Merge branch 'devel' of https://cta-gitlab.irap.omp.eu/ctools/ctools into 2189-ctmodel_trim_models

Josh Cardenzana
2 parents eab52ead 3705c8a9
Showing 4 changed files with 298 additions and 0 deletions
doc/source/users/tutorials/howto/comptel/howto_comptel_1.8MeV_tsmap.png
doc/source/users/tutorials/howto/comptel/howto_comptel_1.8MeV_tsmap_5vp.png
doc/source/users/tutorials/howto/comptel/howto_comptel_dri.rst
doc/source/users/tutorials/howto/comptel/index.rst
+.. _howto_comptel_dri:
+
+Generating your own event selection
+-----------------------------------
+
+  .. admonition:: What you will learn
+
+     You will learn how to use the GammaLib classes to generate your own
+     data cubes and response functions for a COMPTEL analysis.
+
+The data in the
+`HEASARC archive <https://heasarc.gsfc.nasa.gov/xamin/>`_
+comprises counts cubes for the standard COMPTEL energy ranges (0.75-1 MeV,
+1-3 MeV, 3-10 MeV and 10-30 MeV) per viewing period. In case that you want
+to analyse a different energy range, or that you want to perform a different
+event selection, you need to create ``DRE``, ``DRG``, ``DRB`` and ``DRX``
+data and the corresponding ``IAQ`` response function yourself. You can do
+this with GammaLib.
+
+Let's assume you want to make a 1.8 MeV line map of the Galactic centre.
+You can use for this the data of the COMPTEL viewing period 16 in phase 1 of
+the mission. Go to the
+`HEASARC archive <https://heasarc.gsfc.nasa.gov/xamin/>`_
+and download the ``EVP``, ``TIM`` and ``OAD`` datasets. Once this is done,
+create the following
+:ref:`observation definition file <glossary_obsdef>`:
+
+.. code-block:: xml
+
+   <?xml version="1.0" standalone="no"?>
+   <observation_list title="observation library">
+     <observation name="GC" id="000160" instrument="COM">
+       <parameter name="EVP" file="$COMDATA/phase01/vp0016_0/m28846_evp.fits"/>
+       <parameter name="TIM" file="$COMDATA/phase01/vp0016_0/m11765_tim.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20745_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20750_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20753_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20759_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20760_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20761_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20762_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20764_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20770_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20771_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20772_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20785_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20786_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20787_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20788_oad.fits"/>
+       <parameter name="OAD" file="$COMDATA/phase01/vp0016_0/m20789_oad.fits"/>
+     </observation>
+   </observation_list>
+..
+
+  .. note::
+
+     There exist two formats for the
+     :ref:`observation definition file <glossary_obsdef>`
+     for COMPTEL data, one that describes the locations of the COMPTEL
+     data space cubes and response functions, and one that desribes
+     the location of an ``EVP`` event list, a ``TIM`` Good Time
+     Interval file, and an arbitrary number of ``OAD`` Orbit Aspect
+     Data files. In general there exists one ``OAD`` per day, while
+     there is one ``EVP`` event file and one ``TIM`` Good Time Interval
+     file per viewing period.
+
+     In the example above, the environment variable ``$COMDATA`` was set
+     to the root directory of the COMPTEL archive.
+
+Now you are ready to generate the ``DRE``, ``DRG``, ``DRB``, ``DRX`` and
+``IAQ`` datasets that you need for a ctools analysis of COMPTEL data.
+This will take a few minutes. Start
+`Python <https://www.python.org>`_
+in your terminal and type the following:
+
+.. code-block:: python
+
+    # You need GammaLib, of course ;)
+    import gammalib
+
+    # Create sky map for the definition of the DRE and DRG data cubes
+    cube = gammalib.GSkyMap('TAN', 'GAL', 0.0, 20.0, 1.0, 1.0, 80, 80)
+
+    # Create sky map for the definition of the DRX exposure map
+    expo = gammalib.GSkyMap('CAR', 'GAL', 0.0, 0.0, 1.0, 1.0, 360, 180)
+
+    # Allocate DRE, DRG and DRX. DRE and DRG have a 3rd Phibar dimension, starting at 0.0 deg,
+    # with a binsize of 2.0 deg, and 25 Phibar layers.
