Iftach Sadeh / ctools

Commit c18829b41a005d04115d5d63a11d7e9f27867b37

Authored by Jürgen Knödlseder
1 parent f048c13b

Prepare documentation for release

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Showing 6 changed files with 70 additions and 141 deletions
doc/source/_templates/index.html
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... ... @@ -19,7 +19,7 @@ Besides CTA, GammaLib supports also the analysis of Fermi/LAT and COMPTEL data,
19 19 and extensions to support further gamma-ray instruments are planned. An
20 20 interface to virtual observatory ressources does also exist. By making use of
21 21 the GammaLib multi-instrument capabilities, ctools supports the joint analysis
22   -of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT and COMPTEL data.
  22 +of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT, INTEGRAL/SPI and COMPTEL data.
23 23 {%endtrans%}</p>
24 24  
25 25 <p>{%trans%} ctools are developed by a team of enthousiastic gamma-ray
... ...
doc/source/about.rst
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... ... @@ -15,12 +15,13 @@ Creation of shell or Python scripts and pipelines is supported as well.
15 15  
16 16 ctools are based on GammaLib, a versatile toolbox for the scientific
17 17 analysis of astronomical gamma-ray data.
18   -Besides CTA, GammaLib supports also the analysis of Fermi/LAT and COMPTEL
19   -data, and extensions to support further gamma-ray instruments are planned.
  18 +Besides CTA, GammaLib supports also the analysis of Fermi/LAT, INTEGRAL/SPI
  19 +and COMPTEL data, and extensions to support further gamma-ray instruments are
  20 +planned.
20 21 An interface to virtual observatory ressources does also exist.
21 22 By making use of the GammaLib multi-instrument capabilities, ctools
22   -supports the joint analysis of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT and
23   -COMPTEL data.
  23 +supports the joint analysis of CTA, H.E.S.S., MAGIC, VERITAS, Fermi/LAT,
  24 +INTEGRAL/SPI and COMPTEL data.
24 25  
25 26 ctools are developed by a team of enthousiastic gamma-ray astronomers with
26 27 support from engineers. We regularily organise
... ...
doc/source/admin/install_source.rst
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... ... @@ -17,7 +17,7 @@ The procedure for building and installing ctools is modeled on GNU
17 17 software distributions. You will need the following to build the
18 18 software:
19 19  
20   -- About 25 MB of free disk space.
  20 +- About 50 MB of free disk space.
21 21  
22 22 - An ANSI C++ compiler. ctools builds well using GNU g++ or clang.
23 23  
... ... @@ -42,7 +42,7 @@ section and continue with the :ref:`sec_building_ctools` section.
42 42  
43 43 You will need the following to build the GammaLib:
44 44  
45   -- About 200 MB of free disk space.
  45 +- About 300 MB of free disk space.
46 46  
47 47 - An ANSI C++ compiler. We recommend building GammaLib with the GNU g++
48 48 or the clang compilers.
... ... @@ -66,7 +66,7 @@ in an appropriate location (for example ``$HOME/builds``), and type
66 66  
67 67 .. code-block:: bash
68 68  
69   - $ tar xvfz gammalib-1.2.0.tar.gz
  69 + $ tar xvfz gammalib-1.7.0.tar.gz
70 70  
71 71 (the ``$`` symbol indicates the console prompt and is not part of the
72 72 command that you should type in).
... ... @@ -76,25 +76,25 @@ typing
76 76  
77 77 .. code-block:: bash
78 78  
79   - $ cd gammalib-1.2.0
80   - $ ./configure
81   - $ make
82   - $ make check
83   - $ make install
  79 + $ cd gammalib-1.7.0
  80 + $ ./configure
  81 + $ make
  82 + $ make check
  83 + $ make install
84 84  
85 85 The last step may require system administator privileges. In this case,
86 86 use
87 87  
88 88 .. code-block:: bash
89 89  
90   - $ sudo make install
  90 + $ sudo make install
91 91  
92 92 If you do not have system administrator privileges, change the install
93 93 directory by typing for example
94 94  
95 95 .. code-block:: bash
96 96  
97   - $ ./configure --prefix=$HOME/gamma
  97 + $ ./configure --prefix=$HOME/gamma
98 98  
99 99 which then installs GammaLib in the ``gamma`` folder of your home
100 100 directory.
