Final revision of reference manual

Jürgen Knödlseder
1 parent c65f2ac9
Showing 24 changed files with 117 additions and 80 deletions
doc/source/users/reference_manual/csebins.rst
doc/source/users/reference_manual/csfindobs.rst
doc/source/users/reference_manual/csmodelinfo.rst
doc/source/users/reference_manual/csmodelmerge.rst
doc/source/users/reference_manual/csobsdef.rst
doc/source/users/reference_manual/csphagen.rst
doc/source/users/reference_manual/cstsdist.rst
doc/source/users/reference_manual/ctbkgcube.rst
doc/source/users/reference_manual/ctbutterfly.rst
doc/source/users/reference_manual/ctcubemask.rst
doc/source/users/reference_manual/ctedispcube.rst
doc/source/users/reference_manual/cterror.rst
doc/source/users/reference_manual/ctexpcube.rst
doc/source/users/reference_manual/ctlike.rst
doc/source/users/reference_manual/ctmapcube.rst
doc/source/users/reference_manual/ctmodel.rst
doc/source/users/reference_manual/ctobssim.rst
doc/source/users/reference_manual/ctpsfcube.rst
doc/source/users/reference_manual/ctskymap.rst
doc/source/users/reference_manual/cttsmap.rst
@@ -14,7 +14,7 @@ the variation in the effective area and the background template of the response
 functions. The script takes either an observation definition XML file or a
 specific instrument response function on input.
  
-csebins writes an energy boundary extension into a FITS file.
+:ref:`csebins` writes an energy boundary extension into a FITS file.
  
  
 General parameters
@@ -17,7 +17,9 @@ to further constrain criteria to select observations. The user can e.g. select
 all observations within a certain zenith angle range by specifying the hidden
 parameter expression. For example
  
-``csfindobs expression="ZEN_PNT<50&&ZEN_PNT>40"``
+.. code-block:: bash
+
+   $ csfindobs expression="ZEN_PNT<50&&ZEN_PNT>40"
  
 is used to select observations with zenith angle range between 40 and 50 degrees.
  
@@ -17,9 +17,9 @@ quite useful for debugging a fit. Finally the tool also list the TS values of
 each source that was fitted, in order have a quick overview on these quantities
 on the screen.
  
-In addition the tool is also capable of exporting the input model XML container
+In addition the script is also capable of exporting the input model XML container
 to a region file which is compatible to be read with ds9 or other displying
-tools. To create a region file, the hidden parameter "ds9file" needs to be
+tools. To create a region file, the hidden parameter ``ds9file`` needs to be
 specified. There are quite a few further hidden parameters to steer e.g. color,
 font, etc of the region file output.
  
@@ -20,7 +20,7 @@ a list of files that should be merged:
  
 Note that the "@" needs to be specified in case of an ASCII file name. It is
 also important to note that models with the same name cannot be appended. The
-tool will throw and exception if the provided file contain models with the same
+script will throw and exception if the provided file contain models with the same
 name.
  
  
@@ -9,11 +9,10 @@ Generates an observation definition file.
 Synopsis
 --------
  
-The csobsdef script generates an observation definition file from
-a pointing list. The pointing list is a comma-separated value (CSV)
-ASCII file with header keywords in the first row followed by a list
-of pointings (one pointing per row). The following header keywords
-are supported (case sensitive, column order irrelevant):
+This script generates an observation definition file from a pointing list. The
+pointing list is a comma-separated value (CSV) ASCII file with header keywords
+in the first row followed by a list of pointings (one pointing per row). The
+following header keywords are supported (case sensitive, column order irrelevant):
  
 - name     - Observation name string
 - id       - Unique observation identifier string
@@ -29,10 +28,10 @@ are supported (case sensitive, column order irrelevant):
 - caldb    - Calibration database
 - irf      - Response function name
  
-Only the pairs (ra,dec) or (lon,lat) are mandatory header keywords.
-All other keywords are optional and can be specified when calling
-csobsdef as user parameters. The only exception is the "duration"
-keyword that will automatically be queried.
+Only the pairs (ra,dec) or (lon,lat) are mandatory header keywords. All other
+keywords are optional and can be specified when calling :ref:`csobsdef` as user
+parameters. The only exception is the ``duration`` keyword that will automatically
+be queried.
  
