Merge branch 'integration' into devel

# Conflicts: # cscripts/cta_make_nodes.py

Merge branch 'integration' into devel
# Conflicts: # cscripts/cta_make_nodes.py
Jürgen Knödlseder
2 parents 791a04af beadce17
Showing 28 changed files with 900 additions and 329 deletions
.gitignore
Makefile.am
configure.ac
cscripts/Makefile.am
cscripts/csiactobs.py
cscripts/cslightcrv.py
cscripts/csobsinfo.py
cscripts/cspull.py
cscripts/csresmap.py
cscripts/cssens.py
cscripts/csspec.py
cscripts/cstsdist.py
cscripts/cstsmapmerge.py
cscripts/cta_kb_bkgrates.py
cscripts/cta_kb_root2caldb.py
cscripts/cta_make_nodes.py
cscripts/cta_root2caldb.py
pyext/ctool.i
pyext/setup.py.in
src/ctbin/ctbin.cpp
@@ -12,6 +12,8 @@
 *.toc
 *.Pi
 *.Tpi
+*.gcno
+*.gcda
 .DS_Store
 .cproject
 .project
@@ -41,6 +43,7 @@ depcomp
 test-driver
 testconf.sh
 coverage-report-python.xml
+coverage-report-cxx.xml
 doc/html
 doc/man
@@ -93,7 +93,7 @@ cppncss:
 # Add coverage rule
 coverage:
 	@if type gcovr >/dev/null 2>&1; then \
-		gcovr -r . -x -o coverage-report-cxx.xml; \
+		gcovr -r . -x --exclude-unreachable-branches -o coverage-report-cxx.xml; \
 	else \
 		echo "gcovr script not found in PATH."; \
 	fi; \
@@ -87,6 +87,22 @@ AC_CANONICAL_HOST
 #############################################################################
+# Check for --enable-coverage option
+#############################################################################
+AC_MSG_CHECKING(whether to build ctools for code coverage measure)
+AC_ARG_ENABLE([coverage],
+              AS_HELP_STRING([--enable-coverage],
+                             [turn on code coverage measure [default=no]]),
+              [enable_coverage="$enableval"],
+              [enable_coverage="no"])
+if test "x$enable_coverage" = "xyes"; then
+  AC_MSG_RESULT(yes)
+else
+  AC_MSG_RESULT(no)
+fi
+
+
+#############################################################################
 # Check for valid C++ compiler.  This has to come before the check for      #
 # header files, otherwise we won't detect if the C++ compiler is missing.   #
 #                                                                           #
@@ -140,11 +156,23 @@ else
 fi
 AM_CONDITIONAL(IS_ELCAPITAN, test "x$osx_el_capitan" = "xyes")
+# If coverage is selected then save current C++ options
+if test "x$enable_coverage" = "xyes"; then
+  SAVED_CXXFLAGS=$CXXFLAGS
+  SAVED_CFLAGS=$CFLAGS
+fi
+
 # Our language is C++
 AC_LANG(C++)
 AC_PROG_CXX($cxx_list)
 AC_PROG_CC($cc_list)
+# If coverage is selected then restore former C++ options
+if test "x$enable_coverage" = "xyes"; then
+  CXXFLAGS=$SAVED_CXXFLAGS
+  CFLAGS=$SAVED_CFLAGS
+fi
+
 #############################################################################
 # Darwin option: Determine architecture of universal library to be built    #
@@ -758,25 +786,22 @@ fi
 #############################################################################
 # Initialise Python coverage with empty string
 PYTHON_COVERAGE=
+COVERAGE_CXXFLAGS=
-# Check for coverage option
-AC_MSG_CHECKING(whether to build ctools for code coverage measure)
-AC_ARG_ENABLE([coverage],
-              AS_HELP_STRING([--enable-coverage],
-                             [turn on code coverage measure [default=no]]),
-              [enable_coverage="$enableval"],
-              [enable_coverage="no"])
+# If coverage option has been selected then set some variables
 if test "x$enable_coverage" = "xyes"; then
   CXXFLAGS="--coverage $CXXFLAGS"
+  COVERAGE_CXXFLAGS="--coverage"
   LDFLAGS="--coverage $LDFLAGS"
   if test "x$has_python" = "xyes"; then
-    PYTHON_COVERAGE="coverage run --append "
+    PYTHON_COVERAGE="coverage run --branch --append "
   fi
   AC_MSG_RESULT(yes)
 else
   AC_MSG_RESULT(no)
 fi
 AC_SUBST(PYTHON_COVERAGE)
+AC_SUBST(COVERAGE_CXXFLAGS)
 #############################################################################
@@ -937,7 +962,7 @@ OPENMP_LIB_LDFLAGS=
 #fi
 AC_SUBST(OPENMP_LIB_LDFLAGS)
-# Signal if ctools cannot be compiled as gammalibe requires OpenMP but ctools
+# Signal if ctools cannot be compiled as gammalib requires OpenMP but ctools
 # cannot be compiled with OpenMP
 if test "x$enable_openmp" = "xno" && test "x$gammalib_with_openmp" = "xyes"; then
   AC_MSG_ERROR([The GammaLib library has been built with openMP support but OpenMP is not available on this system. Please install OpenMP or re-build GammaLib without OpenMP support.])
@@ -26,13 +26,17 @@ linkscripts = cspull cssens cstsdist cscaldb csresmap \
 # Test scripts to be distributed in $(pyexecdir)/cscripts/tests
 testscripts = tests/__init__.py \
               ../test/test_python_cscripts.py \
-              ../test/test_cscaldb.py
+              ../test/test_cscaldb.py \
+              ../test/test_cslightcrv.py
 # Test data to be distributed in $(pyexecdir)/cscripts/tests/data
-testdata    = 
+testdata    = ../test/data/crab.xml \
+              ../test/data/crab_events.fits.gz \
+              ../test/data/crab_cntmap.fits.gz \
+              ../test/data/exclusion.reg
 # Test IRFs to be distributed in $(pyexecdir)/cscripts/tests/irf
-testirf     = 
+#testirf     = 
 # Distribute scripts and parfiles
 EXTRA_DIST         = $(binscripts) $(pythonscripts)
@@ -46,8 +50,8 @@ testscriptsdir     = $(pyexecdir)/cscripts/tests
 testscripts_DATA   = $(testscripts)
 testdatadir        = $(pyexecdir)/cscripts/tests/data
 testdata_DATA      = $(testdata)
-testirfdir         = $(pyexecdir)/cscripts/tests/irf
-testirf_DATA       = $(testirf)
+#testirfdir         = $(pyexecdir)/cscripts/tests/irf
+#testirf_DATA       = $(testirf)
 # Add hook rule to create symbolic links for cscripts
 install-data-hook:
@@ -501,14 +501,14 @@ class csiactobs(ctools.cscript):
                 self._log("\n")
             # Append observation to XML and set attributes
-            obs = lib.append("observation");
-            obs.attribute("name", object_name);
-            obs.attribute("id", str(obs_id));
-            obs.attribute("instrument", telescope);
+            obs = lib.append("observation")
+            obs.attribute("name", object_name)
+            obs.attribute("id", str(obs_id))
+            obs.attribute("instrument", telescope)
             # Append event file
             ev = gammalib.GXmlElement("parameter name=\"EventList\"")
-            ev.attribute("file", eventfile);
+            ev.attribute("file", eventfile)
             # Append effective area
             aeff = gammalib.GXmlElement("parameter name=\"EffectiveArea\"")
@@ -76,12 +76,15 @@ class cslightcrv(ctools.cscript):
         self._stacked = False
         # Initialise observation container from constructor arguments.
-        self._obs = self._set_input_obs(argv)
+        self._obs, argv = self._set_input_obs(argv)
-        # Initialise application by calling the appropriate class
-        # constructor.
+        # Initialise script by calling the appropriate class constructor.
         self._init_cscript(argv)
+        # Set logger properties
+        self._log_header()
+        self._log.date(True)
+
         # Return
         return
@@ -91,12 +94,10 @@ class cslightcrv(ctools.cscript):
         """
         Get parameters from parfile.
         """
-        # Set observation if not done before
-        if self._obs == None or self._obs.size() == 0:
-            self._require_inobs("cslightcrv::_get_parameters()")
-            self._obs = self._get_observations()
+        # Setup observations
+        self._setup_observations(self._obs)
-        # Set models if we have none
+        # Set models if there are none in the container
         if self._obs.models().size() == 0:
             self._obs.models(self["inmodel"].filename())
@@ -106,11 +107,18 @@ class cslightcrv(ctools.cscript):
         # Get time boundaries             
         self._tbins = self._create_tbounds()
-        # Set stacked analysis flag if the requested number of energy bins
-        # is not zero; otherwise an unbinned analysis will be done.
-        self._stacked = False if self["enumbins"].integer() == 0 else True
+        # Set stacked analysis flag to True if the requested number of
+        # energy bins is positive. Otherwise an unbinned analysis will
+        # be done and the stacked analysis flag will be set to False.
