Restructure front page and add text to the beyond quickstart section.

Jürgen Knödlseder
1 parent fa8e11ff
Showing 3 changed files with 46 additions and 22 deletions
doc/source/_templates/index.html
doc/source/user_manual/getting_started/beyond.rst
doc/source/user_manual/getting_started/resmap-crab.png
@@ -12,15 +12,15 @@ are available in the format defined for CTA. {%endtrans%}&lt;/p&gt;
 <p>{%trans%} ctools comprises a set of ftools-like binary executables with
 a command-line interface allowing for interactive step-wise data analysis.
-ctools comprises also a Python module allowing to control all executables. 
+ctools includes also a Python module allowing to control all executables. 
 Creation of shell or Python scripts and pipelines is supported.
-ctools comprises also cscripts, which are Python scripts that behave like binary 
-ftools executables. Extensions of the ctools package by user defined binary 
-executable or Python scripts is supported. {%endtrans%}</p>
+ctools provides cscripts, which are Python scripts complementing the binary
+executables. Extensions of the ctools package by user defined binary 
+executables or Python scripts is supported. {%endtrans%}</p>
-<p>{%trans%} ctools are based on GammaLib, a versatile toolbox for
-the high-level analysis of astronomical gamma-ray data. Besides CTA,
-GammaLib supports also the analysis of Fermi/LAT and COMPTEL data, 
+<p>{%trans%} ctools are based on <a href="http://cta.irap.omp.eu/gammalib">GammaLib</a>,
+a versatile toolbox for the high-level analysis of astronomical gamma-ray data.
+Besides CTA, GammaLib supports also the analysis of Fermi/LAT and COMPTEL data, 
 and extensions to support further gamma-ray instruments are planned.
 An interface to virtual observatory ressources is also in preparation.
 By making use of the GammaLib multi-instrument capabilities, ctools
@@ -30,13 +30,21 @@ CTA format), Fermi/LAT and COMPTEL data. {%endtrans%}&lt;/p&gt;
 <p>{%trans%} ctools is free software distributed under the
 <a href="http://www.gnu.org/licenses/gpl.html">GNU GPL license version 3</a> {%endtrans%}</p>
-<h2 style="margin-bottom: 0">{%trans%}Documentation{%endtrans%}</h2>
+<h2 style="margin-bottom: 0">{%trans%}Getting started{%endtrans%}</h2>
 <ul>
 <li><a class="smalllink" href="{{ pathto("user_manual/getting") }}">{%trans%}Installation{%endtrans%}</a></li> 
 <li><a class="smalllink" href="{{ pathto("user_manual/getting_started/quickstart") }}">{%trans%}Quickstart{%endtrans%}</a></li> 
+<li><a class="smalllink" href="{{ pathto("user_manual/getting_started/beyond") }}">{%trans%}Beyond the first steps{%endtrans%}</a></li> 
 <li><a class="smalllink" href="{{ pathto("user_manual/getting_started/models") }}">{%trans%}Modelling CTA data{%endtrans%}</a></li> 
 <li><a class="smalllink" href="{{ pathto("user_manual/getting_started/response") }}">{%trans%}CTA response functions{%endtrans%}</a></li> 
+<li><a class="smalllink" href="{{ pathto("user_manual/getting_started/python") }}">{%trans%}Using ctools from Python{%endtrans%}</a></li> 
+<li><a class="smalllink" href="{{ pathto("user_manual/getting_started/faq") }}">{%trans%}Frequently asked questions{%endtrans%}</a></li> 
+</ul>
+
+<h2 style="margin-bottom: 0">{%trans%}Documentation{%endtrans%}</h2>
+
+<ul>
 <li><a class="smalllink" href="{{ pathto("user_manual/index") }}">{%trans%}User Manual{%endtrans%}</a></li> 
 <li><a class="smalllink" href="{{ pathto("reference_manual/index") }}">{%trans%}Reference Manual{%endtrans%}</a></li> 
 <li><a class="smalllink" href="doxygen/index.html">{%trans%}Source code documentation (Doxygen){%endtrans%}</a></li> 
@@ -4,8 +4,7 @@ Beyond the first steps
 ----------------------
 Assuming that you have read the :ref:`quickstart <quickstart>` tutorial,
-here now some information on how to make the following more complex 
-analyses:
+here now some information on how to make more complex analyses:
 - :ref:`sec_combining_obs`
@@ -537,22 +536,22 @@ Real life situations may of course require larger correction factors.
 .. _sec_tsmap:
-Generating a Test Statistics map
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Generating a Test Statistic map
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 In the above examples we were always considering that we knew exactly
 where the source is located, but in real life situations this may not
 necessarily be the case.
 We thus need a mean to search for significant excess emission in our data.
-One possibility to accomplish this task is to compute the Test Statistics
+One possibility to accomplish this task is to compute the Test Statistic
 for a specific source at a grid of trial positions.
 The :ref:`cttsmap` tool will exactly do that job.
-The Test Statistics is defined as twice the log-likelihood difference 
+The Test Statistic is defined as twice the log-likelihood difference 
 between fitting a source at a given position on top of a model or fitting
 no source.
-Roughly speaken, the square root of the Test Statistics value gives
+Roughly speaken, the square root of the Test Statistic value gives
 the source detection significance in Gaussian sigmas, although the
-exact releation depends somewhat on the formulation of the statistical
+exact relation depends somewhat on the formulation of the statistical
 problem.
 Here an example where we apply the :ref:`cttsmap` tool to our two
@@ -580,19 +579,19 @@ nominal position of the Crab nebula with a grid spacing of 0.02 degrees.
   Image scale (in degrees/pixel) [0.02] 
   Size of the X axis in pixels [200] 10
   Size of the Y axis in pixels [200] 10
-  Output Test Statistics map [tsmap.fits]
+  Output Test Statistic map [tsmap.fits]
-:ref:`cttsmap` writes the Test Statistics map in the ``tsmap.fits`` file
-that contains one extension for the Test Statistics value and further
+:ref:`cttsmap` writes the Test Statistic map in the ``tsmap.fits`` file
+that contains one extension for the Test Statistic value and further
 extensions for the spectral parameters that have been fitted for the
 source at each position of the grid.
-The figure below show the Test Statistics map which reaches a maximum
+The figure below show the Test Statistic map which reaches a maximum
 value of 13782 near the centre of the map.
 .. figure:: tsmap-crab.png
    :width: 60%
-   *Test Statistics map of the Crab region*
+   *Test Statistic map of the Crab region*
 .. note::
@@ -607,4 +606,21 @@ value of 13782 near the centre of the map.
 Generating a residual map
 ~~~~~~~~~~~~~~~~~~~~~~~~~
-TBW
+.. code-block:: bash
+
+  $ csresmap
+  Parfile csresmap.par not found. Create default parfile.
+  Event list, counts cube, or observation definition file [events.fits] obs.xml
+  Calibration database [dummy] 
+  Instrument response function [cta_dummy_irf] 
+  Source model [$CTOOLS/share/models/crab.xml] crab_results.xml
+  Output residual map [resmap.fits] 
+  First coordinate of image center in degrees (RA or galactic l) [83.63] 
+  Second coordinate of image center in degrees (DEC or galactic b) [22.01] 
+  Coordinate System (CEL|GAL) [CEL] 
+  Projection method e.g. AIT|AZP|CAR|MER|MOL|STG|TAN (AIT|AZP|CAR|MER|MOL|STG|TAN) [CAR]
+
+.. figure:: resmap-crab.png
+   :width: 60%
+
+   *Residual map of the Crab region*