Pierrick Martin / ctools

Commit 7c7ef2af93bf050e419fd2aa80c11bed4f09ebcd

Authored by Jürgen Knödlseder
1 parent d7c71736

Update cscripts reference manual

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Showing 58 changed files with 895 additions and 842 deletions
cscripts/cslightcrv.par
  View file @7c7ef2a
... ... @@ -16,14 +16,14 @@
16 16 #
17 17 # Input and output parameters
18 18 #============================
19   -inobs, f, a, events.fits,,, "Input event list or observation definition XML file"
20   -inmodel, f, a, $CTOOLS/share/models/crab.xml,,, "Input model definition XML file"
21   -srcname, s, a, Crab,,, "Source name"
22   -caldb, s, a, prod2,,, "Calibration database"
23   -irf, s, a, South_0.5h,,, "Instrument response function"
24   -inexclusion, f, h, NONE,,, "Sky map of exclusion regions for On/Off analysis"
25   -edisp, b, h, no,,, "Apply energy dispersion in Cube analysis?"
26   -outfile, f, a, lightcurve.fits,,, "Output light curve file"
  19 +inobs, f, a, events.fits,,, "Input event list or observation definition XML file"
  20 +inmodel, f, a, $CTOOLS/share/models/crab.xml,,, "Input model definition XML file"
  21 +srcname, s, a, Crab,,, "Source name"
  22 +caldb, s, a, prod2,,, "Calibration database"
  23 +irf, s, a, South_0.5h,,, "Instrument response function"
  24 +inexclusion, f, h, NONE,,, "Sky map of exclusion regions for On/Off analysis"
  25 +edisp, b, h, no,,, "Apply energy dispersion in Cube analysis?"
  26 +outfile, f, a, lightcurve.fits,,, "Output light curve file"
27 27  
28 28 #
29 29 # Script parameters
... ...
cscripts/cslightcrv.py
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... ... @@ -107,7 +107,6 @@ class cslightcrv(ctools.csobservation):
107 107 # Set On/Off analysis flag and query relevant user parameters
108 108 self._onoff = self._is_onoff()
109 109  
110   - # If cube analysis is selected
111 110 # Set stacked analysis flag and query relevant user parameters
112 111 if not self._onoff:
113 112 self._stacked = self._is_stacked()
... ...
cscripts/csresspec.par
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... ... @@ -32,13 +32,13 @@ outfile, f, a, resspec.fits,,, "Output residual spectrum file"
32 32 # Script parameters
33 33 #==================
34 34 statistic, s, h, DEFAULT,DEFAULT|CSTAT|WSTAT|CHI2,, "Optimization statistic"
35   -components,b, h, no,,, "Calculate model for individual components"
36   -ebinalg, s, h, LOG,LIN|LOG|FILE,, "Binning algorithm"
  35 +components,b, h, no,,, "Calculate model for individual components?"
  36 +ebinalg, s, a, LOG,FILE|LIN|LOG,, "Algorithm for defining energy bins"
37 37 emin, r, a, 0.1,,, "Lower energy limit (TeV)"
38 38 emax, r, a, 100.0,,, "Upper energy limit (TeV)"
39 39 enumbins, i, a, 20,,, "Number of model cube energy bins"
40 40 ebinfile, f, a, NONE,,, "Name of the file containing the energy bin definition"
41   -stack, b, a, no,,, "Stack observations"
  41 +stack, b, a, no,,, "Stack observations?"
42 42 coordsys, s, a, CEL,CEL|GAL,, "Coordinate System"
43 43 proj, s, a, CAR,AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN,, "Projection method"
44 44 xref, r, a, 83.63,0,360, "First coordinate of image/source region center in degrees (RA or galactic l)"
... ... @@ -46,11 +46,11 @@ yref, r, a, 22.01,-90,90, "Second coordinate of image/source region center
46 46 nxpix, i, a, 200,,, "Size of the X axis in pixels"
47 47 nypix, i, a, 200,,, "Size of the Y axis in pixels"
48 48 binsz, r, a, 0.02,,, "Pixel size (deg/pixel)"
49   -mask, b, a, no,,, "Mask data to calculate residuals in ROI"
  49 +mask, b, a, no,,, "Mask data to calculate residuals in ROI?"
50 50 ra, r, a, 83.63,0,360, "RA for ROI centre (degrees)"
51 51 dec, r, a, 22.01,-90,90, "Dec for ROI centre (degrees)"
52 52 rad, r, a, 3.0,0,180, "Radius of ROI (degrees)"
53   -regfile, f, a, "NONE",,, "Input exclusion region file in ds9 format"
  53 +regfile, f, a, NONE,,, "Input exclusion region file in ds9 format"
54 54 algorithm, s, a, SIGNIFICANCE,SUB|SUBDIV|SUBDIVSQRT|SIGNIFICANCE,, "Residuals computation algorithm"
55 55  
56 56 #
... ...
cscripts/csroot2caldb.par
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... ... @@ -27,9 +27,9 @@ azimuth, r, a, 0.0,0.0,360.0, "Azimuth Angle (deg)"
27 27 emin, r, h, UNDEF,,, "Minimum energy threshold (TeV)"
28 28 emax, r, h, UNDEF,,, "Maximum energy threshold (TeV)"
29 29 psftype, s, h, Gauss,Gauss|King,, "Point spread function type"
30   -split, b, h, no,,, "Split IRF components into different files"
31   -norm1d, b, h, no,,, "Normalize on 1D histograms"
32   -rebin, b, h, no,,, "Rebin"
  30 +split, b, h, no,,, "Split IRF components into different files?"
  31 +norm1d, b, h, no,,, "Normalize on 1D histograms?"
  32 +rebin, b, h, no,,, "Rebin?"
33 33 eascale, r, h, 1.0,,, "Scaling factor for effective areas"
34 34 bgdscale, r, h, 1.0,,, "Scaling factor for background rates"
35 35 bgdoversample, i, h, 1,,, "Spatial oversampling factor for background template"
... ...
cscripts/cstsmapsplit.par
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... ... @@ -27,7 +27,7 @@ caldb, s, a, prod2,,, "Calibration database"
27 27 irf, s, a, South_0.5h,,, "Instrument response function"
28 28 edisp, b, h, no,,, "Apply energy dispersion?"
29 29 errors, b, h, no,,, "Compute/store parameter errors?"
30   -statistic, s, h, CSTAT,CSTAT|WSTAT|CHI2,, "Optimization statistic"
  30 +statistic, s, h, DEFAULT,DEFAULT|CSTAT|WSTAT|CHI2,, "Optimization statistic"
31 31 outmap, f, a, tsmap.fits,,, "Output Test Statistic map file"
32 32 bins_per_job, i, a, 5,,, "Number of TS map bins per task"
33 33 compute_null, b, a, yes,,,"Compute null hypothesis first?"
... ...
doc/source/admin/release_history/1.5.rst
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... ... @@ -88,4 +88,4 @@ Clean up
88 88 :ref:`csspec` and :ref:`cstsdist` scripts from ``cslikelihood`` base
89 89 class
90 90 * [`1567 <https://cta-redmine.irap.omp.eu/issues/1567>`_] -
91   - Revise :ref:`cstsdist parameters`
  91 + Revise :ref:`cstsdist` parameters
... ...
doc/source/users/reference_manual/cscaldb.rst
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... ... @@ -3,22 +3,22 @@
3 3 cscaldb
4 4 =======
5 5  
6   -Dumps all available instrument response functions into log file.
  6 +Logs all available instrument response functions into log file.
7 7  
8 8  
9 9 Synopsis
10 10 --------
11 11  
12   -This scripts dumps all instrument response functions that are available
  12 +This scripts logs all instrument response functions that are available
13 13 in the calibration database into the log file. If you want the information
14   -on the screen, add the ``debug=yes`` parameter.
  14 +on the screen, specify ``debug=yes``.
15 15  
16 16  
17 17 General parameters
18 18 ------------------
19 19  
20 20 None
21   -
  21 +
22 22  
23 23 Standard parameters
24 24 -------------------
... ... @@ -26,23 +26,23 @@ Standard parameters
26 26 ``(chatter = 2) [integer]``
27 27 Verbosity of the executable:
28 28 ``chatter = 0``: no information will be logged
29   -
  29 +
30 30 ``chatter = 1``: only errors will be logged
31   -
  31 +
32 32 ``chatter = 2``: errors and actions will be logged
33   -
  33 +
34 34 ``chatter = 3``: report about the task execution
35   -
  35 +
36 36 ``chatter = 4``: detailed report about the task execution
37   -
  37 +
38 38 ``(clobber = yes) [boolean]``
39 39 Specifies whether an existing output file should be overwritten.
40   -
  40 +
41 41 ``(debug = no) [boolean]``
42 42 Enables debug mode. In debug mode the executable will dump any log file output to the console.
43   -
  43 +
44 44 ``(mode = ql) [string]``
45   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  45 + Mode of automatic parameters (default is `ql``, i.e. "query and learn").
46 46  
47 47  
48 48 Related tools of scripts
... ...
doc/source/users/reference_manual/csebins.rst
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... ... @@ -25,7 +25,7 @@ General parameters
25 25  
26 26 ``caldb [string]``
27 27 Calibration database.
28   -
  28 +
29 29 ``irf [string]``
30 30 Instrumental response function.
31 31  
... ... @@ -34,7 +34,7 @@ General parameters
34 34  
35 35 ``emin [real]``
36 36 Lower energy limit of energy boundaries (in TeV).
37   -
  37 +
38 38 ``emax [real]``
39 39 Upper energy limit of energy boundaries (in TeV).
40 40  
... ... @@ -53,23 +53,23 @@ Standard parameters
53 53 ``(chatter = 2) [integer]``
54 54 Verbosity of the executable:
55 55 ``chatter = 0``: no information will be logged
56   -
  56 +
57 57 ``chatter = 1``: only errors will be logged
58   -
  58 +
59 59 ``chatter = 2``: errors and actions will be logged
60   -
  60 +
61 61 ``chatter = 3``: report about the task execution
62   -
  62 +
63 63 ``chatter = 4``: detailed report about the task execution
64   -
  64 +
65 65 ``(clobber = yes) [boolean]``
66 66 Specifies whether an existing energy boundaries output file should be overwritten.
67   -
  67 +
68 68 ``(debug = no) [boolean]``
69 69 Enables debug mode. In debug mode the executable will dump any log file output to the console.
70   -
  70 +
71 71 ``(mode = ql) [string]``
72   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  72 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
73 73  
74 74 ``(logfile = csebins.log) [filename]``
75 75 Log filename.
... ...
doc/source/users/reference_manual/csfindobs.rst
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... ... @@ -49,7 +49,7 @@ General parameters
49 49  
50 50 ``dec [real]``
51 51 Declination of search region (invoke "INDEF" to avoid spatial selection).
52   -
  52 +
53 53 ``rad [real]``
54 54 Radius of search region (deg) (invoke "INDEF" or negative values to avoid
55 55 spatial selection)
... ... @@ -70,23 +70,23 @@ Standard parameters
70 70 ``(chatter = 2) [integer]``
71 71 Verbosity of the executable:
72 72 ``chatter = 0``: no information will be logged
73   -
  73 +
74 74 ``chatter = 1``: only errors will be logged
75   -
  75 +
76 76 ``chatter = 2``: errors and actions will be logged
77   -
  77 +
78 78 ``chatter = 3``: report about the task execution
79   -
  79 +
80 80 ``chatter = 4``: detailed report about the task execution
81   -
  81 +
82 82 ``(clobber = yes) [boolean]``
83 83 Specifies whether an existing output runlist should be overwritten.
84   -
  84 +
85 85 ``(debug = no) [boolean]``
86 86 Enables debug mode. In debug mode the executable will dump any log file output to the console.
87   -
  87 +
88 88 ``(mode = ql) [string]``
89   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  89 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
90 90  
91 91 ``(logfile = csfindobs.log) [filename]``
92 92 Log filename.
... ...
doc/source/users/reference_manual/csiactcopy.rst
  View file @7c7ef2a
1 1 .. _csiactcopy:
2 2  
3 3 csiactcopy
4   -===========
  4 +==========
5 5  
6 6 Copies IACT data from one location to another
7 7  
... ... @@ -14,7 +14,7 @@ has to be mounted before running the script. For mounting, e.g. sshfs can be use
14 14  
15 15 .. code-block:: bash
16 16  
17   - $ sshfs user@remote.server.com:/path/to/remote/fits /path/to/mountpoint/
  17 + $ sshfs user@remote.server.com:/path/to/remote/fits /path/to/mountpoint/
18 18  
19 19 The script can optionally take an ASCII file with a list of observation IDs as input.
20 20 In this way the user can copy only a specific subset of the data. Index files and data
... ... @@ -36,7 +36,7 @@ General parameters
36 36  
37 37 ``prodname [string]``
38 38 Name of FITS production to download
39   -
  39 +
40 40 ``outpath [file]``
41 41 Destination path of FITS data
42 42  
... ... @@ -50,23 +50,23 @@ Standard parameters
50 50 ``(chatter = 2) [integer]``
51 51 Verbosity of the executable:
52 52 ``chatter = 0``: no information will be logged
53   -
  53 +
54 54 ``chatter = 1``: only errors will be logged
55   -
  55 +
56 56 ``chatter = 2``: errors and actions will be logged
57   -
  57 +
58 58 ``chatter = 3``: report about the task execution
59   -
  59 +
60 60 ``chatter = 4``: detailed report about the task execution
61   -
  61 +
62 62 ``(clobber = yes) [boolean]``
63 63 Specifies whether existing output files should be overwritten.
64   -
  64 +
65 65 ``(debug = no) [boolean]``
66 66 Enables debug mode. In debug mode the executable will dump any log file output to the console.
67   -
  67 +
68 68 ``(mode = ql) [string]``
69   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  69 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
70 70  
71 71 ``(logfile = csiactdload.log) [filename]``
72 72 Log filename.
... ...
doc/source/users/reference_manual/csiactdata.rst
  View file @7c7ef2a
... ... @@ -23,34 +23,34 @@ General parameters
23 23  
24 24 ``datapath [string]``
25 25 Path were data are located.
26   -
  26 +
27 27 ``(master_index = master.json) [string]``
28 28 Name of master index file.
29   -
30   -
  29 +
  30 +
31 31 Standard parameters
32 32 -------------------
33 33  
34 34 ``(chatter = 2) [integer]``
35 35 Verbosity of the executable:
36 36 ``chatter = 0``: no information will be logged
37   -
  37 +
38 38 ``chatter = 1``: only errors will be logged
39   -
  39 +
40 40 ``chatter = 2``: errors and actions will be logged
41   -
  41 +
42 42 ``chatter = 3``: report about the task execution
43   -
  43 +
44 44 ``chatter = 4``: detailed report about the task execution
45   -
  45 +
46 46 ``(clobber = yes) [boolean]``
47 47 Specifies whether existing output files should be overwritten.
48   -
  48 +
49 49 ``(debug = no) [boolean]``
50 50 Enables debug mode. In debug mode the executable will dump any log file output to the console.
51   -
  51 +
52 52 ``(mode = ql) [string]``
53   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  53 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
54 54  
55 55 ``(logfile = csiactdata.log) [filename]``
56 56 Log filename.
... ...
doc/source/users/reference_manual/csiactobs.rst
  View file @7c7ef2a
1 1 .. _csiactobs:
2 2  
3 3 csiactobs
4   -===========
  4 +=========
5 5  
6 6 Creates an observation XML file for IACTs using a list of observation IDs as
7 7 input.
... ... @@ -37,8 +37,8 @@ that will be in the output XML model.
37 37  
38 38 If an observation that given in the input ASCII file is not available on the user
39 39 machine, the script dumps a warning into the logfile and the observation is
40   -skipped.
41   -
  40 +skipped.
  41 +
42 42  
43 43 General parameters
44 44 ------------------
... ... @@ -48,16 +48,16 @@ General parameters
48 48  
49 49 ``prodname [string]``
50 50 Name of FITS production (Run :doc:`csiactdata` to view your options).
51   -
  51 +
52 52 ``infile [file]``
53 53 Input runlist ASCII file.
54 54  
55 55 ``(inmodel = NONE) [file]``
56 56 Input model XML file.
57   -
  57 +
58 58 ``outobs [file]``
59 59 Output Observation Definition XML file.
60   -
  60 +
61 61 ``outmodel [file]``
62 62 Output model XML file.
63 63  
... ... @@ -66,7 +66,7 @@ General parameters
66 66  
67 67 ``(master_indx = master.json) [file]``
68 68 Name of master index file.
69   -
  69 +
70 70 ``(bkg_scale = yes) [boolean]``
71 71 Specifies whether the background scaling factor from the observation index
72 72 file should be applied if available.
... ... @@ -82,10 +82,10 @@ General parameters
82 82  
83 83 ``(edisp_hiera = edisp_2d) [string]``
84 84 Hierarchy of energy disperson formats.
85   -
  85 +
86 86 ``(bkg_hiera = bkg_3d) [string]``
87 87 Hierarchy of background formats.
88   -
  88 +
89 89 ``(bkg_mod_hiera = irf|aeff|gauss) [string]``
90 90 Hierarchy of background models.
91 91  
... ... @@ -107,30 +107,30 @@ General parameters
107 107 ``(bkg_range_factor = 100.0) [real]``
108 108 Factor to determine range of background normalisation.
109 109  
110   -
  110 +
111 111 Standard parameters
112 112 -------------------
113 113  
114 114 ``(chatter = 2) [integer]``
115 115 Verbosity of the executable:
116 116 ``chatter = 0``: no information will be logged
117   -
  117 +
118 118 ``chatter = 1``: only errors will be logged
119   -
  119 +
120 120 ``chatter = 2``: errors and actions will be logged
121   -
  121 +
122 122 ``chatter = 3``: report about the task execution
123   -
  123 +
124 124 ``chatter = 4``: detailed report about the task execution
125   -
  125 +
126 126 ``(clobber = yes) [boolean]``
127 127 Specifies whether existing output files should be overwritten.
128   -
  128 +
129 129 ``(debug = no) [boolean]``
130 130 Enables debug mode. In debug mode the executable will dump any log file output to the console.
131   -
  131 +
132 132 ``(mode = ql) [string]``
133   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  133 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
134 134  
135 135 ``(logfile = csiactobs.log) [filename]``
136 136 Log filename.
... ...
doc/source/users/reference_manual/cslightcrv.rst
  View file @7c7ef2a
... ... @@ -3,21 +3,35 @@
3 3 cslightcrv
4 4 ==========
5 5  
6   -Computes a lightcurve for a given source.
  6 +Computes a light curve for a given source.