 Here some usage examples:
  
@@ -9,18 +9,50 @@ Creates files necessary to perform a region-based spectral On/Off analysis.
 Synopsis
 --------
  
-This script can be used to derive from an observation or a set of observations
-the count spectra in a source region and in background regions, as well as the
-detector response (effective area, energy redistribution matrix), that can be
-used to perform a classical 1D spectral analysis. Regions can be placed
-automatically or by hand. The output files are saved in the OGIP format normally
-used in X-ray astronomy (PHA, ARF, RMF).
-`See here <https://heasarc.gsfc.nasa.gov/docs/heasarc/ofwg/docs/spectra/ogip_92_007/node5.html>`__.
-
-The outputs are:
-
-1) the PHA, ARF, RMF files, either separately for each observation, or stacked
-   for a set of observations;
+This script generates the files that are necessary for a region-based spectral
+On/Off analysis from one or several event lists. The output files are saved in
+the OGIP format normally used in X-ray astronomy (PHA, ARF, RMF),
+`see here for a description of the format <https://heasarc.gsfc.nasa.gov/docs/heasarc/ofwg/docs/spectra/ogip_92_007/node5.html>`__.
+
+If the ``bkgmethod`` parameter is ``REFLECTED``, the script will use an On region
+shape defined by the ``srcshape`` parameter and generate reflected regions by
+placing regions of the same shape that are reflected with respect to the pointing
+direction. So far only circular regions are supported, with a center that is
+specified by the ``ra`` and ``dec`` parameters if ``coordsys=CEL`` or the ``glon``
+and ``glat`` parameters if ``coordsys=GAL``, and a radius that is specified by the
+``rad`` parameter. Reflected regions are only generated for offset angles with
+respect to the pointing direction that are smaller than the value specified by
+the ``maxoffset`` parameter. If less than ``bkgregmin`` reflected regions can be
+found because the offset angle between source and pointing direction is too small,
+the observation will be skipped. Regions to be excluded for background
+determination can be specified using a mask file that is specified using the
+``inexclusion`` parameter. A mask file is a sky map where all pixel values that
+differ from zero will be used as exclusion region.
+
+Alternatively, if ``bkgmethod=CUSTOM`` is specified, the source and background
+regions will be specified using the ``srcregfile`` and ``bkgregfile`` parameters,
+respectively. Both parameters accept either a ds9 region file or a sky map where
+all non-zero pixel values define a region. In case that an observation definition
+XML file is specified as input using the ``inobs``, background region files can
+be specified separately for each observation using the ``OffRegions`` parameter
+in the format
+
+.. code-block:: xml
+
+   <observation name="Crab" id="00001" instrument="CTA">
+     <parameter name="OffRegions" file="ds9.reg"/>
+     ...
+   </observation>
+
+The :ref:`csphagen` script will produce on output an observation definition XML
+file that points to all relevant files. All relevant files will be prefixed with
+the string specified by the ``prefix`` parameter. If several observations are
+contained in the input observation definition XML file the script can either
+generate region based files for each of the observations or stack all
+observations into single files (controlled via the ``stack`` parameter). The
+script will write out:
+
+1) the PHA, ARF, RMF files;
 2) DS9 regions files listing the source and background regions for each
    observation;
 3) a new observation definition XML file.
@@ -39,8 +71,8 @@ General parameters
     Instrument response function.
  
 ``(inexclusion = NONE) [file]``
-    Optional FITS file containing a WCS map in the first hdu that defines sky
-    regions not to be used for background estimation (where map value != 0).
+    Optional FITS file containing a WCS map in the first extension that defines
+    sky regions not to be used for background estimation (where map value != 0).
  
