Iftach Sadeh / ctools

Commit 6662e9a91c6be50bf003a1a0330b485893bd2d1b

Authored by Jürgen Knödlseder
1 parent bd318829

Do some minor documentation adjustments

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Showing 4 changed files with 105 additions and 108 deletions
doc/source/users/index.rst
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... ... @@ -11,7 +11,7 @@ This documentation will guide you in the process of using ctools.
11 11 tips/index
12 12 user_manual/index
13 13 tutorials/index
  14 + notebooks
14 15 reference_manual/index
15 16 user_contributed/index
16 17 glossary
17   - notebooks
... ...
doc/source/users/tutorials/beyond/combining-observations.ipynb
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... ... @@ -101,16 +101,14 @@
101 101 },
102 102 "outputs": [],
103 103 "source": [
104   - "import xml.etree.cElementTree as ET\n",
105   - "\n",
106   - "obslist = ET.Element(\"observation_list\", title=\"observation library\")\n",
  104 + "xml = gammalib.GXml()\n",
  105 + "obslist = xml.append('observation_list title=\"observation library\"')\n",
107 106 "\n",
108 107 "for i in range(2):\n",
109   - " obs = ET.SubElement(obslist, \"observation\", name=\"Crab\", id=\"{:02d}\".format(i+1), instrument=\"CTA\")\n",
110   - " ET.SubElement(obs, \"parameter\", name=\"EventList\", file=\"events{}.fits\".format(i+1))\n",
  108 + " obs = obslist.append('observation name=\"Crab\" id=\"%02d\" instrument=\"CTA\"' % (i+1))\n",
  109 + " obs.append('parameter name=\"EventList\" file=\"events%d.fits\"' % (i+1))\n",
111 110 "\n",
112   - "tree = ET.ElementTree(obslist)\n",
113   - "tree.write(\"obs.xml\",xml_declaration=True,encoding='UTF-8')"
  111 + "xml.save('obs.xml')"
114 112 ]
115 113 },
116 114 {
... ...
doc/source/users/tutorials/quickstart/butterfly.rst
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... ... @@ -42,7 +42,6 @@ default is set to 100. Below an excerpt of the first lines of the
42 42 110917.48152624 6.81370736945431e-15 6.62965024227895e-15 6.99776449662967e-15
43 43 118850.222743702 5.73964152654309e-15 5.58918876927557e-15 5.89009428381061e-15
44 44 127350.308101666 4.83488401643174e-15 4.71191629605204e-15 4.95785173681143e-15
45   -
46 45 ...
47 46  
48 47 A graphical display of the results is shown below:
... ...
doc/source/users/tutorials/quickstart/onoff.rst
  View file @6662e9a
... ... @@ -40,20 +40,20 @@ excluded from the background computation.
40 40  
41 41 .. code-block:: bash
42 42  
43   - $ csphagen
44   - Input event list or observation definition XML file [obs.xml] events_edisp.fits
45   - Calibration database [prod2]
46   - Instrument response function [South_0.5h]
47   - Binning algorithm (LIN|LOG|FILE) [LOG]
48   - Lower energy limit (TeV) [0.1]
49   - Upper energy limit (TeV) [100.0]
50   - Number of energy bins [120] 30
51   - Coordinate system (CEL - celestial, GAL - galactic) (CEL|GAL) [CEL]
52   - Right Ascension of source region centre (deg) (0-360) [83.63]
53   - Declination of source region centre (deg) (-90-90) [22.01]
54   - Radius of source region circle (deg) (0-180) [0.2]
55   - Stack multiple observations into single PHA, ARF and RMF files? [no]
56   - Output observation definition XML file [onoff_obs.xml]
  43 + $ csphagen
  44 + Input event list or observation definition XML file [obs.xml] events_edisp.fits
  45 + Calibration database [prod2]
  46 + Instrument response function [South_0.5h]
  47 + Binning algorithm (LIN|LOG|FILE) [LOG]
  48 + Lower energy limit (TeV) [0.1]
  49 + Upper energy limit (TeV) [100.0]
  50 + Number of energy bins [120] 30
  51 + Coordinate system (CEL - celestial, GAL - galactic) (CEL|GAL) [CEL]
  52 + Right Ascension of source region centre (deg) (0-360) [83.63]
  53 + Declination of source region centre (deg) (-90-90) [22.01]
  54 + Radius of source region circle (deg) (0-180) [0.2]
  55 + Stack multiple observations into single PHA, ARF and RMF files? [no]
  56 + Output observation definition XML file [onoff_obs.xml]
57 57  
58 58 .. note::
59 59  
... ... @@ -76,15 +76,15 @@ contains a single On/Off observation.
