Integrate code

Jürgen Knödlseder
1 parent 73bec68a
Showing 43 changed files with 235 additions and 233 deletions
cscripts/csresmap.py
doc/source/users/reference_manual/cscaldb.rst
doc/source/users/reference_manual/csebins.rst
doc/source/users/reference_manual/csfindobs.rst
doc/source/users/reference_manual/csiactcopy.rst
doc/source/users/reference_manual/csiactdata.rst
doc/source/users/reference_manual/csiactobs.rst
doc/source/users/reference_manual/cslightcrv.rst
doc/source/users/reference_manual/csmodelinfo.rst
doc/source/users/reference_manual/csmodelmerge.rst
doc/source/users/reference_manual/csmodelselect.rst
doc/source/users/reference_manual/csobs2caldb.rst
doc/source/users/reference_manual/csobsdef.rst
doc/source/users/reference_manual/csobsinfo.rst
doc/source/users/reference_manual/csobsselect.rst
doc/source/users/reference_manual/csphasecrv.rst
doc/source/users/reference_manual/cspull.rst
doc/source/users/reference_manual/csresmap.rst
doc/source/users/reference_manual/cssens.rst
doc/source/users/reference_manual/csspec.rst
@@ -19,6 +19,7 @@
 #
 # ==========================================================================
 import sys
+import math
 import gammalib
 import ctools
@@ -241,21 +242,21 @@ class csresmap(ctools.cscript):
         # Calculate significance from Li&Ma derivation
         elif algorithm == 'SIGNIFICANCE':
+
+            # Compute sign map
             signmap = (self._resmap - modelmap).sign()
+
+            # Compute logarithm of map. For that we mask pixels
             logmap  = self._resmap/modelmap
-            # Masking pixels with zero counts. Put a small value >0 for log
-            # calculation and restore the zero value afterwards
-            mask = []
             for i in range(logmap.npix()):
-                # Testing pixel i and map 0 (there is one map only after stacking)
-                if logmap[i,0] == 0:  
-                    mask.append(i)
-                    logmap[i,0] = 1e-10
-            logmap = logmap.log()
-            for i in mask:
-                logmap[i,0] = 0.
+                if logmap[i] > 0.0:
+                    logmap[i] = math.log(logmap[i])
+                else:
+                    logmap[i] = 0.0
+            
+            # Compute significance map
             signif_squared_map  = (self._resmap*logmap) + modelmap  - self._resmap
-            signif_squared_map *= 2.
+            signif_squared_map *= 2.0
             unsigned_resmap     = signif_squared_map.sqrt()
             self._resmap        = unsigned_resmap * signmap
@@ -25,15 +25,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -52,15 +52,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing energy boundaries output file should be overwritten.
@@ -69,15 +69,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output runlist should be overwritten.
@@ -95,4 +95,4 @@ Standard parameters
 Related tools or scripts
 ------------------------
-:doc:`csiactobs`
 \ No newline at end of file
+:doc:`csiactobs`
@@ -49,15 +49,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -75,4 +75,4 @@ Standard parameters
 Related tools or scripts
 ------------------------
-:doc:`csiactdata`
 \ No newline at end of file
+:doc:`csiactdata`
@@ -33,15 +33,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -59,4 +59,4 @@ Standard parameters
 Related tools or scripts
 ------------------------
-:doc:`csfindobs`
 \ No newline at end of file
+:doc:`csfindobs`
@@ -113,15 +113,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -139,4 +139,4 @@ Standard parameters
 Related tools or scripts
 ------------------------
-:doc:`csiactobs`
 \ No newline at end of file
+:doc:`csiactobs`
@@ -114,15 +114,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing light curve output file should be overwritten.
@@ -72,15 +72,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -39,15 +39,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output model file should be overwritten.
@@ -65,4 +65,4 @@ Standard parameters
 Related tools or scripts
 ------------------------
-None
 \ No newline at end of file
+None
@@ -56,15 +56,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output model file should be overwritten.
@@ -49,15 +49,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -89,15 +89,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing Observation Definition XML file should be overwritten.