 ``outobs [string]``
     Output observation definition XML file.
@@ -72,10 +104,11 @@ General parameters
     You may use :ref:`csebins` to generate a file with appropriate energy binning.
  
 ``(srcshape = CIRCLE) <CIRCLE> [string]``
-    Shape of the source region (``CIRCLE``: circular region around given position).
+    Shape of the source region. So far only ``CIRCLE`` exists which defines a
+    circular region around given position.
  
 ``coordsys <CEL|GAL> [string]``
-    Coordinate system (``CEL``: celestial; ``GAL``: galactic).
+    Coordinate system (CEL - celestial, GAL - galactic).
  
 ``ra [real]``
     Right Ascension of source region centre (deg).
@@ -15,7 +15,7 @@ sets. The Test Statistics is defined as twice the log-likelihood difference
 that is obtained when fitting simulated data with and without a given
 source model component.
  
-cstsdist will create an ASCII file in comma-separated value (CSV) format,
+:red:`cstsdist` will create an ASCII file in comma-separated value (CSV) format,
 containing one row per TS computation. The first row is a header row providing
 the column names. The following rows give the TS value, the log-likelihood 
 values of the fit with or without the source, the number of observed and 
@@ -16,7 +16,7 @@ The energy binning may be either linear, logarithmic, or custom defined using
 an input file. The input model is used to predict the expected number of
 background counts in each background cube bin.
  
-ctbkgcube requires on input the event list or observation definition file 
+:ref:`ctbkgcube` requires on input the event list or observation definition file
 that has been used in the generation of the counts cube using :doc:`ctbin`.
  
 To assure consistency between an existing counts cube and the 
@@ -29,12 +29,12 @@ Note that there should at least be 25 bins per energy decade in the background
 cube to assure that the energy dependence of the background rate is sufficiently
 well sampled (in particular at low energies).
  
-ctbkgcube generates a background cube FITS file comprising two extensions.
+:ref:`ctbkgcube` generates a background cube FITS file comprising two extensions.
 The primary extension contains a 3-dimensional image that contains the 
 background cube values. The next extension named ``ENERGIES`` contains a
 binary table that defines the energies of the background cube.
  
-ctbkgcube generates also an output model XML file that can serve as input 
+:ref:`ctbkgcube` generates also an output model XML file that can serve as input 
 for a maximum likelihood analysis. The output model XML file is a copy of
 the input model XML file where the input background model has been replaced
 by a background model of type ``CTACubeBackground``. The ``CTACubeBackground``
@@ -23,11 +23,11 @@ law models that fall within the error ellipse of the prefactor and index
 parameters. The error ellipse is derived from the covariance matrix of a
 maximum likelihood fit.
  
-ctbutterfly assumes that the input model (parameter ``inmodel``) has been 
+:ref:`ctbutterfly` assumes that the input model (parameter ``inmodel``) has been
 adjusted using :doc:`ctlike` to the data, but if this is not the case you 
 can request a maximum likelihood fit by setting the hidden parameter ``fit=yes``.
  
-ctbutterfly writes the butterfly diagram into an ASCII file with 4 columns 
+:ref:`ctbutterfly` writes the butterfly diagram into an ASCII file with 4 columns 
 separated by a whitespace. Each row in the result file corresponds to a specific
 energy. The meaning of the columns are:
  
@@ -13,7 +13,7 @@ This tool masks out specific regions from a counts cube by setting the
 corresponding bin values to -1. Bins with negative values will be ignored
 in a maximum likelihood analysis. A mask is applied spatially and spectrally.
  
-ctcubemask applies a spatial mask that is comprised of a circular selection
+:ref:`ctcubemask` applies a spatial mask that is comprised of a circular selection
 region and a list of circular exclusion regions. The circular selection region
 is specified by the sky direction of the centre and the radius of the circle.
 The circular exclusion regions are specified by an ASCII file in ds9 format.
@@ -24,10 +24,10 @@ The ASCII file contains one row per exclusion region, given in the format
 where ``83.63`` and ``21.5`` are the Right Ascension and Declination of 
 the centre and ``0.4`` is the radius (in degrees) of the exclusion circle.
  