+        if self["enumbins"].integer() > 0:
+            self._stacked = True
+        else:
+            self._stacked = False
-        # Make sure that other parameters are queried now and not later
+        # Make sure that remaining user parameters are queried now. We
+        # do not store the actual parameter values as we do not want
+        # too many instance attributes with enhances the maintenance
+        # costs.
         self["emin"].real()
         self["emax"].real()
         if self._stacked:
@@ -429,16 +437,26 @@ class cslightcrv(ctools.cscript):
         if self._logExplicit():
             self._log.header3("Creating point spread function cube")
-        # Create psf cube
+        # Compute spatial binning for point spread function and
+        # energy dispersion cubes
+        binsz = 0.1 * self["binsz"].real()
+        nxpix = self["nxpix"].integer() / 10
+        nypix = self["nypix"].integer() / 10
+        if nxpix < 2:
+            nxpix = 2
+        if nypix < 2:
+            nypix = 2
+
+        # Create point spread function cube
         psfcube = ctools.ctpsfcube(obs)
         psfcube["incube"]   = "NONE"
         psfcube["usepnt"]   = False
         psfcube["ebinalg"]  = "LOG"
         psfcube["xref"]     = self["xref"].real()
         psfcube["yref"]     = self["yref"].real()
-        psfcube["binsz"]    = self["binsz"].real()
-        psfcube["nxpix"]    = self["nxpix"].integer()
-        psfcube["nypix"]    = self["nypix"].integer()
+        psfcube["binsz"]    = binsz
+        psfcube["nxpix"]    = nxpix
+        psfcube["nypix"]    = nypix
         psfcube["enumbins"] = self["enumbins"].integer()
         psfcube["emin"]     = self["emin"].real()
         psfcube["emax"]     = self["emax"].real()    
@@ -453,16 +471,16 @@ class cslightcrv(ctools.cscript):
             if self._logExplicit():
                 self._log.header3("Creating energy dispersion cube")
-            # Create edisp cube
+            # Create energy dispersion cube
             edispcube = ctools.ctedispcube(obs)
             edispcube["incube"]   = "NONE"
             edispcube["usepnt"]   = False
             edispcube["ebinalg"]  = "LOG"
             edispcube["xref"]     = self["xref"].real()
             edispcube["yref"]     = self["yref"].real()
-            edispcube["binsz"]    = self["binsz"].real()
-            edispcube["nxpix"]    = self["nxpix"].integer()
-            edispcube["nypix"]    = self["nypix"].integer()
+            edispcube["binsz"]    = binsz
+            edispcube["nxpix"]    = nxpix
+            edispcube["nypix"]    = nypix
             edispcube["enumbins"] = self["enumbins"].integer()
             edispcube["emin"]     = self["emin"].real()
             edispcube["emax"]     = self["emax"].real()    
@@ -52,7 +52,7 @@ class csobsinfo(ctools.cscript):
         self._gti            = gammalib.GGti()
         # Initialise observation container from constructor arguments.
-        self._obs = self._set_input_obs(argv)
+        self._obs, argv = self._set_input_obs(argv)
         # Initialise application by calling the appropriate class
         # constructor.
@@ -18,7 +18,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
-import gammalib
+#import gammalib
 import ctools
 from cscripts import obsutils
 import sys
@@ -62,7 +62,7 @@ class cspull(ctools.cscript):
         self._log_clients = False
         # Initialise observation container from constructor arguments.
-        self._obs = self._set_input_obs(argv)
+        self._obs, argv = self._set_input_obs(argv)
         # Initialise application by calling the appropriate class
         # constructor.
@@ -410,17 +410,17 @@ class cspull(ctools.cscript):
             # Write out result immediately
             if seed == 0:
-                file   = open(self._outfile.url(), 'w')
-                writer = csv.DictWriter(file, result['colnames'])
+                f      = open(self._outfile.url(), 'w')
+                writer = csv.DictWriter(f, result['colnames'])
                 headers = {}
                 for n in result['colnames']:
                     headers[n] = n
                 writer.writerow(headers)
             else:
-                file = open(self._outfile.url(), 'a')
-            writer = csv.DictWriter(file, result['colnames'])
+                f = open(self._outfile.url(), 'a')
+            writer = csv.DictWriter(f, result['colnames'])
             writer.writerow(result['values'])
-            file.close()
+            f.close()
         # Return
         return
@@ -74,7 +74,7 @@ class csresmap(ctools.cscript):
         self._log_clients  = False
         # Initialise observation container from constructor arguments.
-        self._obs = self._set_input_obs(argv)
+        self._obs, argv = self._set_input_obs(argv)
         # Initialise application by calling the appropriate class
         # constructor.
@@ -347,18 +347,18 @@ class cssens(ctools.cscript):
         photon_flux_value = []
         energy_flux_value = []
         sensitivity_value = []
-        iter              = 0
+        iterations        = 0
         test_crab_flux    = 0.1 # Initial test flux in Crab units (100 mCrab)
         # Loop until we break
         while True:
             # Update iteration counter
-            iter += 1
+            iterations += 1
             # Write header
             if self._logExplicit():
-                self._log.header2("Iteration "+str(iter))
+                self._log.header2("Iteration "+str(iterations))
             # Set source model. crab_prefactor is the Prefactor that
             # corresponds to 1 Crab
@@ -370,7 +370,7 @@ class cssens(ctools.cscript):
             self._obs.models(src_model)
             # Simulate events
-            sim = obsutils.sim(self._obs, nbins=self._enumbins, seed=iter,
+            sim = obsutils.sim(self._obs, nbins=self._enumbins, seed=iterations,
                                binsz=self._binsz, npix=self._npix,
                                log=self._log_clients, debug=self._debug,
                                edisp=self._edisp)
@@ -464,8 +464,8 @@ class cssens(ctools.cscript):
             # Get fitted Crab, photon and energy fluxes
             crab_flux     = result_all[self._srcname]['Prefactor'].value() / \
                             crab_prefactor
-            crab_flux_err = result_all[self._srcname]['Prefactor'].error() / \
-                            crab_prefactor
+            #crab_flux_err = result_all[self._srcname]['Prefactor'].error() / \
+            #                crab_prefactor
             photon_flux   = result_all[self._srcname].spectral().flux(emin, emax)
             energy_flux   = result_all[self._srcname].spectral().eflux(emin, emax)
@@ -511,7 +511,7 @@ class cssens(ctools.cscript):
                     for par in model:
                         self._log(str(par)+"\n")
             elif self._logTerse():
-                self._log.parformat("Iteration "+str(iter))
+                self._log.parformat("Iteration "+str(iterations))
                 self._log("TS=")
                 self._log(ts)
                 self._log(" ")
@@ -549,7 +549,7 @@ class cssens(ctools.cscript):
             sensitivity /= num
             # Compare average flux to last average
-            if iter > self._num_avg:
+            if iterations > self._num_avg:
                 if test_crab_flux > 0:
                     ratio = crab_flux/test_crab_flux
@@ -570,7 +570,7 @@ class cssens(ctools.cscript):
             test_crab_flux = crab_flux
             # Exit loop if number of trials exhausted
-            if (iter >= self._max_iter):
+            if (iterations >= self._max_iter):
                 if self._logTerse():
                     self._log(" Test ended after "+str(self._max_iter)+
                               " iterations.\n")
@@ -60,7 +60,7 @@ class csspec(ctools.cscript):
         self._debug       = False
         # Initialise observation container from constructor arguments.
-        self._obs = self._set_input_obs(argv)
+        self._obs, argv = self._set_input_obs(argv)
         # Initialise application by calling the appropriate class
         # constructor.
@@ -158,9 +158,10 @@ class csspec(ctools.cscript):
             # If no layers overlap then throw an exception
             if (len(use_layers) == 0):
-                msg = "Energy range ["+str(cube_ebounds.emin(i))+ \
-                      ", "+str(cube_ebounds.emax(i))+"] of counts "+ \
-                      "cube does not overlap with specified energy range ["+ \
+                msg = "Energy range ["+str(cube_ebounds.emin())+ \
+                      ", "+str(cube_ebounds.emax())+"] of counts "+ \
+                      "cube does not overlap with specified energy "+ \
+                      "range ["+ \
                       str(emin)+", "+str(emax)+"]. Specify "+ \
                       "overlapping energy range."