7 7  
8 8  
9 9 Synopsis
10 10 --------
11 11  
12   -This script computes a lightcurve by performing a maximum likelihood fit
  12 +This script computes a light curve by performing a maximum likelihood fit
13 13 using :doc:`ctlike` in a series of time bins. The time bins can be either
14 14 specified in an ASCII file, as an interval divided into equally sized time
15 15 bins, or can be taken from the Good Time Intervals of the observation(s).
16 16 The format of the ASCII file is one row per time bin, each specifying the
17 17 start of stop value of the bin, separated by a whitespace. The times are
18   -given in Modified Julian Days (MJD).
19   -
20   -cslightcrv writes the fitted model parameters and their statistical errors
  18 +given in Modified Julian Days (MJD).
  19 +
  20 +:ref:`cslightcrv` can perform the light curve fitting in unbinned, stacked or
  21 +On/Off analysis mode; on input the script always requires unbinned data, i.e.
  22 +event list(s), since only event data retain time information for light curve
  23 +fitting. To select unbinned analysis, specify ``method=3D`` and ``enumbins=0``;
  24 +for stacked analysis specify ``method=3D`` and any positive number for ``enumbins``.
  25 +To perform the analysis in On/Off model, specify ``method=ONOFF``.
  26 +
  27 +For a stacked analysis, :ref:`cslightcrv` will query the parameters that define
  28 +the counts cube (``coordsys``, ``proj``, ``xref``, ``yref``, ``nxpix``, ``nypix``,
  29 +``binsz``) while for an On/Off analysis the script will query the parameters that
  30 +are necessary to run internally the :ref:`csphagen` script (``inexclusion``, ``coordsys``,
  31 +``xref``, ``yref``, ``srcshape``, ``rad``, ``bkgmethod``, ``bkgregmin``, ``maxoffset``,
  32 +``etruemin``, ``etruemax``, ``etruebins``).
  33 +
  34 +:ref:`cslightcrv` writes the fitted model parameters and their statistical errors
21 35 in a FITS file. In addition, it computes for each time bin the statistical
22 36 significance of the detection, expressed by the Test Statistics, and the
23 37 upper flux limit.
... ... @@ -44,12 +58,12 @@ General parameters
44 58  
45 59 ``(inexclusion = NONE) [file]``
46 60 Optional FITS file containing a WCS map in the first hdu that defines sky
47   - regions not to be used for background estimation in ``ONOFF`` analysis (where
  61 + regions not to be used for background estimation in On/Off analysis (where
48 62 map value != 0).
49 63  
50 64 ``(edisp = no) [boolean]``
51 65 Applies energy dispersion to response computation (for ``3D`` analysis only,
52   - energy dispersion is always taken into account in ``ONOFF`` analysis).
  66 + energy dispersion is always taken into account in On/Off analysis).
53 67  
54 68 ``outfile [file]``
55 69 Name of the light curve output file.
... ... @@ -90,11 +104,11 @@ General parameters
90 104  
91 105 ``xref [real]``
92 106 Right Ascension / Galactic longitude of image centre for ``3D`` analysis or
93   - source region centre for ``ONOFF`` analysis (J2000, in degrees).
  107 + source region centre for On/Off analysis (J2000, in degrees).
94 108  
95 109 ``yref [real]``
96 110 Declination / Galactic latitude of image centre for ``3D`` analysis or
97   - source region centre for ``ONOFF`` analysis (J2000, in degrees).
  111 + source region centre for On/Off analysis (J2000, in degrees).
98 112  
99 113 ``nxpix [integer]``
100 114 Size of the Right Ascension / Galactic longitude axis for ``3D`` analysis (in pixels).
... ... @@ -106,14 +120,14 @@ General parameters
106 120 Pixel size for ``3D`` analysis (in degrees/pixel).
107 121  
108 122 ``(srcshape = CIRCLE) [string]``
109   - Shape of the source region for ``ONOFF`` analysis.
  123 + Shape of the source region for On/Off analysis.
110 124 ``CIRCLE``: circular region around given position.
111 125  
112 126 ``rad [real]``
113   - Radius of source region circle for ``ONOFF`` analysis (deg)
  127 + Radius of source region circle for On/Off analysis (deg)
114 128  
115 129 ``(bkgmethod = REFLECTED) [string]``
116   - Method for background estimation in ``ONOFF`` analysis.
  130 + Method for background estimation in On/Off analysis.
117 131 ``REFLECTED:`` background evaluated in regions with the same shape as
118 132 source region reflected w.r.t. pointing direction for each observation.
119 133  
... ... @@ -124,17 +138,17 @@ General parameters
124 138  
125 139 ``(maxoffset = 4.0) [real]``
126 140 Maximum offset in degrees of source from camera center to accept the
127   - observation for ``ONOFF`` analysis.
  141 + observation for On/Off analysis.
128 142  
129 143 ``(etruemin = 0.01) [real]``
130   - Minimum true energy to evaluate instrumental response in ``ONOFF`` analysis (TeV).
  144 + Minimum true energy to evaluate instrumental response in On/Off analysis (TeV).
131 145  
132 146 ``(etruemax = 0.01) [real]``
133   - Maximum true energy to evaluate instrumental response in ``ONOFF`` analysis (TeV).
  147 + Maximum true energy to evaluate instrumental response in On/Off analysis (TeV).
134 148  
135 149 ``(etruebins = 30) [integer]``
136 150 Number of bins per decade for true energy bins to evaluate instrumental
137   - response in ``ONOFF`` analysis.
  151 + response in On/Off analysis.
138 152  
139 153 ``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT|CHI2> [string]``
140 154 Optimization statistic. ``DEFAULT`` uses the default statistic for all
... ... @@ -174,16 +188,16 @@ Standard parameters
174 188 ``chatter = 3``: report about the task execution
175 189  
176 190 ``chatter = 4``: detailed report about the task execution
177   -
  191 +
178 192 ``(clobber = yes) [boolean]``
179 193 Specifies whether an existing light curve output file should be overwritten.
180   -
  194 +
181 195 ``(debug = no) [boolean]``
182 196 Enables debug mode. In debug mode the executable will dump any log file
183 197 output to the console.
184   -
  198 +
185 199 ``(mode = ql) [string]``
186   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  200 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
187 201  
188 202 ``(logfile = cslightcrv.log) [filename]``
189 203 Log filename.
... ... @@ -193,3 +207,4 @@ Related tools or scripts
193 207 ------------------------
194 208  
195 209 :doc:`ctlike`
  210 +:doc:`csphagen`
... ...
doc/source/users/reference_manual/csmodelinfo.rst
  View file @7c7ef2a
... ... @@ -3,25 +3,25 @@
3 3 csmodelinfo
4 4 ===========
5 5  
6   -Dumps information about a model container into log file or on screen.
  6 +Logs information about a model container into log file or on screen.
7 7  
8 8  
9 9 Synopsis
10 10 --------
11 11  
12   -This script provides detailled information about a given model container.
13   -It presents the number of parameters, the number of free parameters (sub-
14   -divided by spectral, spatial and temporal type). The tool further creates
15   -information about any parameter that is stuck at the parameter boundaries.
16   -This might be quite useful for debugging a fit. Finally the tool also list
17   -the TS values of each source that was fitted, in order have a quick overview
18   -on these quantities on the screen.
  12 +This script provides detailed information about a given model container. It
  13 +presents the number of parameters, the number of free parameters (sub-divided
  14 +by spectral, spatial and temporal type). The tool further creates information
  15 +about any parameter that is stuck at the parameter boundaries. This might be
  16 +quite useful for debugging a fit. Finally the tool also list the TS values of
  17 +each source that was fitted, in order have a quick overview on these quantities
  18 +on the screen.
19 19  
20 20 In addition the tool is also capable of exporting the input model XML container
21 21 to a region file which is compatible to be read with ds9 or other displying
22 22 tools. To create a region file, the hidden parameter "ds9file" needs to be
23   -specified. There are quite a few further hidden parameters to steer e.g.
24   -color, font, etc of the region file output.
  23 +specified. There are quite a few further hidden parameters to steer e.g. color,
  24 +font, etc of the region file output.
25 25  
26 26  
27 27 General parameters
... ... @@ -36,25 +36,25 @@ General parameters
36 36 ``(pnt_type=cross) <circle|box|diamond|cross|x|arrow|boxcircle> [string]``
37 37 Marker type for point sources
38 38  
39   -``pnt_mark_size [integer]``
  39 +``(pnt_mark_size=12) [integer]``
40 40 Marker size for point sources
41 41  
42 42 ``(show_labels=yes) [boolean]``
43 43 Add source labels?
44   -
  44 +
45 45 ``(width=2) [integer]``
46 46 Line width for regions
47   -
48   - ``(font=helvetica) <helvetica|times|courier> [string]``
  47 +
  48 +``(fontfamily=helvetica) <helvetica|times|courier> [string]``
49 49 Font for source labels
50 50  
51 51 ``(fontsize=12) [integer]``
52 52 Font size for source labels
53 53  
54   -``(fonttype=normal) <normal|bold> [string]``
  54 +``(fontweight=normal) <normal|bold> [string]``
55 55 Use normal or bold font?
56 56  
57   -``(fonttype2=roman) <roman|italic> [string]``
  57 +``(fontslant=roman) <roman|italic> [string]``
58 58 Use roman or italic font?
59 59  
60 60 ``(show_ext_type=yes) [boolean]``
... ... @@ -65,31 +65,31 @@ General parameters
65 65  
66 66 ``(fixed_color=magenta) [string]``
67 67 Color for sources without free parameters (any ds9 color or hex code)
68   -
69   -
  68 +
  69 +
70 70 Standard parameters
71 71 -------------------
72 72  
73 73 ``(chatter = 2) [integer]``
74 74 Verbosity of the executable:
75 75 ``chatter = 0``: no information will be logged
76   -
  76 +
77 77 ``chatter = 1``: only errors will be logged
78   -
  78 +
79 79 ``chatter = 2``: errors and actions will be logged
80   -
  80 +
81 81 ``chatter = 3``: report about the task execution
82   -
  82 +
83 83 ``chatter = 4``: detailed report about the task execution
84   -
  84 +
85 85 ``(clobber = yes) [boolean]``
86 86 Specifies whether existing output files should be overwritten.
87   -
  87 +
88 88 ``(debug = no) [boolean]``
89 89 Enables debug mode. In debug mode the executable will dump any log file output to the console.
90   -
  90 +
91 91 ``(mode = ql) [string]``
92   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  92 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
93 93  
94 94 ``(logfile = csmodelinfo.log) [filename]``
95 95 Log filename.
... ...
doc/source/users/reference_manual/csmodelmerge.rst
  View file @7c7ef2a
... ... @@ -13,10 +13,10 @@ This script merges several model XML file into a single model XML file. The
13 13 files are passed via the ``inmodels`` parameter. There are 4 options to specify
14 14 a list of files that should be merged:
15 15  
16   -* a space-separated list of file names (e.g. ``model1.xml model2.xml``)
17   -* a semi-colon separated list of file names (e.g. ``model1.xml;model2.xml``)
18   -* a wildcard string (e.g. ``mymodel*.xml``)
19   -* an ASCII file containing the file names, one file per line (e.g. ``@mymodels.txt``)
  16 +- a space-separated list of file names (e.g. ``model1.xml model2.xml``)
  17 +- a semi-colon separated list of file names (e.g. ``model1.xml;model2.xml``)
  18 +- a wildcard string (e.g. ``mymodel*.xml``)
  19 +- an ASCII file containing the file names, one file per line (e.g. ``@mymodels.txt``)
20 20  
21 21 Note that the "@" needs to be specified in case of an ASCII file name. It is
22 22 also important to note that models with the same name cannot be appended. The
... ... @@ -32,31 +32,31 @@ General parameters
32 32  
33 33 ``outmodel [file]``
34 34 Output model file
35   -
36   -
  35 +
  36 +
37 37 Standard parameters
38 38 -------------------
39 39  
40 40 ``(chatter = 2) [integer]``
41 41 Verbosity of the executable:
42 42 ``chatter = 0``: no information will be logged
43   -
  43 +
44 44 ``chatter = 1``: only errors will be logged
45   -
  45 +
46 46 ``chatter = 2``: errors and actions will be logged
47   -
  47 +
48 48 ``chatter = 3``: report about the task execution
49   -
  49 +
50 50 ``chatter = 4``: detailed report about the task execution
51   -
  51 +
52 52 ``(clobber = yes) [boolean]``
53 53 Specifies whether an existing output model file should be overwritten.
54   -
  54 +
55 55 ``(debug = no) [boolean]``
56 56 Enables debug mode. In debug mode the executable will dump any log file output to the console.
57   -
  57 +
58 58 ``(mode = ql) [string]``
59   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  59 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
60 60  
61 61 ``(logfile = csmodelmerge.log) [filename]``
62 62 Log filename.
... ...
doc/source/users/reference_manual/csmodelselect.rst
  View file @7c7ef2a
... ... @@ -21,28 +21,28 @@ General parameters
21 21 ------------------
22 22  
23 23 ``inobs [file]``
24   - Input event list or observation definition XML file
  24 + Input event list or observation definition XML file.
25 25  
26 26 ``inmodel [file]``
27   - Input model definition XML file
  27 + Input model definition XML file.
28 28  
29 29 ``outmodel [file]``
30   - Output model definition XML file
  30 + Output model definition XML file.
31 31  
32 32 ``(roilimit = 4.5) [real]``
33   - Maximum RoI radius (degrees)
  33 + Maximum RoI radius (degrees).
34 34  
35 35 ``(roimargin = 0.1) [real]``
36   - Radial margin to be added to RoIs (degrees)
  36 + Radial margin to be added to RoIs (degrees).
37 37  
38 38 ``(ethres = 0.1) [real]``
39   - Energy threshold for source flux selection (TeV)
  39 + Energy threshold for source flux selection (TeV).
40 40  
41 41 ``(fluxlimit = 1.0e-12) [real]``
42   - Minimum source flux for selection (ph/cm2/s)
  42 + Minimum source flux for selection (ph/cm2/s).
43 43  
44 44 ``(tslimit = 10.0) [real]``
45   - Minimum Test Statistic for selection
  45 + Minimum Test Statistic for selection.
46 46  
47 47 ``(fit_pos = yes) [boolean]``
48 48 Fit source positions?
... ... @@ -57,24 +57,24 @@ Standard parameters
57 57 ``(chatter = 2) [integer]``
58 58 Verbosity of the executable:
59 59 ``chatter = 0``: no information will be logged
60   -
  60 +
61 61 ``chatter = 1``: only errors will be logged
62   -
  62 +
63 63 ``chatter = 2``: errors and actions will be logged
64   -
  64 +
65 65 ``chatter = 3``: report about the task execution
66   -
  66 +
67 67 ``chatter = 4``: detailed report about the task execution
68   -
  68 +
69 69 ``(clobber = yes) [boolean]``
70 70 Specifies whether an existing output model file should be overwritten.
71   -
  71 +
72 72 ``(debug = no) [boolean]``
73 73 Enables debug mode. In debug mode the executable will dump any log file
74 74 output to the console.
75   -
  75 +
76 76 ``(mode = ql) [string]``
77   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  77 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
78 78  
79 79 ``(logfile = csmodelselect.log) [filename]``
80 80 Log filename.
... ...
doc/source/users/reference_manual/csmodelsois.rst
  View file @7c7ef2a
... ... @@ -9,43 +9,43 @@ Generate a map cube from a subset of models in an input model.
9 9 Synopsis
10 10 ----------
11 11  
12   -This tool generates a map cube from a subset of sky model components contained
  12 +This script generates a map cube from a subset of sky model components contained
13 13 in an input model. A map cube is a series of sky maps, each spanned by Right
14   -Ascension or Galactic longitude and Declination or Galactic latitude. Each
15   -map corresponds to a specific photon energy. The energy binning of the map
16   -cube may be either linear, logarithmic, or custom defined using an input
17   -file.
  14 +Ascension or Galactic longitude and Declination or Galactic latitude. Each map
  15 +corresponds to a specific photon energy. The energy binning of the map cube may
  16 +be either linear, logarithmic, or custom defined using an input file.
18 17  
19   -csmodelsois generates a map cube FITS file comprising two extensions. The
  18 +:ref:`csmodelsois` generates a map cube FITS file comprising two extensions. The
20 19 primary extension contains a 3-dimensional image containing the map cube
21 20 values. A second extension named ``ENERGIES`` contains a binary table that
22 21 defines the energy values of each map in the cube.
23 22  
24   -Optionally, csmodelsois can also output an updated model XML file in which all
  23 +Optionally, :ref:`csmodelsois` can also output an updated model XML file in which all
25 24 sources from the input model XML file used to generate the map cube are
26 25 replaced with an updated model that uses the generated map cube. This is done
27   -by specifying the 'outmodel' parameter. The 'soilist' parameter specifies a
28   -list of source names (separated by ',') to be excluded from the generated
  26 +by specifying the ``outmodel`` parameter. The ``soilist`` parameter specifies a
  27 +list of source names (separated by ``,``) to be excluded from the generated
29 28 cube.
30 29  
  30 +
31 31 General parameters
32 32 ------------------
33 33  
34 34 ``inmodel [file]``
35 35 Input model XML file.
36 36  
37   -``outmodel [file]``
38   - Output model XML file (not generated if set to ``NONE``).
39   -
40 37 ``outcube [file]``
41 38 Output map cube file.
42 39  
43   -``soilist [string]``
44   - CSV list of sources to be excluded from the generated map cube.
45   -
46 40 ``(ptsrcsig = 1.0) [real]``
47 41 Sigma of Gaussian to be used for point sources (in arcmin).
48 42  
  43 +``soilist [string]``
  44 + CSV list of source names to be excluded from the generated map cube.
  45 +
  46 +``outmodel [file]``
  47 + Output model XML file (not generated if set to ``NONE``).
  48 +
49 49 ``ebinalg <FILE|LIN|LOG> [string]``
50 50 Algorithm for defining energy bins.
51 51  
... ... @@ -62,10 +62,10 @@ General parameters
62 62 Name of the file containing the energy bin definition.
63 63  
64 64 ``nxpix [integer]``
65   - Number of cube bins in Right Ascension or Galactic longitude.
  65 + Number of map cube bins in Right Ascension or Galactic longitude.
66 66  
67 67 ``nypix [integer]``
68   - Number of cube bins in Declination or Galactic latitude.
  68 + Number of map cube bins in Declination or Galactic latitude.
69 69  
70 70 ``binsz [real]``
71 71 Image scale (in degrees/pixel).
... ... @@ -77,16 +77,16 @@ General parameters
77 77 Projection method.
78 78  
79 79 ``ra [real]``
80   - Right Ascension of cube centre (J2000, in degrees).
  80 + Right Ascension of map cube centre (J2000, in degrees).
81 81  
82 82 ``dec [real]``
83   - Declination of cube centre (J2000, in degrees).
  83 + Declination of map cube centre (J2000, in degrees).
84 84  
85 85 ``glon [real]``
86   - Galactic longitude of cube centre (in degrees).
