From d61e31007a67c0a537da1e3466eae8b485477309 Mon Sep 17 00:00:00 2001 From: Jürgen Knödlseder Date: Tue, 3 Feb 2015 01:38:35 +0100 Subject: [PATCH] Convert reference manual into RST format (remove old statis html pages). --- doc/source/_templates/index.html | 2 +- doc/source/contents.rst | 1 + doc/source/fhelp/cspull.html | 373 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/cssens.html | 393 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/cstsdist.html | 356 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/ctbin.html | 377 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/ctbutterfly.html | 300 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ doc/source/fhelp/ctlike.html | 233 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/ctmodel.html | 505 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/ctobssim.html | 354 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ doc/source/fhelp/ctools.css | 21 --------------------- doc/source/fhelp/ctselect.html | 314 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- doc/source/fhelp/ctskymap.html | 306 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ doc/source/fhelp/ftools_usage.html | 126 ------------------------------------------------------------------------------------------------------------------------------ doc/source/reference_manual/cspull.rst | 108 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/cssens.rst | 105 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/cstsdist.rst | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctbin.rst | 106 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctbutterfly.rst | 89 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctlike.rst | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctmodel.rst | 136 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctobssim.rst | 105 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctselect.rst | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/ctskymap.rst | 91 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ doc/source/reference_manual/index.rst | 32 ++++++++++++++++++++++++++++++++ doc/source/reference_manual/usage.rst | 42 ++++++++++++++++++++++++++++++++++++++++++ doc/source/tools_reference.rst | 24 ------------------------ 27 files changed, 1087 insertions(+), 3683 deletions(-) delete mode 100644 doc/source/fhelp/cspull.html delete mode 100644 doc/source/fhelp/cssens.html delete mode 100644 doc/source/fhelp/cstsdist.html delete mode 100644 doc/source/fhelp/ctbin.html delete mode 100644 doc/source/fhelp/ctbutterfly.html delete mode 100644 doc/source/fhelp/ctlike.html delete mode 100644 doc/source/fhelp/ctmodel.html delete mode 100644 doc/source/fhelp/ctobssim.html delete mode 100644 doc/source/fhelp/ctools.css delete mode 100644 doc/source/fhelp/ctselect.html delete mode 100644 doc/source/fhelp/ctskymap.html delete mode 100644 doc/source/fhelp/ftools_usage.html create mode 100644 doc/source/reference_manual/cspull.rst create mode 100644 doc/source/reference_manual/cssens.rst create mode 100644 doc/source/reference_manual/cstsdist.rst create mode 100644 doc/source/reference_manual/ctbin.rst create mode 100644 doc/source/reference_manual/ctbutterfly.rst create mode 100644 doc/source/reference_manual/ctlike.rst create mode 100644 doc/source/reference_manual/ctmodel.rst create mode 100644 doc/source/reference_manual/ctobssim.rst create mode 100644 doc/source/reference_manual/ctselect.rst create mode 100644 doc/source/reference_manual/ctskymap.rst create mode 100644 doc/source/reference_manual/index.rst create mode 100644 doc/source/reference_manual/usage.rst delete mode 100644 doc/source/tools_reference.rst diff --git a/doc/source/_templates/index.html b/doc/source/_templates/index.html index b89285d..414c334 100644 --- a/doc/source/_templates/index.html +++ b/doc/source/_templates/index.html @@ -37,7 +37,7 @@ CTA format), Fermi/LAT and COMPTEL data. {%endtrans%}

  • {%trans%}Quickstart{%endtrans%}
  • {%trans%}CTA response functions{%endtrans%}
  • {%trans%}User Manual{%endtrans%}
    • -
  • {%trans%}ctools Reference{%endtrans%}
    • +
  • {%trans%}Reference Manual{%endtrans%}
  • {%trans%}Source code documentation (Doxygen){%endtrans%}
    • diff --git a/doc/source/contents.rst b/doc/source/contents.rst index 4ffb7b9..63f97f2 100644 --- a/doc/source/contents.rst +++ b/doc/source/contents.rst @@ -10,4 +10,5 @@ Documentation :maxdepth: 2 user_manual/index + reference_manual/index develop \ No newline at end of file diff --git a/doc/source/fhelp/cspull.html b/doc/source/fhelp/cspull.html deleted file mode 100644 index a8f9830..0000000 --- a/doc/source/fhelp/cspull.html +++ /dev/null @@ -1,373 +0,0 @@ - - -cspull - - - - - - -

    cspull

    -

    Generates pull distribution for all model -parameters.

    -
    -

    Synopsis

    -

    Generates -pull distributions for all parameters in a model. The pull is defined -by the fitted value minus the simulated true value, devided by the -statistical uncertainty. For unbiased parameter estimates, the pull -distribution should follow a Gaussian centred on 0 and a sigma -parameter of 1.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     srcmdl -[file]
      XML file that describes the -astrophysical sources and the instrumental background.
       
     outfile -[file]
      ASCII file containing the individual -pull values.
       
     ntrials -[integer]
      Number of samples for generating the -pull distribution.
       
     caldb -[string]
      Calibration database repository.
       
     irf -[string]
      Instrumental response function that -should be used for event generation.
       
     ra -[double]
      Right Ascension of CTA pointing -(J2000, in degrees).
       
     dec -[double]
      Declination of CTA pointing (J2000, -in degrees).
       
     rad -[double]
      Radius of CTA field of view -(simulation cone radius) (in degrees).
       
     emin -[double]
      Lower energy limit of events (in -TeV).
       
     emax -[double]
      Upper energy limit of events (in -TeV).
       
     enumbins -[integer]
      Number of energy bins (0=unbinned).
       
     duration -[double]
      Duration of -observation (in seconds).
       
     (deadc -= 0.95) -[double]
      Average deadtime correction factor.
       