76 76  
77 77 .. code-block:: bash
78 78  
79   - <?xml version="1.0" encoding="UTF-8" standalone="no"?>
80   - <observation_list title="observation list">
81   - <observation name="" id="" instrument="CTAOnOff" statistic="cstat">
82   - <parameter name="Pha_on" file="onoff_pha_on.fits" />
83   - <parameter name="Pha_off" file="onoff_pha_off.fits" />
84   - <parameter name="Arf" file="onoff_arf.fits" />
85   - <parameter name="Rmf" file="onoff_rmf.fits" />
86   - </observation>
87   - </observation_list>
  79 + <?xml version="1.0" encoding="UTF-8" standalone="no"?>
  80 + <observation_list title="observation list">
  81 + <observation name="" id="" instrument="CTAOnOff" statistic="cstat">
  82 + <parameter name="Pha_on" file="onoff_pha_on.fits" />
  83 + <parameter name="Pha_off" file="onoff_pha_off.fits" />
  84 + <parameter name="Arf" file="onoff_arf.fits" />
  85 + <parameter name="Rmf" file="onoff_rmf.fits" />
  86 + </observation>
  87 + </observation_list>
88 88  
89 89 The observation entails four FITS files. ``onoff_pha_on.fits`` and
90 90 ``onoff_pha_off.fits`` contain the On and Off spectra, respectively.
... ... @@ -126,27 +126,27 @@ background component that we are dealing with a ``CTAOnOff`` analysis.
126 126  
127 127 .. code-block:: bash
128 128  
129   - <?xml version="1.0" standalone="no"?>
130   - <source_library title="source library">
131   - <source name="Crab" type="PointSource">
132   - <spectrum type="PowerLaw">
133   - <parameter name="Prefactor" scale="1e-16" value="5.7" min="1e-07" max="1000.0" free="1"/>
134   - <parameter name="Index" scale="-1" value="2.48" min="0.0" max="+5.0" free="1"/>
135   - <parameter name="PivotEnergy" scale="1e6" value="0.3" min="0.01" max="1000.0" free="0"/>
136   - </spectrum>
137   - <spatialModel type="PointSource">
138   - <parameter name="RA" scale="1.0" value="83.6331" min="-360" max="360" free="0"/>
139   - <parameter name="DEC" scale="1.0" value="22.0145" min="-90" max="90" free="0"/>
140   - </spatialModel>
141   - </source>
142   - <source name="CTABackgroundModel" type="CTAIrfBackground" instrument="CTAOnOff">
143   - <spectrum type="PowerLaw">
144   - <parameter name="Prefactor" scale="1.0" value="1.0" min="1e-3" max="1e+3" free="1"/>
145   - <parameter name="Index" scale="1.0" value="0.0" min="-5.0" max="+5.0" free="1"/>
146   - <parameter name="PivotEnergy" scale="1e6" value="1.0" min="0.01" max="1000.0" free="0"/>
147   - </spectrum>
148   - </source>
149   - </source_library>
  129 + <?xml version="1.0" standalone="no"?>
  130 + <source_library title="source library">
  131 + <source name="Crab" type="PointSource">
  132 + <spectrum type="PowerLaw">
  133 + <parameter name="Prefactor" scale="1e-16" value="5.7" min="1e-07" max="1000.0" free="1"/>
  134 + <parameter name="Index" scale="-1" value="2.48" min="0.0" max="+5.0" free="1"/>
  135 + <parameter name="PivotEnergy" scale="1e6" value="0.3" min="0.01" max="1000.0" free="0"/>
  136 + </spectrum>
  137 + <spatialModel type="PointSource">
  138 + <parameter name="RA" scale="1.0" value="83.6331" min="-360" max="360" free="0"/>
  139 + <parameter name="DEC" scale="1.0" value="22.0145" min="-90" max="90" free="0"/>
  140 + </spatialModel>
  141 + </source>
  142 + <source name="CTABackgroundModel" type="CTAIrfBackground" instrument="CTAOnOff">
  143 + <spectrum type="PowerLaw">
  144 + <parameter name="Prefactor" scale="1.0" value="1.0" min="1e-3" max="1e+3" free="1"/>
  145 + <parameter name="Index" scale="1.0" value="0.0" min="-5.0" max="+5.0" free="1"/>
  146 + <parameter name="PivotEnergy" scale="1e6" value="1.0" min="0.01" max="1000.0" free="0"/>
  147 + </spectrum>
  148 + </source>
  149 + </source_library>
150 150  
151 151 At this point we can run an On/Off analysis just by passing the On/Off
152 152 observation container to :ref:`ctlike`.
