Merge branch 'bugfix-1.0.1' into integration

# Conflicts: # NEWS # README

Merge branch 'bugfix-1.0.1' into integration
# Conflicts: # NEWS # README
Jürgen Knödlseder
2 parents 6aea09e8 12238f81
Showing 6 changed files with 63 additions and 31 deletions
ChangeLog
NEWS
README
doc/source/reference_manual/csresmap.rst
src/ctmodel/ctmodel.cpp
src/support/ctool.cpp
-2016-01-06  Juergen Knoedlseder  <jurgen.knodlseder@irap.omp.eu>
+2016-01-11  Juergen Knoedlseder  <jurgen.knodlseder@irap.omp.eu>
         * Version 1.1.0 released
         ========================
-2016-01-06  Juergen Knoedlseder  <jurgen.knodlseder@irap.omp.eu>
+2016-01-11  Juergen Knoedlseder  <jurgen.knodlseder@irap.omp.eu>
         * Bug fix version 1.0.1 released
         ================================
@@ -2,7 +2,7 @@ New Features and Important Changes in ctools 1.1.0
 Author(s) : Juergen Knoedlseder
-6 January 2016
+11 January 2016
 1. Introduction
 ctools information
 ==================
-Version:             1.1.0dev (6 January 2016)
+Version:             1.1.0dev (11 January 2016)
 Author:              Juergen Knodlseder (jurgen.knodlseder@irap.omp.eu)
 GammaLib dependency: 1.1.0dev
@@ -31,18 +31,33 @@ General parameters
 ``inobs [file]``
     Input event list, counts cube or observation definition XML file.
+``modcube [file]``
+    Input model cube file (generated with ctmodel).
+
+``expcube [file]``
+    Input exposure cube file (only needed for stacked analysis).
+
+``psfcube [file]``
+    Input PSF cube file (only needed for stacked analysis).
+
+``bkgcube [file]``
+    Input background cube file (only needed for stacked analysis).
+
 ``inmodel [file]``
     Input model XML file.
-``outmap [file]``
-    Output residual counts map file.
-
 ``caldb [string]``
     Calibration database.
 ``irf [string]``
     Instrument response function.
+``(edisp = no) [boolean]``
+    Apply energy dispersion?
+
+``outmap [file]``
+    Output residual counts map file.
+
 ``(ebinalg = LOG) <FILE|LIN|LOG> [string]``
     Algorithm for defining energy bins.
@@ -58,27 +73,27 @@ General parameters
 ``(ebinfile = NONE) [file]``
     Name of the file containing the energy bin definition.
-``nxpix [integer]``
-    Number of cube bins in Right Ascension or Galactic longitude.
- 	 	 
-``nypix [integer]``
-    Number of cube bins in Declination or Galactic latitude.
- 	 	 
-``binsz [real]``
-    Cube bin size (in degrees/pixel).
- 	 	 
 ``coordsys <CEL|GAL> [string]``
     Coordinate system (CEL - celestial, GAL - galactic).
+``proj <AIT|AZP|CAR|MER|MOL|STG|TAN> [string]``
+    Projection method.
+
 ``xref [real]``
     Right Ascension / Galactic longitude of cube centre (J2000, in degrees).
 ``yref [real]``
     Declination / Galactic latitude of cube centre (J2000, in degrees).
-``proj <AIT|AZP|CAR|MER|MOL|STG|TAN> [string]``
-    Projection method.
-
+``nxpix [integer]``
+    Number of cube bins in Right Ascension or Galactic longitude.
+ 	 	 
+``nypix [integer]``
+    Number of cube bins in Declination or Galactic latitude.
+ 	 	 
+``binsz [real]``
+    Cube bin size (in degrees/pixel).
+ 	 	 
 ``(algorithm = SUBDIV) <SUB|SUBDIV|SUBDIVSQRT> [string]``
     Algorithm used to generate the residual map.