... ... @@ -114,16 +114,16 @@ machine:
114 114  
115 115 .. code-block:: bash
116 116  
117   - export GAMMALIB=/usr/local/gamma
118   - source $GAMMALIB/bin/gammalib-init.sh
  117 + export GAMMALIB=/usr/local/gamma
  118 + source $GAMMALIB/bin/gammalib-init.sh
119 119  
120 120 If you use C shell or a variant then add the following to your
121 121 ``$HOME/.cshrc`` or ``$HOME/.tcshrc`` script:
122 122  
123 123 .. code-block:: csh
124 124  
125   - setenv GAMMALIB /usr/local/gamma
126   - source $GAMMALIB/bin/gammalib-init.csh
  125 + setenv GAMMALIB /usr/local/gamma
  126 + source $GAMMALIB/bin/gammalib-init.csh
127 127  
128 128  
129 129 .. _sec_building_ctools:
... ... @@ -136,7 +136,7 @@ an appropriate location (for example ``$HOME/builds``), and type
136 136  
137 137 .. code-block:: bash
138 138  
139   - $ tar xvfz ctools-1.2.0.tar.gz
  139 + $ tar xvfz ctools-1.7.0.tar.gz
140 140  
141 141 (the ``$`` symbol indicates the console prompt and is not part of the
142 142 command that you should type in).
... ... @@ -145,9 +145,9 @@ Step in the directory and build the ctools by typing
145 145  
146 146 .. code-block:: bash
147 147  
148   - $ cd ctools-1.2.0
149   - $ ./configure
150   - $ make
  148 + $ cd ctools-1.7.0
  149 + $ ./configure
  150 + $ make
151 151  
152 152 at the operating system prompt. The ``./configure`` command customizes
153 153 the Makefiles for the particular system, the ``make`` command compiles
... ... @@ -159,7 +159,7 @@ You can get the full list of configuration options by typing
159 159  
160 160 .. code-block:: bash
161 161  
162   - $ ./configure --help
  162 + $ ./configure --help
163 163  
164 164  
165 165 Testing ctools
... ... @@ -170,7 +170,7 @@ make sure that ctools have been built correctly. For this, type
170 170  
171 171 .. code-block:: bash
172 172  
173   - $ make check
  173 + $ make check
174 174  
175 175 If you have automake version 1.13 or newer installed, you should see the
176 176 following output at the end of the unit testing:
... ... @@ -181,7 +181,7 @@ following output at the end of the unit testing:
181 181 PASS: test_python_cscripts.sh
182 182 PASS: test_examples.py
183 183 ============================================================================
184   - Testsuite summary for ctools 1.2.0
  184 + Testsuite summary for ctools 1.7.0
185 185 ============================================================================
186 186 # TOTAL: 3
187 187 # PASS: 3
... ... @@ -199,34 +199,36 @@ For older automake version, you should see
199 199 ***********************
200 200 * ctools unit testing *
201 201 ***********************
202   - Test ctobssim on command line: ..... ok
203   - Test ctobssim from Python: ................................................. ok
204   - Test ctselect on command line: ....... ok
205   - Test ctselect from Python: ..... ok
206   - Test ctbin on command line: ..... ok
207   - Test ctbin from Python: ............................................. ok
  202 + Test ctobssim on command line: ...... ok
  203 + Test ctobssim from Python: ........................................... ok
  204 + Test ctselect on command line: ........ ok
  205 + Test ctselect from Python: .............................................................. ok
  206 + Test ctphase on command line: ...... ok
  207 + Test ctphase from Python: .............. ok
208 208 ...