                 raise RuntimeError(msg)
@@ -419,17 +419,17 @@ class cstsdist(ctools.cscript):
             # Write out result immediately
             if seed == 0:
-                file   = open(self._outfile.url(), 'w')
-                writer = csv.DictWriter(file, result['colnames'])
+                f      = open(self._outfile.url(), 'w')
+                writer = csv.DictWriter(f, result['colnames'])
                 headers = {}
                 for n in result['colnames']:
                     headers[n] = n
                 writer.writerow(headers)
             else:
-                file = open(self._outfile.url(), 'a')
-            writer = csv.DictWriter(file, result['colnames'])
+                f = open(self._outfile.url(), 'a')
+            writer = csv.DictWriter(f, result['colnames'])
             writer.writerow(result['values'])
-            file.close()
+            f.close()
         # Return
         return
@@ -414,8 +414,8 @@ class cstsmapmerge(ctools.cscript):
         # Delete TS input maps if requested
         if self._delete:
             for filename in self._merged_files:
-                 os.remove(filename)
-                 if self._logTerse():
+                os.remove(filename)
+                if self._logTerse():
                     self._log(gammalib.parformat("Deleted input file"))
                     self._log(filename)
                     self._log("\n")
@@ -4,7 +4,7 @@
 # into a column separated file function table. The table is automatically
 # named "bkg_XXX.txt" where "XXX" is for example "kb_E_50h_v3".
 #
-# Copyright (C) 2011-2014 Juergen Knoedlseder
+# Copyright (C) 2011-2016 Juergen Knoedlseder
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -38,8 +38,8 @@ def make_file_function(irfname, filename):
      filename - File function filename
     """
     # Open performance file and file function
-    irf  = open(irfname, "r")
-    file = open(filename, "w")
+    irf = open(irfname, "r")
+    f   = open(filename, "w")
     # Read data
     for row in irf:
@@ -53,12 +53,12 @@ def make_file_function(irfname, filename):
         # Extract data
         fields = row.replace(" ",",").replace(",,",",").rstrip("\n").split(",")
         logE   = float(fields[0])
-        aeff   = float(fields[1])
-        r68    = float(fields[2])
+        #aeff   = float(fields[1])
+        #r68    = float(fields[2])
         r80    = float(fields[3])
-        eres   = float(fields[4])
+        #eres   = float(fields[4])
         bgd    = float(fields[5])
-        sens   = float(fields[6])
+        #sens   = float(fields[6])
         # Compute energy (in MeV)
         energy = math.pow(10.0, logE)*1.0e6
@@ -76,11 +76,11 @@ def make_file_function(irfname, filename):
             bkg_rate = 0.0
         # Write
-        file.write(str(energy)+" "+str(bkg_rate)+"\n")
+        f.write(str(energy)+" "+str(bkg_rate)+"\n")
     # Close files
     irf.close()
-    file.close()
+    f.close()
     # Return
     return
@@ -90,9 +90,7 @@ def make_file_function(irfname, filename):
 # Main entry point #
 # ================ #
 if __name__ == '__main__':
-    """
-    Main entry point
-    """
+
     # Set parameters
     caldb = "/usr/local/gamma/share/caldb/data/cta/kb/"
@@ -23,7 +23,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
-from ROOT import TFile, TH1F, TH2F
+#from ROOT import TFile, TH1F, TH2F
+from ROOT import TFile, TH1F
 from datetime import datetime
 import gammalib
 import math
@@ -506,11 +507,11 @@ if __name__ == &#39;__main__&#39;:
     """
     """
     # Get ROOT filename from command line argument
-    if (len(sys.argv) > 1):
-        filename = sys.argv[1]
-    else:
-        db = "/Users/jurgen/Documents/Travail/Projects/CTA/WP-MC/root/Kb_all_20deg_root"
-        #db = "/Users/jurgen/Documents/Travail/Projects/CTA/WP-MC/root/Kb_all_50deg_root"
+    #if (len(sys.argv) > 1):
+    #    filename = sys.argv[1]
+    #else:
+    db = "/Users/jurgen/Documents/Travail/Projects/CTA/WP-MC/root/Kb_all_20deg_root"
+    #db = "/Users/jurgen/Documents/Travail/Projects/CTA/WP-MC/root/Kb_all_50deg_root"
     # Get list of all performance files
     files = glob.glob(db+"/*.root")
@@ -520,26 +521,26 @@ if __name__ == &#39;__main__&#39;:
     irf = caldb("kb")
     # Loop over all files
-    for file in files:
+    for f in files:
         # Get filename
-        head, tail = os.path.split(file)
+        head, tail = os.path.split(f)
         # Build name
         name = tail.strip(".root")
         if name.find("kb_") != -1:
             name = name.replace("_20deg", "")
         elif name.find("IFAE_") != -1:
-            name = name.replace("Subarray", "")
-            name = name.replace("IFAE_", "")
-            name = "IFAE_"+name
-            i    = name.find("hours")
-            if i != -1:
-                name = name[0:i+1]
+            name  = name.replace("Subarray", "")
+            name  = name.replace("IFAE_", "")
+            name  = "IFAE_"+name
+            index = name.find("hours")
+            if index != -1:
+                name = name[0:index+1]
         print(tail)
         # Open calibration file
         irf.add(name)
         # Translate ROOT to CALDB information
-        irf.root2caldb(file)
+        irf.root2caldb(f)
@@ -20,7 +20,6 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
-#import gammalib
 import sys
 import math
@@ -28,7 +27,7 @@ import math
 # ============== #
 # Write one node #
 # ============== #
-def write_node(file, energy, scale):
+def write_node(f, energy, scale):
     """
     Writes one node to XML file.
     """
@@ -37,22 +36,22 @@ def write_node(file, energy, scale):
     str_scale  = str(scale)
     # Write start tag
-    file.write('      <node>\n')
+    f.write('      <node>\n')
     # Write energy
-    file.write('        <parameter scale="1e6"   name="Energy"')
-    file.write('    min="'+str_energy+'"   max="'+str_energy+'"')
-    file.write(' value="'+str_energy+'"')
-    file.write(' free="0"/>\n')
+    f.write('        <parameter scale="1e6"   name="Energy"')
+    f.write('    min="'+str_energy+'"   max="'+str_energy+'"')
+    f.write(' value="'+str_energy+'"')
+    f.write(' free="0"/>\n')
     # Write intensity
-    file.write('        <parameter scale="'+str_scale+'"   name="Intensity"')
-    file.write(' min="1e-5"   max="1e5"')
-    file.write(' value="1.0"')
-    file.write(' free="1"/>\n')
+    f.write('        <parameter scale="'+str_scale+'"   name="Intensity"')
+    f.write(' min="1e-5"   max="1e5"')
+    f.write(' value="1.0"')
+    f.write(' free="1"/>\n')
     # Write end tag
-    file.write('      </node>\n')
+    f.write('      </node>\n')
     # Return
     return
@@ -66,7 +65,7 @@ def create_nodes(emin, emax, enumbins):
     Create nodes (energies in TeV).
     """
     # Open file
-    file = open("nodes.xml", "w")
+    f = open("nodes.xml", "w")
     # Set node boundaries
     elogmin = math.log10(float(emin))
@@ -83,14 +82,14 @@ def create_nodes(emin, emax, enumbins):
         scale = 3.45e-17 * math.pow(energy, -2.63)
         # Write node
-        write_node(file, energy, scale)
+        write_node(f, energy, scale)
         # Debug
         #sys.stdout.write(energy)
         #sys.stdout.write(math.pow(10.0, int(math.log10(scale))-1.0)±"\n")
     # Close file
-    file.close()
+    f.close()
     # Return
     return
@@ -100,9 +99,7 @@ def create_nodes(emin, emax, enumbins):
 # Main script entry point #
 # ======================= #
 if __name__ == '__main__':
-    """
-    Compute nodes.
-    """
+
     # Check command line
     usage = "Usage: cta_make_nodes emin emax enumbins"
     if len(sys.argv) < 3:
@@ -3,7 +3,7 @@
 # This script generates IRFs in the CALDB format of HEASARC using ROOT
 # offaxis performance files.
 # -------------------------------------------------------------------------
-# Copyright (C) 2011-2015 Juergen Knoedlseder
+# Copyright (C) 2011-2016 Juergen Knoedlseder
 # -------------------------------------------------------------------------
 #
 # This program is free software: you can redistribute it and/or modify
@@ -24,12 +24,13 @@
 # - gammalib
 # - pyroot
 # ==========================================================================
-from ROOT import TFile, TH1F, TH2F, TH3F
+#from ROOT import TFile, TH1F, TH2F, TH3F
+from ROOT import TFile, TH2F, TH3F
 import gammalib
 from datetime import datetime
 import math
-import sys
-import glob
+#import sys
+#import glob
 import os
@@ -87,6 +87,7 @@ public:
     %rename(_read_ahead)           read_ahead() const;
     %rename(_time_reference)       time_reference() const;
     %rename(_get_observations)     get_observations(const bool& get_response = true);
+    %rename(_setup_observations)   setup_observations(GObservations& obs);
     %rename(_create_ebounds)       create_ebounds();
     %rename(_create_map)           create_map(const GObservations& obs);
     %rename(_create_cube)          create_cube(const GObservations& obs);
@@ -105,6 +106,7 @@ public:
     const bool&           read_ahead(void) const;
     const GTimeReference& time_reference(void) const;
     GObservations         get_observations(const bool& get_response = true);
+    void                  setup_observations(GObservations& obs);
     // Protected methods that create objects from user parameters
     GEbounds        create_ebounds(void);
@@ -170,14 +172,15 @@ public:
 # Initialise observation container from constructor arguments. In case that
 # an observation container is provided as argument, this container will be
-# used to initialise the class.