@@ -284,7 +284,7 @@ void ctmodel::run(void)
         // Fill cube and leave loop if we are binned mode (meaning we 
         // only have one binned observation)
-        if (m_binned && m_obs.size() == 1) {
+        if (m_binned) {
             fill_cube(obs);
             break;
         }
@@ -464,13 +464,16 @@ void ctmodel::get_parameters(void)
     m_append_cube = false;
     // If there are no observations in container then load them via user
-    // parameters
+    // parameters.
     if (m_obs.size() == 0) {
         get_obs();
     }
-    // Check if we got excactly one binned CTA observation
-    if (m_obs.size() == 1) {
+    // If we have now excactly one CTA observation (but no cube has yet been
+    // appended to the observation) then check whether this observation
+    // is a binned observation, and if yes, extract the counts cube for
+    // model generation
+    if ((m_obs.size() == 1) && (m_append_cube == false)) {
         // Get CTA observation
         GCTAObservation* obs = dynamic_cast<GCTAObservation*>(m_obs[0]);
@@ -498,7 +501,6 @@ void ctmodel::get_parameters(void)
     } // endif: had exactly one observation
-
     // Read model definition file if required
     if (m_obs.models().size() == 0) {
@@ -513,7 +515,9 @@ void ctmodel::get_parameters(void)
     // Get energy dispersion flag parameters
     m_apply_edisp = (*this)["edisp"].boolean();
-    // Optionally get input counts cube for model cube definition
+    // If we do not have yet a counts cube for model computation then check
+    // whether we should read it from the "incube" parameter or whether we
+    // should create it from scratch using the task parameters
     if (!m_has_cube) {
         // Read cube definition file
@@ -544,18 +548,21 @@ void ctmodel::get_parameters(void)
         // Signal that cube has been set
         m_has_cube = true;
-    }
+
+    } // endif: we had no cube yet
     // Read optionally output cube filenames
     if (read_ahead()) {
-           m_outcube = (*this)["outcube"].filename();
+        m_outcube = (*this)["outcube"].filename();
     }
     // If cube should be appended to first observation then do that now.
     // This is a kluge that makes sure that the cube is passed as part
     // of the observation in case that a cube response is used. The kluge
     // is needed because the GCTACubeSourceDiffuse::set method needs to
-    // get the full event cube from the observation.
+    // get the full event cube from the observation. It is also at this
+    // step that the GTI, which may just be a dummy GTI when create_cube()
+    // has been used, will be set.
     if (m_append_cube) {
         //TODO: Check that energy boundaries are compatible
@@ -588,6 +595,11 @@ void ctmodel::get_parameters(void)
  * If no file names are specified for the "expcube", "psfcube" or "bkgcube"
  * parameters, the method reads the necessary parameters to build a CTA
  * observation from scratch.
+ *
+ * The method sets m_append_cube = true and m_binned = true in case that
+ * a stacked observation is requested (as detected by the presence of the
+ * "expcube", "psfcube", and "bkgcube" parameters). In that case, it appended
+ * a dummy event cube to the observation.
  ***************************************************************************/
 void ctmodel::get_obs(void)
 {
@@ -620,7 +632,6 @@ void ctmodel::get_obs(void)
             // Create dummy sky map cube
             GSkyMap map("CAR","GAL",0.0,0.0,1.0,1.0,1,1,ebounds.size());
-            m_append_cube = true;
             // Create event cube
             GCTAEventCube cube(map, ebounds, exposure.gti());
@@ -633,6 +644,12 @@ void ctmodel::get_obs(void)
             // Append observation to container
             m_obs.append(cta);
+            // Signal that we are in binned mode
+            m_binned = true;
+
+            // Signal that we appended a cube
+            m_append_cube = true;
+
         } // endif: cube response information was available
         // ... otherwise build an observation from IRF response information
@@ -646,7 +663,7 @@ void ctmodel::get_obs(void)
             // Append observation to container
             m_obs.append(cta);
-            
+
         }
     } // endif: filename was "NONE" or ""
@@ -652,7 +652,7 @@ GCTAObservation ctool::create_cta_obs(void)
     list.gti(gti);
     list.ebounds(ebounds);
-    // Attach event list to CTA observation
+    // Attach empty event list to CTA observation
     obs.events(list);
     // Set observation ontime, livetime and deadtime correction factor