     (rad -= 5.0) -[double]
      ROI radius (in degrees).
       
     (npix -= 200) -[integer]
      Number of pixels for binned analysis.
       
     (binsz -= 0.05) -[double]
      Pixel size for binned analysis.
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -event list should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 21 December -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/cssens.html b/doc/source/fhelp/cssens.html deleted file mode 100644 index 653e8b7..0000000 --- a/doc/source/fhelp/cssens.html +++ /dev/null @@ -1,393 +0,0 @@ - - -cssens - - - - - - -

    cssens

    -

    Computes the CTA sensitivity for a number -of energy bins.

    -
    -

    Synopsis

    -

    Computes -the CTA sensitivity for a number of energy bins using ctlike. Crab spectra are fitted -in narrow energy bins to simulated data, and the flux level is -determined that leads to a particular significance.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     outfile -[file]
      ASCII file containing the -sensitivity -values.
       
     caldb -[string]
      Calibration database repository.
       
     irf -[string]
      Instrumental response function that -should be used for event generation.
       
     type -[string]
      Source model type -(point/gauss/shell/disk).
       
     offset -[double]
      Source offset angle (in -degrees).
       
     bkg -[string]
      Background model file function -(none=power law for subarray E).
       
     duration -[double]
      Effective exposure time (in seconds).
       
     rad -[double]
      Radius of ROI (in degrees).
       
     (enumbins = 0) -[integer]
      Number of energy bins (0=unbinned).
       
     (npix = 200) -[integer]
      Number of pixels for binned analysis.
       
     (binsz = 0.05) -[double]
      Pixel size for binned analysis.
       
     (sigma = 5.0) -[double]
      Significance threshold.
       
     (ts_use = yes) -[boolean]
      Use TS for signifiance estimation?
       
     (index = -2.48) -[double]
      Spectral index for source model.
       
     (radius = 0.1) -[double]
      Extended source model radius (in degrees).
       
     (width = 0.05) -[double]
      Extended source model width (in degrees).
       
     (max_iter = 50) -[integer]
      Maximum number of iterations.
       
     (num_avg = 3) -[integer]
      Number of iterations for sliding average.
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -event list should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 21 December -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/cstsdist.html b/doc/source/fhelp/cstsdist.html deleted file mode 100644 index 9a50c5c..0000000 --- a/doc/source/fhelp/cstsdist.html +++ /dev/null @@ -1,356 +0,0 @@ - - -cstsdist - - - - - - -

    cstsdist

    -

    Generates the TS distribution for a -particular model.

    -
    -

    Synopsis

    -

    Generates -the Test Statistics (TS) distribution for a particular model based on -Monte-Carlo simulations.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (outfile -= ts.dat) -[file]
      ASCII file containing the TS -distribution values.
       
     ntrials -[integer]
      Number of Monte Carlo samples.
       
     caldb -[string]
      Calibration database repository.
       
     irf -[string]
      Instrumental response function that -should be used for event generation.
       
     type -[string]
      Source model type -(point/gauss/shell/disk).
       
     (index -= -2.48) -[double]
      Spectral index for source model.
       
     offset -[double]
      Source offset angle (in -degrees).
       
     bkg -[string]
      Background model file function -(none=power law for subarray E).
       
       
     emin -[double]
      Lower energy limit (in TeV).
       
     emax -[double]
      Upper energy limit (in TeV).
       
     enumbins -[integer]
      Number of energy bins (0=unbinned).
       
     duration -[double]
      Effective exposure time (in seconds).
       
     (rad -= 5.0) -[double]
      Radius of ROI (in degrees).
       
     (npix -= 200) -[integer]
      Number of pixels for binned analysis.
       
     (binsz -= 0.05) -[double]
      Pixel size for binned analysis.
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -event list should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 21 December -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctbin.html b/doc/source/fhelp/ctbin.html deleted file mode 100644 index 54a5bbb..0000000 --- a/doc/source/fhelp/ctbin.html +++ /dev/null @@ -1,377 +0,0 @@ - - -ctbin - - - - - - -

    ctbin

    -

    Calculates counts maps for binned maximum -likelihood analysis.

    -
    -

    Synopsis

    -

    This -tool computes the counts cube for use in a binned likelihood analysis. -The maps are data cubes in Right Ascension or Galactic longitude, -Declination or Galactic latitude, and log(energy).

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     evfile -[file]
      Input event list or observation -definition XML file.
       
     outfile -[file]
      Output counts cube file.
       
     (prefix = "cntmap_") -[string]
      Prefix for counts maps (no longer used).
       
     (ebinalg -= LOG) -<FILE|LIN|LOG> [string]
      Algorithm for defining energy bins. -Currently, only LOG is supported.
       
     emin -[double]
      Lower energy value for first energy -bin (in -TeV).
       
     emax -[double]
      Upper energy value for last energy -bin -(in -TeV).
       
     enumbins -[integer]
      Number of energy bins.
       
     (ebinfile -= NONE) -[file]
      Name of the file containing the -energy bin definition (not -yet implemented).
       
     nxpix -[integer]
      Size of the Right Ascension / -Galactic longitude axis (in pixels).
       
     nypix -[integer]
      Size of the Declination / Galactic -latitude axis (in pixels).
       
     binsz -[double]
      Pixel size (in degrees/pixel).
       
     coordsys -= CEL <CEL|GAL> [string]
      Coordinate system (CEL -- celestial, GAL - galactic).
       
     xref -[double]
      Right Ascension / Galactic longitude -of image centre -(J2000, in degrees).
       
     yref -[double]
      Declination / Galactic latitude of -image centre (J2000, -in degrees).
       