+# used to initialise the class. The function returns a tuple containing the
+# observation container and the eventually reduced argument list.
 def _set_input_obs(self, argv):
     if len(argv) > 0 and isinstance(argv[0],gammalib.GObservations):
         obs  = argv[0]
         argv = argv[1:]
     else:      
         obs = gammalib.GObservations()
-    return obs
+    return (obs, argv)
 cscript._set_input_obs = _set_input_obs 
 # Initialise application by calling the appropriate class constructor.
 #############################################################################
 # Disutils setup file for ctools Python extension module                    #
 # ------------------------------------------------------------------------- #
-# Copyright (C) 2011-2014 Juergen Knoedlseder                               #
+# Copyright (C) 2011-2016 Juergen Knoedlseder                               #
 # ------------------------------------------------------------------------- #
 #                                                                           #
 #  This program is free software: you can redistribute it and/or modify     #
@@ -27,35 +27,35 @@ import sys
 # Detect execution mode
 is_build = True
 if (len(sys.argv) >= 2):
-	if (sys.argv[1] == 'install'):
-		is_build = False
+    if (sys.argv[1] == 'install'):
+        is_build = False
 if is_build:
-	sys.stdout.write("Python extension module building:\n")
+    sys.stdout.write("Python extension module building:\n")
 else:
-	sys.stdout.write("Python extension module installation:\n")
+    sys.stdout.write("Python extension module installation:\n")
 # Darwin MacPorts kluge: Remove -L/opt/local/lib path from LDSHARED as this
 # overrides the GammaLib settings. Otherwise, MacPorts libraries would be
 # used instead of the libraries selected by GammaLib
 if sys.platform.lower().startswith("darwin"):
-	
-	# Get configuration variables
-	cvars = sysconfig.get_config_vars()
-	
-	# Extract LDSHARED
-	ldshared_old = cvars.get('LDSHARED')
-	ldshared_new = ''
-	ldshared_rm  = ''
-	for option in ldshared_old.split(' '):
-		if option.lstrip().find('-L/opt/local/lib') != 0:
-			ldshared_new += option + ' '
-		else:
-			ldshared_rm += option + ' '
-	if (len(ldshared_rm) > 0):
-		sys.stdout.write("Removed following option(s) from LDSHARED: "+ldshared_rm+"\n");
-	
-	# Set LDSHARED
-	cvars['LDSHARED'] = ldshared_new
+    
+    # Get configuration variables
+    cvars = sysconfig.get_config_vars()
+    
+    # Extract LDSHARED
+    ldshared_old = cvars.get('LDSHARED')
+    ldshared_new = ''
+    ldshared_rm  = ''
+    for option in ldshared_old.split(' '):
+        if option.lstrip().find('-L/opt/local/lib') != 0:
+            ldshared_new += option + ' '
+        else:
+            ldshared_rm += option + ' '
+    if (len(ldshared_rm) > 0):
+        sys.stdout.write("Removed following option(s) from LDSHARED: "+ldshared_rm+"\n");
+    
+    # Set LDSHARED
+    cvars['LDSHARED'] = ldshared_new
 # Set default include directories and data files
 include_dirs         = ['@prefix@/include/gammalib']
@@ -66,8 +66,8 @@ libraries            = [&#39;ctools&#39;,&#39;gamma&#39;]
 # Add install directory to runtime library path
 if os.path.exists('@prefix@/lib'):
-	library_dirs.append('@prefix@/lib')
-	runtime_library_dirs.append('@prefix@/lib')
+    library_dirs.append('@prefix@/lib')
+    runtime_library_dirs.append('@prefix@/lib')
 # Add application include files. The method we use here is not very
 # intelligent as it simple will add all names that start with 'ct'
@@ -75,44 +75,49 @@ if os.path.exists(&#39;@prefix@/lib&#39;):
 # add an explicit filter to avoid appending those.
 dirs = glob.glob('../src/ct*')
 for dir in dirs:
-	if len(dir) > 0 and 'ctools' not in dir:
-		path = os.path.abspath(dir)
-		include_dirs.append(path)
+    if len(dir) > 0 and 'ctools' not in dir:
+        path = os.path.abspath(dir)
+        include_dirs.append(path)
 include_dirs.append(os.path.abspath('../src/support'))
 # Add extra libraries
 extra_libs = ('@PYTHON_EXTRA_LIBS@').split(',')
 for extra_lib in extra_libs:
-	if len(extra_lib) > 0:
-		libraries.append(extra_lib)
+    if len(extra_lib) > 0:
+        libraries.append(extra_lib)
 # Get extra library paths
 extra_lib_paths = ('@LDFLAGS@').split(' ')
 for extra_lib_path in extra_lib_paths:
-	if extra_lib_path.lstrip().find('-L') == 0:
-		dir = extra_lib_path.lstrip().lstrip('-L')
-		if len(dir) > 0:
-			library_dirs.append(dir)
-			runtime_library_dirs.append(dir)
+    if extra_lib_path.lstrip().find('-L') == 0:
+        dir = extra_lib_path.lstrip().lstrip('-L')
+        if len(dir) > 0:
+            library_dirs.append(dir)
+            runtime_library_dirs.append(dir)
 # Get extra include directories
 extra_include_dirs = ('@CPPFLAGS@').split(' ')
 for extra_include_dir in extra_include_dirs:
-	if extra_include_dir.lstrip().find('-I') == 0:
-		dir = extra_include_dir.lstrip().lstrip('-I')
-		if len(dir) > 0:
-			include_dirs.append(dir)
+    if extra_include_dir.lstrip().find('-I') == 0:
+        dir = extra_include_dir.lstrip().lstrip('-I')
+        if len(dir) > 0:
+            include_dirs.append(dir)
 # Set data files to install.
 data_files=[('@prefix@/share/ctools/swig', install_files)]
 # Optionally enable OpenMP
 if '@OPENMP_TRUE@' != '#':
-	extra_compile_args = ['@OPENMP_CXXFLAGS@']
-	extra_link_args    = ['@OPENMP_CXXFLAGS@']
+    extra_compile_args = ['@OPENMP_CXXFLAGS@']
+    extra_link_args    = ['@OPENMP_CXXFLAGS@']
 else:
-	extra_compile_args = []
-	extra_link_args    = []
+    extra_compile_args = []
+    extra_link_args    = []
+
+# Append coverage CXXFLAGS
+if len('@COVERAGE_CXXFLAGS@') > 0:
+    extra_compile_args.append('@COVERAGE_CXXFLAGS@')
+    extra_link_args.append('@COVERAGE_CXXFLAGS@')
 # Optionally add link flag for El Capitan post-processing of modules
 if '@IS_ELCAPITAN_TRUE@' != '#':
@@ -133,25 +138,25 @@ setup(name=&#39;@PACKAGE_NAME@&#39;,
                              runtime_library_dirs=runtime_library_dirs,
                              extra_compile_args=extra_compile_args,
                              extra_link_args=extra_link_args)],
-	  data_files=data_files,
-	  license="GNU GPL v3",
-	  long_description="CTA science analysis tools",
-	  platforms=["Linux", "Solaris", "Mac OS-X", "Unix", "BSD"],
+      data_files=data_files,
+      license="GNU GPL v3",
+      long_description="CTA science analysis tools",
+      platforms=["Linux", "Solaris", "Mac OS-X", "Unix", "BSD"],
       )
 # Post-processing. A symbolic link is created to the directory containing the
 # shared wrapper libraries so that we can add this directory to the PYTHONPATH
 # for testing.
 if is_build:
-	try:
-		os.chdir('build')
-		os.remove('ctools')
-		sys.stdout.write("Removed symbolic link build/ctools.\n")
-	except:
-		pass
-	try:
-		path = glob.glob('lib.*')
-		os.symlink(path[0], 'ctools')
-		sys.stdout.write("Created symbolic link build/ctools.\n")
-	except:
-		sys.stdout.write("WARNING: Failed to create symbolic link build/ctools.\n")
+    try:
+        os.chdir('build')
+        os.remove('ctools')
+        sys.stdout.write("Removed symbolic link build/ctools.\n")
+    except:
+        pass
+    try:
+        path = glob.glob('lib.*')
+        os.symlink(path[0], 'ctools')
+        sys.stdout.write("Created symbolic link build/ctools.\n")
+    except:
+        sys.stdout.write("WARNING: Failed to create symbolic link build/ctools.\n")
@@ -62,7 +62,7 @@ ctbin::ctbin(void) : ctool(CTBIN_NAME, CTBIN_VERSION)
     // Return
     return;
-}
+} // GCOV_EXCL_LINE
 /***********************************************************************//**
@@ -49,6 +49,7 @@
 /* __ Method name definitions ____________________________________________ */
+#define G_SETUP_OBSERVATION       "ctool::setup_observations(GObservations&)"
 #define G_GET_MEAN_POINTING        "ctool::get_mean_pointing(GObservations&)"
 #define G_CREATE_EBOUNDS                            "ctool::create_ebounds()"
 #define G_PROVIDE_HELP                                "ctool::provide_help()"
@@ -378,7 +379,98 @@ GObservations ctool::get_observations(const bool&amp; get_response)
     // Return observation container
     return obs;
+}
+
+
+/***********************************************************************//**
+ * @brief Setup observation container
+ *
+ * @param[in] obs Observation container
+ *
+ * @exception GException::invalid_value
+ *            Invalid "inobs" parameter encountered.
+ *
+ * Setup an observation container by appending all required information that
+ * is missing using user parameters.
+ *
+ * If the observation container @p obs is empty, the method will extract the
+ * filename from the "inobs" parameter, and if the filename is neither empty
+ * nor "NONE", will load the observation container from the specified file.