... ... @@ -164,61 +164,61 @@ always be the case, especially if the background is not well known a priori.
164 164  
165 165 .. code-block:: bash
166 166  
167   - 2017-11-28T17:26:56: +=================================+
168   - 2017-11-28T17:26:56: | Maximum likelihood optimisation |
169   - 2017-11-28T17:26:56: +=================================+
170   - 2017-11-28T17:26:56: >Iteration 0: -logL=-48350.908, Lambda=1.0e-03
171   - 2017-11-28T17:26:56: >Iteration 1: -logL=-48352.759, Lambda=1.0e-03, delta=1.852, step=1.0e+00, max(|grad|)=2.829489 [Index:7]
172   - 2017-11-28T17:26:56: >Iteration 2: -logL=-48352.760, Lambda=1.0e-04, delta=0.000, step=1.0e+00, max(|grad|)=0.002408 [Index:3]
173   - 2017-11-28T17:26:56:
174   - 2017-11-28T17:26:56: +=========================================+
175   - 2017-11-28T17:26:56: | Maximum likelihood optimisation results |
176   - 2017-11-28T17:26:56: +=========================================+
177   - 2017-11-28T17:26:56: === GOptimizerLM ===
178   - 2017-11-28T17:26:56: Optimized function value ..: -48352.760
179   - 2017-11-28T17:26:56: Absolute precision ........: 0.005
180   - 2017-11-28T17:26:56: Acceptable value decrease .: 2
181   - 2017-11-28T17:26:56: Optimization status .......: converged
182   - 2017-11-28T17:26:56: Number of parameters ......: 10
183   - 2017-11-28T17:26:56: Number of free parameters .: 4
184   - 2017-11-28T17:26:56: Number of iterations ......: 2
185   - 2017-11-28T17:26:56: Lambda ....................: 1e-05
186   - 2017-11-28T17:26:56: Maximum log likelihood ....: 48352.760
187   - 2017-11-28T17:26:56: Observed events (Nobs) ...: 6656.000
188   - 2017-11-28T17:26:56: Predicted events (Npred) ..: 6655.663 (Nobs - Npred = 0.337440257160779)
189   - 2017-11-28T17:26:56: === GModels ===
190   - 2017-11-28T17:26:56: Number of models ..........: 2
191   - 2017-11-28T17:26:56: Number of parameters ......: 10
192   - 2017-11-28T17:26:56: === GModelSky ===
193   - 2017-11-28T17:26:56: Name ......................: Crab
194   - 2017-11-28T17:26:56: Instruments ...............: all
195   - 2017-11-28T17:26:56: Instrument scale factors ..: unity
196   - 2017-11-28T17:26:56: Observation identifiers ...: all
197   - 2017-11-28T17:26:56: Model type ................: PointSource
198   - 2017-11-28T17:26:56: Model components ..........: "PointSource" * "PowerLaw" * "Constant"
199   - 2017-11-28T17:26:56: Number of parameters ......: 6
200   - 2017-11-28T17:26:56: Number of spatial par's ...: 2
201   - 2017-11-28T17:26:56: RA .......................: 83.6331 [-360,360] deg (fixed,scale=1)
202   - 2017-11-28T17:26:56: DEC ......................: 22.0145 [-90,90] deg (fixed,scale=1)
203   - 2017-11-28T17:26:56: Number of spectral par's ..: 3
204   - 2017-11-28T17:26:56: Prefactor ................: 5.69533666063277e-16 +/- 7.77619410705106e-18 [1e-23,1e-13] ph/cm2/s/MeV (free,scale=1e-16,gradient)