-ctcubemask also selects only counts cube energy layers that are fully comprised
+:ref:`ctcubemask` also selects only counts cube energy layers that are fully comprised
 in the energy interval specified by the ``emin`` and ``emax`` parameters.
  
-ctcubemask generates a counts cube FITS file that is a copy of the input 
+:ref:`ctcubemask` generates a counts cube FITS file that is a copy of the input 
 counts cube and for which all masked bins have been set to -1.
  
  
@@ -16,7 +16,7 @@ which is the ratio between reconstructed and true photon energy. The energy
 binning of the cube may be either linear, logarithmic, or custom defined
 using an input file
  
-ctedispcube requires on input the event list or observation definition XML
+:ref:`ctedispcube` requires on input the event list or observation definition XML
 file that has been used in the generation of the counts cube using :doc:`ctbin`.
  
 It is not recommended to use the counts cube for the energy dispersion 
@@ -28,7 +28,7 @@ only little over the field of view of the camera it is recommended to use a
 rather coarse spatial binning to keep the file size manageable (with a typical
 value of ``binsz=1.0``).
  
-ctedispcube generates an energy dispersion cube FITS file comprising three
+:ref:`ctedispcube` generates an energy dispersion cube FITS file comprising three
 extensions. The primary extension contains a 4-dimensional image that contains
 the energy disperison values. The next extension named ``ENERGIES`` contains
 a binary table that defines the energies of the energy dispersion cube. The
@@ -16,7 +16,7 @@ of the likelihood that corresponds to a given confidence level. By default a
 confidence level of 68% is used, but this level can be adjusted using the hidden
 ``confidence`` parameter.
  
-cterror generates an output model XML file that contains the values of the 
+:ref:`cterror` generates an output model XML file that contains the values of the
 best fitting model parameters. For all free parameters, an ``error`` attribute
 is added that provides the statistical uncertainty in the parameter estimate
 as obtained from the likelihood profile. While cterror computes asymmetrical
@@ -15,7 +15,7 @@ Declination or Galactic latitude, and energy, that gives the exposure
 as function of true sky direction and energy. The energy binning of the cube 
 may be either linear, logarithmic, or custom defined using an input file.
  
-ctexpcube requires on input the event list or observation definition file 
+:ref:`ctexpcube` requires on input the event list or observation definition file
 that has been used in the generation of the counts cube using :doc:`ctbin`.
  
 The binning of an exposure cube does not need to correspond to the binning
@@ -36,7 +36,7 @@ Note that there should at least be 25 bins per energy decade in the exposure
 cube to assure that the energy dependence of the exposure is sufficiently
 well sampled (in particular at low energies).
  
-ctexpcube generates an exposure cube FITS file comprising three extensions.
+:ref:`ctexpcube` generates an exposure cube FITS file comprising three extensions.
 The primary extension contains a 3-dimensional image that contains the 
 exposure values. The next extension named ``ENERGIES`` contains a binary table
 that defines the energies of the exposure cube. The last extension named ``GTI``
@@ -17,12 +17,12 @@ The tool can mix the analysis of unbinned and binned data, and is also able
 to perform a joint maximum likelihood analysis of data collected in 
 separate observations or with different instruments.
  
-ctlike will automatically switch between unbinned, binned and joint analysis
+:ref:`ctlike` will automatically switch between unbinned, binned and joint analysis
 on basis of the file provided on input (parameter ``inobs``). Providing an 
 event list will lead to an unbinned analysis while providing a counts cube 
 will lead to a binned analysis. If several observations have been stacked
 into a single counts cube, an exposure cube, a point spread function cube and
-a background cube need also to be provided. ctlike will automatically prompt
+a background cube need also to be provided. :ref:`ctlike` will automatically prompt
 for these parameters in case that a counts cube is given. Answering ``NONE``
 will ignore the exposure cube, point spread function cube and background cube
 and handle the data as a single observation using the specified instrument
@@ -33,19 +33,19 @@ can be handled by specifying an observation definition file on input. Each of
 the observations will be kept separately and  associated with its appropriate
 instrument response functions, as opposed to a stacked analysis where average
 response functions, computed using :doc:`ctexpcube`, :doc:`ctpsfcube` and :doc:`ctbkgcube`,
-are used. If an observation definition file is provided, ctlike will use the
+are used. If an observation definition file is provided, :ref:`ctlike` will use the
 joint likelihood of all the observations for parameter optimisation.
  
