash
+
+  $ csmodelinfo debug=yes
+  Input model XML file [$CTOOLS/share/models/crab.xml] 
+  2016-02-19T15:50:40: +=========+
+  2016-02-19T15:50:40: | Summary |
+  2016-02-19T15:50:40: +=========+
+  2016-02-19T15:50:40: === Instrument specific models ===
+  2016-02-19T15:50:40:  All .......................: 1
+  2016-02-19T15:50:40:  CTA .......................: 1
+  2016-02-19T15:50:40: === Model types ===
+  2016-02-19T15:50:40:  PointSource ...............: 1
+  2016-02-19T15:50:40:  CTAIrfBackground ..........: 1
+  2016-02-19T15:50:40: 
+  2016-02-19T15:50:40: +=======================+
+  2016-02-19T15:50:40: | Parameter information |
+  2016-02-19T15:50:40: +=======================+
+  2016-02-19T15:50:40:  All parameters ............: 10
+  2016-02-19T15:50:40:  Fixed parameters ..........: 6
+  2016-02-19T15:50:40:  Free parameters (total) ...: 4
+  2016-02-19T15:50:40:  Free background parameters : 2
+  2016-02-19T15:50:40:  Free source parameters ....: 2
+  2016-02-19T15:50:40:  Free spectral parameters ..: 2
+  2016-02-19T15:50:40:  Parameters at limit .......: 0
+
  
 Compute upper limit
 -------------------
+Very often in gamma-ray astronomy sources are at the verge of detection or even not detectable.
+In such cases, it is useful to derive an upper limit using :ref:`ctulimit`.
+
+.. code-block:: bash
+
+	$ ctulimit
+	Input event list, counts cube or observation definition XML file [selected_obs.xml]
+	Input model XML file [crab_models.xml]  
+	Source of interest [Crab] 
+	
+The upper limit will be stored in the log file. To get the limit printed on screen, use the hidden parameter
+``debug=yes``.
  
 Compute asymmetric errors
 -------------------------
+When an analysis approaches its final state, it makes sense to have asymmetric errors on the parameters of the
+source of interest. For this purpose, the tool :ref:`cterror` can be used:
+
+.. code-block:: bash
+
+	$ cterror debug=yes
+	Input event list, counts cube or observation definition XML file [selected_obs.xml] 
+	Input model XML file [crab_models.xml] 
+	Source of interest [Crab] 
+
  
 Compute spectral points
 -----------------------
@@ -21,6 +21,9 @@ Split TS map computation
 Accessing fit parameters in python
 ----------------------------------
  
+Accessing upper limits in python
+--------------------------------
+
 Manipulate models in python
 ---------------------------