.. include:: images.rst


Commands
********

This page lists the commands for performing analyses with cWB. The
commands are implemented as shell scripts (tcsh/bash) and are based on
ROOT macros.


Pre-Production
^^^^^^^^^^^^^^
 
.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Pre-Production

   commands/cwb_mkdir
   commands/cwb_clonedir
   commands/cwb_setpars
   commands/cwb_setppars
   commands/cwb_condor
   commands/cwb_lsf
   commands/cwb_xtalk
   commands/cwb_compile

+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_mkdir <commands/cwb_mkdir.html#cwb-mkdir>`__           |  creates the working directory and subdirectories                                      |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_clonedir <commands/cwb_clonedir.html#cwb-clonedir>`__  |  creates the working directory and subdirectories by copying an existing one           |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_setpars <commands/cwb_setpars.html#cwb-setpars>`__     |  sets the user parameters file (default: config/user_parameters.C)                     |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_setppars <commands/cwb_setppars.html#cwb-setppars>`__  |  sets the user pparamters file (default: config/user_pparameters.C)                    |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_condor <commands/cwb_condor.html#cwb-condor>`__        |  creates and submits the dag and sub condor files                                      |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_lsf <commands/cwb_lsf.html#cwb-lsf>`__                 |  creates and submits job with LSF Job System (implemented in the CNAF cluster)         |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_xtalk <commands/cwb_xtalk.html#cwb-xtalk>`__           |  creates the xtalk catalog (used for the multiresolution analysis)                     |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+
| `cwb_compile <commands/cwb_compile.html#cwb-compile>`__     |  compiles ROOT macros, e.g. the cwb plugins                                            |
+-------------------------------------------------------------+----------------------------------------------------------------------------------------+


Production
^^^^^^^^^^
 
.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Production

   commands/cwb_inet
   commands/cwb_inet2G
   commands/cwb_eced
   commands/cwb_eced2G
   commands/cwb_dump

+------------------------------------------------------+---------------------------------------------------------------------------+
| `cwb_inet <commands/cwb_inet.html#cwb-inet>`__       |  runs the interactive cWB pipeline (both 1G and 2G pipelines available)   |
+------------------------------------------------------+---------------------------------------------------------------------------+
| `cwb_inet2G <commands/cwb_inet2G.html#cwb-inet2g>`__ |  runs the interactive 2G cWB pipeline in the multistage mode              |
+------------------------------------------------------+---------------------------------------------------------------------------+
| `cwb_eced <commands/cwb_eced.html#cwb-eced>`__       |  generates the CED with the 1G cWB pipeline                               |
+------------------------------------------------------+---------------------------------------------------------------------------+
| `cwb_eced2G <commands/cwb_eced2G.html#cwb-eced2g>`__ |  generates the CED with the 2G cWB pipeline                               |
+------------------------------------------------------+---------------------------------------------------------------------------+
| `cwb_dump <commands/cwb_dump.html#cwb-dump>`__       |  dumps the output messages generated by the cWB pipeline                  |
+------------------------------------------------------+---------------------------------------------------------------------------+


Post-Production
^^^^^^^^^^^^^^^
 
.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Post-Production

   commands/cwb_condor_benchmark
   commands/cwb_merge
   commands/cwb_setchunk
   commands/cwb_setifar
   commands/cwb_setcuts
   commands/cwb_setveto
   commands/cwb_report
   commands/cwb_report_cbc
   commands/cwb_mkfad
   commands/cwb_mkprc
   commands/cwb_xgboost