  86 + Galactic longitude of map cube centre (in degrees).
87 87  
88 88 ``glat [real]``
89   - Galactic latitude of cube centre (in degrees).
  89 + Galactic latitude of map cube centre (in degrees).
90 90  
91 91  
92 92 Standard parameters
... ... @@ -114,7 +114,7 @@ Standard parameters
114 114 Enables debug mode. In debug mode the executable will dump any log file output to the console.
115 115  
116 116 ``(mode = ql) [string]``
117   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  117 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
118 118  
119 119 ``(logfile = csmodelsois.log) [string]``
120 120 Name of log file.
... ...
doc/source/users/reference_manual/csobs2caldb.rst
  View file @7c7ef2a
... ... @@ -11,15 +11,15 @@ Synopsis
11 11  
12 12 This script creates an entry in the local calibration database from an
13 13 input observation container. The caldb entry can be used for simulations
14   -with :doc:`ctobssim` later on. On default csobs2caldb uses the first observation
15   -in the given container. This can be modified using the hidden parameter "index"
16   -(e.g. index=3 instructs the tool to use the third observation in the container).
  14 +with :doc:`ctobssim` later on. On default :ref:`csobs2caldb` uses the first observation
  15 +in the given container. This can be modified using the hidden parameter ``index``
  16 +(e.g. ``index=3`` instructs the tool to use the third observation in the container).
17 17 Note that for the moment, the script only works for unbinned observations which
18   -use the latest CTA IRF format (i.e. 2D/3D FITS binary tables).
  18 +use the latest CTA IRF format (i.e. 2D/3D FITS binary tables).
19 19  
20 20 In particular this script might be useful for simulations of current IACT data.
21   -Provided a specific observation with IRFs e.g. at certain zenith/azimuth angle,
22   -the user can create a caldb entry using this tool and subsequently simulate e.g.
  21 +Provided a specific observation with IRFs e.g. at certain zenith/azimuth angle,
  22 +the user can create a caldb entry using this tool and subsequently simulate e.g.
23 23 50 hours using this configuration.
24 24  
25 25 General parameters
... ... @@ -50,23 +50,23 @@ Standard parameters
50 50 ``(chatter = 2) [integer]``
51 51 Verbosity of the executable:
52 52 ``chatter = 0``: no information will be logged
53   -
  53 +
54 54 ``chatter = 1``: only errors will be logged
55   -
  55 +
56 56 ``chatter = 2``: errors and actions will be logged
57   -
  57 +
58 58 ``chatter = 3``: report about the task execution
59   -
  59 +
60 60 ``chatter = 4``: detailed report about the task execution
61   -
  61 +
62 62 ``(clobber = yes) [boolean]``
63 63 Specifies whether an existing output file should be overwritten.
64   -
  64 +
65 65 ``(debug = no) [boolean]``
66 66 Enables debug mode. In debug mode the executable will dump any log file output to the console.
67   -
  67 +
68 68 ``(mode = ql) [string]``
69   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  69 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
70 70  
71 71 ``(logfile = csobs2caldb.log) [filename]``
72 72 Log filename.
... ...
doc/source/users/reference_manual/csobsdef.rst
  View file @7c7ef2a
... ... @@ -14,28 +14,28 @@ a pointing list. The pointing list is a comma-separated value (CSV)
14 14 ASCII file with header keywords in the first row followed by a list
15 15 of pointings (one pointing per row). The following header keywords
16 16 are supported (case sensitive, column order irrelevant):
17   -
18   -* name - Observation name string
19   -* id - Unique observation identifier string
20   -* ra - Right Ascension of pointing (deg)
21   -* dec - Declination of pointing (deg)
22   -* lon - Galactic longitude of pointing (deg)
23   -* lat - Galactic latitude of pointing (deg)
24   -* duration - Duration of pointing (seconds)
25   -* emin - Lower energy limit (TeV)
26   -* emax - Upper energy limit (TeV)
27   -* rad - Radius of region of interest (deg)
28   -* deadc - Deadtime correction factor [0-1]
29   -* caldb - Calibration database
30   -* irf - Response function name
31   -
  17 +
  18 +- name - Observation name string
  19 +- id - Unique observation identifier string
  20 +- ra - Right Ascension of pointing (deg)
  21 +- dec - Declination of pointing (deg)
  22 +- lon - Galactic longitude of pointing (deg)
  23 +- lat - Galactic latitude of pointing (deg)
  24 +- duration - Duration of pointing (seconds)
  25 +- emin - Lower energy limit (TeV)
  26 +- emax - Upper energy limit (TeV)
  27 +- rad - Radius of region of interest (deg)
  28 +- deadc - Deadtime correction factor [0-1]
  29 +- caldb - Calibration database
  30 +- irf - Response function name
  31 +
32 32 Only the pairs (ra,dec) or (lon,lat) are mandatory header keywords.
33 33 All other keywords are optional and can be specified when calling
34 34 csobsdef as user parameters. The only exception is the "duration"
35 35 keyword that will automatically be queried.
36   -
  36 +
37 37 Here some usage examples:
38   -
  38 +
39 39 ``csobsdef``
40 40 Creates minimal observation definition file.
41 41  
... ... @@ -62,27 +62,27 @@ General parameters
62 62 ``duration [real]``
63 63 Duration of observation (in seconds).
64 64  
65   -``(name = "") [string]``
  65 +``(name = None) [string]``
66 66 Observation name.
67 67  
68 68 ``(caldb = "") [string]``
69 69 Calibration database.
70   -
  70 +
71 71 ``(irf = "") [string]``
72 72 Instrumental response function.
73 73  
74 74 ``(emin = UNDEF) [real]``
75 75 Lower energy limit of events (in TeV).
76   -
  76 +
77 77 ``(emax = UNDEF) [real]``
78 78 Upper energy limit of events (in TeV).
79   -
  79 +
80 80 ``(rad = UNDEF) [real]``
81 81 ROI radius (in degrees).
82 82  
83 83 ``(deadc = 0.95) [real]``
84 84 Average deadtime correction factor.
85   -
  85 +
86 86  
87 87 Standard parameters
88 88 -------------------
... ... @@ -90,23 +90,23 @@ Standard parameters
90 90 ``(chatter = 2) [integer]``
91 91 Verbosity of the executable:
92 92 ``chatter = 0``: no information will be logged
93   -
  93 +
94 94 ``chatter = 1``: only errors will be logged
95   -
  95 +
96 96 ``chatter = 2``: errors and actions will be logged
97   -
  97 +
98 98 ``chatter = 3``: report about the task execution
99   -
  99 +
100 100 ``chatter = 4``: detailed report about the task execution
101   -
  101 +
102 102 ``(clobber = yes) [boolean]``
103 103 Specifies whether an existing Observation Definition XML file should be overwritten.
104   -
  104 +
105 105 ``(debug = no) [boolean]``
106 106 Enables debug mode. In debug mode the executable will dump any log file output to the console.
107   -
  107 +
108 108 ``(mode = ql) [string]``
109   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  109 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
110 110  
111 111 ``(logfile = csobsdef.log) [string]``
112 112 Log filename.
... ...
doc/source/users/reference_manual/csobsinfo.rst
  View file @7c7ef2a
... ... @@ -3,8 +3,7 @@
3 3 csobsinfo
4 4 =========
5 5  
6   -Dumps information about an observation container into log file or on
7   -screen.
  6 +Logs information about an observation container into log file or on screen.
8 7  
9 8  
10 9 Synopsis
... ... @@ -15,43 +14,43 @@ For IACT observations usually several observations with different configurations
15 14 are combined. The script computes e.g. the overall energy range which could be
16 15 an important input for :doc:`ctbin` to create a suitable energy range. In
17 16 addition the script prints the pointing attributes like the average
18   -zenith/azimuth angle. If the hidden boolean parameter "offset" is specified to
19   -"yes", the script queries for the target position and computes the run-by-run
20   -offset as well as its average. In the observation summary, the time range of
21   -the observations including total ontime and (dead-time corrected) livetime is
22   -shown.
  17 +zenith/azimuth angle. If the hidden boolean parameter ``offset`` is set to ``yes``,
  18 +the script queries for the target position and computes the run-by-run offset as
  19 +well as its average. In the observation summary, the time range of the
  20 +observations including total ontime and (dead-time corrected) livetime is shown.
23 21  
24   -The script further contains the hidden parameter "ds9file". If specified with
  22 +The script further contains the hidden parameter ``ds9file``. If specified with
25 23 a file name, the tool writes out a ds9 region file including a cross for each
26 24 pointing position in the sky.
27 25  
28   -When executed from within python, the script provides methods to return arrays
  26 +When executed from within Python, the script provides methods to return arrays
29 27 containing observation-wise parameters. This might be useful for graphical
30 28 display within a script. The following methods are implemented:
31   -- zeniths (returning all zenith angles)
32   -- azimuths (returning all azimuth angles)
33   -- offsets (returning all offset angles, provided the hidden parameter offset=yes)
34   -- ebounds (returning energy boundaries)
35   -- gtis (returning good time intervals)
  29 +
  30 +- ``zeniths`` (return zenith angles)
  31 +- ``azimuths`` (return azimuth angles)
  32 +- ``offsets`` (return offset angles, provided the hidden parameter ``offset=yes``)
  33 +- ``ebounds`` (return energy boundaries)
  34 +- ``gti`` (return good time intervals)
36 35  
37 36  
38 37 General parameters
39 38 ------------------
40 39  
41 40 ``inobs [file]``
42   - Event list, counts cube, or observation definition file
  41 + Event list, counts cube, or observation definition file.
43 42  
44 43 ``outds9file [file]``
45   - DS9 region file containing pointing directions
  44 + DS9 region file containing pointing directions.
46 45  
47 46 ``(offset = no) [file]``
48   - Compute offset from target to pointing positions
  47 + Compute offset from target to pointing positions.
49 48  
50 49 ``ra [real]``
51   - Target right ascension for offset computation (only queried if offset=yes)
  50 + Target right ascension for offset computation (only queried if ``offset=yes``).
52 51  
53 52 ``dec [real]``
54   - Target declination for offset computation (only queried if offset=yes)
  53 + Target declination for offset computation (only queried if ``offset=yes``).
55 54  
56 55  
57 56 Standard parameters
... ... @@ -60,23 +59,23 @@ Standard parameters
60 59 ``(chatter = 2) [integer]``
61 60 Verbosity of the executable:
62 61 ``chatter = 0``: no information will be logged
63   -
  62 +
64 63 ``chatter = 1``: only errors will be logged
65   -
  64 +
66 65 ``chatter = 2``: errors and actions will be logged
67   -
  66 +
68 67 ``chatter = 3``: report about the task execution
69   -
  68 +
70 69 ``chatter = 4``: detailed report about the task execution
71   -
  70 +
72 71 ``(clobber = yes) [boolean]``
73 72 Specifies whether an existing output file should be overwritten.
74   -
  73 +
75 74 ``(debug = no) [boolean]``
76 75 Enables debug mode. In debug mode the executable will dump any log file output to the console.
77   -
  76 +
78 77 ``(mode = ql) [string]``
79   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  78 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
80 79  
81 80 ``(logfile = csobsinfo.log) [filename]``
82 81 Log filename.
... ...
doc/source/users/reference_manual/csobsselect.rst
  View file @7c7ef2a
... ... @@ -19,63 +19,63 @@ General parameters
19 19 ------------------
20 20  
21 21 ``inobs [file]``
22   - Input event list or observation definition XML file
  22 + Input event list or observation definition XML file.
23 23  
24 24 ``outobs [file]``
25   - Output observation definition XML file
  25 + Output observation definition XML file.
26 26  
27 27 ``pntselect <CIRCLE|BOX> [string]``
28   - Pointing selection region shape
  28 + Pointing selection region shape.
29 29  
30 30 ``coordsys <CEL|GAL> [string]``
31   - Coordinate system (CEL - celestial, GAL - galactic)
  31 + Coordinate system (CEL - celestial, GAL - galactic).
32 32  
33 33 ``ra [real]``
34   - Right Ascension of pointing selection centre (J2000, in degrees)
35   -
  34 + Right Ascension of pointing selection centre (J2000, in degrees).
  35 +
36 36 ``dec [real]``
37   - Declination of pointing selection centre (J2000, in degrees)
  37 + Declination of pointing selection centre (J2000, in degrees).
38 38  
39 39 ``glon [real]``
40   - Galactic longitude of pointing selection centre (degrees)
41   -
  40 + Galactic longitude of pointing selection centre (degrees).
  41 +
42 42 ``glat [real]``
43   - Galactic latitude of pointing selection centre (degrees)
  43 + Galactic latitude of pointing selection centre (degrees).
44 44  
45 45 ``rad [real]``
46   - Radius of selection circle (degrees)
  46 + Radius of selection circle (degrees).
47 47  
48 48 ``width [real]``
49   - Width of selection box (degrees)
  49 + Width of selection box (degrees).
50 50  
51 51 ``height [real]``
52   - Height of selection box (degrees)
  52 + Height of selection box (degrees).
  53 +
53 54  
54   -
55 55 Standard parameters
56 56 -------------------
57 57  
58 58 ``(chatter = 2) [integer]``
59 59 Verbosity of the executable:
60 60 ``chatter = 0``: no information will be logged
61   -
  61 +
62 62 ``chatter = 1``: only errors will be logged
63   -
  63 +
64 64 ``chatter = 2``: errors and actions will be logged
65   -
  65 +
66 66 ``chatter = 3``: report about the task execution
67   -
  67 +
68 68 ``chatter = 4``: detailed report about the task execution
69   -
  69 +
70 70 ``(clobber = yes) [boolean]``
71 71 Specifies whether an existing output model file should be overwritten
72   -
  72 +
73 73 ``(debug = no) [boolean]``
74 74 Enables debug mode. In debug mode the executable will dump any log file
75 75 output to the console
76   -
  76 +
77 77 ``(mode = ql) [string]``
78   - Mode of automatic parameters (default is "ql", i.e. "query and learn")
  78 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn")
79 79  
80 80 ``(logfile = csobsselect.log) [filename]``
81 81 Log filename
... ...
doc/source/users/reference_manual/csphagen.rst
  View file @7c7ef2a
... ... @@ -3,8 +3,7 @@
3 3 csphagen
4 4 ========
5 5  
6   -Creates files necessary to perform a classical region-based spectral analysis
7   -on IACT data, i.e., source and background PHA files, ARF and RMF files.
  6 +Creates files necessary to perform a region-based spectral On/Off analysis.
8 7  
9 8  
10 9 Synopsis
... ... @@ -21,7 +20,7 @@ used in X-ray astronomy (PHA, ARF, RMF).
21 20 The outputs are:
22 21  
23 22 1) the PHA, ARF, RMF files, either separately for each observation, or stacked
24   - for a set of observations,
  23 + for a set of observations;
25 24 2) DS9 regions files listing the source and background regions for each
26 25 observation;
27 26 3) a new observation definition XML file.
... ... @@ -31,29 +30,29 @@ General parameters
31 30 ------------------
32 31  
33 32 ``inobs [file]``
34   - Input event list or observation definition XML file
  33 + Input event list or observation definition XML file.
35 34  
36 35 ``caldb [string]``
37   - Calibration database
  36 + Calibration database.
38 37  
39 38 ``irf [string]``
40   - Instrument response function
  39 + Instrument response function.
41 40  
42 41 ``(inexclusion = NONE) [file]``
43 42 Optional FITS file containing a WCS map in the first hdu that defines sky
44   - regions not to be used for background estimation (where map value != 0)
  43 + regions not to be used for background estimation (where map value != 0).
45 44  
46 45 ``outobs [string]``
47   - Output observation definition XML file
  46 + Output observation definition XML file.
48 47  
49 48 ``(prefix = onoff) [string]``
50   - Prefix of the file name for output PHA, ARF, RMF, XML, and DS9 region files
  49 + Prefix of the file name for output PHA, ARF, RMF, XML, and DS9 region files.
51 50  
52 51 ``emin [real]``
53   - Lower energy limit (TeV) if ``LIN`` or ``LOG`` binning algorithms are used
  52 + Lower energy limit (TeV) if ``LIN`` or ``LOG`` binning algorithms are used.
54 53  
55 54 ``emax [real]``
56   - Upper energy limit (TeV) if ``LIN`` or ``LOG`` binning algorithms are used
  55 + Upper energy limit (TeV) if ``LIN`` or ``LOG`` binning algorithms are used.
57 56  
58 57 ``enumbins [integer]``
59 58 Number of energy bins. At least 30 bins per decade are recommended for
... ... @@ -62,35 +61,35 @@ General parameters
62 61 ``ebinalg <FILE|LIN|LOG> [string]``
63 62 Algorithm for defining energy bins (``FILE``: energy bounds retrieved from
64 63 file, see ``ebinfile`` parameter; ``LIN``: linearly spaced energy bins;
65   - ``LOG``: logarithmically spaced energy bins)
  64 + ``LOG``: logarithmically spaced energy bins).
66 65  
67 66 ``ebinfile [file]``
68 67 Name of the file containing the energy bin definition if ``FILE`` algorithm
69   - is used
  68 + is used.
70 69  
71 70 ``(srcshape = CIRCLE) <CIRCLE> [string]``
72   - Shape of the source region (``CIRCLE``: circular region around given position)
  71 + Shape of the source region (``CIRCLE``: circular region around given position).
73 72  
74 73 ``coordsys <CEL|GAL> [string]``
75   - Coordinate system (``CEL``: celestial; ``GAL``: galactic)
  74 + Coordinate system (``CEL``: celestial; ``GAL``: galactic).
76 75  
77 76 ``ra [real]``
78   - Right Ascension of source region centre (deg)
  77 + Right Ascension of source region centre (deg).
79 78  
80 79 ``dec [real]``
81   - Declination of source region centre (deg)
  80 + Declination of source region centre (deg).
82 81  
83 82 ``glon [real]``
84   - Galactic longitude of source region centre (deg)
  83 + Galactic longitude of source region centre (deg).
85 84  
86 85 ``glat [real]``
87   - Galactic latitude of source region centre (deg)
  86 + Galactic latitude of source region centre (deg).
88 87  
89 88 ``rad [real]``
90   - Radius of source region circle (deg)
  89 + Radius of source region circle (deg).
91 90  
92 91 ``srcregfile [file]``
93   - Source region file (ds9 or FITS WCS map)
  92 + Source region file (ds9 or FITS WCS map).
94 93  
95 94 ``bkgmethod <REFLECTED|CUSTOM> [string]``
96 95 Method for background estimation:
... ... @@ -107,7 +106,7 @@ General parameters
107 106 XML file. Off region files can be either ds9 region files or FITS WCS maps.
108 107  
109 108 ``bkgregfile [file]``
110   - Background regions file (ds9 or FITS WCS map)
  109 + Background regions file (ds9 or FITS WCS map).