+    dre = gammalib.GCOMDri(cube, 0.0, 2.0, 25)
+    drg = gammalib.GCOMDri(cube, 0.0, 2.0, 25)
+    drx = gammalib.GCOMDri(expo)
+
+    # Set DRE energy range to 1.7-1.9 MeV, DRG and DRX are energy independent
+    dre.ebounds(gammalib.GEbounds(gammalib.GEnergy(1.7, 'MeV'),
+                                  gammalib.GEnergy(1.9, 'MeV')))
+
+    # Load observation definition XML file 'obs.xml' (the file you created above)
+    obsdef = gammalib.GObservations('obs.xml')
+
+    # Compute DRE, DRG and DRX for the first observation in the XML file
+    dre.compute_dre(obsdef[0])
+    drg.compute_drg(obsdef[0])
+    drx.compute_drx(obsdef[0])
+
+    # Save DRE, DRG and DRX ('True' indicates to overwrite any existing file)
+    dre.save('dre.fits', True)
+    drg.save('drg.fits', True)
+    drx.save('drx.fits', True)
+
+    # Load DRE and DRG to generate a DRB background model cube
+    dre = gammalib.GCOMDri('dre.fits')
+    drb = gammalib.GCOMDri('drg.fits')
+
+    # Normalise DRB on the Phibar distribution of the DRE cube
+    npix = dre.nchi() * dre.npsi()
+    for k in range(dre.nphibar()):
+        sum_dre = 0.0
+        sum_drb = 0.0
+        for i in range(npix):
+            index    = i + k * npix
+            sum_dre += dre[index]
+            sum_drb += drb[index]
+        if sum_drb > 0:
+            for i in range(npix):
+                index       = i + k * npix
+                drb[index] *= sum_dre / sum_drb
+
+    # Save DRB
+    drb.save('drb.fits', True)
+
+    # Initialise IAQ that will hold the response function
+    iaq = gammalib.GCOMIaq(55.0, 1.0, 50.0, 2.0)
+
+    # Compute IAQ for a line energy of 1.809 MeV and an energy band of 1.7-1.9 MeV
+    iaq.set(gammalib.GEnergy(1.809, 'MeV'),
+            gammalib.GEbounds(gammalib.GEnergy(1.7, 'MeV'),
+                              gammalib.GEnergy(1.9, 'MeV')))
+
+    # Save IAQ and you are done
+    iaq.save('iaq.fits', True)
+
+Now you have everything at hand to perform a COMPTEL maximum likelihood
+analysis. For that purpoe you need to gather all the datasets that you
+just created in a new
+:ref:`observation definition file <glossary_obsdef>`
+that should look as follows:
+
+.. code-block:: xml
+
+   <?xml version="1.0" standalone="no"?>
+   <observation_list title="observation library">
+     <observation name="GC" id="000160" instrument="COM">
+       <parameter name="DRE" file="dre.fits"/>
+       <parameter name="DRB" file="drb.fits"/>
+       <parameter name="DRG" file="drg.fits"/>
+       <parameter name="DRX" file="drx.fits"/>
+       <parameter name="IAQ" value="iaq.fits"/>
+     </observation>
+   </observation_list>
+..
+
+  .. warning::
+
+     Be aware that the attribute for the ``IAQ`` parameter is ``value`` and
+     not ``file`` since the ``IAQ`` parameter is not necessarily a file
+     but can be also a response name of the calibration database.
+
+Before doing a model fit you need a model. Create the following
+:ref:`model definition file <glossary_moddef>`:
+
+.. code-block:: xml
+
+   <?xml version="1.0" encoding="UTF-8" standalone="no"?>
+   <source_library title="source library">
+     <source name="GC" type="PointSource" tscalc="1">
+       <spectrum type="Constant">
+         <parameter name="Normalization" scale="1.0e-5" value="1.0"  min="-100.0" max="100.0" free="1"/>
+       </spectrum>
+       <spatialModel type="PointSource">
+         <parameter name="RA"  scale="1.0" value="266.40" min="-360" max="360" free="0"/>
+         <parameter name="DEC" scale="1.0" value="-28.94" min="-90"  max="90"  free="0"/>
+       </spatialModel>
+     </source>
+     <source name="Background" type="DRBFitting" instrument="COM">
+       <node>
+         <parameter name="Phibar"        value="9"   scale="1" min="0" max="50"   free="0" />
+         <parameter name="Normalization" value="1.0" scale="1" min="0" max="1000" free="1" />
+       </node>
+       <node>
+         <parameter name="Phibar"        value="11"  scale="1" min="0" max="50"   free="0" />
+         <parameter name="Normalization" value="1.0" scale="1" min="0" max="1000" free="1" />
+       </node>
+       ...
+       <node>
+         <parameter name="Phibar"        value="49"  scale="1" min="0" max="50"   free="0" />
+         <parameter name="Normalization" value="1.0" scale="1" min="0" max="1000" free="1" />
+       </node>
+     </source>
+   </source_library>
+
+This file contains a single point source at the position of the Galactic
+Centre. The spectral model is a simple constant normalisation that will
+return the gamma-ray line flux in units of
+:math:`{\rm photons}\,{\rm cm}^{-2}\,{\rm s}^{-1}`.