+ * If the file is a FITS file, and dependent on the information that is found
+ * in the FITS file, the method will append a single CTA observation to the
+ * observation container, containing either an event list or a counts cube.
+ * Otherwise, the method assumes that the file is an observation definition
+ * XML file and will load that file into the observation container.
+ *
+ * If the filename is empty or "NONE", the method will throw an exception.
+ *
+ * The method will then setup the response for all CTA observations in the
+ * container (see the set_response() method for more information).
+ * 
+ * The method will furthermore setup the observation boundaries for all CTA
+ * observations in the container that contain event lists (see the
+ * set_obs_bounds() method for more information).
+ ***************************************************************************/
+void ctool::setup_observations(GObservations& obs)
+{
+    // Load observations if there are none in the container
+    if (obs.size() == 0) {
+
+        // Get the filename from the "inobs" parameter
+        GFilename filename((*this)["inobs"].filename());
+        
+        // Load observation container from file if the filename is neither
+        // "NONE" nor empty ...
+        if ((gammalib::toupper(filename.url()) != "NONE") &&
+            !filename.is_empty()) {
+
+            // If file does not exist then throw an exceptions
+            if (!filename.exists()) {
+                std::string msg = "The \"inobs\" parameter \""+filename+
+                                  "\" specifies a file that does not "
+                                  "exist. Please specify  a valid event "
+                                  "list, counts cube or  observation "
+                                  "definition XML file.";
+                throw GException::invalid_value(G_SETUP_OBSERVATION, msg);
+            }
+
+            // If the file is a FITS file then load it into a CTA
+            // observation and append that observation to the container ...
+            else if (filename.is_fits()) {
+                GCTAObservation cta(filename);
+                obs.append(cta);
+            }
+
+            // ... otherwise it is assumed that the file is an observation
+            // definition XML file and the file is loaded into the
+            // observation container
+            else {
+                obs.load(filename);
+            }
+
+        }
+
+        // ... otherwise, if the filename is "NONE" or empty then throw
+        // an exception.
+        else {
+            std::string msg = "The \"inobs\" parameter \""+filename+
+                              "\" is not a valid filename. Please specify "
+                              "a valid event list, counts cube or "
+                              "observation definition XML file.";
+            throw GException::invalid_value(G_SETUP_OBSERVATION, msg);
+        }
+
+    } // endif: there were no observations in the container
+
+    // Setup the response for all CTA observations in the observation
+    // container
+    set_response(obs);
+    // Setup boundaries for all CTA observations containing event lists
+    set_obs_bounds(obs);
+
+    // Return
+    return;
 }
@@ -595,15 +687,16 @@ GCTAEventCube ctool::create_cube(const GObservations&amp; obs)
  * method furthermore sets the ontime, livetime and deadtime correction
  * factor.
  *
- * The following parameters are read:
- *      ra - Right Ascension of pointing and RoI centre (deg)
- *      dec - Declination of pointing and RoI centre (deg)
- *      rad - Radius of RoI (deg)
- *      deadc - Deadtime correction factor
- *      tmin - Start time
- *      tmax - Stop time
- *      emin - Minimum energy (TeV)
- *      emax - Maximum energy (TeV)
+ * The following parameters are read
+ *
+ *      ra:    Right Ascension of pointing and RoI centre (deg)
+ *      dec:   Declination of pointing and RoI centre (deg)
+ *      rad:   Radius of RoI (deg)
+ *      deadc: Deadtime correction factor
+ *      tmin:  Start time
+ *      tmax:  Stop time
+ *      emin:  Minimum energy (TeV)
+ *      emax:  Maximum energy (TeV)
  ***************************************************************************/
 GCTAObservation ctool::create_cta_obs(void)
 {
@@ -804,12 +897,9 @@ void ctool::require_inobs_nocube(const std::string&amp; method)
  *
  * @param[in,out] obs Observation container
  *
- * Set the response for a CTA observations in the container that so far have
- * no response using the "caldb" and "irf" task parameters.
- *
- * The following parameters are read:
- *      caldb - Calibration database
- *      irf - Instrument response function
+ * Set the response for all CTA observations in the container that so far
+ * have no response information available. See the set_obs_response()
+ * method for more information about the user parameters that are read.
  ***************************************************************************/
 void ctool::set_response(GObservations& obs)
 {
@@ -841,69 +931,83 @@ void ctool::set_response(GObservations&amp; obs)
  *
  * @param[in,out] obs CTA observation
  *
- * Set the response for a CTA observation. If the CTA observation contains
+ * Set the response for one CTA observation. If the CTA observation contains
  * a counts cube the method first attempts to set the response information
- * using the @a expcube and @a psfcube user parameters. If this is not
- * successful (for example because the parameters do not exist or their
- * value is NONE or blank), the method will set the response information
- * from the @a caldb and @a irf user parameters.
+ * using the following user parameters
+ *
+ *      expcube:   Exposure cube file
+ *      psfcube:   Point spread function cube file
+ *      edispcube: Energy dispersion cube file (optional)
+ *      bkgcube:   Background cube file
+ *
+ * If none of the @p expcube, @p psfcube and @p bkgcube parameters is
+ * "NONE" or empty, the method will allocate a stacked response for the
+ * observation. In case that an energy dispersion cube is provided using
+ * the @p edispcube parameter, this energy dispersion cube is also loaded
+ * and attached to the stacked response function.
+ *
+ * In case that any of the @p expcube, @p psfcube and @p bkgcube parameters
+ * is "NONE" or empty, the method will assume that a IRF response should
+ * be used, and will attempty to set the response information using the
+ * following user parameters
+ *
+ *      caldb:     Calibration database
+ *      irf:       Instrument response function
  *
- * The following parameters are read:
- *      expcube - Exposure cube file (optional)
- *      psfcube - PSF cube file (optional)
- *      caldb - Calibration database (optional)
- *      irf - Instrument response function (optional)
  ***************************************************************************/
 void ctool::set_obs_response(GCTAObservation* obs)
 {
     // Initialise response flag
     bool has_response = false;
-    // If the observation contains a counts cube, then first check whether
-    // the expcube and psfcube parameters exist and are not NONE
+    // If the observation contains a counts cube, then check whether
+    // response information for a stacked analysis is provided, and if so,
+    // set that response information for the CTA observation
     if (dynamic_cast<const GCTAEventCube*>(obs->events()) != NULL) {
         if (has_par("expcube")   && has_par("psfcube") &&
             has_par("edispcube") && has_par("bkgcube")) {
             // Get filenames
-            std::string expcube   = (*this)["expcube"].filename();
-            std::string psfcube   = (*this)["psfcube"].filename();
-            std::string edispcube = (*this)["edispcube"].filename();
-            std::string bkgcube   = (*this)["bkgcube"].filename();
-
-            // Extract response information if available
-            if ((expcube != "NONE") && (psfcube != "NONE") &&
-                (bkgcube != "NONE") &&
-                (gammalib::strip_whitespace(expcube) != "") &&
-                (gammalib::strip_whitespace(psfcube) != "") &&
-                (gammalib::strip_whitespace(bkgcube) != "")) {
+            GFilename expcube((*this)["expcube"].filename());
+            GFilename psfcube((*this)["psfcube"].filename());
+            GFilename edispcube((*this)["edispcube"].filename());
+            GFilename bkgcube((*this)["bkgcube"].filename());
+
+            // Extract stacked response information if available
+            if ((gammalib::toupper(expcube.url()) != "NONE") &&
+                (gammalib::toupper(psfcube.url()) != "NONE") &&
+                (gammalib::toupper(bkgcube.url()) != "NONE") &&
+                !expcube.is_empty() &&
+                !psfcube.is_empty() &&
+                !bkgcube.is_empty()) {
                 // Get exposure, PSF and background cubes
                 GCTACubeExposure   exposure(expcube);
                 GCTACubePsf        psf(psfcube);
                 GCTACubeBackground background(bkgcube);
-                // Optionally load energy dispersion cube
-                if ((edispcube != "NONE") &&
-                    (gammalib::strip_whitespace(edispcube) != "")) {
+                // If an energy dispersion cube is available, get also
+                // this cube, and set all information as stacked response
+                // for this CTA observation
+                if ((gammalib::toupper(edispcube.url()) != "NONE") &&
+                    !edispcube.is_empty()) {
                 	GCTACubeEdisp edisp(edispcube);
                 	obs->response(exposure, psf, edisp, background);
                 }
                 else {
-					// Set reponse
 					obs->response(exposure, psf, background);
                 }
-                // Signal response availability
+                // Signal that response is available
                 has_response = true;
             } // endif: filenames were available
-        } // endif: expcube and psfcube parameters exist
+        } // endif: expcube, psfcube and bkdcube parameters valid
     } // endif: observation contains a counts cube
-    // If we have not yet response information then get it now
-    // from the caldb and irf parameters
+    // If we have not yet response information then get it now from the
+    // caldb and irf user parameters
     if (!has_response) {
         // Load response information
@@ -938,59 +1042,70 @@ void ctool::set_obs_response(GCTAObservation* obs)
 /***********************************************************************//**
- * @brief Set observation boundaries
+ * @brief Set observation boundaries for all CTA observations
  *
  * @param[in,out] obs Observation container
+ *
+ * Sets the observation boundaries for all CTA observations in the container
+ * that contain event lists. If the energy boundaries of an event list are
+ * empty, the method gets the 
+ *
+ *      emin:   Minimum energy (TeV)
+ *      emax:   Maximum energy (TeV)
+ *
+ * user parameters and sets a single energy boundary element @p [emin,emax].