111 110  
112 111 ``(bkgregmin = 2) [integer]``
113 112 Minimum number of background regions that are required for an observation.
... ... @@ -116,20 +115,20 @@ General parameters
116 115  
117 116 ``(maxoffset = 4.0) [real]``
118 117 Maximum offset in degrees of source from camera center to accept the
119   - observation
  118 + observation.
120 119  
121 120 ``stack [boolean]``
122 121 Specifies whether multiple observations should be stacked (``yes``) or
123   - whether run-wise PHA, ARF and RMF files should be produced (``no``)
  122 + whether run-wise PHA, ARF and RMF files should be produced (``no``).
124 123  
125 124 ``(etruemin = 0.01) [real]``
126   - Minimum true energy (TeV)
  125 + Minimum true energy (TeV).
127 126  
128 127 ``(etruemax = 0.01) [real]``
129   - Maximum true energy (TeV)
  128 + Maximum true energy (TeV).
130 129  
131 130 ``(etruebins = 30) [integer]``
132   - Number of bins per decade for true energy bins
  131 + Number of bins per decade for true energy bins.
133 132  
134 133  
135 134 Standard parameters
... ... @@ -138,22 +137,22 @@ Standard parameters
138 137 ``(chatter = 2) [integer]``
139 138 Verbosity of the executable:
140 139 ``chatter = 0``: no information will be logged
141   -
  140 +
142 141 ``chatter = 1``: only errors will be logged
143   -
  142 +
144 143 ``chatter = 2``: errors and actions will be logged
145   -
  144 +
146 145 ``chatter = 3``: report about the task execution
147   -
  146 +
148 147 ``chatter = 4``: detailed report about the task execution
149   -
  148 +
150 149 ``(clobber = yes) [boolean]``
151 150 Specifies whether an existing output runlist should be overwritten.
152   -
  151 +
153 152 ``(debug = no) [boolean]``
154 153 Enables debug mode. In debug mode the executable will dump any log file
155 154 output to the console.
156   -
  155 +
157 156 ``(mode = ql) [string]``
158 157 Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
159 158  
... ... @@ -161,3 +160,8 @@ Standard parameters
161 160 Log filename.
162 161  
163 162  
  163 +Related tools or scripts
  164 +------------------------
  165 +
  166 +None
  167 +
... ...
doc/source/users/reference_manual/csphasecrv.rst
  View file @7c7ef2a
... ... @@ -12,15 +12,27 @@ Synopsis
12 12 This script computes spectra by performing a maximum likelihood fit using
13 13 :doc:`ctlike` in a series of phase bins for periodic sources. The input event
14 14 list must have a ``PHASE`` column containing the phase values, that can be
15   -assigned using :doc:`ctphase`. The phase bins can be
16   -either specified in an ASCII file or as an interval divided into equally sized
17   -phase bins. The format of the ASCII file is one row per phase bin, each
18   -specifying the start of stop value of the phase bin, separated by a whitespace.
19   -The phase goes from 0.0 to 1.0.
  15 +assigned using :doc:`ctphase`. The phase bins can be either specified in an ASCII
  16 +file or as an interval divided into equally sized phase bins. The format of the
  17 +ASCII file is one row per phase bin, each specifying the start of stop value of
  18 +the phase bin, separated by a whitespace. The phase goes from 0.0 to 1.0.
20 19  
21   -The script writes the fit results into a FITS file. The script
22   -also produces one XML file per phase bin that contains the best-fit model for
23   -that bin.
  20 +:ref:`csphasecrv` can perform the phase curve fitting in unbinned, stacked or
  21 +On/Off analysis mode; on input the script always requires unbinned data, i.e.
  22 +event list(s), since only event data retain phase information for phase curve
  23 +fitting. To select unbinned analysis, specify ``method=3D`` and ``enumbins=0``;
  24 +for stacked analysis specify ``method=3D`` and any positive number for ``enumbins``.
  25 +To perform the analysis in On/Off model, specify ``method=ONOFF``.
  26 +
  27 +For a stacked analysis, :ref:`csphasecrv` will query the parameters that define
  28 +the counts cube (``coordsys``, ``proj``, ``xref``, ``yref``, ``nxpix``, ``nypix``,
  29 +``binsz``) while for an On/Off analysis the script will query the parameters that
  30 +are necessary to run internally the :ref:`csphagen` script (``inexclusion``, ``coordsys``,
  31 +``xref``, ``yref``, ``srcshape``, ``rad``, ``bkgmethod``, ``bkgregmin``, ``maxoffset``,
  32 +``etruemin``, ``etruemax``, ``etruebins``).
  33 +
  34 +The script writes the fit results into a FITS file. The script also produces one
  35 +XML file per phase bin that contains the best-fit model for that bin.
24 36  
25 37  
26 38 General parameters
... ... @@ -43,7 +55,7 @@ General parameters
43 55  
44 56 ``(inexclusion = NONE) [file]``
45 57 Optional FITS file containing a WCS map in the first hdu that defines sky
46   - regions not to be used for background estimation in ``ONOFF`` analysis (where
  58 + regions not to be used for background estimation in On/Off analysis (where
47 59 map value != 0).
48 60  
49 61 ``(edisp = no) [boolean]``
... ... @@ -74,7 +86,7 @@ General parameters
74 86 Upper energy limit of events (in TeV).
75 87  
76 88 ``enumbins [integer]``
77   - Number of energy bins per phase bin (0=unbinned).
  89 + Number of energy bins per phase bin (0=unbinned for ``3D`` analysis only).
78 90  
79 91 ``coordsys <CEL|GAL> [string]``
80 92 Coordinate system (CEL - celestial, GAL - galactic).
... ... @@ -84,11 +96,11 @@ General parameters
84 96  
85 97 ``xref [real]``
86 98 Right Ascension / Galactic longitude of image centre for ``3D`` analysis or
87   - source region centre for ``ONOFF`` analysis (J2000, in degrees).
  99 + source region centre for On/Off analysis (J2000, in degrees).
88 100  
89 101 ``yref [real]``
90 102 Declination / Galactic latitude of image centre for ``3D`` analysis or
91   - source region centre for ``ONOFF`` analysis (J2000, in degrees).
  103 + source region centre for On/Off analysis (J2000, in degrees).
92 104  
93 105 ``nxpix [integer]``
94 106 Size of the Right Ascension / Galactic longitude axis for ``3D`` analysis (in pixels).
... ... @@ -100,35 +112,35 @@ General parameters
100 112 Pixel size for ``3D`` analysis (in degrees/pixel).
101 113  
102 114 ``(srcshape = CIRCLE) [string]``
103   - Shape of the source region for ``ONOFF`` analysis.
  115 + Shape of the source region for On/Off analysis.
104 116 ``CIRCLE``: circular region around given position.
105 117  
106 118 ``rad [real]``
107   - Radius of source region circle for ``ONOFF`` analysis (deg)
  119 + Radius of source region circle for On/Off analysis (deg)
108 120  
109 121 ``(bkgmethod = REFLECTED) [string]``
110   - Method for background estimation in ``ONOFF`` analysis.
  122 + Method for background estimation in On/Off analysis.
111 123 ``REFLECTED:`` background evaluated in regions with the same shape as
112 124 source region reflected w.r.t. pointing direction for each observation.
113 125  
114 126 ``(bkgregmin = 2) [integer]``
115 127 Minimum number of background regions that are required for an observation in
116   - ``ONOFF`` analysis. If this number of background regions is not available the
  128 + On/Off analysis. If this number of background regions is not available the
117 129 observation is skipped.
118 130  
119 131 ``(maxoffset = 4.0) [real]``
120 132 Maximum offset in degrees of source from camera center to accept the
121   - observation for ``ONOFF`` analysis.
  133 + observation for On/Off analysis.
122 134  
123 135 ``(etruemin = 0.01) [real]``
124   - Minimum true energy to evaluate instrumental response in ``ONOFF`` analysis (TeV).
  136 + Minimum true energy to evaluate instrumental response in On/Off analysis (TeV).
125 137  
126 138 ``(etruemax = 0.01) [real]``
127   - Maximum true energy to evaluate instrumental response in ``ONOFF`` analysis (TeV).
  139 + Maximum true energy to evaluate instrumental response in On/Off analysis (TeV).
128 140  
129 141 ``(etruebins = 30) [integer]``
130 142 Number of bins per decade for true energy bins to evaluate instrumental
131   - response in ``ONOFF`` analysis.
  143 + response in On/Off analysis.
132 144  
133 145 ``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT|CHI2> [string]``
134 146 Optimization statistic. ``DEFAULT`` uses the default statistic for all
... ... @@ -156,7 +168,7 @@ Standard parameters
156 168 ``chatter = 3``: report about the task execution
157 169  
158 170 ``chatter = 4``: detailed report about the task execution
159   -
  171 +
160 172 ``(clobber = yes) [boolean]``
161 173 Specifies whether an existing light curve output file should be overwritten.
162 174  
... ... @@ -165,7 +177,7 @@ Standard parameters
165 177 output to the console.
166 178  
167 179 ``(mode = ql) [string]``
168   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  180 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
169 181  
170 182 ``(logfile = csphasecrv.log) [filename]``
171 183 Log filename.
... ...
doc/source/users/reference_manual/cspull.rst
  View file @7c7ef2a
... ... @@ -11,14 +11,25 @@ Synopsis
11 11  
12 12 This script generates pull distributions for all free model parameters.
13 13 The pull is defined as the fitted model parameter value minus the true
14   -value, divided by the parameter error. cspull will perform ``ntrials``
  14 +value, divided by the parameter error. :ref:`cspull` will perform ``ntrials``
15 15 statistically independent Monte Carlo simulations followed by maximum
16 16 likelihood model fitting to derive the pull distribution for each free
17 17 model parameter. If the model fit is unbiased and the parameters are
18 18 correct, the pull distribution should follow a Gaussian centred on 0
19 19 and with a sigma parameter of 1.
20 20  
21   -cspull will generate an ASCII file in comma-separated value (CSV) format,
  21 +The script can generate pull distributions for unbinned, binned, stacked or
  22 +On/Off analyses. The script always starts from simulating an event list. If
  23 +the ``enumbins`` parameter is zero and ``onsrc=NONE`` an unbinned analysis will
  24 +be performed. If ``enumbins`` is positive and ``onsrc=NONE`` the script will
  25 +perform a binned analysis. To perform a stacked analysis, an observation definition
  26 +XML file with response cube information has to be specified for the ``inobs``
  27 +parameter. Finally, if the ``onsrc`` parameter is set to the name of a source in
  28 +the input model (specified via the ``inmodel`` parameter), the script will perform
  29 +an On/Off analysis using the ``REFLECTED`` method and a On region radius that is
  30 +given by the ``onrad`` parameter.
  31 +
  32 +:ref:`cspull` will generate an ASCII file in comma-separated value (CSV) format,
22 33 containing one row per pull. The first row is a header row providing the
23 34 column names. The following rows give the pull results, one row per pull.
24 35 This includes for each parameter the parameter value, error and pull. The
... ... @@ -35,7 +46,7 @@ of trials. Both scripts require matplotlib for plotting.
35 46 General parameters
36 47 ------------------
37 48  
38   -``inobs [file]``
  49 +``(inobs = NONE) [file]``
39 50 Event list, counts cube, or observation definition XML file.
40 51  
41 52 ``inmodel [file]``
... ... @@ -99,7 +110,7 @@ General parameters
99 110 Number of pixels for binned analysis.
100 111  
101 112 ``binsz [real]``
102   - Pixel size for binned analysis.
  113 + Pixel size for binned analysis (degrees/pixel).
103 114  
104 115 ``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT|CHI2> [string]``
105 116 Optimization statistic. ``DEFAULT`` uses the default statistic for all
... ... @@ -139,7 +150,7 @@ Standard parameters
139 150 output to the console.
140 151  
141 152 ``(mode = ql) [string]``
142   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  153 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
143 154  
144 155 ``(logfile = cspull.log) [string]``
145 156 Log filename.
... ...
doc/source/users/reference_manual/csresmap.rst
  View file @7c7ef2a
... ... @@ -18,10 +18,10 @@ binning and used for residual computation. Before residual computation,
18 18 the counts and model cubes are collapsed into maps by summing over all
19 19 energies. Four options exist then for residual computation:
20 20  
21   -* the subtraction of the model from the counts (SUB)
22   -* the subtraction and division by the model (SUBDIV)
23   -* the subtraction and division by the square root of the model (SUBDIVSQRT)
24   -* the computation of the significance using Li & Ma (SIGNIFICANCE)
  21 +- the subtraction of the model from the counts (SUB)
  22 +- the subtraction and division by the model (SUBDIV)
  23 +- the subtraction and division by the square root of the model (SUBDIVSQRT)
  24 +- the computation of the significance using Li & Ma (SIGNIFICANCE)
25 25  
26 26 The residual map is written into a FITS file.
27 27  
... ... @@ -32,6 +32,9 @@ General parameters
32 32 ``inobs [file]``
33 33 Input event list, counts cube or observation definition XML file.
34 34  
  35 +``inmodel [file]``
  36 + Input model XML file.
  37 +
35 38 ``modcube [file]``
36 39 Input model cube file (generated with ctmodel).
37 40  
... ... @@ -47,9 +50,6 @@ General parameters
47 50 ``bkgcube [file]``
48 51 Input background cube file.
49 52  
50   -``inmodel [file]``
51   - Input model XML file.
52   -
53 53 ``caldb [string]``
54 54 Calibration database.
55 55  
... ... @@ -135,7 +135,7 @@ Standard parameters
135 135 Enables debug mode. In debug mode the executable will dump any log file output to the console.
136 136  
137 137 ``(mode = ql) [string]``
138   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  138 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
139 139  
140 140 ``(logfile = csresmap.log) [string]``
141 141 Log filename.
... ...
doc/source/users/reference_manual/csresspec.rst
  View file @7c7ef2a
... ... @@ -9,19 +9,18 @@ Generates residual spectrum.
9 9 Synopsis
10 10 --------
11 11  
12   -This scripts generates a residual spectrum for a given model. It works for
13   -event lists, counts cubes, On/Off observations or observation definition files.
14   -For event lists parameters that define the spectral binning need to
15   -be provided so that the script can bin the data internally. The model
16   -is then convolved with the instrumental response function for the chosen
17   -binning (either specified by the user or intrinsic to the observations)
18   -and used for residual computation. It is possible to compute the model
19   -contributions from individual model components.
20   -
21   -If starting from event lists or count cubes,
22   -before residual computation the 3D counts and model cubes are collapsed into
23   -spectra by summing over all spatial direction. It is possible to specify a mask
24   -to compute counts, model, and residuals only for a region of interest.
  12 +This scripts generates a residual spectrum for a given model. It works for event
  13 +lists, counts cubes, On/Off observations or observation definition files. For
  14 +event lists parameters that define the spectral binning need to be provided so
  15 +that the script can bin the data internally. The model is then convolved with
  16 +the instrumental response function for the chosen binning (either specified by
  17 +the user or intrinsic to the observations) and used for residual computation. It
  18 +is possible to compute the model contributions from individual model components.
  19 +
  20 +If starting from event lists or count cubes, before residual computation the 3D
  21 +counts and model cubes are collapsed into spectra by summing over all spatial
  22 +direction. It is possible to specify a mask to compute counts, model, and
  23 +residuals only for a region of interest.
25 24  
26 25 For On/Off observations, counts, model, and residual spectra for the Off regions
27 26 are computed as well.
... ... @@ -33,10 +32,10 @@ residuals are calculated separately for each observation.
33 32  
34 33 Four options exist then for residual computation:
35 34  
36   -* the subtraction of the model from the counts (SUB)
37   -* the subtraction and division by the model (SUBDIV)
38   -* the subtraction and division by the square root of the model (SUBDIVSQRT)
39   -* the computation of the significance using Li & Ma (SIGNIFICANCE)
  35 +- the subtraction of the model from the counts (SUB)
  36 +- the subtraction and division by the model (SUBDIV)
  37 +- the subtraction and division by the square root of the model (SUBDIVSQRT)
  38 +- the computation of the significance using Li & Ma (SIGNIFICANCE)
40 39  
41 40 The counts, model, and residual spectra are written into a FITS file.
42 41  
... ... @@ -47,12 +46,12 @@ General parameters
47 46 ``inobs [file]``
48 47 Input event list, counts cube or observation definition XML file.
49 48  
50   -``modcube [file]``
51   - Input model cube file (generated with ctmodel).
52   -
53 49 ``inmodel [file]``
54 50 Input model XML file.
55 51  
  52 +``modcube [file]``
  53 + Input model cube file (generated with ctmodel).
  54 +
56 55 ``expcube [file]``
57 56 Input exposure cube file.
58 57  
... ... @@ -75,13 +74,18 @@ General parameters
75 74 Apply energy dispersion?
76 75  
77 76 ``outfile [file]``
78   - Output file.
  77 + Output residual spectrum file.
  78 +
  79 +``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT|CHI2> [string]``
  80 + Optimization statistic. ``DEFAULT`` uses the default statistic for all
  81 + observations, which is ``CSTAT`` or the statistic specified in the
  82 + observation definition XML file. ``CSTAT`` uses the C statistic for
  83 + all observations, ``WSTAT`` uses the W statistic for all On/Off
  84 + observations, and ``CHI2`` uses the Chi squared statistic for all
  85 + binned or stacked observations.
79 86  
80   -``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT> [string]``
81   - Optimization statistic. For On/Off observations determines how
82   - the background counts are computed. ``DEFAULT``, i.e., ``CSTAT``,
83   - will use the input background model. ``WSTAT`` uses the background
84   - counts from likelihood profiling as defined for the W statistic.
  87 +``(components = no) [boolean]``
  88 + Calculate model for individual components?
85 89  
86 90 ``ebinalg <FILE|LIN|LOG> [string]``
87 91 Algorithm for defining energy bins.
... ... @@ -98,35 +102,37 @@ General parameters
98 102 ``ebinfile [file]``
99 103 Name of the file containing the energy bin definition.
100 104  
101   -``(stack = no) [boolean]``
102   - Stack multiple observations for residual calculation.
  105 +``stack [boolean]``
  106 + Stack multiple observations for residual calculation?
103 107  
104 108 ``coordsys <CEL|GAL> [string]``
105 109 Coordinate system (CEL - celestial, GAL - galactic) for stacking
106 110 multiple event lists.
107 111  
108 112 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
109   - Projection method for stacking multiple event lists.
  113 + Projection method for stacking multiple event lists.
110 114  
111 115 ``xref [real]``
112 116 Right Ascension / Galactic longitude of cube centre (J2000, in degrees)
113 117 for stacking multiple event lists.
114 118  
115 119 ``yref [real]``
116   - Declination / Galactic latitude of cube centre (J2000, in degrees) for stacking
117   - multiple event lists.