     (axisrot -= h) [double]
      Rotation angle of image axes (in -degrees).
       
     proj -= CAR [string]
      Projection method (only AZP,CAR,STG,TAN -are supported so far).
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 1) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -counts map should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 4 April -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctbutterfly.html b/doc/source/fhelp/ctbutterfly.html deleted file mode 100644 index f170cd6..0000000 --- a/doc/source/fhelp/ctbutterfly.html +++ /dev/null @@ -1,300 +0,0 @@ - - -ctbutterfly - - - - - - -

    ctbutterfly

    -

    Butterfly calculation tool.

    -
    -

    Synopsis

    -

    Calculates -the confidence band of a spectral model, taking into account the -covariance matrix of a likelihood fit. -

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     infile -[file]
      XML or fits file that defines the observation
       
     srcmdl -[file]
      Model XML file containing the source and background definitions
       
     srcname - [file]
      Name of model for which butterfly should be computed
       
     caldb - [string]
      Calibration database repository.
       
     irf - [string]
      Instrumental response function that - should be used for event generation.
       
     outfile - [file]
      Output butterfly file name
       
     (matrix = "NONE") - [file]
      Input covariance matrix file (not used)
       
     emin - [double]
      Minimum energy of butterfly (in - TeV).
       
     emax - [double]
      Maximum energy of butterfly (in - TeV).
       
     (ebinalg - = "LOG") <FILE|LIN|LOG> - [string]
      Butterfly binning algorithm
       
     (enumbins - = 100) - [string]
      Number of energy bins of butterfly
       
     (ebinfile - = "NONE") - [string]
      File for energy binning algorithm
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -event list should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Michael -Mayer 30 October -2014 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctlike.html b/doc/source/fhelp/ctlike.html deleted file mode 100644 index 5bc7841..0000000 --- a/doc/source/fhelp/ctlike.html +++ /dev/null @@ -1,233 +0,0 @@ - - -ctlike - - - - - -

    ctlike

    -

    Performs binned and unbinned maximum -likelihood analysis of CTA data.

    -
    -

    Synopsis

    -

    Determines -source model parameters, such as flux, spectral index, source position, -and source extent from a maximum likelihood analysis of CTA data. The -analysis can be done in a binned or an unbinned formulation of the -log-likelihood function. For binned analysis, a counts map producted by -ctbin is required. For -unbinned analysis, an events list processed by ctselect -is required. Based on the input file format, ctlike automatically -selects between binned and unbinned maximum likelihood analysis.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     infile -[file]
      Input event list, counts map or -observation definition XML file.
       
     (stat -= POISSON) [string]
      Fitting statistics (only affects -binned analysis).
       
     (refit -= no) [boolean]
      Performs refitting of solution after -initial fit.
       
     caldb -[string]
      Calibration database.
       
     irf -[string]
      Instrument response function.
       
     srcmdl -[string]
      Source model input XML file.
       
     outmdl -[string]
      Source model result XML file.
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing source -model result file should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    - -
    -
    -

    Last updated by: Jürgen -Knödlseder 3 April -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctmodel.html b/doc/source/fhelp/ctmodel.html deleted file mode 100644 index 0d8412a..0000000 --- a/doc/source/fhelp/ctmodel.html +++ /dev/null @@ -1,505 +0,0 @@ - - -ctmodel - - - - - - -

    ctmodel

    -

    Calculates model counts maps.

    -
    -

    Synopsis

    -

    This -tool computes model counts maps based on an XML model. -The maps are data cubes in Right Ascension or Galactic longitude, -Declination or Galactic latitude, and log(energy).

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     infile -[file]
      Input counts map or observation -definition XML file.
       
     outfile -[file]
      Output model counts map or -observation definition XML file.
       
     (prefix -= "modmap_") -[string]
      Prefix for model counts maps in -observation definition file.
       
     caldb -[string]
      Calibration database.
       
     irf -[string]
      Instrument response function.
       
     srcmdl -[string]
      Source model input XML file.
       
     ra -[double]
      Right Ascension of pointing -(J2000, in degrees).
       
     dec -[double]
      Declination of pointing (J2000, -in degrees).
       
     (deadc -= 0.95) -[double]
      Average deadtime correction factor.
       
     tmin -[double]
      CTA mission elapsed start time (in -seconds).
       
     tmax -[double]
      CTA mission elapsed stop time -(in -seconds).
       
     (ebinalg -= LOG) -<FILE|LIN|LOG> [string]
      Algorithm for defining energy bins. -Currently, only LOG is supported.
       
     emin -[double]
      Lower energy value for first energy -bin (in -TeV).
       
     emax -[double]
      Upper energy value for last energy -bin -(in -TeV).
       
     enumbins -[integer]
      Number of energy bins.
       
     (ebinfile -= NONE) -[file]
      Name of the file containing the -energy bin definition (not -yet implemented).
       
     nxpix -[integer]
      Size of the Right Ascension / -Galactic longitude axis (in pixels).
       
     nypix -[integer]
      Size of the Declination / Galactic -latitude axis (in pixels).
       
     binsz -[double]
      Pixel size (in degrees/pixel).
       
     coordsys -= CEL <CEL|GAL> [string]
      Coordinate system (CEL -- celestial, GAL - galactic).
       
     xref -[double]
      Right Ascension / Galactic longitude -of image centre -(J2000, in degrees).
       
     yref -[double]
      Declination / Galactic latitude of -image centre (J2000, -in degrees).
       
     (axisrot -= h) [double]
      Rotation angle of image axes (in -degrees).
       
     proj -= CAR [string]
      Projection method (only AZP,CAR,STG,TAN -are supported so far).
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 1) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -counts map should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 18 December -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctobssim.html b/doc/source/fhelp/ctobssim.html deleted file mode 100644 index bdbe093..0000000 --- a/doc/source/fhelp/ctobssim.html +++ /dev/null @@ -1,354 +0,0 @@ - - -ctobssim - - - - - - -

    ctobssim

    -

    Observation simulator.