205   - 2017-11-28T17:26:56: Index ....................: -2.47347083803876 +/- 0.0114544870463654 [-0,-5] (free,scale=-1,gradient)
206   - 2017-11-28T17:26:56: PivotEnergy ..............: 300000 [10000,1000000000] MeV (fixed,scale=1000000,gradient)
207   - 2017-11-28T17:26:56: Number of temporal par's ..: 1
208   - 2017-11-28T17:26:56: Normalization ............: 1 (relative value) (fixed,scale=1,gradient)
209   - 2017-11-28T17:26:56: === GCTAModelIrfBackground ===
210   - 2017-11-28T17:26:56: Name ......................: CTABackgroundModel
211   - 2017-11-28T17:26:56: Instruments ...............: CTAOnOff
212   - 2017-11-28T17:26:56: Instrument scale factors ..: unity
213   - 2017-11-28T17:26:56: Observation identifiers ...: all
214   - 2017-11-28T17:26:56: Model type ................: "PowerLaw" * "Constant"
215   - 2017-11-28T17:26:56: Number of parameters ......: 4
216   - 2017-11-28T17:26:56: Number of spectral par's ..: 3
217   - 2017-11-28T17:26:56: Prefactor ................: 1.00017594707712 +/- 0.0373732914079376 [0.001,1000] ph/cm2/s/MeV (free,scale=1,gradient)
218   - 2017-11-28T17:26:56: Index ....................: 0.0190520959815092 +/- 0.0220805114253248 [-5,5] (free,scale=1,gradient)
219   - 2017-11-28T17:26:56: PivotEnergy ..............: 1000000 [10000,1000000000] MeV (fixed,scale=1000000,gradient)
220   - 2017-11-28T17:26:56: Number of temporal par's ..: 1
221   - 2017-11-28T17:26:56: Normalization ............: 1 (relative value) (fixed,scale=1,gradient)
  167 + 2017-11-28T17:26:56: +=================================+
  168 + 2017-11-28T17:26:56: | Maximum likelihood optimisation |
  169 + 2017-11-28T17:26:56: +=================================+
  170 + 2017-11-28T17:26:56: >Iteration 0: -logL=-48350.908, Lambda=1.0e-03
  171 + 2017-11-28T17:26:56: >Iteration 1: -logL=-48352.759, Lambda=1.0e-03, delta=1.852, step=1.0e+00, max(|grad|)=2.829489 [Index:7]
  172 + 2017-11-28T17:26:56: >Iteration 2: -logL=-48352.760, Lambda=1.0e-04, delta=0.000, step=1.0e+00, max(|grad|)=0.002408 [Index:3]
  173 + 2017-11-28T17:26:56:
  174 + 2017-11-28T17:26:56: +=========================================+
  175 + 2017-11-28T17:26:56: | Maximum likelihood optimisation results |
  176 + 2017-11-28T17:26:56: +=========================================+
  177 + 2017-11-28T17:26:56: === GOptimizerLM ===
  178 + 2017-11-28T17:26:56: Optimized function value ..: -48352.760
  179 + 2017-11-28T17:26:56: Absolute precision ........: 0.005
  180 + 2017-11-28T17:26:56: Acceptable value decrease .: 2
  181 + 2017-11-28T17:26:56: Optimization status .......: converged
  182 + 2017-11-28T17:26:56: Number of parameters ......: 10
  183 + 2017-11-28T17:26:56: Number of free parameters .: 4
  184 + 2017-11-28T17:26:56: Number of iterations ......: 2
  185 + 2017-11-28T17:26:56: Lambda ....................: 1e-05
  186 + 2017-11-28T17:26:56: Maximum log likelihood ....: 48352.760
  187 + 2017-11-28T17:26:56: Observed events (Nobs) ...: 6656.000