+ *
+ * If the RoI radius of the event list is invalid, the method gets the
+ *
+ *      rad:    Region of Interest radius (deg)
+ *
+ * user parameter to set the radius of the RoI, and uses the CTA pointing
+ * direction to set the centre of the RoI.
  ***************************************************************************/
 void ctool::set_obs_bounds(GObservations& obs)
 {
-    // Setup response for all observations
+    // Loop over all observations in the container
     for (int i = 0; i < obs.size(); ++i) {
-        // Is this observation a CTA observation?
+        // Get pointer to CTA observation
         GCTAObservation* cta = dynamic_cast<GCTAObservation*>(obs[i]);
-        // Continue only if observation is CTA and has events
-        if ((cta != NULL) && (cta->has_events())) {
-
-            // Get pointer on event list
-            GCTAEventList* list = const_cast<GCTAEventList*>(dynamic_cast<const GCTAEventList*>(cta->events()));
-
-            // Continue only if it's valid
-            if (list != NULL) {
-
-                // If there are no energy boundaries then read the user
-                // parameters and add them
-                if (list->ebounds().is_empty()) {
-
-                    // If there are "emin" and "emax" parameters then use
-                    // them
-                    if (has_par("emin") && has_par("emax")) {
-                        double emin = (*this)["emin"].real();
-                        double emax = (*this)["emax"].real();
-                        GEbounds ebounds(GEnergy(emin, "TeV"),
-                                         GEnergy(emax, "TeV"));
-                        list->ebounds(ebounds);
-                    }
-                    
-                }
+        // Fall through if observation is not a CTA observation or if it
+        // does not contain events
+        if ((cta == NULL) || (!cta->has_events())) {
+            continue;
+        }
-                // If there is no ROI then read the user parameters and add
-                // them
-                if (list->roi().radius() == 0) {
-                    
-                    // If there is a "rad" parameter then use it
-                    if (has_par("rad")) {
-                        double rad = (*this)["rad"].real();
-                        GCTARoi roi(GCTAInstDir(cta->pointing().dir()), rad);
-                        list->roi(roi);
-                    }
+        // Get pointer on CTA event list
+        GCTAEventList* list = const_cast<GCTAEventList*>
+                       (dynamic_cast<const GCTAEventList*>(cta->events()));
-                }
+        // Fall through if CTA observation does not contain an event list
+        if (list == NULL) {
+            continue;
+        }
-            } // endif: list was valid
+        // If there are no energy boundaries then read the "emin" and "emax"
+        // user parameters and add them
+        if (list->ebounds().is_empty()) {
+            if (has_par("emin") && has_par("emax")) {
+                double emin((*this)["emin"].real());
+                double emax((*this)["emax"].real());
+                GEbounds ebounds(GEnergy(emin, "TeV"),
+                                 GEnergy(emax, "TeV"));
+                list->ebounds(ebounds);
+            }
+        }
-        } // endif: observation was CTA
+        // If there is no RoI then read the "rad" user parameters and use
+        // the pointing direction to set the RoI
+        if (list->roi().radius() == 0) {
+            if (has_par("rad")) {
+                double rad = (*this)["rad"].real();
+                GCTARoi roi(GCTAInstDir(cta->pointing().dir()), rad);
+                list->roi(roi);
+            }
+        }
     } // endfor: looped over observations
@@ -72,6 +72,7 @@ protected:
     const bool&           read_ahead(void) const;
     const GTimeReference& time_reference(void) const;
     GObservations         get_observations(const bool& get_response = true);
+    void                  setup_observations(GObservations& obs);
     // Protected methods that create objects from user parameters
     GEbounds        create_ebounds(void);
@@ -18,6 +18,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
+import os
 import gammalib
 import cscripts
@@ -28,7 +29,11 @@ import cscripts
 class Test(gammalib.GPythonTestSuite):
     """
     Test class for cscaldb script.
+
+    This test class makes unit tests for the cslightcrv script by using it
+    from the command line and from Python.
     """
+
     # Constructor
     def __init__(self):
         """
@@ -49,15 +54,15 @@ class Test(gammalib.GPythonTestSuite):
         self.name("cscaldb")
         # Append tests
-        self.append(self._test_functional, "Test cscaldb functionality")
+        self.append(self._test_python, "Test cscaldb from Python")
         # Return
         return
-    # Test cscaldb functionality
-    def _test_functional(self):
+    # Test cscaldb from Python
+    def _test_python(self):
         """
-        Test cscaldb functionality.
+        Test cscaldb from Python.
         """
         # Set-up cscaldb
         caldb = cscripts.cscaldb()
+#! /usr/bin/env python
+# ==========================================================================
+# This scripts performs unit tests for the cslightcrv script.
+#
+# Copyright (C) 2016 Juergen Knoedlseder
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# ==========================================================================
+import os
+import gammalib
+import cscripts
+
+
+# ================================ #
+# Test class for cslightcrv script #
+# ================================ #
+class Test(gammalib.GPythonTestSuite):
+    """
+    Test class for cslightcrv script.
+
+    This test class makes unit tests for the cslightcrv script by using it
+    from the command line and from Python.
+    """
+    
+    # Constructor
+    def __init__(self):
+        """
+        Constructor.
+        """
+        # Call base class constructor
+        gammalib.GPythonTestSuite.__init__(self)
+
+        # Set members
+        self._events_name = "data/crab_events.fits"
+        self._model_name  = "data/crab.xml"
+
+        # Return
+        return
+
+    # Set test functions
+    def set(self):
+        """
+        Set all test functions.
+        """
+        # Set test name
+        self.name("cslightcrv")
+
+        # Append tests
+        self.append(self._test_cmd, "Test cslightcrv on command line")
+        self.append(self._test_python, "Test cslightcrv from Python")
+
+        # Return
+        return
+
+    # Test cslightcrv on command line
+    def _test_cmd(self):
+        """
+        Test cslightcrv on the command line.
+        """
+        # Kluge to set the command (installed version has no README file)
+        if os.path.isfile("README"):
+            cslightcrv = "../cscripts/cslightcrv.py"
+        else:
+            cslightcrv = "cslightcrv"
+
+        # Setup cslightcrv command
+        cmd = cslightcrv+' inobs="'+self._events_name+'"'+ \
+                         ' inmodel="'+self._model_name+'"'+ \
+                         ' srcname="Crab" caldb="prod2" irf="South_0.5h"'+ \
+                         ' tbinalg="LIN" tmin=51544.50 tmax=51544.53'+ \
+                         ' tbins=3 enumbins=0 emin=0.1 emax=100.0'+ \
+                         ' outfile="lightcurve_cmd1.fits"'
+
+        # Execute cslightcrv, make sure we catch any exception
+        try:
+            rc = os.system(cmd+" >/dev/null 2>&1")
+        except:
+            pass
+
+        # Check if execution was successful
+        self.test_assert(rc == 0,
+                         "Successful cslightcrv execution on command line")
+
+        # Check light curve
+        self._check_light_curve("lightcurve_cmd1.fits", 3)
+
+        # Setup cslightcrv command
+        cmd = cslightcrv+' inobs="events_that_do_not_exist.fits"'+ \
+                         ' inmodel="'+self._model_name+'"'+ \
+                         ' srcname="Crab" caldb="prod2" irf="South_0.5h"'+ \
+                         ' tbinalg="LIN" tmin=51544.50 tmax=51544.53'+ \
+                         ' tbins=3 enumbins=0 emin=0.1 emax=100.0'+ \
+                         ' outfile="lightcurve_cmd1.fits"'
+
+        # Execute cslightcrv, make sure we catch any exception
+        try:
+            rc = os.system(cmd+" >/dev/null 2>&1")
+        except:
+            pass
+
+        # Check if execution failed
+        self.test_assert(rc != 0,
+                         "Failure of cslightcrv execution on command line")
+
+        # Return
+        return
+
+    # Test cslightcrv from Python
+    def _test_python(self):
+        """
+        Test cslightcrv from Python.
+        """
+        # Set-up unbinned cslightcrv
+        lcrv = cscripts.cslightcrv()
+        lcrv["inobs"]    = self._events_name
+        lcrv["inmodel"]  = self._model_name
+        lcrv["srcname"]  = "Crab"
+        lcrv["caldb"]    = "prod2"
+        lcrv["irf"]      = "South_0.5h"
+        lcrv["tbinalg"]  = "LIN"
+        lcrv["tmin"]     = 51544.50
+        lcrv["tmax"]     = 51544.53
+        lcrv["tbins"]    = 3
+        lcrv["enumbins"] = 0
+        lcrv["emin"]     = 0.1
+        lcrv["emax"]     = 100.0
+        lcrv["outfile"]  = "lightcurve_py1.fits"
+
+        # Run cslightcrv script and save light curve
+        lcrv.run()
+        lcrv.save()
+
+        # Check light curve
+        self._check_light_curve("lightcurve_py1.fits", 3)
+
+        # Now use FILE as time bin algorithm. For this we need first to
+        # create an ASCII file. We use now 6 time bins. The ASCII file
+        # is saved into the file "lightcurve_py2.dat".