209 209 PASS test_python_ctools.sh
210 210  
211 211 *************************
212 212 * cscripts unit testing *
213 213 *************************
214   - Test cscaldb on command line: .. ok
215   - Test cscaldb from Python: . ok
216   - Test cslightcrv on command line: ............... ok
217   - Test cslightcrv from Python: ................................................. ok
218   - Test csmodelinfo on command line: ..... ok
219   - Test csmodelinfo from Python: ..... ok
  214 + Test cscript base class: ............................................................................................................................... ok
  215 + Test ctobservation base class: ............................................. ok
  216 + Test ctlikelihood base class: ... ok
  217 + Test csbkgmodel on command line: ..... ok
  218 + Test csbkgmodel from Python: ........... ok
  219 + Test csbkgmodel pickeling: ...... ok
220 220 ...
221 221 PASS test_python_cscripts.sh
222 222  
223 223 ********************
224 224 * Examples testing *
225 225 ********************
226   - Test generate_prod3_irfs.py: .. ok
227 226 Test make_pointings.py: ....... ok
228   - Test make_spectrum.py: .. ok
229   - Test make_ts_distributions.py: .. ok
  227 + Test show_butterfly.py: .. ok
  228 + Test show_irf.py: .. ok
  229 + Test show_lightcurve.py: .. ok
  230 + Test show_model.py: ... ok
  231 + Test show_obs.py: ... ok
230 232 ...
231 233 PASS test_examples.py
232 234 ==================
... ... @@ -239,9 +241,9 @@ versions, but there it is written in log files that you can find in the
239 241  
240 242 .. code-block:: bash
241 243  
242   - test_python_ctools.sh.log
243   - test_python_cscripts.sh.log
244   - test_examples.py.log
  244 + test_python_ctools.sh.log
  245 + test_python_cscripts.sh.log
  246 + test_examples.py.log
245 247  
246 248 If you do not see the same output, but a failure message, please check
247 249 first the :ref:`issues` section. If you cannot fix the problem, please
... ... @@ -256,7 +258,7 @@ Now you are ready to install the ctools by typing
256 258  
257 259 .. code-block:: bash
258 260  
259   - $ make install
  261 + $ make install
260 262  
261 263 If the destination directory is owned by ``root`` (which is normally the
262 264 case when using the default), administrator privileges are needed for
... ... @@ -264,7 +266,7 @@ installation. In this case, type
264 266  
265 267 .. code-block:: bash
266 268  
267   - $ sudo make install
  269 + $ sudo make install
268 270  
269 271 By default, the install directory is set to ``/usr/local/gamma``. To
270 272 change the install directory (for example in case that you do not
... ... @@ -273,7 +275,7 @@ can be given, for example:
273 275  
274 276 .. code-block:: bash
275 277  
276   - $ ./configure --prefix=$HOME/gamma
  278 + $ ./configure --prefix=$HOME/gamma
277 279  
278 280  
279 281 Setting up the ctools environment
... ... @@ -288,16 +290,16 @@ on a Linux machine:
288 290  
289 291 .. code-block:: bash
290 292  
291   - export CTOOLS=/usr/local/gamma
292   - source $CTOOLS/bin/ctools-init.sh
  293 + export CTOOLS=/usr/local/gamma
  294 + source $CTOOLS/bin/ctools-init.sh
293 295  
294 296 If you use C shell or a variant then add the following to your
295 297 ``$HOME/.cshrc`` or ``$HOME/.tcshrc`` script:
296 298  
297 299 .. code-block:: csh
298 300  
299   - setenv CTOOLS /usr/local/gamma
300   - source $CTOOLS/bin/ctools-init.csh
  301 + setenv CTOOLS /usr/local/gamma
  302 + source $CTOOLS/bin/ctools-init.csh
301 303  
302 304  
303 305 Checking your setup
... ... @@ -309,17 +311,17 @@ As a quick check that your setup is okay you can run ``csinfo check``:
309 311  
310 312 .. code-block:: bash
311 313  
312   - $ csinfo check
  314 + $ csinfo check
313 315  
314   - Gammalib / ctools setup check:
  316 + Gammalib / ctools setup check:
315 317  
316   - GAMMALIB environment variable ... ok
317   - CTOOLS environment variable ... ok
318   - gammalib Python import .......... ok
319   - ctools Python import .......... ok
320   - cscripts Python import .......... ok
  318 + GAMMALIB environment variable ... ok
  319 + CTOOLS environment variable ... ok
  320 + gammalib Python import .......... ok
  321 + ctools Python import .......... ok
  322 + cscripts Python import .......... ok
321 323  
322   - ===> Your Gammalib / ctools setup is OK.