  120 + Declination / Galactic latitude of cube centre (J2000, in degrees) for
  121 + stacking multiple event lists.
118 122  
119 123 ``nxpix [integer]``
120   - Number of cube bins in Right Ascension or Galactic longitude for stacking
  124 + Number of cube bins in Right Ascension or Galactic longitude for stacking
121 125 multiple event lists.
122 126  
123 127 ``nypix [integer]``
124   - Number of cube bins in Declination or Galactic latitude for stacking
  128 + Number of cube bins in Declination or Galactic latitude for stacking
125 129 multiple event lists.
126 130  
127 131 ``binsz [real]``
128   - Cube bin size (in degrees/pixel) for stacking
129   - multiple event lists.
  132 + Cube bin size (in degrees/pixel) for stacking multiple event lists.
  133 +
  134 +``mask [boolean]``
  135 + Mask data to calculate residuals in ROI?
130 136  
131 137 ``ra [real]``
132 138 Right Ascension of circular selection region centre (J2000, in degrees).
... ... @@ -177,7 +183,7 @@ Standard parameters
177 183 Enables debug mode. In debug mode the executable will dump any log file output to the console.
178 184  
179 185 ``(mode = ql) [string]``
180   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  186 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
181 187  
182 188 ``(logfile = csresspec.log) [string]``
183 189 Log filename.
... ...
doc/source/users/reference_manual/csroot2caldb.rst
  View file @7c7ef2a
... ... @@ -19,7 +19,7 @@ General parameters
19 19 ``infile [file]``
20 20 Input ROOT performance file file.
21 21  
22   -``(outdir = ) [string]``
  22 +``(outdir = "") [string]``
23 23 Output CALDB directory.
24 24  
25 25 ``inst [string]``
... ... @@ -46,17 +46,17 @@ General parameters
46 46 ``(emax = UNDEF) [real]``
47 47 Maximum energy threshold (TeV).
48 48  
49   -``(psftype = Gauss) [string]``
  49 +``(psftype = Gauss) <Gauss|King> [string]``
50 50 Point spread function type.
51 51  
52 52 ``(split = no) [boolean]``
53   - Split IRF components into different files.
  53 + Split IRF components into different files?
54 54  
55 55 ``(norm1d = no) [boolean]``
56   - Normalize on 1D histograms.
  56 + Normalize on 1D histograms?
57 57  
58 58 ``(rebin = no) [boolean]``
59   - Rebin.
  59 + Rebin?
60 60  
61 61 ``(eascale = 1.0) [real]``
62 62 Scaling factor for effective areas.
... ... @@ -71,7 +71,7 @@ General parameters
71 71 Energy above which to replace background by power law (TeV).
72 72  
73 73 ``(bgdinfill = no) [boolean]``
74   - Infill of background template?.
  74 + Infill of background template?
75 75  
76 76  
77 77 Standard parameters
... ... @@ -80,23 +80,23 @@ Standard parameters
80 80 ``(chatter = 2) [integer]``
81 81 Verbosity of the executable:
82 82 ``chatter = 0``: no information will be logged
83   -
  83 +
84 84 ``chatter = 1``: only errors will be logged
85   -
  85 +
86 86 ``chatter = 2``: errors and actions will be logged
87   -
  87 +
88 88 ``chatter = 3``: report about the task execution
89   -
  89 +
90 90 ``chatter = 4``: detailed report about the task execution
91   -
  91 +
92 92 ``(clobber = yes) [boolean]``
93 93 Specifies whether an existing output file should be overwritten.
94   -
  94 +
95 95 ``(debug = no) [boolean]``
96 96 Enables debug mode. In debug mode the executable will dump any log file output to the console.
97   -
  97 +
98 98 ``(mode = ql) [string]``
99   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  99 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
100 100  
101 101 ``(logfile = csroot2caldb.log) [filename]``
102 102 Log filename.
... ...
doc/source/users/reference_manual/cssens.rst
  View file @7c7ef2a
... ... @@ -10,33 +10,30 @@ Synopsis
10 10 --------
11 11  
12 12 This script computes the differential or integrated CTA sensitivity using
13   -maximum likelihood fitting of a test source. The differential sensitivity
14   -is determined for a number of energy bins, the integral sensitivity is
15   -determined for a number of energy thresholds. The test source is fitted to
16   -simulated data using :doc:`ctlike` to determine it's detection significance
17   -as a function of source flux. The source flux is then varied until the
18   -source significance achieves a given level, specified by the (hidden)
19   -significance parameter ``sigma``. To damp variations between individual
20   -Monte Carlo simulations, a sliding average is applied in the significance
21   -computation (controlled by hidden ``num_avg`` parameter).
22   -
23   -The significance is estimated using the Test Statistic value, defined as
24   -twice the log-likelihood difference that is obtained when fitting the
25   -simulated data with and without the test source. The simplified assumption
26   -is made that the significance (in Gaussian sigma) is the square root of
27   -the Test Statistic.
28   -
29   -cssens will generate an ASCII file in comma-separated value (CSV) format
30   -containing the sensitivity as function of energy. The first row is a header
31   -row providing the column names. The following rows provide the mean
32   -logarithmic energy and the boundaries of the energy bin for which the
33   -sensitivity was computed. They also provide the flux within the energy bin
34   -in Crab units, in photons (ph/cm2/s) and in energy (erg/cm2/s). Finally,
35   -the sensitivity is given as the test source spectrum evaluated at the mean
36   -logarithmic energy multiplied by the energy squared (erg/cm2/s).
37   -
38   -The sensitivity can be displayed using the ``show_sensitivity.py`` script
39   -in the example folder. Matplotlib is required to execute the script.
  13 +maximum likelihood fitting of a test source. The differential sensitivity is
  14 +determined for a number of energy bins, the integral sensitivity is determined
  15 +for a number of energy thresholds. The test source is fitted to simulated data
  16 +using :doc:`ctlike` to determine it's detection significance as a function of
  17 +source flux. The source flux is then varied until the source significance
  18 +achieves a given level, specified by the (hidden) significance parameter
  19 +``sigma``.
  20 +
  21 +The significance is estimated using the Test Statistic value, defined as twice
  22 +the log-likelihood difference that is obtained when fitting the simulated data
  23 +with and without the test source. The simplified assumption is made that the
  24 +significance (in Gaussian sigma) is the square root of the Test Statistic.
  25 +
  26 +:ref:`cssens` will generate an ASCII file in comma-separated value (CSV) format
  27 +containing the sensitivity as function of energy. The first row is a header row
  28 +providing the column names. The following rows provide the mean logarithmic
  29 +energy and the boundaries of the energy bin for which the sensitivity was
  30 +computed. They also provide the flux within the energy bin in Crab units, in
  31 +photons (ph/cm2/s) and in energy (erg/cm2/s). Finally, the sensitivity is given
  32 +as the test source spectrum evaluated at the mean logarithmic energy multiplied
  33 +by the energy squared (erg/cm2/s).
  34 +
  35 +The sensitivity can be displayed using the ``show_sensitivity.py`` script in the
  36 +example folder. Matplotlib is required to execute the script.
40 37  
41 38  
42 39 General parameters
... ... @@ -61,7 +58,7 @@ General parameters
61 58 ``(edisp = no) [boolean]``
62 59 Apply energy dispersion to response computation?
63 60  
64   -``(deadc = 0.95) [real]``
  61 +``(deadc = 0.98) [real]``
65 62 Average deadtime correction factor.
66 63  
67 64 ``outfile [file]``
... ... @@ -135,7 +132,7 @@ Standard parameters
135 132 output to the console.
136 133  
137 134 ``(mode = ql) [string]``
138   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  135 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
139 136  
140 137 ``(logfile = cssens.log) [filename]``
141 138 Log filename.
... ...
doc/source/users/reference_manual/csspec.rst
  View file @7c7ef2a
... ... @@ -19,23 +19,28 @@ significance of the source detection. Optionally, it also computes an upper
19 19 flux limit that is particularly useful in case that the source is not
20 20 significantly detected within a spectral bin (hidden parameter ``calc_ulim``).
21 21  
22   -The script works on binned and unbinned data.
23   -
24   -For unbinned data, the spectral binning is either defined by a FITS file
25   -containing the energy boundaries of each bin (option ``ebinalg=FILE``) or
26   -as ``enumbins`` bins spread linearly (option ``ebinalg=LIN``) or
27   -logarithmically (option ``ebinalg=LOG``) from a minimum energy given by
28   -``emin`` to a maximum energy given by ``emax``.
29   -
30   -For binned data, all energy bins within the counts cube that overlap with
31   -the energy range spanned by ``emin`` and ``emax`` are considered. The number
32   -of spectral bins is only approximately determined by the ``enumbins`` parameter.
33   -Naturally, the script cannot create more spectral bins than the number of
34   -energy bins that are available in the cube. Also, in case that ``enumbins``
35   -is smaller than the number of energy bins in the cube, the script will fit
36   -several layers of the counts cube for each spectral bin. The number of
37   -layers fit is determined by the total number of energy bins divided by the
38   -``enumbins`` parameter.
  22 +There are two fundamental methods to run the script depending on the value of
  23 +the ``method`` parameter. If ``method=SLICE`` the energy interval defined by the
  24 +``emin`` and ``emax`` parameters is divided into a number of energy bins and an
  25 +independent maximum likelihood fit is performed in each of the energy bins,
  26 +while if ``method=NODES`` the spectral model will be replaced by a node function
  27 +that will be fit to all data. The latter is particularly useful if non-CTA data
  28 +should be fitted such as data from Fermi/LAT or COMPTEL. By default, ``method`` is
  29 +set to ``AUTO`` which will automatically select the method based on the input data.
  30 +For CTA-only observations ``SLICE`` will be used, otherwise ``NODES`` will be used.
  31 +
  32 +The spectral binning is either defined by a FITS file containing the energy
  33 +boundaries of each bin (option ``ebinalg=FILE``) or as ``enumbins`` bins spread
  34 +linearly (option ``ebinalg=LIN``) or logarithmically (option ``ebinalg=LOG``)
  35 +from a minimum energy, given by ``emin``, to a maximum energy, given by ``emax``.
  36 +
  37 +For binned, stacked or On/Off CTA data, all energy bins that overlap with the
  38 +energy range spanned by ``emin`` and ``emax`` are considered. The number of spectral
  39 +bins is only approximately determined by the ``enumbins`` parameter. Naturally,
  40 +:ref:`csspec` cannot create more spectral bins than the number of energy bins that
  41 +are available in the data. In case that there are more energy bins in the data
  42 +than the number of spectral bins that are requested, :ref:`csspec` will fit the
  43 +data in all energy bins that overlap with a given spectral bin simultaneously.
39 44  
40 45 On output, the script will provide a FITS file with the fitted source
41 46 spectrum in form of a binary table. Each row corresponds to a spectral bin.
... ... @@ -44,11 +49,14 @@ the fitted flux and flux error, the Test Statistics value (option
44 49 ``calc_ts=yes``), the upper flux limit (option ``calc_ulim=yes``) and the
45 50 predicted number of events (only for unbinned data).
46 51  
  52 +.. warning::
  53 + The upper limit computation is not yet implemented for the ``NODES`` method.
  54 +
47 55  
48 56 General parameters
49 57 ------------------
50 58  
51   -``(inobs = NONE) [file]``
  59 +``inobs [file]``
52 60 Input event list, counts cube or observation definition XML file.
53 61  
54 62 ``inmodel [file]``
... ... @@ -84,11 +92,11 @@ General parameters
84 92  
85 93 ``method <SLICE|NODES|AUTO> [string]``
86 94 Spectrum generation method.
87   - ``SLICE``: Slice energy interval into ``enumbins`` independent bins.
88   - ``NODES``: Replace spectral model by node function with ``enumbins`` nodes.
89   - ``AUTO`` : Automatically select method based on input data. Will use
90   - ``SLICE`` for CTA-only observations and ``NODES`` for
91   - observations including non-CTA data.
  95 + ``SLICE`` will slice energy interval into ``enumbins`` independent bins,
  96 + ``NODES`` will replace spectral model by node function with ``enumbins``
  97 + nodes, and ``AUTO`` will automatically select the method based on the input
  98 + data. For CTA-only observations ``SLICE`` will be used, otherwise ``NODES``
  99 + will be used.
92 100  
93 101 ``emin [real]``
94 102 Lower energy limit of events (in TeV).
... ... @@ -153,7 +161,7 @@ Standard parameters
153 161 output to the console.
154 162  
155 163 ``(mode = ql) [string]``
156   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  164 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
157 165  
158 166 ``(logfile = csspec.log) [filename]``
159 167 Log filename.
... ...
doc/source/users/reference_manual/cssrcdetect.rst
  View file @7c7ef2a
... ... @@ -61,31 +61,31 @@ General parameters
61 61 ``(fit_shape = yes) [boolean]``
62 62 Enable fitting of source shapes in model definiton XML file?
63 63  
64   -
  64 +
65 65 Standard parameters
66 66 -------------------
67 67  
68 68 ``(chatter = 2) [integer]``
69 69 Verbosity of the executable:
70 70 ``chatter = 0``: no information will be logged
71   -
  71 +
72 72 ``chatter = 1``: only errors will be logged
73   -
  73 +
74 74 ``chatter = 2``: errors and actions will be logged
75   -
  75 +
76 76 ``chatter = 3``: report about the task execution
77   -
  77 +
78 78 ``chatter = 4``: detailed report about the task execution
79   -
  79 +
80 80 ``(clobber = yes) [boolean]``
81 81 Specifies whether an existing output model file should be overwritten.
82   -
  82 +
83 83 ``(debug = no) [boolean]``
84 84 Enables debug mode. In debug mode the executable will dump any log file
85 85 output to the console.
86   -
  86 +
87 87 ``(mode = ql) [string]``
88   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  88 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
89 89  
90 90 ``(logfile = cssrcdetect.log) [filename]``
91 91 Log filename.
... ...
doc/source/users/reference_manual/cstsdist.rst
  View file @7c7ef2a
... ... @@ -106,7 +106,7 @@ Standard parameters
106 106 output to the console.
107 107  
108 108 ``(mode = ql) [string]``
109   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  109 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
110 110  
111 111 ``(logfile = cstsdist.log) [string]``
112 112 Log filename.
... ... @@ -117,4 +117,3 @@ Related tools or scripts
117 117  
118 118 :doc:`ctlike`
119 119 :doc:`cspull`
120   -
... ...
doc/source/users/reference_manual/cstsmapmerge.rst
  View file @7c7ef2a
... ... @@ -16,10 +16,10 @@ map again. Running :doc:`cttsmap` with the hidden parameters ``binmin`` and
16 16 them into one FITS file. The input slices can be passed via the ``inmaps``
17 17 parameter. There are 4 options to specify a list of files that should be merged:
18 18  
19   -* a space-separated list of file names (e.g. tsmap1.fits tsmap2.fits)
20   -* a comma-separated list of file names (e.g. tsmap1.fits,tsmap2.fits)
21   -* a wildcard string (e.g. tsmap*.xml)
22   -* an ASCII file containing the file names, one file per line (e.g. @mymaps.txt)
  19 +- a space-separated list of file names (e.g. tsmap1.fits tsmap2.fits)
  20 +- a comma-separated list of file names (e.g. tsmap1.fits,tsmap2.fits)
  21 +- a wildcard string (e.g. tsmap*.xml)
  22 +- an ASCII file containing the file names, one file per line (e.g. @mymaps.txt)
23 23  
24 24 Note that the "@" needs to be specified in case of an ASCII file name.
25 25  
... ... @@ -31,37 +31,37 @@ General parameters
31 31  
32 32 ``outmap [file]``
33 33 Output TS map FITS file
34   -
  34 +
35 35 ``(overwrite=yes) [boolean]``
36 36 Overwrite previously filled bins?
37 37  
38 38 ``(delete=no) [boolean]``
39 39 Delete merged files?
40   -
41   -
  40 +
  41 +
42 42 Standard parameters
43 43 -------------------
44 44  
45 45 ``(chatter = 2) [integer]``
46 46 Verbosity of the executable:
47 47 ``chatter = 0``: no information will be logged
48   -
  48 +
49 49 ``chatter = 1``: only errors will be logged
50   -
  50 +
51 51 ``chatter = 2``: errors and actions will be logged
52   -
  52 +
53 53 ``chatter = 3``: report about the task execution
54   -
  54 +
55 55 ``chatter = 4``: detailed report about the task execution
56   -
  56 +
57 57 ``(clobber = yes) [boolean]``
58 58 Specifies whether an existing output TS map file should be overwritten.
59   -
  59 +
60 60 ``(debug = no) [boolean]``
61 61 Enables debug mode. In debug mode the executable will dump any log file output to the console.
62   -
  62 +
63 63 ``(mode = ql) [string]``
64   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  64 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
65 65  
66 66 ``(logfile = cstsmapmerge.log) [filename]``
67 67 Log filename.
... ...
doc/source/users/reference_manual/cstsmapsplit.rst
  View file @7c7ef2a
... ... @@ -3,7 +3,7 @@
3 3 cstsmapsplit
4 4 ============
5 5  
6   -Generate commands to split the Test Statistic map computation
  6 +Generate commands to split the Test Statistic map computation.
7 7  
8 8  
9 9 Synopsis
... ... @@ -48,21 +48,24 @@ General parameters
48 48 Instrumental response function.
49 49  
50 50 ``(edisp = no) [boolean]``
51   - Applies energy dispersion to response computation.
  51 + Applies energy dispersion to response computation?
52 52  
53 53 ``(errors = no) [boolean]``
54 54 Compute and store parameter errors?
55 55  
56   -``(statistic = CSTAT) <CSTAT|WSTAT|CHI2> [string]``
57   - Optimization statistic. ``CSTAT`` applies to all types of observations,
58   - ``WSTAT``applies only to On/Off observations, and ``CHI2`` applies only
59   - to binned or stacked observations.
  56 +``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT|CHI2> [string]``
  57 + Optimization statistic. ``DEFAULT`` uses the default statistic for all
  58 + observations, which is ``CSTAT`` or the statistic specified in the
  59 + observation definition XML file. ``CSTAT`` uses the C statistic for
  60 + all observations, ``WSTAT`` uses the W statistic for all On/Off
  61 + observations, and ``CHI2`` uses the Chi squared statistic for all
  62 + binned or stacked observations.
60 63  
61 64 ``outmap [file]``
62 65 Output Test Statistic map file.
63 66  
64 67 ``bins_per_job [integer]``
65   - Number of bins of the TS map that should be computed within one command
  68 + Number of bins of the TS map that should be computed within one command.
66 69  
67 70 ``compute_null [boolean]``
68 71 Pre-computes the null hypothesis globally and passes the value to the
... ... @@ -78,28 +81,28 @@ General parameters
78 81  
79 82 ``(usepnt = no) [boolean]``
80 83 Use CTA pointing direction for map centre instead of xref/yref parameters?