@@ -59,15 +59,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -57,15 +57,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output model file should be overwritten
@@ -94,15 +94,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing light curve output file should be overwritten.
@@ -110,15 +110,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -16,11 +16,12 @@ be provided so that the script can bin the data internally. The model
 is then convolved with the instrumental response function for that
 binning and used for residual computation. Before residual computation,
 the counts and model cubes are collapsed into maps by summing over all
-energies. Three options exist then for residual computation:
+energies. Four options exist then for residual computation:
 * the subtraction of the model from the counts (SUB)
 * the subtraction and division by the model (SUBDIV)
 * the subtraction and division by the square root of the model (SUBDIVSQRT)
+* the computation of the significance using Li & Ma (SIGNIFICANCE)
 The residual map is written into a FITS file.  
@@ -95,16 +96,16 @@ General parameters
     Cube bin size (in degrees/pixel).
 ``(algorithm = SUBDIV) <SUB|SUBDIV|SUBDIVSQRT|SIGNIF> [string]``
-    Algorithm used to generate the residual map.
+    Algorithm used to generate the residual map:
-    SUB:         DATA - MODEL
+     ``SUB``: :math:`DATA - MODEL`
-    SUBDIV:     (DATA - MODEL)/MODEL
+     ``SUBDIV``: :math:`\frac{DATA - MODEL}{MODEL}`
-    SUBDIVSQRT: (DATA - MODEL)/sqrt(MODEL)
+     ``SUBDIVSQRT``: :math:`\frac{DATA - MODEL}{\sqrt{MODEL}}`
+
+     ``SIGNIFICANCE``: :math:`{\rm sign}(DATA-MODEL) \times \sqrt{ 2 \times ( DATA \times \ln \left(\frac{DATA}{MODEL} \right) + MODEL - DATA ) }`
-    SIGNIF:     sign(DATA-MODEL) * sqrt( 2*( DATA*log(DATA/MODEL) + MODEL - DATA ) )
-     	 	 
 Standard parameters
 -------------------
@@ -114,15 +115,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing residual map file should be overwritten.
@@ -106,15 +106,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -115,15 +115,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing source spectrum output file should be overwritten.
@@ -67,15 +67,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output model file should be overwritten.
@@ -117,15 +117,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -44,15 +44,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output TS map file should be overwritten.
@@ -95,15 +95,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output TS map file should be overwritten.
@@ -63,15 +63,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing visibility cube file should be overwritten.
@@ -83,15 +83,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output counts cube file should be overwritten.
@@ -123,15 +123,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output background cube file should be overwritten.
@@ -107,15 +107,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -74,15 +74,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output counts cube file should be overwritten.
@@ -109,15 +109,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output energy dispersion cube file should be overwritten.
@@ -74,15 +74,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.
@@ -113,15 +113,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output exposure cube file should be overwritten.
@@ -106,15 +106,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output model file should be overwritten.
@@ -79,15 +79,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output counts cube file should be overwritten.
@@ -143,15 +143,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output model cube file should be overwritten.
@@ -114,15 +114,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing files should be overwritten.
@@ -63,15 +63,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -50,15 +50,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -109,15 +109,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output point spread function cube file should be overwritten.
@@ -109,15 +109,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether existing output files should be overwritten.
@@ -86,15 +86,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output sky map file should be overwritten.
@@ -105,15 +105,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output TS map file should be overwritten.
@@ -86,15 +86,15 @@ Standard parameters
 ``(chatter = 2) [integer]``
     Verbosity of the executable:
-     chatter = 0: no information will be logged
+     ``chatter = 0``: no information will be logged
-     chatter = 1: only errors will be logged
+     ``chatter = 1``: only errors will be logged
-     chatter = 2: errors and actions will be logged
+     ``chatter = 2``: errors and actions will be logged
-     chatter = 3: report about the task execution
+     ``chatter = 3``: report about the task execution
-     chatter = 4: detailed report about the task execution
+     ``chatter = 4``: detailed report about the task execution
 ``(clobber = yes) [boolean]``
     Specifies whether an existing output file should be overwritten.