Add links to User Manual

Jürgen Knödlseder
1 parent da319f54
Showing 5 changed files with 33 additions and 27 deletions
doc/source/users/user_manual/data.rst
doc/source/users/user_manual/irf_cta.rst
doc/source/users/user_manual/irf_intro.rst
doc/source/users/user_manual/models_implementation.rst
doc/source/users/user_manual/observations.rst
@@ -12,6 +12,7 @@ is shown below.
  
 .. figure:: eventlist.png
    :width: 70%
+   :align: center
  
 Metadata, such as the telescope pointing direction, the live time, or any other
 information that may be relevant for data processing, is stored in the FITS
@@ -21,15 +22,17 @@ below.
  
 .. figure:: eventheader.png
    :width: 70%
+   :align: center
  
-Every event list needs to be accompanied by a table with so-called Good Time
-Intervals (GTIs) where each row corresponds to a time interval of continuous
-data taking, and the two columns correspond to the start and stop times of these
-time intervals. An exemple for the GTIs of the H.E.S.S. event lists comprising
-a single GTI is shown below.
+Every event list needs to be accompanied by a table with so-called
+:ref:`Good Time Intervals (GTIs) <glossary_gti>` where each row corresponds
+to a time interval of continuous data taking, and the two columns correspond
+to the start and stop times of these time intervals. An exemple for the GTIs
+of the H.E.S.S. event lists comprising a single GTI is shown below.
  
 .. figure:: gti.png
    :width: 40%
+   :align: center
  
 Note that times are given in so-called Mission-Elapsed Time (MET) in seconds,
 and that the zero-point of the MET is specified by the ``MJDREFI`` and
@@ -6,8 +6,8 @@ CTA response functions
 Formulation
 ~~~~~~~~~~~
  
-The instrument response functions for CTA (as well as the other IACTs such as
-H.E.S.S., VERITAS and MAGIC) are factorised into
+The :ref:`instrument response functions <glossary_irf>` for CTA (as well as the
+other IACTs such as H.E.S.S., VERITAS and MAGIC) are factorised into
 the effective area :math:`A_{\rm eff}(p,E,t)` (units :math:`cm^2`),
 the point spread function :math:`PSF(p'|p,E,t)`,
 and the energy dispersion :math:`E_{\rm disp}(E'|p,E,t)`
@@ -109,9 +109,9 @@ In total, the following six instrument response functions are available:
 Specifying CTA response functions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
-The specification of the CTA Instrument Response Functions depends on the 
-way how ctools are used. Common to all methods is that the IRFs are 
-defined by a response name and a calibration database name.
+The specification of the CTA :ref:`Instrument Response Functions <glossary_irf>`
+depends on the way how ctools are used. Common to all methods is that the IRFs
+are defined by a response name and a calibration database name.
 ctools makes use of HEASARC's CALDB format to index and store
 IRFs, and specification of the database and response names is
 sufficient to access the response.
@@ -120,8 +120,9 @@ sufficient to access the response.
 Specifying the response function as input parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
-ctools that require instrument response functions have two parameters
-to specify the calibration database name and the response function name.
+ctools that require :ref:`instrument response functions <glossary_irf>` have
+two parameters to specify the calibration database name and the response
+function name.
 The following example shows a ``ctobssim`` run using the ``prod2``
 calibration database and the ``South_0.5h`` response function:
  
@@ -3,11 +3,11 @@
 What are instrument response functions?
 ---------------------------------------
  
-The instrument response functions provide a mathematical description that
-links the reconstructed photon arrival direction :math:`p'`, energy :math:`E'`
-and trigger time :math:`t'` of an event to the true incident direction
-:math:`p`, energy :math:`E` and time :math:`t` of a photon. The following
-figure illustrates this relationship:
+The :ref:`instrument response functions <glossary_irf>` provide a mathematical
+description that links the reconstructed photon arrival direction :math:`p'`,
+energy :math:`E'` and trigger time :math:`t'` of an event to the true incident
+direction :math:`p`, energy :math:`E` and time :math:`t` of a photon. The
+following figure illustrates this relationship:
  
 .. figure:: irfs.jpg
    :width: 70%
@@ -3,7 +3,8 @@
 Implementation
 --------------
  
-The general model is describe in ctools using a model definition XML file. 
+The general model is describe in ctools using a
+:ref:`model definition XML file <glossary_moddef>`.
 Below is a simple example of such a file comprising one source and one 
 background model.
 Each model is factorised into
@@ -87,9 +88,9 @@ term will be appended to each ``&lt;parameter&gt;`` tag.
  
 .. note::
  
-   The syntax of the model definition XML file has been inspired from the
-   syntax used by the Fermi/LAT ScienceTools, but for reasons of clarity and
-   homogenity of the various model and parameter names we have made some
-   modifications.
+   The syntax of the :ref:`model definition XML file <glossary_moddef>` has been
+   inspired from the syntax used by the Fermi/LAT ScienceTools, but for reasons
+   of clarity and homogenity of the various model and parameter names we have
+   made some modifications.
    Nevertheless, the format used by the Fermi/LAT ScienceTools is also
    supported.
@@ -23,8 +23,9 @@ log-likelihood
  
 for the maximum likelihood estimations, where the sum is taken over the
 individual observations :math:`k`. Below you will see the first lines of an
-observation definition XML file that describe the first three observations of
-the Galactic Plane survey for the first CTA Data Challenge:
+:ref:`observation definition XML file <glossary_obsdef>` that describe the
+first three observations of the Galactic Plane survey for the first CTA Data
+Challenge:
  
 .. code-block:: xml
  
@@ -198,7 +199,7 @@ where :math:`B_k(p&#39;,E&#39;,t&#39;)` is the background model of observation :math:`k`.
 The sum is taken over all observations :math:`k`.
  
 The files for a stacked binned observation are specified as follows in an
-observation definition XML file:
+:ref:`observation definition XML file <glossary_obsdef>`:
  
 .. code-block:: xml
  
@@ -255,8 +256,8 @@ and the effective background response vectors using
  
 where :math:`\tau_k` is the live time (or exposure) of observation :math:`k`.
  
-The XML file for a stacked On/Off observation has the same format as for
-a single On/Off observation:
+The :ref:`observation definition XML file <glossary_obsdef>` for a stacked
+On/Off observation has the same format as for a single On/Off observation:
  
 .. code-block:: xml