    -
    -

    Synopsis

    -

    Generate -photon events from astrophysical sources and process those photons -according to the specified instrument response functions and generate -instrumental background events.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     infile -[file]
      XML file that describes the -astrophysical sources and the instrumental background.
       
     outfile -[file]
      Output event list or observation definition file.
       
     (prefix -= "sim_") -[string]
      Prefix for event list in -observation definition file.
       
     caldb -[string]
      Calibration database repository.
       
     irf -[string]
      Instrumental response function that -should be used for event generation.
       
     (seed -= 1) [integer]
      Integer seed value to be used for -Monte Carlo simulations.
       
     ra -[double]
      Right Ascension of CTA pointing -(J2000, in degrees).
       
     dec -[double]
      Declination of CTA pointing (J2000, -in degrees).
       
     rad -[double]
      Radius of CTA field of view -(simulation cone radius) (in degrees).
       
     tmin -[double]
      Mission elapsed start time of -observation (in seconds).
       
     tmax -[double]
      Mission elapsed stop time of -observation (in seconds).
       
     emin -[double]
      Lower energy limit of events (in -TeV).
       
     emax -[double]
      Upper energy limit of events (in -TeV).
       
     edisp -[bool]
      Apply energy dispersion?
       
     (deadc -= 0.95) -[double]
      Average deadtime correction factor.
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -event list should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 14 September -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctools.css b/doc/source/fhelp/ctools.css deleted file mode 100644 index 2c636aa..0000000 --- a/doc/source/fhelp/ctools.css +++ /dev/null @@ -1,21 +0,0 @@ -.Body { color: #404040; font-family: 'Arial', 'Arial', 'Arial', sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: 0; line-height: 17px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; opacity: 1.00; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; } .Header { color: #666666; font-family: 'Arial', 'Arial', 'Arial', 'Arial', sans-serif; font-size: 30px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: 0; line-height: 44px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; opacity: 1.00; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; } .Title { color: #404040; font-family: 'Arial', 'Arial', 'Arial', sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: bold; letter-spacing: 0; line-height: 17px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; opacity: 1.00; padding-bottom: 10px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; } .Menu { color: #404040; font-family: 'Arial', 'Arial', 'Arial', sans-serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: bold; letter-spacing: 0; line-height: 17px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; opacity: 1.00; padding-bottom: 10px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; } .Code { border-style: solid; border-width: 0.1em; margin: 1em 0.5em; padding: 0.6em 0.5em 0.5em; font-family: Courier New,Courier,monospace; font-size: smaller; background-color: rgb(255, 255, 204); display: block; } .irafpar { - color: #404040; - font-family: Courier New,Courier,monospace; - font-size: 13px; - font-style: normal; - font-variant: normal; - font-weight: normal; - letter-spacing: 0; - line-height: 17px; - margin-bottom: 0px; - margin-left: 0px; - margin-right: 0px; - margin-top: 0px; - opacity: 1.00; - padding-bottom: 0px; - padding-top: 0px; - text-align: left; - text-decoration: none; - text-indent: 0px; - text-transform: none; -} diff --git a/doc/source/fhelp/ctselect.html b/doc/source/fhelp/ctselect.html deleted file mode 100644 index 2f32fde..0000000 --- a/doc/source/fhelp/ctselect.html +++ /dev/null @@ -1,314 +0,0 @@ - - -ctselect - - - - - - -

    ctselect

    -

    Performs sub-selections of event data -which are needed for unbinned maximum likelihood analysis.

    -
    -

    Synopsis

    -

    Creates -a new FITS file of selected events from an input event list based on -spatial, temporal, and energy cuts. Event selection is mandatory for -unbinned maximum likelihood analysis.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     infile -[file]
      Input event list of observation -definition XML file
       
     outfile -[file]
      Output event list or observation -definition XML file.
       
     (prefix -= "selected_") -[string]
      Prefix for output event lists in -observation definition file.
       
     (usepnt = no) -[boolean]
      Use pointing instead of RA/DEC parameters?
       
     ra -[double]
      Right Ascension of acceptance cone -(or ROI) centre -(J2000, in degrees).
       
     dec -[double]
      Declination of acceptance cone (or -ROI) centre (J2000, -in degrees).
       
     rad -[double]
      Radius of acceptance cone (or -ROI) centre (in degrees).
       
     tmin -[double]
      CTA mission elapsed start time defining -the earliest event (in -seconds).
       
     tmax -[double]
      CTA mission elapsed stop time defining -the latest event (in -seconds).
       
     emin -[double]
      Lower energy limit of events (in -TeV).
       
     emax -[double]
      Upper energy limit of events (in -TeV).
       
     (expr -= "") -[string]
      Additional event selection -expression (cfitsio syntax).
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 2) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -event list should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 18 December -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ctskymap.html b/doc/source/fhelp/ctskymap.html deleted file mode 100644 index 54744cd..0000000 --- a/doc/source/fhelp/ctskymap.html +++ /dev/null @@ -1,306 +0,0 @@ - - -ctskymap - - - - - - -

    ctskymap

    -

    Computes sky map from CTA data.

    -
    -

    Synopsis

    -

    This -tool generates a sky maps from CTA data.

    -
    -

    Links

    - -

    -
    -

    General parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     evfile -[file]
      Input event list or observation -definition XML file.
       
     outfile -[file]
      Output sky map.
       
     emin -[double]
      Minimum energy in map (in -TeV).
       
     emax -[double]
      Maximum energy in map (in -TeV).
       
     nxpix -[integer]
      Size of the Right Ascension / -Galactic longitude axis (in pixels).
       
     nypix -[integer]
      Size of the Declination / Galactic -latitude axis (in pixels).
       
     binsz -[double]
      Pixel size (in degrees/pixel).
       
     coordsys -= CEL <CEL|GAL> [string]
      Coordinate system (CEL -- celestial, GAL - galactic).
       
     xref -[double]
      Right Ascension / Galactic longitude -of image centre -(J2000, in degrees).
       
     yref -[double]
      Declination / Galactic latitude of -image centre (J2000, -in degrees).
       