81   -
  84 +
82 85 ``nxpix [integer]``
83 86 Number of map pixels in Right Ascension or Galactic longitude.
84   -
  87 +
85 88 ``nypix [integer]``
86 89 Number of map pixels in Declination or Galactic latitude.
87   -
  90 +
88 91 ``binsz [real]``
89 92 Map pixel size (in degrees/pixel).
90   -
  93 +
91 94 ``coordsys <CEL|GAL> [string]``
92 95 Coordinate system (CEL - celestial, GAL - galactic).
93   -
  96 +
94 97 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
95 98 Projection method.
96 99  
97 100 ``xref [real]``
98 101 Right Ascension / Galactic longitude of map centre (J2000, in degrees).
99   -
  102 +
100 103 ``yref [real]``
101 104 Declination / Galactic latitude of map centre (J2000, in degrees).
102   -
  105 +
103 106  
104 107 Standard parameters
105 108 -------------------
... ... @@ -107,24 +110,24 @@ Standard parameters
107 110 ``(chatter = 2) [integer]``
108 111 Verbosity of the executable:
109 112 ``chatter = 0``: no information will be logged
110   -
  113 +
111 114 ``chatter = 1``: only errors will be logged
112   -
  115 +
113 116 ``chatter = 2``: errors and actions will be logged
114   -
  117 +
115 118 ``chatter = 3``: report about the task execution
116   -
  119 +
117 120 ``chatter = 4``: detailed report about the task execution
118   -
  121 +
119 122 ``(clobber = yes) [boolean]``
120 123 Specifies whether an existing output TS map file should be overwritten.
121   -
  124 +
122 125 ``(debug = no) [boolean]``
123 126 Enables debug mode. In debug mode the executable will dump any log file
124 127 output to the console.
125   -
  128 +
126 129 ``(mode = ql) [string]``
127   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  130 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
128 131  
129 132 ``(logfile = cstsmapsplit.log) [string]``
130 133 Name of log file.
... ...
doc/source/users/reference_manual/csviscube.rst
  View file @7c7ef2a
... ... @@ -64,23 +64,23 @@ Standard parameters
64 64 ``(chatter = 2) [integer]``
65 65 Verbosity of the executable:
66 66 ``chatter = 0``: no information will be logged
67   -
  67 +
68 68 ``chatter = 1``: only errors will be logged
69   -
  69 +
70 70 ``chatter = 2``: errors and actions will be logged
71   -
  71 +
72 72 ``chatter = 3``: report about the task execution
73   -
  73 +
74 74 ``chatter = 4``: detailed report about the task execution
75   -
  75 +
76 76 ``(clobber = yes) [boolean]``
77 77 Specifies whether an existing visibility cube file should be overwritten.
78   -
  78 +
79 79 ``(debug = no) [boolean]``
80 80 Enables debug mode. In debug mode the executable will dump any log file output to the console.
81   -
  81 +
82 82 ``(mode = ql) [string]``
83   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  83 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
84 84  
85 85 ``(logfile = csviscube.log) [filename]``
86 86 Log filename.
... ...
doc/source/users/reference_manual/ctbin.rst
  View file @7c7ef2a
... ... @@ -34,46 +34,46 @@ General parameters
34 34  
35 35 ``outcube [file]``
36 36 Output counts cube file.
37   -
  37 +
38 38 ``ebinalg <FILE|LIN|LOG> [string]``
39 39 Algorithm for defining energy bins.
40   -
  40 +
41 41 ``emin [real]``
42 42 Lower energy value for first energy bin (in TeV).
43   -
  43 +
44 44 ``emax [real]``
45 45 Upper energy value for last energy bin (in TeV).
46   -
  46 +
47 47 ``enumbins [integer]``
48 48 Number of energy bins.
49   -
  49 +
50 50 ``ebinfile [file]``
51 51 Name of the file containing the energy bin definition.
52   -
  52 +
53 53 ``(usepnt = no) [boolean]``
54 54 Use CTA pointing direction for cube centre instead of xref/yref parameters?
55   -
  55 +
56 56 ``nxpix [integer]``
57 57 Number of cube bins in Right Ascension or Galactic longitude.
58   -
  58 +
59 59 ``nypix [integer]``
60 60 Number of cube bins in Declination or Galactic latitude.
61   -
  61 +
62 62 ``binsz [real]``
63 63 Cube bin size (in degrees/pixel).
64   -
  64 +
65 65 ``coordsys <CEL|GAL> [string]``
66 66 Coordinate system (CEL - celestial, GAL - galactic).
67   -
  67 +
68 68 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
69 69 Projection method.
70   -
  70 +
71 71 ``xref [real]``
72 72 Right Ascension / Galactic longitude of cube centre (J2000, in degrees).
73   -
  73 +
74 74 ``yref [real]``
75 75 Declination / Galactic latitude of cube centre (J2000, in degrees).
76   -
  76 +
77 77  
78 78 Standard parameters
79 79 -------------------
... ... @@ -84,23 +84,23 @@ Standard parameters
84 84 ``(chatter = 2) [integer]``
85 85 Verbosity of the executable:
86 86 ``chatter = 0``: no information will be logged
87   -
  87 +
88 88 ``chatter = 1``: only errors will be logged
89   -
  89 +
90 90 ``chatter = 2``: errors and actions will be logged
91   -
  91 +
92 92 ``chatter = 3``: report about the task execution
93   -
  93 +
94 94 ``chatter = 4``: detailed report about the task execution
95   -
  95 +
96 96 ``(clobber = yes) [boolean]``
97 97 Specifies whether an existing output counts cube file should be overwritten.
98   -
  98 +
99 99 ``(debug = no) [boolean]``
100 100 Enables debug mode. In debug mode the executable will dump any log file output to the console.
101   -
  101 +
102 102 ``(mode = ql) [string]``
103   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  103 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
104 104  
105 105 ``(logfile = ctbin.log) [string]``
106 106 Name of log file.
... ...
doc/source/users/reference_manual/ctbkgcube.rst
  View file @7c7ef2a
... ... @@ -47,7 +47,6 @@ as spectral component, but you can replace this by any component of your
47 47 choice.
48 48  
49 49  
50   -
51 50 General parameters
52 51 ------------------
53 52  
... ... @@ -74,16 +73,16 @@ General parameters
74 73  
75 74 ``ebinalg <FILE|LIN|LOG> [string]``
76 75 Algorithm for defining energy bins.
77   -
  76 +
78 77 ``emin [real]``
79 78 Lower energy value for first energy bin (in TeV).
80   -
  79 +
81 80 ``emax [real]``
82 81 Upper energy value for last energy bin (in TeV).
83   -
  82 +
84 83 ``enumbins [integer]``
85 84 Number of energy bins.
86   -
  85 +
87 86 ``ebinfile [file]``
88 87 Name of the file containing the energy bin definition.
89 88  
... ... @@ -92,28 +91,28 @@ General parameters
92 91  
93 92 ``(usepnt = no) [boolean]``
94 93 Use CTA pointing direction for cube centre instead of xref/yref parameters?
95   -
  94 +
96 95 ``nxpix [integer]``
97 96 Number of cube bins in Right Ascension or Galactic longitude.
98   -
  97 +
99 98 ``nypix [integer]``
100 99 Number of cube bins in Declination or Galactic latitude.
101   -
  100 +
102 101 ``binsz [real]``
103 102 Cube bin size (in degrees/pixel).
104   -
  103 +
105 104 ``coordsysL <CEL|GAL> [string]``
106 105 Coordinate system (CEL - celestial, GAL - galactic).
107   -
  106 +
108 107 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
109 108 Projection method.
110   -
  109 +
111 110 ``xref [real]``
112 111 Right Ascension / Galactic longitude of cube centre (J2000, in degrees).
113   -
  112 +
114 113 ``yref [real]``
115 114 Declination / Galactic latitude of cube centre (J2000, in degrees).
116   -
  115 +
117 116  
118 117 Standard parameters
119 118 -------------------
... ... @@ -124,23 +123,23 @@ Standard parameters
124 123 ``(chatter = 2) [integer]``
125 124 Verbosity of the executable:
126 125 ``chatter = 0``: no information will be logged
127   -
  126 +
128 127 ``chatter = 1``: only errors will be logged
129   -
  128 +
130 129 ``chatter = 2``: errors and actions will be logged
131   -
  130 +
132 131 ``chatter = 3``: report about the task execution
133   -
  132 +
134 133 ``chatter = 4``: detailed report about the task execution
135   -
  134 +
136 135 ``(clobber = yes) [boolean]``
137 136 Specifies whether an existing output background cube file should be overwritten.
138   -
  137 +
139 138 ``(debug = no) [boolean]``
140 139 Enables debug mode. In debug mode the executable will dump any log file output to the console.
141   -
  140 +
142 141 ``(mode = ql) [string]``
143   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  142 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
144 143  
145 144 ``(logfile = ctbkgcube.log) [string]``
146 145 Name of log file.
... ...
doc/source/users/reference_manual/ctbutterfly.rst
  View file @7c7ef2a
... ... @@ -31,10 +31,10 @@ ctbutterfly writes the butterfly diagram into an ASCII file with 4 columns
31 31 separated by a whitespace. Each row in the result file corresponds to a specific
32 32 energy. The meaning of the columns are:
33 33  
34   -* Energy in MeV
35   -* Fitted intensity for that energy in ph/cm2/s/MeV
36   -* Minimum intensity for that energy in ph/cm2/s/MeV
37   -* Maximum intensity for that energy in ph/cm2/s/MeV
  34 +- Energy in MeV
  35 +- Fitted intensity for that energy in ph/cm2/s/MeV
  36 +- Minimum intensity for that energy in ph/cm2/s/MeV
  37 +- Maximum intensity for that energy in ph/cm2/s/MeV
38 38  
39 39 The butterfly diagram can be displayed using the ``show_butterfly.py`` script
40 40 in the example folder.
... ... @@ -45,13 +45,13 @@ General parameters
45 45  
46 46 ``inobs [file]``
47 47 Input event list, counts cube or observation definition XML file.
48   -
  48 +
49 49 ``inmodel [file]``
50 50 Input model XML file.
51   -
  51 +
52 52 ``srcname [string]``
53 53 Name of source model for which the butterfly diagram should be computed.
54   -
  54 +
55 55 ``expcube [file]``
56 56 Input exposure cube file.
57 57  
... ... @@ -66,16 +66,16 @@ General parameters
66 66  
67 67 ``caldb [string]``
68 68 Calibration database.
69   -
  69 +
70 70 ``irf [string]``
71 71 Instrumental response function.
72 72  
73 73 ``(edisp = no) [boolean]``
74 74 Applies energy dispersion to response computation.
75   -
  75 +
76 76 ``outfile [file]``
77 77 Output butterfly ASCII file name.
78   -
  78 +
79 79 ``(fit = no) [boolean]``
80 80 Performs maximum likelihood fitting of input model ignoring any provided
81 81 covariance matrix.
... ... @@ -85,7 +85,7 @@ General parameters
85 85  
86 86 ``(confidence = 0.68) [real]``
87 87 Confidence level for error computation.
88   -
  88 +
89 89 ``(statistic = DEFAULT) <DEFAULT|CSTAT|WSTAT|CHI2> [string]``
90 90 Optimization statistic. ``DEFAULT`` uses the default statistic for all
91 91 observations, which is ``CSTAT`` or the statistic specified in the
... ... @@ -119,23 +119,23 @@ Standard parameters
119 119 ``(chatter = 2) [integer]``
120 120 Verbosity of the executable:
121 121 ``chatter = 0``: no information will be logged
122   -
  122 +
123 123 ``chatter = 1``: only errors will be logged
124   -
  124 +
125 125 ``chatter = 2``: errors and actions will be logged
126   -
  126 +
127 127 ``chatter = 3``: report about the task execution
128   -
  128 +
129 129 ``chatter = 4``: detailed report about the task execution
130   -
  130 +
131 131 ``(clobber = yes) [boolean]``
132 132 Specifies whether an existing output file should be overwritten.
133   -
  133 +
134 134 ``(debug = no) [boolean]``
135 135 Enables debug mode. In debug mode the executable will dump any log file output to the console.
136   -
  136 +
137 137 ``(mode = ql) [string]``
138   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  138 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
139 139  
140 140 ``(logfile = ctbutterfly.log) [string]``
141 141 Name of log file.
... ...
doc/source/users/reference_manual/ctcubemask.rst
  View file @7c7ef2a
... ... @@ -46,10 +46,10 @@ General parameters
46 46  
47 47 ``(usepnt = no) [boolean]``
48 48 Use CTA pointing direction instead of ra/dec parameters?
49   -
  49 +
50 50 ``ra [real]``
51 51 Right Ascension of circular selection region centre (J2000, in degrees).
52   -
  52 +
53 53 ``dec [real]``
54 54 Declination of circular selection region centre (J2000, in degrees).
55 55  
... ... @@ -61,10 +61,10 @@ General parameters
61 61  
62 62 ``emin [real]``
63 63 Lower energy limit (in TeV).
64   -
  64 +
65 65 ``emax [real]``
66 66 Upper energy limit (in TeV).
67   -
  67 +
68 68  
69 69 Standard parameters
70 70 -------------------
... ... @@ -75,23 +75,23 @@ Standard parameters
75 75 ``(chatter = 2) [integer]``
76 76 Verbosity of the executable:
77 77 ``chatter = 0``: no information will be logged
78   -
  78 +
79 79 ``chatter = 1``: only errors will be logged
80   -
  80 +
81 81 ``chatter = 2``: errors and actions will be logged
82   -
  82 +
83 83 ``chatter = 3``: report about the task execution
84   -
  84 +
85 85 ``chatter = 4``: detailed report about the task execution
86   -
  86 +
87 87 ``(clobber = yes) [boolean]``
88 88 Specifies whether an existing output counts cube file should be overwritten.
89   -
  89 +
90 90 ``(debug = no) [boolean]``
91 91 Enables debug mode. In debug mode the executable will dump any log file output to the console.
92   -
  92 +
93 93 ``(mode = ql) [string]``
94   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  94 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
95 95  
96 96 ``(logfile = ctcubemask.log) [string]``
97 97 Name of log file.
... ...
doc/source/users/reference_manual/ctedispcube.rst
  View file @7c7ef2a
... ... @@ -57,52 +57,52 @@ General parameters
57 57  
58 58 ``ebinalg <FILE|LIN|LOG> [string]``
59 59 Algorithm for defining energy bins.
60   -
  60 +
61 61 ``emin [real]``
62 62 Lower energy value for first energy bin (in TeV).
63   -
  63 +
64 64 ``emax [real]``
65 65 Upper energy value for last energy bin (in TeV).
66   -
  66 +
67 67 ``enumbins [integer]``
68 68 Number of energy bins.
69   -
  69 +
70 70 ``ebinfile [file]``
71 71 Name of the file containing the energy bin definition.
72   -
  72 +
73 73 ``(addbounds = no) [boolean]``
74 74 Add energies to the energy dispersion cube at the observation energy boundaries?
75 75  
76 76 ``(usepnt = no) [boolean]``
77 77 Use CTA pointing direction for cube centre instead of xref/yref parameters?
78   -
  78 +
79 79 ``nxpix [integer]``
80 80 Number of cube bins in Right Ascension or Galactic longitude.
81   -
  81 +
82 82 ``nypix [integer]``
83 83 Number of cube bins in Declination or Galactic latitude.
84   -
  84 +
85 85 ``binsz [real]``
86 86 Cube bin size (in degrees/pixel).
87   -
  87 +
88 88 ``coordsys <CEL|GAL> [string]``
89 89 Coordinate system (CEL - celestial, GAL - galactic).
90   -
  90 +
91 91 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
92 92 Projection method.
93 93  
94 94 ``xref [real]``
95 95 Right Ascension / Galactic longitude of cube centre (J2000, in degrees).
96   -
  96 +
97 97 ``yref [real]``
98 98 Declination / Galactic latitude of cube centre (J2000, in degrees).
99   -
  99 +
100 100 ``(migramax = 2.0) [real]``
101 101 Upper bound of ratio between reconstructed and true photon energy.
102 102  
103 103 ``(migrabins = 100) [integer]``
104 104 Number of migration bins.
105   -
  105 +
106 106  
107 107 Standard parameters
108 108 -------------------
... ... @@ -110,23 +110,23 @@ Standard parameters
110 110 ``(chatter = 2) [integer]``
111 111 Verbosity of the executable:
112 112 ``chatter = 0``: no information will be logged
113   -
  113 +
114 114 ``chatter = 1``: only errors will be logged
115   -
  115 +
116 116 ``chatter = 2``: errors and actions will be logged
117   -
  117 +
118 118 ``chatter = 3``: report about the task execution
119   -
  119 +
120 120 ``chatter = 4``: detailed report about the task execution
121   -
  121 +
122 122 ``(clobber = yes) [boolean]``
123 123 Specifies whether an existing output energy dispersion cube file should be overwritten.
124   -
  124 +
125 125 ``(debug = no) [boolean]``
126 126 Enables debug mode. In debug mode the executable will dump any log file output to the console.
127   -
  127 +
128 128 ``(mode = ql) [string]``
129   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  129 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
130 130  
131 131 ``(logfile = ctedispcube.log) [string]``
132 132 Name of log file.
... ...
doc/source/users/reference_manual/cterror.rst
  View file @7c7ef2a
... ... @@ -86,23 +86,23 @@ Standard parameters
86 86 ``(chatter = 2) [integer]``
87 87 Verbosity of the executable:
88 88 ``chatter = 0``: no information will be logged
89   -
  89 +
90 90 ``chatter = 1``: only errors will be logged
91   -
  91 +
92 92 ``chatter = 2``: errors and actions will be logged
93   -
  93 +
94 94 ``chatter = 3``: report about the task execution
95   -
  95 +
96 96 ``chatter = 4``: detailed report about the task execution
97   -
  97 +
98 98 ``(clobber = yes) [boolean]``
99 99 Specifies whether an existing output file should be overwritten.
100   -
  100 +
101 101 ``(debug = no) [boolean]``
102 102 Enables debug mode. In debug mode the executable will dump any log file output to the console.
103   -
  103 +
104 104 ``(mode = ql) [string]``
105   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  105 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
106 106  
107 107 ``(logfile = cterror.log) [string]``
108 108 Name of log file.
... ...
doc/source/users/reference_manual/ctexpcube.rst
  View file @7c7ef2a
... ... @@ -64,16 +64,16 @@ General parameters
64 64  
65 65 ``ebinalg <FILE|LIN|LOG> [string]``
66 66 Algorithm for defining energy bins.
67   -
  67 +
68 68 ``emin [real]``
69 69 Lower energy value for first energy bin (in TeV).
70   -
  70 +
71 71 ``emax [real]``
72 72 Upper energy value for last energy bin (in TeV).