-By default, ctlike will use the Poisson statistics for likelihood computation,
+By default, :ref:`ctlike` will use the Poisson statistics for likelihood computation,
 but for binned analysis also Gaussian statistics can be specified (parameter
 ``stat``). Optionally, a refit can be requested after an initial fit (parameter
 ``refit``), but normally this is not needed. For all model components that
-have the ``tscalc="1"`` attribute set, ctlike will also compute the Test
+have the ``tscalc="1"`` attribute set, :ref:`ctlike` will also compute the Test
 Statistics value that is a measure of the source significance. Optionally,
 the spatial model parameters can be kept fixed during that computation
 (parameter ``fix_spat_for_ts``).
  
-ctlike generates an output model XML file that contains the values of the 
+:ref:`ctlike` generates an output model XML file that contains the values of the
 best fitting model parameters. For all free parameters, an ``error`` attribute
 is added that provides the statistical uncertainty in the parameter estimate.
 If computation of the Test Statistics has been requested for a model component,
@@ -16,7 +16,7 @@ map corresponds to a specific photon energy. The energy binning of the map
 cube may be either linear, logarithmic, or custom defined using an input
 file.
  
-ctmapcube generates a map cube FITS file comprising two extensions. The
+:ref:`ctmapcube` generates a map cube FITS file comprising two extensions. The
 primary extension contains a 3-dimensional image containing the map cube
 values. A second extension named ``ENERGIES`` contains a binary table that
 defines the energy values of each map in the cube.
@@ -15,10 +15,10 @@ function of Right Ascension or Galactic longitude, Declination or Galactic
 latitude, and energy. The energy binning may be either linear, logarithmic,
 or custom defined using an input file.
  
-ctmodel requires on input either a counts cube, an event list or an observation
+:ref:`ctmodel` requires on input either a counts cube, an event list or an observation
 definition file.
  
-If a counts cube is provided, ctmodel will use the definition of this cube
+If a counts cube is provided, :ref:`ctmodel` will use the definition of this cube
 (such as sky coordinates and projection, number of pixels, pixel scale,
 energy binning) to compute a model cube. In case that the counts cube combines
 multiple observations (i.e. for a so-called "stacked cube"), an exposure cube,
@@ -26,17 +26,17 @@ a point spread function cube and a background cube have to be provided
 (otherwise you may just enter ``NONE`` when the names of these files are
 queried).
  
-If an event list is provided, ctmodel will query for a counts cube to 
+If an event list is provided, :ref:`ctmodel` will query for a counts cube to
 extract the model cube definition (parameter ``incube``). If no counts cube
-is  provided (``incube=NONE``), ctmodel tools will query for cube definition
+is  provided (``incube=NONE``), :ref:`ctmodel` will query for cube definition
 parameters.
  
-If an observation definition file is provided, ctmodel will query for a counts
+If an observation definition file is provided, :ref:`ctmodel` will query for a counts
 cube to extract the model cube definition, unless the observation definition
 file contains a single binned observation (in that case, the counts cube of
 that observation will be used to extract the model cube definition).
  
-ctmodel generates a model cube FITS file comprising three extensions. The
+:ref:`ctmodel` generates a model cube FITS file comprising three extensions. The
 primary extension contains a 3-dimensional image that contains the model 
 cube values. The next extension named ``EBOUNDS`` contains a binary table
 that defines the energy boundaries of the background cube. The last extension
@@ -21,14 +21,14 @@ a numerical random number generator for the simulations with a seed value
 provided by the hidden ``seed`` parameter. Changing this parameter for
 subsequent runs will lead to different event samples.
  