+        csv    = gammalib.GCsv(2,2)
+        tmin   = 51544.50
+        tdelta = 0.01
+        for i in range(csv.nrows()):
+            csv[i,0] = "%.5f" % (tmin +  i    * tdelta)
+            csv[i,1] = "%.5f" % (tmin + (i+1) * tdelta)
+        csv.save("lightcurve_py2.dat", " ", True)
+
+        # Set-up unbinned cslightcrv
+        lcrv = cscripts.cslightcrv()
+        lcrv["inobs"]    = self._events_name
+        lcrv["inmodel"]  = self._model_name
+        lcrv["srcname"]  = "Crab"
+        lcrv["caldb"]    = "prod2"
+        lcrv["irf"]      = "South_0.5h"
+        lcrv["tbinalg"]  = "FILE"
+        lcrv["tbinfile"] = "lightcurve_py2.dat"
+        lcrv["enumbins"] = 0
+        lcrv["emin"]     = 0.1
+        lcrv["emax"]     = 100.0
+        lcrv["outfile"]  = "lightcurve_py2.fits"
+
+        # Execute cslightcrv script
+        lcrv.execute()
+
+        # Check light curve
+        self._check_light_curve("lightcurve_py2.fits", 2)
+
+        # Now we setup an observation container on input. We attached the
+        # model to the observation container so that cslightcrv should
+        # no longer query for the parameter.
+        cta = gammalib.GCTAObservation(self._events_name)
+        obs = gammalib.GObservations()
+        obs.append(cta)
+        obs.models(self._model_name)
+
+        # Set-up unbinned cslightcrv from observation container. Now use
+        # the GTI algorithm so that we test all timing algorithms.
+        lcrv = cscripts.cslightcrv(obs)
+        lcrv["srcname"]  = "Crab"
+        lcrv["caldb"]    = "prod2"
+        lcrv["irf"]      = "South_0.5h"
+        lcrv["tbinalg"]  = "GTI"
+        lcrv["enumbins"] = 0
+        lcrv["emin"]     = 0.1
+        lcrv["emax"]     = 100.0
+        lcrv["outfile"]  = "lightcurve_py3.fits"
+
+        # Execute cslightcrv script
+        lcrv.execute()
+
+        # Check light curve
+        self._check_light_curve("lightcurve_py3.fits", 1)
+
+        # Finally we set-up a binned cslightcrv
+        lcrv = cscripts.cslightcrv()
+        lcrv["inobs"]    = self._events_name
+        lcrv["inmodel"]  = self._model_name
+        lcrv["srcname"]  = "Crab"
+        lcrv["caldb"]    = "prod2"
+        lcrv["irf"]      = "South_0.5h"
+        lcrv["tbinalg"]  = "LIN"
+        lcrv["tmin"]     = 51544.50
+        lcrv["tmax"]     = 51544.53
+        lcrv["tbins"]    = 2
+        lcrv["emin"]     = 0.1
+        lcrv["emax"]     = 100.0
+        lcrv["enumbins"] = 10
+        lcrv["coordsys"] = "CEL"
+        lcrv["proj"]     = "TAN"
+        lcrv["xref"]     = 83.63
+        lcrv["yref"]     = 22.01
+        lcrv["nxpix"]    = 20
+        lcrv["nypix"]    = 20
+        lcrv["binsz"]    = 0.02
+        lcrv["outfile"]  = "lightcurve_py4.fits"
+
+        # Execute cslightcrv script
+        lcrv.execute()
+
+        # Check light curve
+        self._check_light_curve("lightcurve_py4.fits", 2)
+
+        # Return
+        return
+
+    # Check light curve result file
+    def _check_light_curve(self, filename, bins):
+        """
+        Check light curve file.
+        """
+        # Expected column names
+        cols = ["MJD", "e_MJD", "Prefactor", "e_Prefactor",
+                "Index", "e_Index", "TS", "UpperLimit"]
+
+        # Open FITS file
+        fits = gammalib.GFits(filename)
+
+        # Check FITS file structure
+        self.test_value(fits.size(), 2,
+             'Check for 2 extensions in light curve FITS file')
+        self.test_assert(fits.contains("LIGHTCURVE"),
+             'FITS file contains "LIGHTCURVE" extension')
+
+        # Get LIGHTCURVE table
+        table = fits["LIGHTCURVE"]
+
+        # Check FITS table structure
+        self.test_value(table.ncols(), len(cols),
+             'Check for %d columns in light curve FITS table' % len(cols))
+        self.test_value(table.nrows(), bins,
+             'Check for %d rows in light curve FITS table' % bins)
+        for col in cols:
+            self.test_assert(table.contains(col),
+                 'FITS file contains "'+col+'" column')
+
+        # Close FITS file
+        fits.close()
+        
+        # Return
+        return
 #! /usr/bin/env python
 # ==========================================================================
-# This scripts performs unit tests for the ctbin module.
+# This scripts performs unit tests for the ctbin tool.
 #
 # Copyright (C) 2014-2016 Juergen Knoedlseder
 #
@@ -18,16 +18,20 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
+import os
 import gammalib
 import ctools
-# =========================== #
-# Test class for ctbin module #
-# =========================== #
+# ========================= #
+# Test class for ctbin tool #
+# ========================= #
 class Test(gammalib.GPythonTestSuite):
     """
-    Test class for ctbin module.
+    Test class for ctbin tool.
+    
+    This test class makes unit tests for the ctbin tool by using it from
+    the command line and from Python.
     """
     # Constructor
@@ -53,15 +57,68 @@ class Test(gammalib.GPythonTestSuite):
         self.name("ctbin")
         # Append tests
-        self.append(self._test_ctbin, "Test ctbin")
+        self.append(self._test_cmd, "Test ctbin on command line")
+        self.append(self._test_python, "Test ctbin from Python")
         # Return
         return
-    # Test ctbin
-    def _test_ctbin(self):
+    # Test ctbin on command line
+    def _test_cmd(self):
         """
-        Test ctbin.
+        Test ctbin on the command line.
+        """
+        # Kluge to set the command (installed version has no README file)
+        if os.path.isfile("README"):
+            ctbin = "../src/ctbin/ctbin"
+        else:
+            ctbin = "ctbin"
+
+        # Setup ctbin command
+        cmd = ctbin+' inobs="'+self._events_name+'"'+ \
+                    ' outcube="cntmap_cmd1.fits"'+\
+                    ' emin=0.1 emax=100.0 enumbins=20 ebinalg="LOG"'+ \
+                    ' nxpix=200 nypix=200 binsz=0.02 coordsys="CEL"'+ \
+                    ' xref=83.63 yref=22.01 proj="CAR"'
+
+        # Execute ctbin, make sure we catch any exception
+        try:
+            rc = os.system(cmd+" >/dev/null 2>&1")
+        except:
+            pass
+
+        # Check if execution was successful
+        self.test_assert(rc == 0,
+                         "Successful ctbin execution on command line")
+
+        # Load counts cube and check content.
+        evt = gammalib.GCTAEventCube("cntmap_cmd1.fits")
+        self._check_cube(evt, 5542)
+
+        # Setup ctbin command
+        cmd = ctbin+' inobs="events_that_do_not_exist.fits"'+ \
+                    ' outcube="cntmap_cmd2.fits"'+\
+                    ' emin=0.1 emax=100.0 enumbins=20 ebinalg="LOG"'+ \
+                    ' nxpix=200 nypix=200 binsz=0.02 coordsys="CEL"'+ \
+                    ' xref=83.63 yref=22.01 proj="CAR"'
+
+        # Execute ctbin, make sure we catch any exception
+        try:
+            rc = os.system(cmd+" >/dev/null 2>&1")
+        except:
+            pass
+
+        # Check if execution failed
+        self.test_assert(rc != 0,
+                         "Failure of ctbin execution on command line")
+
+        # Return
+        return
+
+    # Test ctbin from Python
+    def _test_python(self):
+        """
+        Test ctbin from Python.