73   -
  73 +
74 74 ``enumbins [integer]``
75 75 Number of energy bins.
76   -
  76 +
77 77 ``ebinfile [file]``
78 78 Name of the file containing the energy bin definition.
79 79  
... ... @@ -82,25 +82,25 @@ General parameters
82 82  
83 83 ``(usepnt = no) [boolean]``
84 84 Use CTA pointing direction for cube centre instead of xref/yref parameters?
85   -
  85 +
86 86 ``nxpix [integer]``
87 87 Number of cube bins in Right Ascension or Galactic longitude.
88   -
  88 +
89 89 ``nypix [integer]``
90 90 Number of cube bins in Declination or Galactic latitude.
91   -
  91 +
92 92 ``binsz [real]``
93 93 Cube bin size (in degrees/pixel).
94   -
  94 +
95 95 ``coordsys <CEL|GAL> [string]``
96 96 Coordinate system (CEL - celestial, GAL - galactic).
97   -
  97 +
98 98 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
99 99 Projection method.
100 100  
101 101 ``xref [real]``
102 102 Right Ascension / Galactic longitude of cube centre (J2000, in degrees).
103   -
  103 +
104 104 ``yref [real]``
105 105 Declination / Galactic latitude of cube centre (J2000, in degrees).
106 106  
... ... @@ -114,23 +114,23 @@ Standard parameters
114 114 ``(chatter = 2) [integer]``
115 115 Verbosity of the executable:
116 116 ``chatter = 0``: no information will be logged
117   -
  117 +
118 118 ``chatter = 1``: only errors will be logged
119   -
  119 +
120 120 ``chatter = 2``: errors and actions will be logged
121   -
  121 +
122 122 ``chatter = 3``: report about the task execution
123   -
  123 +
124 124 ``chatter = 4``: detailed report about the task execution
125   -
  125 +
126 126 ``(clobber = yes) [boolean]``
127 127 Specifies whether an existing output exposure cube file should be overwritten.
128   -
  128 +
129 129 ``(debug = no) [boolean]``
130 130 Enables debug mode. In debug mode the executable will dump any log file output to the console.
131   -
  131 +
132 132 ``(mode = ql) [string]``
133   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  133 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
134 134  
135 135 ``(logfile = ctexpcube.log) [string]``
136 136 Name of log file.
... ...
doc/source/users/reference_manual/ctlike.rst
  View file @7c7ef2a
... ... @@ -65,7 +65,7 @@ General parameters
65 65  
66 66 ``inmodel [string]``
67 67 Input model XML file.
68   -
  68 +
69 69 ``expcube [file]``
70 70 Input exposure cube file.
71 71  
... ... @@ -80,10 +80,10 @@ General parameters
80 80  
81 81 ``caldb [string]``
82 82 Calibration database.
83   -
  83 +
84 84 ``irf [string]``
85 85 Instrument response function.
86   -
  86 +
87 87 ``(edisp = no) [boolean]``
88 88 Applies energy dispersion to response computation.
89 89  
... ... @@ -115,23 +115,23 @@ Standard parameters
115 115 ``(chatter = 2) [integer]``
116 116 Verbosity of the executable:
117 117 ``chatter = 0``: no information will be logged
118   -
  118 +
119 119 ``chatter = 1``: only errors will be logged
120   -
  120 +
121 121 ``chatter = 2``: errors and actions will be logged
122   -
  122 +
123 123 ``chatter = 3``: report about the task execution
124   -
  124 +
125 125 ``chatter = 4``: detailed report about the task execution
126   -
  126 +
127 127 ``(clobber = yes) [boolean]``
128 128 Specifies whether an existing output model file should be overwritten.
129   -
  129 +
130 130 ``(debug = no) [boolean]``
131 131 Enables debug mode. In debug mode the executable will dump any log file output to the console.
132   -
  132 +
133 133 ``(mode = ql) [string]``
134   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  134 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
135 135  
136 136 ``(logfile = ctlike.log) [string]``
137 137 Name of log file.
... ...
doc/source/users/reference_manual/ctmapcube.rst
  View file @7c7ef2a
... ... @@ -96,7 +96,7 @@ Standard parameters
96 96 Enables debug mode. In debug mode the executable will dump any log file output to the console.
97 97  
98 98 ``(mode = ql) [string]``
99   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  99 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
100 100  
101 101 ``(logfile = ctmapcube.log) [string]``
102 102 Name of log file.
... ...
doc/source/users/reference_manual/ctmodel.rst
  View file @7c7ef2a
... ... @@ -70,73 +70,73 @@ General parameters
70 70  
71 71 ``caldb [string]``
72 72 Calibration database.
73   -
  73 +
74 74 ``irf [string]``
75 75 Instrument response function.
76   -
  76 +
77 77 ``(edisp = no) [boolean]``
78 78 Apply energy dispersion to response computation.
79 79  
80 80 ``outcube [file]``
81 81 Output model cube file.
82   -
  82 +
83 83 ``ra [real]``
84 84 Right Ascension of pointing (J2000, in degrees).
85   -
  85 +
86 86 ``dec [real]``
87 87 Declination of pointing (J2000, in degrees).
88 88  
89 89 ``rad [real]``
90 90 Radius of field of view (in degrees).
91   -
  91 +
92 92 ``tmin [time]``
93 93 Start time (UTC string, JD, MJD or MET in seconds).
94   -
  94 +
95 95 ``tmax [time]``
96 96 Stop time (UTC string, JD, MJD or MET in seconds).
97   -
  97 +
98 98 ``(deadc = 0.95) [real]``
99 99 Average deadtime correction factor.
100 100  
101 101 ``(ebinalg = LOG) <FILE|LIN|LOG> [string]``
102 102 Algorithm for defining energy bins.
103   -
  103 +
104 104 ``emin [real]``
105 105 Lower energy value for first energy bin (in TeV).
106   -
  106 +
107 107 ``emax [real]``
108 108 Upper energy value for last energy bin (in TeV).
109   -
  109 +
110 110 ``enumbins [integer]``
111 111 Number of energy bins.
112   -
  112 +
113 113 ``(ebinfile = NONE) [file]``
114 114 Name of the file containing the energy bin definition.
115 115  
116 116 ``(usepnt = no) [boolean]``
117 117 Use pointing instead of xref/yref parameters?
118   -
  118 +
119 119 ``nxpix [integer]``
120 120 Size of the Right Ascension / Galactic longitude axis (in pixels).
121   -
  121 +
122 122 ``nypix [integer]``
123 123 Size of the Declination / Galactic latitude axis (in pixels).
124   -
  124 +
125 125 ``binsz [real]``
126 126 Pixel size (in degrees/pixel).
127   -
  127 +
128 128 ``coordsys <CEL|GAL> [string]``
129 129 Coordinate system (CEL - celestial, GAL - galactic).
130   -
  130 +
131 131 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
132 132 Projection method.
133 133  
134 134 ``xref [real]``
135 135 Right Ascension / Galactic longitude of image centre (J2000, in degrees).
136   -
  136 +
137 137 ``yref [real]``
138 138 Declination / Galactic latitude of image centre (J2000, in degrees).
139   -
  139 +
140 140  
141 141 Standard parameters
142 142 -------------------
... ... @@ -147,23 +147,23 @@ Standard parameters
147 147 ``(chatter = 2) [integer]``
148 148 Verbosity of the executable:
149 149 ``chatter = 0``: no information will be logged
150   -
  150 +
151 151 ``chatter = 1``: only errors will be logged
152   -
  152 +
153 153 ``chatter = 2``: errors and actions will be logged
154   -
  154 +
155 155 ``chatter = 3``: report about the task execution
156   -
  156 +
157 157 ``chatter = 4``: detailed report about the task execution
158   -
  158 +
159 159 ``(clobber = yes) [boolean]``
160 160 Specifies whether an existing output model cube file should be overwritten.
161   -
  161 +
162 162 ``(debug = no) [boolean]``
163 163 Enables debug mode. In debug mode the executable will dump any log file output to the console.
164   -
  164 +
165 165 ``(mode = ql) [string]``
166   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  166 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
167 167  
168 168 ``(logfile = ctmodel.log) [string]``
169 169 Name of log file.
... ...
doc/source/users/reference_manual/ctobssim.rst
  View file @7c7ef2a
... ... @@ -49,19 +49,19 @@ General parameters
49 49  
50 50 ``inmodel [file]``
51 51 Input model XML file.
52   -
  52 +
53 53 ``caldb [string]``
54 54 Calibration database.
55   -
  55 +
56 56 ``irf [string]``
57 57 Instrumental response function.
58   -
  58 +
59 59 ``(edisp = no) [boolean]``
60 60 Apply energy dispersion?
61   -
  61 +
62 62 ``outevents [file]``
63 63 Output event list or observation definition XML file.
64   -
  64 +
65 65 ``(prefix = sim_events_) [string]``
66 66 Prefix for event list in observation definition XML file.
67 67  
... ... @@ -73,28 +73,28 @@ General parameters
73 73 parameter at the same value for repeatable simulations, or increment
74 74 this value for subsequent runs if non-repeatable simulations are
75 75 required.
76   -
  76 +
77 77 ``ra [real]``
78 78 Right Ascension of CTA pointing (J2000, in degrees).
79   -
  79 +
80 80 ``dec [real]``
81 81 Declination of CTA pointing (J2000, in degrees).
82   -
  82 +
83 83 ``rad [real]``
84 84 Radius of CTA field of view (simulation cone radius) (in degrees).
85   -
  85 +
86 86 ``tmin [time]``
87 87 Start time (UTC string, JD, MJD or MET in seconds).
88   -
  88 +
89 89 ``tmax [time]``
90 90 Stop time (UTC string, JD, MJD or MET in seconds).
91 91  
92 92 ``emin [real]``
93 93 Lower energy limit of simulated events (in TeV).
94   -
  94 +
95 95 ``emax [real]``
96 96 Upper energy limit of simulated events (in TeV).
97   -
  97 +
98 98 ``(deadc = 0.95) [real]``
99 99 Average deadtime correction factor.
100 100  
... ... @@ -115,23 +115,23 @@ Standard parameters
115 115 ``(chatter = 2) [integer]``
116 116 Verbosity of the executable:
117 117 ``chatter = 0``: no information will be logged
118   -
  118 +
119 119 ``chatter = 1``: only errors will be logged
120   -
  120 +
121 121 ``chatter = 2``: errors and actions will be logged
122   -
  122 +
123 123 ``chatter = 3``: report about the task execution
124   -
  124 +
125 125 ``chatter = 4``: detailed report about the task execution
126   -
  126 +
127 127 ``(clobber = yes) [boolean]``
128 128 Specifies whether existing files should be overwritten.
129   -
  129 +
130 130 ``(debug = no) [boolean]``
131 131 Enables debug mode. In debug mode the executable will dump any log file output to the console.
132   -
  132 +
133 133 ``(mode = ql) [string]``
134   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  134 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
135 135  
136 136 ``(logfile = ctobssim.log) [string]``
137 137 Name of log file.
... ...
doc/source/users/reference_manual/ctphase.rst
  View file @7c7ef2a
... ... @@ -23,13 +23,13 @@ General parameters
23 23  
24 24 ``inobs [file]``
25 25 Input event list or observation definition XML file.
26   -
  26 +
27 27 ``outobs [file]``
28 28 Output event list or observation definition XML file.
29   -
  29 +
30 30 ``(prefix = "phased_") [string]``
31 31 Prefix for output event lists in observation definition XML file.
32   -
  32 +
33 33 ``inmodel [string]``
34 34 Input model definition XML file. If ``NONE`` is specified the phase
35 35 computation will be based on the ``mjd``, ``phase``, ``f0``, ``f1``, and ``f2``
... ... @@ -64,23 +64,23 @@ Standard parameters
64 64 ``(chatter = 2) [integer]``
65 65 Verbosity of the executable:
66 66 ``chatter = 0``: no information will be logged
67   -
  67 +
68 68 ``chatter = 1``: only errors will be logged
69   -
  69 +
70 70 ``chatter = 2``: errors and actions will be logged
71   -
  71 +
72 72 ``chatter = 3``: report about the task execution
73   -
  73 +
74 74 ``chatter = 4``: detailed report about the task execution
75   -
  75 +
76 76 ``(clobber = yes) [boolean]``
77 77 Specifies whether existing output files should be overwritten.
78   -
  78 +
79 79 ``(debug = no) [boolean]``
80 80 Enables debug mode. In debug mode the executable will dump any log file output to the console.
81   -
  81 +
82 82 ``(mode = ql) [string]``
83   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  83 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
84 84  
85 85 ``(logfile = ctphase.log) [string]``
86 86 Name of log file.
... ...
doc/source/users/reference_manual/ctprob.rst
  View file @7c7ef2a
... ... @@ -22,22 +22,22 @@ General parameters
22 22  
23 23 ``inobs [file]``
24 24 Input event list or observation definition XML file
25   -
  25 +
26 26 ``outobs [file]``
27 27 Output event list or observation definition XML file.
28   -
  28 +
29 29 ``(prefix = "prob_") [string]``
30 30 Prefix for output event lists in observation definition XML file.
31   -
  31 +
32 32 ``inmodel [string]``
33 33 Input model definition XML file.
34 34  
35 35 ``caldb [string]``
36 36 Calibration database.
37   -
  37 +
38 38 ``irf [string]``
39 39 Instrument response function.
40   -
  40 +
41 41 ``(edisp = no) [boolean]``
42 42 Applies energy dispersion to response computation.
43 43  
... ... @@ -51,23 +51,23 @@ Standard parameters
51 51 ``(chatter = 2) [integer]``
52 52 Verbosity of the executable:
53 53 ``chatter = 0``: no information will be logged
54   -
  54 +
55 55 ``chatter = 1``: only errors will be logged
56   -
  56 +
57 57 ``chatter = 2``: errors and actions will be logged
58   -
  58 +
59 59 ``chatter = 3``: report about the task execution
60   -
  60 +
61 61 ``chatter = 4``: detailed report about the task execution
62   -
  62 +
63 63 ``(clobber = yes) [boolean]``
64 64 Specifies whether existing output files should be overwritten.
65   -
  65 +
66 66 ``(debug = no) [boolean]``
67 67 Enables debug mode. In debug mode the executable will dump any log file output to the console.
68   -
  68 +
69 69 ``(mode = ql) [string]``
70   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  70 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
71 71  
72 72 ``(logfile = ctprob.log) [string]``
73 73 Name of log file.
... ...
doc/source/users/reference_manual/ctpsfcube.rst
  View file @7c7ef2a
... ... @@ -56,53 +56,53 @@ General parameters
56 56  
57 57 ``ebinalg <FILE|LIN|LOG> [string]``
58 58 Algorithm for defining energy bins.
59   -
  59 +
60 60 ``emin [real]``
61 61 Lower energy value for first energy bin (in TeV).
62   -
  62 +
63 63 ``emax [real]``
64 64 Upper energy value for last energy bin (in TeV).
65   -
  65 +
66 66 ``enumbins [integer]``
67 67 Number of energy bins.
68   -
  68 +
69 69 ``ebinfile [file]``
70 70 Name of the file containing the energy bin definition.
71   -
  71 +
72 72 ``(addbounds = no) [boolean]``
73 73 Add energies to the point spread function cube at the observation energy boundaries?
74 74  
75 75 ``(usepnt = no) [boolean]``
76 76 Use CTA pointing direction for cube centre instead of xref/yref parameters?
77   -
  77 +
78 78 ``nxpix [integer]``
79 79 Number of cube bins in Right Ascension or Galactic longitude.
80   -
  80 +
81 81 ``nypix [integer]``
82 82 Number of cube bins in Declination or Galactic latitude.
83   -
  83 +
84 84 ``binsz [real]``
85 85 Cube bin size (in degrees/pixel).
86   -
  86 +
87 87 ``coordsys <CEL|GAL> [string]``
88 88 Coordinate system (CEL - celestial, GAL - galactic).
89   -
  89 +
90 90 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
91 91 Projection method.
92 92  
93 93 ``xref [real]``
94 94 Right Ascension / Galactic longitude of cube centre (J2000, in degrees).
95   -
  95 +
96 96 ``yref [real]``
97 97 Declination / Galactic latitude of cube centre (J2000, in degrees).
98   -
  98 +
99 99 ``(amax = 0.3) [real]``
100 100 Upper bound of angular separation between true and measued photon
101 101 direction (in degrees).
102 102  
103 103 ``(anumbins = 200) [integer]``
104 104 Number of angular separation bins.
105   -
  105 +
106 106  
107 107 Standard parameters
108 108 -------------------
... ... @@ -110,23 +110,23 @@ Standard parameters
110 110 ``(chatter = 2) [integer]``
111 111 Verbosity of the executable:
112 112 ``chatter = 0``: no information will be logged
113   -
  113 +
114 114 ``chatter = 1``: only errors will be logged
115   -
  115 +
116 116 ``chatter = 2``: errors and actions will be logged
117   -
  117 +
118 118 ``chatter = 3``: report about the task execution
119   -
  119 +
120 120 ``chatter = 4``: detailed report about the task execution
121   -
  121 +
122 122 ``(clobber = yes) [boolean]``
123 123 Specifies whether an existing output point spread function cube file should be overwritten.
124   -
  124 +
125 125 ``(debug = no) [boolean]``
126 126 Enables debug mode. In debug mode the executable will dump any log file output to the console.
127   -
  127 +
128 128 ``(mode = ql) [string]``
129   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  129 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
130 130  
131 131 ``(logfile = ctpsfcube.log) [string]``
132 132 Name of log file.
... ...
doc/source/users/reference_manual/ctselect.rst
  View file @7c7ef2a
... ... @@ -40,60 +40,60 @@ General parameters
40 40  
41 41 ``inobs [file]``
42 42 Input event list or observation definition XML file
43   -
  43 +
44 44 ``outobs [file]``
45 45 Output event list or observation definition XML file.
46   -
  46 +
47 47 ``(prefix = "selected_") [string]``
48 48 Prefix for output event lists in observation definition file.
49   -
  49 +
50 50 ``(usepnt = no) [boolean]``
51 51 Use pointing instead of RA/DEC parameters?
52   -
  52 +
53 53 ``ra [real]``
54 54 Right Ascension of acceptance cone (or ROI) centre (J2000, in degrees).
55 55 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no ROI
56 56 selection will be performed.
57   -
  57 +
58 58 ``dec [real]``
59 59 Declination of acceptance cone (or ROI) centre (J2000, in degrees).
60 60 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no ROI
61 61 selection will be performed.
62   -
  62 +
63 63 ``rad [real]``
64 64 Radius of acceptance cone (or ROI) centre (in degrees).
65 65 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no ROI
66 66 selection will be performed.
67   -
  67 +
68 68 ``tmin [time]``
69 69 Start time (UTC string, JD, MJD or time in seconds).