     (axisrot -= h) [double]
      Rotation angle of image axes (in -degrees).
       
     proj -= CAR [string]
      Projection method (only AZP,CAR,STG,TAN -are supported so far).
       
    -

    Standard parameters

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     (chatter -= 1) [integer]
      Verbosity of the executable:
    -chatter = 0: no information will be -logged
    -chatter = 1: only errors will be logged
    -chatter = 2: errors and actions will be -logged
    -chatter = 3: report about the task -execution
    -chatter = 4: detailed report about the -task execution
       
     (clobber -= yes) [boolean]
      Specifies whether an existing output -counts map should be overwritten.
       
     (debug -= no) [boolean]
      Enables debug mode. In debug mode -the executable will dump any log file output in the console.
       
     (mode -= ql) [string]
      Mode of automatic parameters.
       
    -
    -

    Related FTOOLS

    -
    -
    -

    Last updated by: Jürgen -Knödlseder 18 December -2012 -

    -
    - \ No newline at end of file diff --git a/doc/source/fhelp/ftools_usage.html b/doc/source/fhelp/ftools_usage.html deleted file mode 100644 index 341ede1..0000000 --- a/doc/source/fhelp/ftools_usage.html +++ /dev/null @@ -1,126 +0,0 @@ - - -Basic FTOOL Parameter Usage - - - - - - -

    Basic FTOOL Parameter Usage

    -
    -

    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.
    -
    -

    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.
    -
    -

    Examples:

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     infile -[file]
      Describes an -automatic (queried) file-type parameter with no default value.
       
     irf -= kb_E_50h_v3 <kb_E_50h_v3|kb_H_50h_v3> [string]
      Describes an automatic (quiered) -string-type parameter with two value options.
       
     (plot -= yes) [bool]
      Describes a -hidden bool-type parameter named plot, whose default value is yes -(true).
       
    -

    Note: To set hidden parameters at runtime, -specify them explicitly at the command line; for example:

    -
    -

    gtobssim start_time=900

    -
    -
    -
    -
    -

    Last updated by: Jürgen Knödlseder 8 March -2011 -

    -
    - diff --git a/doc/source/reference_manual/cspull.rst b/doc/source/reference_manual/cspull.rst new file mode 100644 index 0000000..054eda4 --- /dev/null +++ b/doc/source/reference_manual/cspull.rst @@ -0,0 +1,108 @@ +cspull +====== + +Generates pull distribution for all model parameters. + + +Synopsis +-------- + +Generates pull distributions for all parameters in a model. +The pull is defined by the fitted value minus the simulated true value, +devided by the statistical uncertainty. +For unbiased parameter estimates, the pull distribution should follow a +Gaussian centred on 0 and a sigma parameter of 1. + + +Links +----- + + +General parameters +------------------ + +``inmodel [file]`` + XML file that describes the astrophysical sources and the instrumental + background. + +``outfile [file]`` + ASCII file containing the individual pull values. + +``ntrials [integer]`` + Number of samples for generating the pull distribution. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrumental response function. + +``(edisp = no) [boolean]`` + Apply energy dispersion to response computation. + +``ra [double]`` + Right Ascension of CTA pointing (J2000, in degrees). + +``dec [double]`` + Declination of CTA pointing (J2000, in degrees). + +``emin [double]`` + Lower energy limit of events (in TeV). + +``emax [double]`` + Upper energy limit of events (in TeV). + +``enumbins [integer]`` + Number of energy bins (0=unbinned). + +``duration [double]`` + Duration of observation (in seconds). + +``(deadc = 0.95) [double]`` + Average deadtime correction factor. + +``(rad = 5.0) [double]`` + ROI radius (in degrees). + +``(pattern = single) [string]`` + Pattern for pointing simulation (single/four). + +``(offset = 1.5) [double]`` + Observation pattern offset (in degrees). + +``(npix = 200) [integer]`` + Number of pixels for binned analysis. + +``(binsz = 0.05) [double]`` + Pixel size for binned analysis. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/cssens.rst b/doc/source/reference_manual/cssens.rst new file mode 100644 index 0000000..fccce0c --- /dev/null +++ b/doc/source/reference_manual/cssens.rst @@ -0,0 +1,105 @@ +cssens +====== + +Computes the CTA sensitivity for a number of energy bins. + + +Synopsis +-------- + +Computes the CTA sensitivity for a number of energy bins using :doc:`ctlike`. +Crab spectra are fitted in narrow energy bins to simulated data, and the +flux level is determined that leads to a particular significance. + + +Links +----- + + +General parameters +------------------ + +``outfile [file]`` + ASCII file containing the sensitivity values. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrumental response function. + +``type [string]`` + Source model type. + +``offset [double]`` + Source offset angle (in degrees). + +``bkg [string]`` + Background model file function (none=power law for subarray E). + +``duration [double]`` + Effective exposure time (in seconds). + +``rad [double]`` + Radius of ROI (in degrees). + +``(enumbins = 0) [integer]`` + Number of energy bins (0=unbinned). + +``(npix = 200) [integer]`` + Number of pixels for binned analysis. + +``(binsz = 0.05) [double]`` + Pixel size for binned analysis. + +``(sigma = 5.0) [double]`` + Significance threshold. + +``(ts_use = yes) [boolean]`` + Use TS for signifiance estimation? + +``(index = -2.48) [double]`` + Spectral index for source model. + +``(radius = 0.1) [double]`` + Extended source model radius (in degrees). + +``(width = 0.05) [double]`` + Extended source model width (in degrees). + +``(max_iter = 50) [integer]`` + Maximum number of iterations. + +``(num_avg = 3) [integer]`` + Number of iterations for sliding average. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/cstsdist.rst b/doc/source/reference_manual/cstsdist.rst new file mode 100644 index 0000000..03fa4c0 --- /dev/null +++ b/doc/source/reference_manual/cstsdist.rst @@ -0,0 +1,95 @@ +cstsdist +======== + +Generates the TS distribution for a particular model. + + +Synopsis +-------- + +Generates the Test Statistics (TS) distribution for a particular model based on +Monte-Carlo simulations. + + +Links +----- + + +General parameters +------------------ + +``(outfile = ts.dat) [file]`` + ASCII file containing the TS distribution values. + +``ntrials [integer]`` + Number of Monte Carlo samples. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrumental response function. + +``type [string]`` + Source model type. + +``(index = -2.48) [double]`` + Spectral index for source model. + +``offset [double]`` + Source offset angle (in degrees). + +``bkg [string]`` + Background model file function (none=power law for subarray E). + +``emin [double]`` + Lower energy limit (in TeV). + +``emax [double]`` + Upper energy limit (in TeV). + +``enumbins [integer]`` + Number of energy bins (0=unbinned). + +``duration [double]`` + Effective exposure time (in seconds). + +``(rad = 5.0) [double]`` + Radius of ROI (in degrees). + +``(npix = 200) [integer]`` + Number of pixels for binned analysis. + +``(binsz = 0.05) [double]`` + Pixel size for binned analysis. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctbin.rst b/doc/source/reference_manual/ctbin.rst new file mode 100644 index 0000000..e7f5644 --- /dev/null +++ b/doc/source/reference_manual/ctbin.rst @@ -0,0 +1,106 @@ +ctbin +===== + +Generate a counts cube for binned maximum likelihood analysis. + + +Synopsis +-------- + +This tool computes the counts cube for use in a binned maximum likelihood +analysis. +The counts cubes are 3-dimensional data cubes spanned by Right Ascension or +Galactic longitude, Declination or Galactic latitude, and energy. +The energy binning may be either linear, logarithmic, or custom defined. +If an observation definition XML file containing several observations is +provided on input, the tool will stack all data into a single counts cube. + + +Links +----- + + +General parameters +------------------ + +``inobs [file]`` + Input event list or observation definition XML file. + +``outcube [file]`` + Output counts cube file. + +``ebinalg = LOG [string]`` + Algorithm for defining energy bins. + +``emin [double]`` + Lower energy value for first energy bin (in TeV). + +``emax [double]`` + Upper energy value for last energy bin (in TeV). + +``enumbins [integer]`` + Number of energy bins. + +``ebinfile = NONE [file]`` + Name of the file containing the energy bin definition. + +``(usepnt = no) [boolean]`` + Use CTA pointing direction for cube centre instead of xref/yref parameters? + +``nxpix [integer]`` + Size of the Right Ascension / Galactic longitude axis (in pixels). + +``nypix [integer]`` + Size of the Declination / Galactic latitude axis (in pixels). + +``binsz [double]`` + Pixel size (in degrees/pixel). + +``coordsys = CEL [string]`` + Coordinate system (CEL - celestial, GAL - galactic). + +``xref [double]`` + Right Ascension / Galactic longitude of cube centre (J2000, in degrees). + +``yref [double]`` + Declination / Galactic latitude of cube centre (J2000, in degrees). + +``(axisrot = h) [double]`` + Rotation angle of image axes (in degrees). + +``proj = CAR [string]`` + Projection method. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctbin.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctbutterfly.rst b/doc/source/reference_manual/ctbutterfly.rst new file mode 100644 index 0000000..17e0ad5 --- /dev/null +++ b/doc/source/reference_manual/ctbutterfly.rst @@ -0,0 +1,89 @@ +ctbutterfly +=========== + +Computes butterfly. + + +Synopsis +-------- + +Calculates the confidence band of a spectral model, taking into account the +covariance matrix of a likelihood fit. + + +Links +----- + + +General parameters +------------------ + +``inobs [file]`` + Input event list, counts cube or observation definition XML file. + +``inmodel [file]`` + Model XML file containing the source and background definitions. + +``srcname [string]`` + Name of model component for which butterfly should be computed. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrumental response function. + +``outfile [file]`` + Output butterfly ASCII file name. + +``(matrix = "NONE") [file]`` + Input covariance matrix file (not used) + +``(ebinalg = "LOG") [string]`` + Butterfly energy binning algorithm. + +``emin [double]`` + Minimum energy of butterfly (in TeV). + +``emax [double]`` + Maximum energy of butterfly (in TeV). + +``(enumbins = 100) [string]`` + Number of energy bins of butterfly. + +``(ebinfile = "NONE") [string]`` + File for energy binning algorithm. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctskymap.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctlike.rst b/doc/source/reference_manual/ctlike.rst new file mode 100644 index 0000000..71bb648 --- /dev/null +++ b/doc/source/reference_manual/ctlike.rst @@ -0,0 +1,84 @@ +ctlike +====== + +Performs binned and unbinned maximum likelihood analysis of CTA data. + + +Synopsis +-------- + +Determines source model parameters, such as flux, spectral index, source +position, and source extent from a maximum likelihood analysis of CTA data. +The analysis can be done in a binned or an unbinned formulation of the +log-likelihood function. +For binned analysis, a counts cube produced by :doc:`ctbin` is required. +For unbinned analysis, an event list processed by :doc:`ctselect` is required. +Based on the input file format, ctlike automatically selects between binned +and unbinned maximum likelihood analysis. + + +Links +----- + + +General parameters +------------------ + +``inobs [file]`` + Input event list, counts cube or observation definition XML file. + +``(stat = POISSON) [string]`` + Fitting statistics (POISSON or GAUSSIAN; only affects binned analysis). + +``(edisp = no) [boolean]`` + Applies energy dispersion to response computation. + +``(refit = no) [boolean]`` + Performs refitting of solution after initial fit. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrument response function. + +``inmodel [string]`` + Source model input XML file. + +``outmodel [string]`` + Source model result XML file with values and uncertainties updated by + the maximum likelihood fit. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctlike.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctmodel.rst b/doc/source/reference_manual/ctmodel.rst new file mode 100644 index 0000000..e98f92a --- /dev/null +++ b/doc/source/reference_manual/ctmodel.rst @@ -0,0 +1,136 @@ +ctmodel +======= + +Computes model counts cube. + + +Synopsis +-------- + +This tool computes a model counts cube based on an XML model. +The counts cube is a 3-dimensional data cube spanned by Right Ascension or +Galactic longitude, Declination or Galactic latitude, and energy. + + +Links +----- + + +General parameters +------------------ + +``incube [file]`` + Input counts cube. If the parameter is not NONE or blank, the specified + counts cube will be used to define the dimensions of the model cube. + +``outcube [file]`` + Output model counts cube. + +``inmodel [string]`` + Source model XML file. + +``(edisp = no) [boolean]`` + Apply energy dispersion to response computation. + +``inobs [file]`` + Input event list, counts cube or observation definition XML file. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrument response function. + +``ra [double]`` + Right Ascension of pointing (J2000, in degrees). + +``dec [double]`` + Declination of pointing (J2000, in degrees). + +``rad [double]`` + Radius of field of view (in degrees). + +``tmin [double]`` + CTA mission elapsed start time (in seconds). + +``tmax [double]`` + CTA mission elapsed stop time (in seconds). + +``(deadc = 0.95) [double]`` + Average deadtime correction factor. + +``(ebinalg = LOG) [string]`` + Algorithm for defining energy bins. + +``emin [double]`` + Lower energy value for first energy bin (in TeV). + +``emax [double]`` + Upper energy value for last energy bin (in TeV). + +``enumbins [integer]`` + Number of energy bins. + +``(ebinfile = NONE) [file]`` + Name of the file containing the energy bin definition. + +``(usepnt = no) [boolean]`` + Use pointing instead of xref/yref parameters? + +``nxpix [integer]`` + Size of the Right Ascension / Galactic longitude axis (in pixels). + +``nypix [integer]`` + Size of the Declination / Galactic latitude axis (in pixels). + +``binsz [double]`` + Pixel size (in degrees/pixel). + +``coordsys = CEL [string]`` + Coordinate system (CEL - celestial, GAL - galactic). + +``xref [double]`` + Right Ascension / Galactic longitude of image centre (J2000, in degrees). + +``yref [double]`` + Declination / Galactic latitude of image centre (J2000, in degrees). + +``(axisrot = h) [double]`` + Rotation angle of image axes (in degrees). + +``proj = CAR [string]`` + Projection method. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctmodel.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctobssim.rst b/doc/source/reference_manual/ctobssim.rst new file mode 100644 index 0000000..ba06532 --- /dev/null +++ b/doc/source/reference_manual/ctobssim.rst @@ -0,0 +1,105 @@ +ctobssim +======== + +Simulates CTA events. + + +Synopsis +-------- + +Generate photon events from astrophysical sources and process those photons +according to the specified instrument response functions and generate +instrumental background events. + +Links +----- + + +General parameters +------------------ + +``inobs [file]`` + Input event list or observation definition XML file. If provided (i.e. the + parameter is not blank or NONE), the pointing definition and eventually the + response information will be extracted from the input file for event + simulation. + +``inmodel [file]`` + XML file that describes the astrophysical sources and the instrumental + background. + +``outevents [file]`` + Output event list or observation definition XML file. + +``(prefix = sim_events_) [string]`` + Prefix for event list in observation definition XML file. + +``caldb [string]`` + Calibration database. + +``irf [string]`` + Instrumental response function. + +``(seed = 1) [integer]`` + Integer seed value to be used for Monte Carlo simulations. + +``ra [double]`` + Right Ascension of CTA pointing (J2000, in degrees). + +``dec [double]`` + Declination of CTA pointing (J2000, in degrees). + +``rad [double]`` + Radius of CTA field of view (simulation cone radius) (in degrees). + +``tmin [double]`` + Mission elapsed start time of observation (in seconds). + +``tmax [double]`` + Mission elapsed stop time of observation (in seconds). + +``emin [double]`` + Lower energy limit of events (in TeV). + +``emax [double]`` + Upper energy limit of events (in TeV). + +``(edisp = no) [boolean]`` + Apply energy dispersion? + +``(deadc = 0.95) [double]`` + Average deadtime correction factor. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctobssim.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctselect.rst b/doc/source/reference_manual/ctselect.rst new file mode 100644 index 0000000..173dbe6 --- /dev/null +++ b/doc/source/reference_manual/ctselect.rst @@ -0,0 +1,92 @@ +ctselect +======== + +Performs sub-selections of event data. + + +Synopsis +-------- + +Creates a new FITS file of selected events from an input event list based +on spatial, temporal, and energy cuts. + + +Links +----- + + +General parameters +------------------ + +``inobs [file]`` + Input event list or observation definition XML file + +``outobs [file]`` + Output event list or observation definition XML file. + +``(prefix = "selected_") [string]`` + Prefix for output event lists in observation definition file. + +``(usepnt = no) [boolean]`` + Use pointing instead of RA/DEC parameters? + +``ra [double]`` + Right Ascension of acceptance cone (or ROI) centre (J2000, in degrees). + +``dec [double]`` + Declination of acceptance cone (or ROI) centre (J2000, in degrees). + +``rad [double]`` + Radius of acceptance cone (or ROI) centre (in degrees). + +``tmin [double]`` + CTA mission elapsed start time defining the earliest event (in seconds). + +``tmax [double]`` + CTA mission elapsed stop time defining the latest event (in seconds). + +``emin [double]`` + Lower energy limit of events (in TeV). + +``emax [double]`` + Upper energy limit of events (in TeV). + +``(expr = "") [string]`` + Additional event selection expression (cfitsio syntax). + +``(usethres = NONE) [string]`` + Energy threshold type (one of NONE, DEFAULT or USER). + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctlike.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/ctskymap.rst b/doc/source/reference_manual/ctskymap.rst new file mode 100644 index 0000000..15c4cfc --- /dev/null +++ b/doc/source/reference_manual/ctskymap.rst @@ -0,0 +1,91 @@ +ctskymap +======== + +Computes sky map from CTA data. + + +Synopsis +-------- + +This tool generates a sky map from CTA data. + + +Links +----- + + +General parameters +------------------ + +``inobs [file]`` + Input event list or observation definition XML file. + +``outmap [file]`` + Output sky map. + +``emin [double]`` + Minimum energy in map (in TeV). + +``emax [double]`` + Maximum energy in map (in TeV). + +``(usepnt = no) [boolean]`` + Use pointing instead of xref/yref parameters? + +``nxpix [integer]`` + Size of the Right Ascension / Galactic longitude axis (in pixels). + +``nypix [integer]`` + Size of the Declination / Galactic latitude axis (in pixels). + +``binsz [double]`` + Pixel size (in degrees/pixel). + +``coordsys = CEL [string]`` + Coordinate system (CEL - celestial, GAL - galactic). + +``xref [double]`` + Right Ascension / Galactic longitude of image centre (J2000, in degrees). + +``yref [double]`` + Declination / Galactic latitude of image centre (J2000, in degrees). + +``(axisrot = h) [double]`` + Rotation angle of image axes (in degrees). + +``proj = CAR [string]`` + Projection method. + + +Standard parameters +------------------- + +``(chatter = 2) [integer]`` + Verbosity of the executable: + chatter = 0: no information will be logged + + chatter = 1: only errors will be logged + + chatter = 2: errors and actions will be logged + + chatter = 3: report about the task execution + + chatter = 4: detailed report about the task execution + +``(clobber = yes) [boolean]`` + Specifies whether an existing output counts cube should be overwritten. + +``(debug = no) [boolean]`` + Enables debug mode. In debug mode the executable will dump any log file output to the console. + +``(mode = ql) [string]`` + Mode of automatic parameters (default is "ql", i.e. "query and learn"). + +``(logfile = ctskymap.log) [string]`` + Name of log file. + + +Related tools +------------- + +None diff --git a/doc/source/reference_manual/index.rst b/doc/source/reference_manual/index.rst new file mode 100644 index 0000000..766c0f3 --- /dev/null +++ b/doc/source/reference_manual/index.rst @@ -0,0 +1,32 @@ +ctools reference manual +======================= + +General information on ctools usage can be found `here `__. + +Below you find links to the command line reference for the tools and scripts +that are available. + +ctools +------ + +.. toctree:: + :maxdepth: 1 + + ctbin --- Generates counts cube + ctbutterfly --- Compute butterfly + ctlike --- Performs maximum likelihood fitting + ctmodel --- Computes model counts cube + ctobssim --- Simulate CTA observations + ctselect --- Selects event data + ctskymap --- Generate sky map + + +cscripts +-------- + +.. toctree:: + :maxdepth: 1 + + cspull --- Generate pull distribution + cssens --- Computes CTA sensitivity + cstsdist --- Generate TS distribution diff --git a/doc/source/reference_manual/usage.rst b/doc/source/reference_manual/usage.rst new file mode 100644 index 0000000..b82450e --- /dev/null +++ b/doc/source/reference_manual/usage.rst @@ -0,0 +1,42 @@ +Basic ctools parameter usage +============================ + +Automatic parameters +-------------------- + +``par_name [ = value ] 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. + + +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. + + +Examples +-------- + +``infile [file]`` + Describes an automatic (queried) file-type parameter with no default value. + +``irf = kb_E_50h_v3 [string]`` + Describes an automatic (queried) string-type parameter with two value + options. + +``(plot = yes) [boolean]`` + Describes a hidden bool-type parameter named plot, whose default value + is yes (true). + +.. note:: + + To set hidden parameters at runtime, specify them explicitly at + the command line; for example: + + ``gtobssim start_time=900`` diff --git a/doc/source/tools_reference.rst b/doc/source/tools_reference.rst deleted file mode 100644 index 082a6e8..0000000 --- a/doc/source/tools_reference.rst +++ /dev/null @@ -1,24 +0,0 @@ -ctools reference manual -======================= - -General information on FTOOLS usage can be found `here `__. - -Below you can find links to the command line tools help pages that are available in ctools. - -ctools ------- - -* `ctbin `__ --- Calculates counts maps for binned maximum likelihood analysis. -* `ctlike `__ --- Performs binned and unbinned maximum likelihood analysis of CTA data. -* `ctmodel `__ --- Calculates model counts maps. -* `ctobssim `__ --- Observation simulator. -* `ctselect `__ --- Performs sub-selections of event data which are needed for unbinned maximum likelihood analysis. -* `ctskymap `__ --- Computes sky map from CTA data. -* `ctbutterfly `__ --- Computes a butterfly from a spectral model. - -cscripts --------- - -* `cspull `__ --- Generates pull distribution for all model parameters. -* `cssens `__ --- Computes the CTA sensitivity for a number of energy bins. -* `cstsdist `__ --- Generates the TS distribution for a particular model. -- libgit2 0.21.4