         """
         # Set-up ctbin
         bin = ctools.ctbin()
@@ -83,15 +140,15 @@ class Test(gammalib.GPythonTestSuite):
         bin.run()
         # Check content of observation and cube
-        self._test_observation(bin, 5542)
-        self._test_cube(bin.cube(), 5542)
+        self._check_observation(bin, 5542)
+        self._check_cube(bin.cube(), 5542)
         # Test copy constructor
         cpy_bin = bin.copy()
         # Check content of observation and cube
-        self._test_observation(cpy_bin, 5542)
-        self._test_cube(cpy_bin.cube(), 5542)
+        self._check_observation(cpy_bin, 5542)
+        self._check_cube(cpy_bin.cube(), 5542)
         # Run copy of ctbin tool again
         cpy_bin.run()
@@ -100,8 +157,8 @@ class Test(gammalib.GPythonTestSuite):
         # event cube as on input the observation is binned, and any binned
         # observation will be skipped, hence the counts cube should be
         # empty.
-        self._test_observation(cpy_bin, 0)
-        self._test_cube(cpy_bin.cube(), 0)
+        self._check_observation(cpy_bin, 0)
+        self._check_cube(cpy_bin.cube(), 0)
         # Clear and run copy of ctbin again
         #cpy_bin.clear()
@@ -115,7 +172,7 @@ class Test(gammalib.GPythonTestSuite):
         # Load counts cube and check content.
         evt = gammalib.GCTAEventCube("cntmap.fits")
-        self._test_cube(evt, 5542)
+        self._check_cube(evt, 5542)
         # Prepare observation container for stacked analysis
         cta = gammalib.GCTAObservation(self._events_name)
@@ -147,13 +204,12 @@ class Test(gammalib.GPythonTestSuite):
         # Check content of observation and cube (need multiplier=3 since
         # three identical observations have been appended)
-        self._test_observation(bin, 5542, multiplier=3)
-        self._test_cube(bin.cube(), 5542, multiplier=3)
+        self._check_observation(bin, 5542, multiplier=3)
+        self._check_cube(bin.cube(), 5542, multiplier=3)
-        # Set-up ctbin with invalid event file
-        bin = ctools.ctbin()
-        bin["inobs"]    = "event_file_that_does_not_exist.fits"
-        bin["outcube"]  = "cntmap.fits"
+        # Set-up ctbin using an observation container
+        bin = ctools.ctbin(obs)
+        bin["outcube"]  = "cntmap2.fits"
         bin["ebinalg"]  = "LOG"
         bin["emin"]     = 0.1
         bin["emax"]     = 100.0
@@ -166,21 +222,29 @@ class Test(gammalib.GPythonTestSuite):
         bin["xref"]     = 83.63
         bin["yref"]     = 22.01
-        # Run ctbin tool
-        self.test_try("Run ctbin with invalid event file")
-        try:
-            bin.run()
-            self.test_try_failure()
-        except:
-            self.test_try_success()
+        # Execute ctbin tool
+        bin.execute()
+
+        # Load counts cube and check content.
+        evt = gammalib.GCTAEventCube("cntmap2.fits")
+        self._check_cube(evt, 5542, multiplier=3)
+
+        # Clear tool
+        #bin.clear()
+#what():  *** ERROR in GApplicationPars::write(std::string&): Unable to open parameter file "pfiles/".
+
+        # Check content of observation and cube
+        #self.test_value(bin.obs().size(), 0, "There is no observation")
+        #self.test_value(bin.cube().size(), 0, "0 event bins")
+        #self.test_value(bin.cube().number(), 0, "0 events")
         # Return
         return
     # Check observation
-    def _test_observation(self, ctbin, nevents, multiplier=1):
+    def _check_observation(self, ctbin, nevents, multiplier=1):
         """
-        Test content of an observation.
+        Check content of an observation.
         Args:
             ctbin:   ctbin instance
@@ -206,15 +270,15 @@ class Test(gammalib.GPythonTestSuite):
                         "Pointing Declination is 22.01 deg")
         # Test event cube
-        self._test_cube(obs.events(), nevents, multiplier=multiplier)
+        self._check_cube(obs.events(), nevents, multiplier=multiplier)
         # Return
         return
     # Check event cube
-    def _test_cube(self, cube, nevents, multiplier=1):
+    def _check_cube(self, cube, nevents, multiplier=1):
         """
-        Test content of event cube."
+        Check content of event cube."
         Args:
             cube:    Event cube
 #! /usr/bin/env python
 # ==========================================================================
-# This scripts performs unit tests for the ctobssim module.
+# This scripts performs unit tests for the ctobssim tool.
 #
 # Copyright (C) 2014-2016 Juergen Knoedlseder
 #
@@ -18,17 +18,21 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
+import os
 import gammalib
 import ctools
 from cscripts import obsutils
-# ============================== #
-# Test class for ctobssim module #
-# ============================== #
+# ============================ #
+# Test class for ctobssim tool #
+# ============================ #
 class Test(gammalib.GPythonTestSuite):
     """
-    Test class for ctobssim module.
+    Test class for ctobssim tools.
+    
+    This test class makes unit tests for the ctobssim tool by using it from
+    the command line and from Python.
     """
     # Constructor
@@ -56,16 +60,67 @@ class Test(gammalib.GPythonTestSuite):
         self.name("ctobssim")
         # Append tests
-        self.append(self._test_ctobssim, "Test ctobssim")
-        #self.append(self._test_container, "Test ctobssim on observation container")
+        self.append(self._test_ctobssim_cmd, "Test ctobssim on command line")
+        self.append(self._test_ctobssim_python, "Test ctobssim from Python")
         # Return
         return
-    # Test ctobssim
-    def _test_ctobssim(self):
+    # Test ctobssim on command line
+    def _test_ctobssim_cmd(self):
         """
-        Test ctobssim.
+        Test ctobssim on the command line.
+        """
+        # Kluge to set the command (installed version has no README file)
+        if os.path.isfile("README"):
+            ctobssim = "../src/ctobssim/ctobssim"
+        else:
+            ctobssim = "ctobssim"
+
+        # Setup ctobssim command
+        cmd = ctobssim+' inmodel="data/crab.xml" outevents="events.fits"'+ \
+                       ' caldb="irf" irf="cta_dummy_irf" '+ \
+                       ' ra=83.63 dec=22.01 rad=10.0'+ \
+                       ' tmin=0.0 tmax=1800.0 emin=0.1 emax=100.0'
+
+        # Execute ctobssim, make sure we catch any exception
+        try:
+            rc = os.system(cmd+" >/dev/null 2>&1")
+        except:
+            pass
+
+        # Check if execution was successful
+        self.test_assert(rc == 0,
+                         "Successful ctobssim execution on command line")
+
+        # Load counts cube and check content.
+        evt = gammalib.GCTAEventList("events.fits")
+        self._test_list(evt, 4119)
+
+        # Setup ctobssim command
+        cmd = ctobssim+' inmodel="model_that_does_not_exist.xml"'+ \
+                       ' outevents="events.fits"'+ \
+                       ' caldb="irf" irf="cta_dummy_irf" '+ \
+                       ' ra=83.63 dec=22.01 rad=10.0'+ \
+                       ' tmin=0.0 tmax=1800.0 emin=0.1 emax=100.0'
+
+        # Execute ctobssim, make sure we catch any exception
+        try:
+            rc = os.system(cmd+" >/dev/null 2>&1")
+        except:
+            pass
+
+        # Check if execution failed
+        self.test_assert(rc != 0,
+                         "Failure of ctobssim execution on command line")
+
+        # Return
+        return
+
+    # Test ctobssim from Python
+    def _test_ctobssim_python(self):
+        """
+        Test ctobssim from Python.
         """
         # Set-up ctobssim
         sim = ctools.ctobssim()
@@ -18,12 +18,13 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # ==========================================================================
+import os
+import sys
 import gammalib
 import cscripts
-import sys
-import os
 sys.path.append(os.path.dirname(os.path.abspath(__file__)))
 import test_cscaldb
+import test_cslightcrv
 # ================== #
@@ -37,13 +38,16 @@ def test(installed=False):
     suites = gammalib.GTestSuites("cscripts Python module unit testing")
     # Allocate test suites and append them to the container
-    suite_cscaldb = test_cscaldb.Test()
+    suite_cscaldb    = test_cscaldb.Test()
+    suite_cslightcrv = test_cslightcrv.Test()
     # Setup unit tests
     suite_cscaldb.set()
+    suite_cslightcrv.set()
     # Append tests to container
     suites.append(suite_cscaldb)
+    suites.append(suite_cslightcrv)
     # If we have an installed version then create a temporary directory and
     # copy over all information that is needed
@@ -60,9 +64,13 @@ def test(installed=False):
         dirname = os.path.dirname(testdir)
         # Copy over test data and irf
-        #os.system("cp -r %s %s" % (dirname+"/data", "data"))
+        os.system("cp -r %s %s" % (dirname+"/data", "data"))
         #os.system("cp -r %s %s" % (dirname+"/irf",  "irf"))
+    # ... otherwise set the calibration database
+    else:
+        os.environ['CALDB'] = "../caldb"
+
     # Set PFILES environment variable
     try:
         os.mkdir("pfiles")
@@ -97,8 +105,6 @@ def test(installed=False):
 # Main routine entry point #
 # ======================== #
 if __name__ == '__main__':
-    """
-    Perform unit testing for cscripts used from Python.
-    """
+
     # Run tests
     test()
@@ -40,15 +40,15 @@ import test_cterror
 import test_pipelines
-# ================== #
-# Perform unit tests #
-# ================== #
+# ========================= #
+# Perform ctools unit tests #
+# ========================= #
 def test(installed=False):
     """
-    Perform unit testing for Python interface.
+    Perform unit testing for ctools.
     """
     # Allocate test suite container
-    suites = gammalib.GTestSuites("ctools Python module unit testing")
+    suites = gammalib.GTestSuites("ctools unit testing")
     # Allocate test suites and append them to the container
     suite_ctobssim    = test_ctobssim.Test()
@@ -153,8 +153,6 @@ def test(installed=False):
 # Main routine entry point #
 # ======================== #
 if __name__ == '__main__':
-    """
-    Perform unit testing for Python interface.
-    """
+
     # Run tests
     test()