+For the background we do a Phibar fitting of the ``DRB`` cube. Since the
+first four layers of the ``DRE`` cube are empty we start the nodes at the
+fifth layer which corresponds to a Phibar value of 9 degrees. There are
+subsequent nodes spaced by 2 degrees (not shown) up to a Phibar value of
+49 degrees.
+
+Now it's time for model fitting. You can produce for example a Test Statistic
+map of the region around the Galactic centre as follows:
+
+.. code-block:: bash
+
+   $ cttsmap
+   Input event list, counts cube or observation definition XML file [events.fits] obs_dri.xml
+   Test source name [Crab] GC
+   Input model definition XML file [$CTOOLS/share/models/crab.xml] models.xml
+   First coordinate of image center in degrees (RA or galactic l) (0-360) [83.63] 0.0
+   Second coordinate of image center in degrees (DEC or galactic b) (-90-90) [22.01] 0.0
+   Projection method (AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN) [CAR]
+   Coordinate system (CEL - celestial, GAL - galactic) (CEL|GAL) [CEL] GAL
+   Image scale (in degrees/pixel) [0.02] 1.0
+   Size of the X axis in pixels [200] 50
+   Size of the Y axis in pixels [200] 30
+   Output Test Statistic map file [tsmap.fits] tsmap.fits
+
+Below is the resulting Test Statistic map that shows 1.8 MeV emission
+following the Galactic plane and peaking near the Galactic centre.
+
+.. figure:: howto_comptel_1.8MeV_tsmap.png
+   :width: 500px
+   :align: center
+
+   *1.8 MeV Test Statistic map for COMPTEL viewing period 16 of the Galactic Centre*
+
+It is left to you as an exercise to extend this example. To get a better
+statistics you may for example combine observations. For that purpose you
+can add the ``DRI`` datasets of multiple observations into single ``DRE``,
+``DRG``, ``DRB`` and ``DRX`` datasets,
+that's the way how the COMPTEL analysis was done. You can however also leave
+the ``DRI`` datasets separate and combine their description in the
+:ref:`observation definition file <glossary_obsdef>`.
+To combine for example the data of viewing periods 5, 7.5, 13, 16 and 27
+the
+:ref:`observation definition file <glossary_obsdef>`
+should look like this:
+
+.. code-block:: xml
+
+   <?xml version="1.0" standalone="no"?>
+   <observation_list title="observation library">
+     <observation name="GC" id="000050" instrument="COM">
+       <parameter name="DRE" file="dre_0050.fits"/>
+       <parameter name="DRB" file="drb_0050.fits"/>
+       <parameter name="DRG" file="drg_0050.fits"/>
+       <parameter name="DRX" file="drx_0050.fits"/>
+       <parameter name="IAQ" value="iaq.fits"/>
+     </observation>
+     <observation name="GC" id="000075" instrument="COM">
+       <parameter name="DRE" file="dre_0075.fits"/>
+       <parameter name="DRB" file="drb_0075.fits"/>
+       <parameter name="DRG" file="drg_0075.fits"/>
+       <parameter name="DRX" file="drx_0075.fits"/>
+       <parameter name="IAQ" value="iaq.fits"/>
+     </observation>
+     <observation name="GC" id="000130" instrument="COM">
+       <parameter name="DRE" file="dre_0130.fits"/>
+       <parameter name="DRB" file="drb_0130.fits"/>
+       <parameter name="DRG" file="drg_0130.fits"/>
+       <parameter name="DRX" file="drx_0130.fits"/>
+       <parameter name="IAQ" value="iaq.fits"/>
+     </observation>
+     <observation name="GC" id="000160" instrument="COM">
+       <parameter name="DRE" file="dre_0160.fits"/>
+       <parameter name="DRB" file="drb_0160.fits"/>
+       <parameter name="DRG" file="drg_0160.fits"/>
+       <parameter name="DRX" file="drx_0160.fits"/>
+       <parameter name="IAQ" value="iaq.fits"/>
+     </observation>
+     <observation name="GC" id="000270" instrument="COM">
+       <parameter name="DRE" file="dre_0270.fits"/>
+       <parameter name="DRB" file="drb_0270.fits"/>
+       <parameter name="DRG" file="drg_0270.fits"/>
+       <parameter name="DRX" file="drx_0270.fits"/>
+       <parameter name="IAQ" value="iaq.fits"/>
+     </observation>
+   </observation_list>
+
+The corresponding Test Statistic map is shown below.
+
+.. figure:: howto_comptel_1.8MeV_tsmap_5vp.png
+   :width: 500px
+   :align: center
+
+   *1.8 MeV Test Statistic map for COMPTEL viewing periods 5, 7.5, 13, 16 and 27 of the Galactic Centre*
@@ -22,3 +22,4 @@ In this tutorial you will learn how to do that with a simple analysis.
    howto_comptel_spectrum
    howto_comptel_tsmap
    howto_comptel_ulimit
+   howto_comptel_dri