70 70 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no time
71 71 selection will be performed.
72   -
  72 +
73 73 ``tmax [time]``
74 74 Stop time (UTC string, JD, MJD or time in seconds).
75 75 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no time
76 76 selection will be performed.
77   -
  77 +
78 78 ``emin [real]``
79 79 Lower energy limit of events (in TeV).
80 80 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no energy
81 81 selection will be performed.
82   -
  82 +
83 83 ``emax [real]``
84 84 Upper energy limit of events (in TeV).
85 85 If INDEF, NONE, UNDEF or UNDEFINED is passed as value, no energy
86 86 selection will be performed.
87   -
  87 +
88 88 ``(phase = NONE) [string]``
89 89 String to apply a phase selection. The string must contain the boundaries
90 90 of the phase interval to be selected separated be a colon. More than one
91 91 interval can be specified at the same time. In this case intervals must be
92   - separated by a comma. Examples of valid strings are: phase = "0.3:0.6",
93   - phase = "0.3:0.6,0.8:0.9" or phase = "0.8:0.2". In the last case, events
  92 + separated by a comma. Examples of valid strings are: ``phase = 0.3:0.6``,
  93 + ``phase = 0.3:0.6,0.8:0.9`` or ``phase = 0.8:0.2``. In the last case, events
94 94 with phases in the intervals [0.8,1.0] and [0.0,0.2] are selected. If NONE
95 95 is passed as value, no phase selection will be performed.
96   -
  96 +
97 97 ``(expr = "") [string]``
98 98 Additional event selection expression (cfitsio syntax).
99 99  
... ... @@ -110,23 +110,23 @@ Standard parameters
110 110 ``(chatter = 2) [integer]``
111 111 Verbosity of the executable:
112 112 ``chatter = 0``: no information will be logged
113   -
  113 +
114 114 ``chatter = 1``: only errors will be logged
115   -
  115 +
116 116 ``chatter = 2``: errors and actions will be logged
117   -
  117 +
118 118 ``chatter = 3``: report about the task execution
119   -
  119 +
120 120 ``chatter = 4``: detailed report about the task execution
121   -
  121 +
122 122 ``(clobber = yes) [boolean]``
123 123 Specifies whether existing output files should be overwritten.
124   -
  124 +
125 125 ``(debug = no) [boolean]``
126 126 Enables debug mode. In debug mode the executable will dump any log file output to the console.
127   -
  127 +
128 128 ``(mode = ql) [string]``
129   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  129 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
130 130  
131 131 ``(logfile = ctlike.log) [string]``
132 132 Name of log file.
... ...
doc/source/users/reference_manual/ctskymap.rst
  View file @7c7ef2a
... ... @@ -43,37 +43,37 @@ General parameters
43 43  
44 44 ``outmap [file]``
45 45 Output sky map file.
46   -
  46 +
47 47 ``emin [real]``
48 48 Minimum energy in map (in TeV).
49   -
  49 +
50 50 ``emax [real]``
51 51 Maximum energy in map (in TeV).
52 52  
53 53 ``(usepnt = no) [boolean]``
54 54 Use pointing instead of xref/yref parameters?
55   -
  55 +
56 56 ``nxpix [integer]``
57 57 Size of the Right Ascension / Galactic longitude axis (in pixels).
58   -
  58 +
59 59 ``nypix [integer]``
60 60 Size of the Declination / Galactic latitude axis (in pixels).
61   -
  61 +
62 62 ``binsz [real]``
63 63 Pixel size (in degrees/pixel).
64   -
  64 +
65 65 ``coordsys <CEL|GAL> [string]``
66 66 Coordinate system (CEL - celestial, GAL - galactic).
67   -
  67 +
68 68 ``proj <AIT|AZP|CAR|GLS|MER|MOL|SFL|SIN|STG|TAN> [string]``
69 69 Projection method.
70 70  
71 71 ``xref [real]``
72 72 Right Ascension / Galactic longitude of image centre (J2000, in degrees).
73   -
  73 +
74 74 ``yref [real]``
75 75 Declination / Galactic latitude of image centre (J2000, in degrees).
76   -
  76 +
77 77  
78 78 Background subtraction configuration parameters
79 79 -----------------------------------------------
... ... @@ -103,24 +103,24 @@ Standard parameters
103 103 ``(chatter = 2) [integer]``
104 104 Verbosity of the executable:
105 105 ``chatter = 0``: no information will be logged
106   -
  106 +
107 107 ``chatter = 1``: only errors will be logged
108   -
  108 +
109 109 ``chatter = 2``: errors and actions will be logged
110   -
  110 +
111 111 ``chatter = 3``: report about the task execution
112   -
  112 +
113 113 ``chatter = 4``: detailed report about the task execution
114   -
  114 +
115 115 ``(clobber = yes) [boolean]``
116 116 Specifies whether an existing output sky map file should be overwritten.
117   -
  117 +
118 118 ``(debug = no) [boolean]``
119 119 Enables debug mode. In debug mode the executable will dump any log file
120 120 output to the console.
121   -
  121 +
122 122 ``(mode = ql) [string]``
123   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  123 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
124 124  
125 125 ``(logfile = ctskymap.log) [string]``
126 126 Name of log file.
... ...
doc/source/users/reference_manual/cttsmap.rst
  View file @7c7ef2a
... ... @@ -117,23 +117,23 @@ Standard parameters
117 117 ``(chatter = 2) [integer]``
118 118 Verbosity of the executable:
119 119 ``chatter = 0``: no information will be logged
120   -
  120 +
121 121 ``chatter = 1``: only errors will be logged
122   -
  122 +
123 123 ``chatter = 2``: errors and actions will be logged
124   -
  124 +
125 125 ``chatter = 3``: report about the task execution
126   -
  126 +
127 127 ``chatter = 4``: detailed report about the task execution
128   -
  128 +
129 129 ``(clobber = yes) [boolean]``
130 130 Specifies whether an existing output TS map file should be overwritten.
131   -
  131 +
132 132 ``(debug = no) [boolean]``
133 133 Enables debug mode. In debug mode the executable will dump any log file output to the console.
134   -
  134 +
135 135 ``(mode = ql) [string]``
136   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  136 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
137 137  
138 138 ``(logfile = cttsmap.log) [string]``
139 139 Name of log file.
... ...
doc/source/users/reference_manual/ctulimit.rst
  View file @7c7ef2a
... ... @@ -97,24 +97,24 @@ Standard parameters
97 97 ``(chatter = 2) [integer]``
98 98 Verbosity of the executable:
99 99 ``chatter = 0``: no information will be logged
100   -
  100 +
101 101 ``chatter = 1``: only errors will be logged
102   -
  102 +
103 103 ``chatter = 2``: errors and actions will be logged
104   -
  104 +
105 105 ``chatter = 3``: report about the task execution
106   -
  106 +
107 107 ``chatter = 4``: detailed report about the task execution
108   -
  108 +
109 109 ``(clobber = yes) [boolean]``
110 110 Specifies whether an existing output file should be overwritten.
111   -
  111 +
112 112 ``(debug = no) [boolean]``
113 113 Enables debug mode. In debug mode the executable will dump any log file
114 114 output to the console.
115   -
  115 +
116 116 ``(mode = ql) [string]``
117   - Mode of automatic parameters (default is "ql", i.e. "query and learn").
  117 + Mode of automatic parameters (default is ``ql``, i.e. "query and learn").
118 118  
119 119 ``(logfile = ctulimit.log) [string]``
120 120 Name of log file.
... ...
doc/source/users/reference_manual/index.rst
  View file @7c7ef2a
... ... @@ -63,8 +63,8 @@ cscripts
63 63 csspec --- Computes spectral points <csspec>
64 64 cssrcdetect --- Detects sources in sky map <cssrcdetect>
65 65 cstsdist --- Generates Test Statistic distribution <cstsdist>
66   - cstsmapsplit --- Creates commands to split the Test Statistic map computations <cstsmapsplit>
67 66 cstsmapmerge --- Merges slices from Test Statistic map computations <cstsmapmerge>
  67 + cstsmapsplit --- Creates commands to split the Test Statistic map computations <cstsmapsplit>
68 68 csviscube --- Computes visibility cube <csviscube>
69 69  
70 70  
... ...
doc/source/users/reference_manual/usage.rst
  View file @7c7ef2a
1   -Description of ctools parameters in the reference manual
2   -=====================================
  1 +.. _sec_usage:
3 2  
4   -For a generic introduction to ctools and user parameters see `here <../user_manual/introduction.html>`__.
  3 +Description of ctools parameters in the :ref:`reference`
  4 +========================================================
  5 +
  6 +For a generic introduction to ctools and user parameters see
  7 +`here <../user_manual/introduction.html>`__.
5 8  
6 9 Automatic parameters
7 10 --------------------
... ... @@ -27,18 +30,18 @@ Examples
27 30  
28 31 ``infile [file]``
29 32 Describes an automatic (queried) file-type parameter with no default value.
30   -
  33 +
31 34 ``irf = South_50h <North_50h|South_50h> [string]``
32 35 Describes an automatic (queried) string-type parameter with two value
33 36 options.
34   -
  37 +
35 38 ``(plot = yes) [boolean]``
36 39 Describes a hidden bool-type parameter named plot, whose default value
37 40 is yes (true).
38   -
  41 +
39 42 .. note::
40 43  
41   - You can set hidden parameters at runtime by specifying them explicitly on
42   - the command line; for example:
  44 + You can set hidden parameters at runtime by specifying them explicitly on
  45 + the command line; for example:
43 46  
44   - ``ctobssim start_time=900``
  47 + ``ctobssim start_time=900``
... ...
doc/source/users/tutorials/1dc/getting_tools.rst
  View file @7c7ef2a
... ... @@ -24,7 +24,7 @@ After downloading, configure GammaLib and ctools as follows:
24 24 $ export CTOOLS=/usr/local/gamma
25 25 $ source $CTOOLS/bin/ctools-init.sh
26 26  
27   -Have a look at :ref:`getting the ctools <sec_install>` if you need more
  27 +Have a look at :ref:`getting the ctools <sec_admin>` if you need more
28 28 information about the installation and configuration process.
29 29  
30 30 .. note::
... ...
doc/source/users/tutorials/beyond/beyond_residual_spectrum.rst
  View file @7c7ef2a
1 1 .. _sec_residual_spectrum:
2 2  
3 3 Generating a residual spectrum
4   -~~~~~~~~~~~~~~~~~~~~~~~~~
  4 +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5 5  
6 6 In the previous tutorial you have used the :ref:`csresmap` script to
7 7 inspect the spatial residuals. You can also inspect the spectral
... ...
doc/source/users/user_manual/introduction.rst
  View file @7c7ef2a
... ... @@ -13,7 +13,7 @@ And you should read the :ref:`sec_develop` section if you would like to
13 13 contribute to the ctools developments.
14 14  
15 15 Running ctools
16   ----------------
  16 +--------------
17 17  
18 18 ctools comprises a set of ftools-like binary executables,
19 19 written in C++, with a command-line interface allowing for interactive
... ... @@ -22,74 +22,71 @@ type the name of the ctool:
22 22  
23 23 .. code-block:: bash
24 24  
25   - $ ctobssim
26   - RA of pointing (degrees) (0-360) [83.63]
  25 + $ ctobssim
  26 + RA of pointing (degrees) (0-360) [83.63]
27 27  
28 28 The ctool will query all user parameters and execute. User parameters can
29 29 also be specified as arguments separated by a whitespace to the ctool:
30 30  
31 31 .. code-block:: bash
32 32  
33   - $ ctobssim ra=83.63 dec=22.01 rad=5.0 tmin=0 tmax=1800 emin=0.1 emax=100.0 caldb=prod2 irf=South_0.5h \
34   - inmodel=$CTOOLS/share/models/crab.xml outevents=events.fits
  33 + $ ctobssim ra=83.63 dec=22.01 rad=5.0 tmin=0 tmax=1800 emin=0.1 emax=100.0 caldb=prod2 irf=South_0.5h \
  34 + inmodel=$CTOOLS/share/models/crab.xml outevents=events.fits
35 35  
36 36 If you need help about the usage of a ctool or a cscript, type the name of
37 37 the ctool or cscript followed by the ``--help`` option:
38 38  
39 39 .. code-block:: bash
40 40  
41   - $ ctobssim --help
  41 + $ ctobssim --help
42 42  
43 43 ctools includes also a Python module that declares every ctool as a
44 44 Python class. The following example illustrates the usage:
45 45  
46   -.. code-block:: bash
  46 +.. code-block:: python
47 47  
48   - $ python
49   - >>> import ctools
50   - >>> sim = ctools.ctobssim()
51   - >>> sim["ra"] = 83.63
52   - >>> sim["dec"] = 22.01
53   - >>> sim.execute()
54   - Radius of FOV (degrees) (0-180) [5.0]
  48 + $ python
  49 + >>> import ctools
  50 + >>> sim = ctools.ctobssim()
  51 + >>> sim["ra"] = 83.63
  52 + >>> sim["dec"] = 22.01
  53 + >>> sim.execute()
  54 + Radius of FOV (degrees) (0-180) [5.0]
55 55  
56 56 ctools comprise also cscripts, which are Python scripts that have the same
57 57 user interface as the ctools binaries. cscripts can be started from the
58 58 command line or used as Python classes, as illustrated below:
59 59  
60   -.. code-block:: bash
  60 +.. code-block:: python
61 61  
62   - $ python
63   - >>> import cscripts
64   - >>> pull = cscripts.cspull()
  62 + $ python
  63 + >>> import cscripts
  64 + >>> pull = cscripts.cspull()
65 65  
66 66 User parameters and parameter files
67   ------------------------------
  67 +-----------------------------------
68 68  
69 69 Each ctool and cscript has a defined list of user parameters. You can
70   -find a complete description `here
71   -<../reference_manual/reference.html>`_.
  70 +find a complete description `here <../reference_manual/reference.html>`_.
72 71  
73   -User parameters are stored in
74   -par files. A ctools installation comprises a set of default par files
75   -stored at ``$CTOOLS/syspfiles``. When you run a tool/script the latest
76   -parameter values will be stored in a copy of the file at
77   -``$HOME/pfiles`` (e.g., ``ctlike`` will save there a file called ``ctlike.par`` ).
  72 +User parameters are stored in par files. A ctools installation comprises a set
  73 +of default par files stored at ``$CTOOLS/syspfiles``. When you run a tool/script
  74 +the latest parameter values will be stored in a copy of the file at
  75 +``$HOME/pfiles`` (e.g., ``ctlike`` will save there a file called ``ctlike.par``).
78 76  
79   -When a tool/script is executed again, it will look for a par file
80   -first in ``$HOME/pfiles``, and propose you to use the latest values
81   -stored there. If no par file is found there, it will use the default
82   -in ``$CTOOLS/syspfiles``.
  77 +When a tool/script is executed again, it will look for a par file first in
  78 +``$HOME/pfiles``, and propose you to use the latest values stored there. If no
  79 +par file is found there, it will use the default in ``$CTOOLS/syspfiles``.
83 80  
84 81 If you update your ctools installation you may get an error such as
85 82  
86 83 .. code-block:: bash
87 84  
88   - *** ERROR encounterted in the execution of ctlike. Run aborted ...
89   - *** ERROR in GApplicationPars::load(GFilename&,
90   - std::vector<std::string>&): Invalid command line parameter
91   - encountered (invalid parameter name "XX"): XX=2
  85 + *** ERROR encounterted in the execution of ctlike. Run aborted ...
  86 + *** ERROR in GApplicationPars::load(GFilename&,
  87 + std::vector<std::string>&): Invalid command line parameter
  88 + encountered (invalid parameter name "XX"): XX=2
92 89  
93   -Remove the stale file ``ctlike.par`` from ``$HOME/pfiles`` and run
94   -again to solve the issue.
  90 +Remove the stale file ``ctlike.par`` from ``$HOME/pfiles`` and run again to
  91 +solve the issue.
95 92  
... ...
test/test_csresspec.py
  View file @7c7ef2a
... ... @@ -77,7 +77,7 @@ class Test(test):
77 77 ' outfile="csresspec_cmd1.fits"' + \
78 78 ' inmodel="' + self._model + '"' + \
79 79 ' caldb="' + self._caldb + '" irf="' + self._irf + '"' + \
80   - ' emin=0.1 emax=100.0 enumbins=20' + \
  80 + ' emin=0.1 emax=100.0 enumbins=20 ebinalg="LOG"' + \
81 81 ' mask=no algorithm="SUB"' + \
82 82 ' logfile="csresspec_cmd1.log" chatter=4'
83 83  
... ... @@ -93,7 +93,7 @@ class Test(test):
93 93 ' outfile="csresspec_cmd2.fits"' + \
94 94 ' inmodel="' + self._model + '"' + \
95 95 ' caldb="' + self._caldb + '" irf="' + self._irf + '"' + \
96   - ' emin=0.1 emax=100.0 enumbins=20' + \
  96 + ' emin=0.1 emax=100.0 enumbins=20 ebinalg="LOG"' + \
97 97 ' mask=no algorithm="SUBDIVSQRT"' + \
98 98 ' logfile="csresspec_cmd2.log" debug=yes chatter=2'
99 99  
... ... @@ -119,6 +119,7 @@ class Test(test):
119 119 resspec['inmodel'] = self._model
120 120 resspec['caldb'] = self._caldb
121 121 resspec['irf'] = self._irf
  122 + resspec['ebinalg'] = 'LOG'
122 123 resspec['emin'] = 0.1
123 124 resspec['emax'] = 100.0
124 125 resspec['enumbins'] = 20
... ... @@ -135,14 +136,15 @@ class Test(test):
135 136 # Check result file
136 137 self._check_result_file('csresspec_py1.fits', 20, 5)
137 138  
138   - # Set-up csresspec for event list
139   - # with computation of individual model components
  139 + # Set-up csresspec for event list with computation of individual
  140 + # model components
140 141 resspec = cscripts.csresspec()
141 142 resspec['inobs'] = self._events
142 143 resspec['outfile'] = 'csresspec_py2.fits'
143 144 resspec['inmodel'] = self._model
144 145 resspec['caldb'] = self._caldb
145 146 resspec['irf'] = self._irf
  147 + resspec['ebinalg'] = 'LOG'
146 148 resspec['emin'] = 0.1
147 149 resspec['emax'] = 100.0
148 150 resspec['enumbins'] = 20
... ... @@ -181,8 +183,7 @@ class Test(test):
181 183 # Check result file
182 184 self._check_result_file('csresspec_py3.fits', 20, 5)
183 185  
184   - # Set-up csresspec for counts cube
185   - # with source mask
  186 + # Set-up csresspec for counts cube with source mask
186 187 resspec = cscripts.csresspec()
187 188 resspec['inobs'] = self._cntcube
188 189 resspec['modcube'] = 'NONE'
... ...