  188 + 2017-11-28T17:26:56: Predicted events (Npred) ..: 6655.663 (Nobs - Npred = 0.337440257160779)
  189 + 2017-11-28T17:26:56: === GModels ===
  190 + 2017-11-28T17:26:56: Number of models ..........: 2
  191 + 2017-11-28T17:26:56: Number of parameters ......: 10
  192 + 2017-11-28T17:26:56: === GModelSky ===
  193 + 2017-11-28T17:26:56: Name ......................: Crab
  194 + 2017-11-28T17:26:56: Instruments ...............: all
  195 + 2017-11-28T17:26:56: Instrument scale factors ..: unity
  196 + 2017-11-28T17:26:56: Observation identifiers ...: all
  197 + 2017-11-28T17:26:56: Model type ................: PointSource
  198 + 2017-11-28T17:26:56: Model components ..........: "PointSource" * "PowerLaw" * "Constant"
  199 + 2017-11-28T17:26:56: Number of parameters ......: 6
  200 + 2017-11-28T17:26:56: Number of spatial par's ...: 2
  201 + 2017-11-28T17:26:56: RA .......................: 83.6331 [-360,360] deg (fixed,scale=1)
  202 + 2017-11-28T17:26:56: DEC ......................: 22.0145 [-90,90] deg (fixed,scale=1)
  203 + 2017-11-28T17:26:56: Number of spectral par's ..: 3
  204 + 2017-11-28T17:26:56: Prefactor ................: 5.69533666063277e-16 +/- 7.77619410705106e-18 [1e-23,1e-13] ph/cm2/s/MeV (free,scale=1e-16,gradient)
  205 + 2017-11-28T17:26:56: Index ....................: -2.47347083803876 +/- 0.0114544870463654 [-0,-5] (free,scale=-1,gradient)
  206 + 2017-11-28T17:26:56: PivotEnergy ..............: 300000 [10000,1000000000] MeV (fixed,scale=1000000,gradient)
  207 + 2017-11-28T17:26:56: Number of temporal par's ..: 1
  208 + 2017-11-28T17:26:56: Normalization ............: 1 (relative value) (fixed,scale=1,gradient)
  209 + 2017-11-28T17:26:56: === GCTAModelIrfBackground ===
  210 + 2017-11-28T17:26:56: Name ......................: CTABackgroundModel
  211 + 2017-11-28T17:26:56: Instruments ...............: CTAOnOff
  212 + 2017-11-28T17:26:56: Instrument scale factors ..: unity
  213 + 2017-11-28T17:26:56: Observation identifiers ...: all
  214 + 2017-11-28T17:26:56: Model type ................: "PowerLaw" * "Constant"
  215 + 2017-11-28T17:26:56: Number of parameters ......: 4
  216 + 2017-11-28T17:26:56: Number of spectral par's ..: 3
  217 + 2017-11-28T17:26:56: Prefactor ................: 1.00017594707712 +/- 0.0373732914079376 [0.001,1000] ph/cm2/s/MeV (free,scale=1,gradient)
  218 + 2017-11-28T17:26:56: Index ....................: 0.0190520959815092 +/- 0.0220805114253248 [-5,5] (free,scale=1,gradient)
  219 + 2017-11-28T17:26:56: PivotEnergy ..............: 1000000 [10000,1000000000] MeV (fixed,scale=1000000,gradient)
  220 + 2017-11-28T17:26:56: Number of temporal par's ..: 1
  221 + 2017-11-28T17:26:56: Normalization ............: 1 (relative value) (fixed,scale=1,gradient)
222 222  
223 223 :ref:`ctlike` has a hidden parameter called ``statistic`` that sets the
224 224 statistic used for the fit.
... ...