-ctobssim performs a safety check on the maximum photon rate for all model 
+:ref:`ctobssim` performs a safety check on the maximum photon rate for all model
 components to avoid that the tool locks up and requests huge memory 
 resources, which may happen if a mistake was made in setting up the input 
 model (for example if an error in the flux units is made). The maximum allowed
 photon rate is controlled by the hidden ``maxrate`` parameter, which by default 
 is set to 1e6.
  
-ctobssim can also generate multiple event lists if an observation definition 
+:ref:`ctobssim` can also generate multiple event lists if an observation definition 
 file is specified on input using the hidden ``inobs`` parameter. In that 
 case, simulation information will be gathered from the file, and for each 
 observation an event list will be created.
@@ -16,7 +16,7 @@ and offset angle between true and measured arrival direction of a photon.
 The energy binning of the cube may be either linear, logarithmic, or custom
 defined using an input file.
  
-ctpsfcube requires on input the event list or observation definition XML
+:ref:`ctpsfcube` requires on input the event list or observation definition XML
 file that has been used in the generation of the counts cube using :doc:`ctbin`.
  
 It is not recommended to use the counts cube for the point spread function 
@@ -28,7 +28,7 @@ function varies only slowly over the field of view of the camera it is
 recommended to use a rather coarse spatial binning to keep the file size 
 manageable (with a typical value of ``binsz=1.0``).
  
-ctpsfcube generates a point spread function cube FITS file comprising three
+:ref:`ctpsfcube` generates a point spread function cube FITS file comprising three
 extensions. The primary extension contains a 4-dimensional image that contains
 the point spread function values. The next extension named ``ENERGIES`` contains
 a binary table that defines the energies of the point spread function cube.
@@ -20,7 +20,7 @@ parameter. By default, no background model is subtracted (method ``NONE``).
 If ``IRF`` is selected, the background template that are shipped with the
 Instrument Response Functions will be used for background subtraction.
  
-ctskymap generates a FITS file comprising a sky map as primary extension.
+:ref:`ctskymap` generates a FITS file comprising a sky map as primary extension.
 If a background subtraction method was selected, the FITS file will contain
 the additional extensions ``BACKGROUND`` and ``SIGNIFICANCE`` that contain
 the background map and a significance map, respectively. For the latter, the
@@ -19,7 +19,7 @@ that excludes the specified source. The square-root of the TS values
 corresponds roughly to the pre-trial detection significance of the source (in
 Gaussian sigma).
  
-cttsmap generates a FITS file comprising a sky map of TS values followed by 
+:ref:`cttsmap` generates a FITS file comprising a sky map of TS values followed by
 one extension per free parameter that contains sky maps of the fitted 
 parameter values. To save computation time, the errors are not computed by
 default. Specifying the hidden parameter ``errors=yes`` will switch on the
@@ -16,7 +16,7 @@ to a decrease of the likelihood that corresponds to a given confidence level.
 By default a confidence level of 95% is used, but this level can be adjusted
 using the hidden ``confidence`` parameter.
  
-ctulimit writes the differential upper flux limit at a given reference 
+:ref:`ctulimit` writes the differential upper flux limit at a given reference
 energy (specified by the hidden parameter ``eref``) and the integrated 
 upper flux limit (specified by the hidden parameters ``emin`` and ``emax``)
 into the log file.
 .. _sec_usage:
  
-Description of ctools parameters in the :ref:`reference`
-========================================================
+ctools parameter interface
+==========================
  
 For a generic introduction to ctools and user parameters see
 `here <../user_manual/introduction.html>`__.
@@ -9,29 +9,27 @@ For a generic introduction to ctools and user parameters see
 Automatic parameters
 --------------------
  
-``par_name [ = value ] <valid values> type``
-    Where par_name is the name of the parameter, value is the default value,
-    valid values are valid parameter values, separated by | characters, and
-    type is the type of the parameter.
-    The type is enclosed in square brackets.
+``par_name <first valid value|second valid value|...> [type]``
+    Where ``par_name`` is the name of the parameter, ``first valid value`` and
+    ``second valid value`` are valid parameter values, separated by ``|`` characters,
+    and ``type`` is the type of the parameter.
  