+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_condor benchmark <commands/cwb_condor.html#cwb-condor-benchmark>`__ |  (is a `cwb_condor <commands/cwb_condor.html#cwb-condor>`__ option) draws plots on the computational load |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_merge <commands/cwb_merge.html#cwb-merge>`__                        |  merges the output root files                                                                             |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_setchunk <commands/cwb_setchunk.html#cwb-setchunk>`__               |  adds chunk id leaf to the merged root files                                                              |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_setifar <commands/cwb_setifar.html#cwb-setifar>`__                  |  adds ifar leaf to the merged simulation root files                                                       |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_setcuts <commands/cwb_setcuts.html#cwb-setcuts>`__                  |  applies selection cuts to the TTree leaves contained in the merged root file                             |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_setveto <commands/cwb_setveto.html#cwb-setveto>`__                  |  applies vetoes to merged root files                                                                      |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_report <commands/cwb_report.html#cwb-report>`__                     |  creates analysis reports                                                                                 |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_report_cbc <commands/cwb_report_cbc.html#cwb-report-cbc>`__         |  creates cbc analysis reports                                                                             |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_mkfad <commands/cwb_mkfad.html#cwb-mkfad>`__                        |  calculates the false-alarm rate density statistic                                                        |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_mkprc <commands/cwb_mkprc.html#cwb-mkprc>`__                        |  produces FOM for sky localizations                                                                       |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
| `cwb_xgboost <commands/cwb_xgboost.html#cwb-xgboost>`__                  |  post production using XGBoost                                                                            |
+--------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+


Utility
^^^^^^^

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Utility

   commands/cwb_mplugin
   commands/cwb_mkhtml
   commands/cwb_mkrep
   commands/cwb_draw_sensitivity
   commands/cwb_draw_antpat
   commands/cwb_gwosc

+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_mplugin <commands/cwb_mplugin.html#cwb-mplugin>`__                               |  merges multiple plugins into one                  |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_mkhtml <commands/cwb_mkhtml.html#cwb-mkhtml>`__                                  |  creates html pages from texi files                |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_mkrep <commands/cwb_mkrep.html#cwb-mkrep>`__                                     |  creates customised reports                        |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_draw_sensitivity <commands/cwb_draw_sensitivity.html#cwb-draw-sensitivity>`__    |  draws sensitivity curves                          |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_draw_antpat <commands/cwb_draw_antpat.html#cwb-draw-antpat>`__                   |  draws the network antenna pattern                 |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_gwosc <commands/cwb_gwosc.html#cwb-gwosc>`__                                     |  analysis of GWOSC O2 catalog events               |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| cwb_watenv                                                                            |  print cWB environment variables                   |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_json2dat <commands/cwb_json2dat.html#cwb-json2dat>`__                            |  convert posterior samples from json to dat format |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_petools <commands/cwb_petools.html#cwb-petools>`__                               |  tools for pe analysis                             |
+---------------------------------------------------------------------------------------+----------------------------------------------------+
| `cwb_pereport <commands/cwb_pereport.html#cwb-pereport>`__                            |  report for pe analysis                            |
+---------------------------------------------------------------------------------------+----------------------------------------------------+


Chunk-wise commands
^^^^^^^^^^^^^^^^^^^

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Chunk-wise commands

   commands/cwb_mkchunk
   commands/cwb_clchunk
   commands/cwb_ppchunk
   commands/cwb_lschunk
   commands/cwb_mksdirs
   commands/cwb_obchunk

+----------------------------------------------------------+-------------------------------------+
| `cwb_mkchunk <commands/cwb_mkchunk.html#cwb-mkchunk>`__  |  creates a working directory        |
+----------------------------------------------------------+-------------------------------------+
| `cwb_clchunk <commands/cwb_clchunk.html#cwb-clchunk>`__  |  clones a working directory         |
+----------------------------------------------------------+-------------------------------------+
| `cwb_ppchunk <commands/cwb_ppchunk.html#cwb-ppchunk>`__  |  post-production analysis           |
+----------------------------------------------------------+-------------------------------------+
| `cwb_lschunk <commands/cwb_lschunk.html#cwb-lschunk>`__  |  lists available chunks             |
+----------------------------------------------------------+-------------------------------------+
| `cwb_mksdirs <commands/cwb_mksdirs.html#cwb-mksdirs>`__  |  creates the search directories     |
+----------------------------------------------------------+-------------------------------------+
| `cwb_obchunk <commands/cwb_obchunk.html#cwb-obchunk>`__  |  open-box analysis                  |
+----------------------------------------------------------+-------------------------------------+