  
 Hidden parameters
 -----------------
  
-``(par_name = value) type``
-    Where par_name is the name of the parameter, value is the default value,
-    and type is the type of the parameter.
-    The type is enclosed in square brackets.
+``(par_name = value) [type]``
+    Where ``par_name`` is the name of the parameter, ``value`` is the default value,
+    and ``type`` is the type of the parameter.
  
  
 Examples
 --------
  
 ``infile [file]``
-    Describes an automatic (queried) file-type parameter with no default value.
+    Describes an automatic (queried) file-type parameter.
  
-``irf = South_50h <North_50h|South_50h> [string]``
+``irf <North_50h|South_50h> [string]``
     Describes an automatic (queried) string-type parameter with two value
     options.
  
 #############################################################################
 # Makefile.am for ctools module                                             #
 # ------------------------------------------------------------------------- #
-# Copyright (C) 2016-2017 Juergen Knoedlseder                               #
+# Copyright (C) 2016-2018 Juergen Knoedlseder                               #
 # ------------------------------------------------------------------------- #
 #                                                                           #
 #  This program is free software: you can redistribute it and/or modify     #
@@ -101,6 +101,8 @@ help-install:
         $(INSTALL_DATA) "$$file" $(DESTDIR)$(datadir)/help/"$$helpname" ; \
         sed -i.bak -e 's/``//g' -e 's/`//g' -e 's/:ref://g' -e 's/:doc://g' \
             -e 's/.. note::/Note/g' -e 's/.. warning::/Warning/g' -e '1d' \
+            -e 's/.. code-block:: bash//g' -e 's/.. code-block:: xml//g' \
+            -e 's/>__/>/g' -e 's/>_/>/g' \
             $(DESTDIR)$(datadir)/help/"$$helpname" ; \
         rm -rf $(DESTDIR)$(datadir)/help/"$$helpname".bak ; \
     done
@@ -72,7 +72,8 @@ class Test(test):
                       ' inmodel="'+self._model+'"'+ \
                       ' caldb="'+self._caldb+'" irf="'+self._irf+'"'+ \
                       ' rad=5.0 ra=83.63 dec=22.01 tmin=0.0 tmax=1800'+ \
-                      ' emin=0.1 emax=100.0 enumbins=10 nxpix=40 nypix=40'+ \
+                      ' emin=0.1 emax=100.0 enumbins=10  ebinalg="LOG"'+ \
+                      ' nxpix=40 nypix=40'+ \
                       ' binsz=0.1 coordsys="CEL" proj="CAR"'+ \
                       ' xref=83.63 yref=22.01'+ \
                       ' logfile="ctmodel_cmd1.log" chatter=1'
@@ -91,7 +92,8 @@ class Test(test):
                       ' inmodel="model_that_does_not_exist.xml"'+ \
                       ' caldb="'+self._caldb+'" irf="'+self._irf+'"'+ \
                       ' rad=5.0 ra=83.63 dec=22.01 tmin=0.0 tmax=1800'+ \
-                      ' emin=0.1 emax=100.0 enumbins=10 nxpix=40 nypix=40'+ \
+                      ' emin=0.1 emax=100.0 enumbins=10  ebinalg="LOG"'+ \
+                      ' nxpix=40 nypix=40'+ \
                       ' binsz=0.1 coordsys="CEL" proj="CAR"'+ \
                       ' xref=83.63 yref=22.01'+ \
                       ' logfile="ctmodel_cmd2.log" debug=yes chatter=1'
@@ -142,6 +144,7 @@ class Test(test):
         model['dec']      = 22.01
         model['tmin']     = 0
         model['tmax']     = 1800
+        model['ebinalg']  = 'LOG'
         model['emin']     = 0.1
         model['emax']     = 100.0
         model['enumbins'] = 10