  324 + ===> Your Gammalib / ctools setup is OK.
323 325  
324 326 If the setup is not okay, run the ``csinfo info`` command to print
325 327 detailed information about your setup. There's also a ``csinfo list``
... ...
doc/source/users/reference_manual/csspec.rst
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... ... @@ -158,7 +158,7 @@ General parameters
158 158 ``(dll_sigmax = 5.0) [real]``
159 159 Maximum number of standard deviations for log-like profiles. The final number
160 160 of bins generated in the likelihood profile will be:
161   - 2*(dll_sigmax/dll_sigstep) + 1
  161 + ``2*(dll_sigmax/dll_sigstep) + 1``
162 162 ensuring that the central flux will always be evaluated.
163 163  
164 164 ``(dll_freenodes = no) [boolean]``
... ...
doc/source/users/reference_manual/csviscube.rst
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... ... @@ -15,6 +15,7 @@ that a given position on the sky is observable under a given zenith angle
15 15 by an IACT array during a given time period.
16 16  
17 17 For the moment, the script takes into account:
  18 +
18 19 - a Sun constraint, specified as a minimum zenith angle of the Sun (hidden
19 20 parameter ``sunzenith``). If the Sun is higher in the sky than this zenith
20 21 angle the corresponding times are excluded
... ...
doc/source/users/tutorials/1dc/getting_data.rst
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... ... @@ -3,89 +3,14 @@
3 3 Getting the data
4 4 ================
5 5  
6   -The
  6 +The data for the
7 7 :ref:`first CTA Data Challenge <glossary_1dc>`
8   -data are available on the
9   -`CTA ownCloud server <https://owncloud.cta-observatory.org>`_.
10   -Only CTA Consortium members are entitled to access the data.
11   -You need your usual CTA credentials to download the data.
  8 +are only available to members of the CTA Consortium.
  9 +Instructions for CTA Consortium of how to download the data can be found
  10 +`here <https://forge.in2p3.fr/projects/data-challenge-1-dc-1/wiki/Getting_data>`_
  11 +(access to the instructions are restricted).
12 12  
13   -The release contains simulated data for the Galactic Plane Survey, the
14   -Galactic Centre Survey, the Extragalactic Survey and the AGN monitoring program,
15   -:ref:`instrument response functions (IRFs) <glossary_irf>`, and the
16   -:ref:`model definition files <glossary_moddef>`
17   -that were used for the simulation.
18   -
19   -The data were split into the separate files that can be downloaded
20   -by clicking on the following links:
21   -
22   -* `Galactic Plane Survey <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gps.tar.gz>`_ (8.3 GB)
23   -* `Galactic Centre Survey <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gc.tar.gz>`_ (4.4 GB)
24   -* `Extragalactic Survey <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/egal.tar.gz>`_ (2.5 GB)
25   -* `AGN monitoring program <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/agn.wobble.tar.gz>`_ (4.7 GB)
26   -* `Instrument Response Functions <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/caldb.tar.gz>`_ (1.2 MB)
27   -* `Sky and background models <https://owncloud.cta-observatory.org/remote.php/webdav/1dc/models.tar.gz>`_ (0.9 GB)
28   -
29   -You can also download the files using the ``wget`` tool from the command
30   -line by typing:
31   -
32   -.. code-block:: bash
33   -
34   - $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gps.tar.gz --user=<user> --ask-password
35   - $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/gc.tar.gz --user=<user> --ask-password
36   - $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/egal.tar.gz --user=<user> --ask-password
37   - $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/agn.wobble.tar.gz --user=<user> --ask-password
38   - $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/caldb.tar.gz --user=<user> --ask-password
39   - $ wget https://owncloud.cta-observatory.org/remote.php/webdav/1dc/models.tar.gz --user=<user> --ask-password
40   -
41   -.. warning::
42   - ``<user>`` needs to be replaced by your CTA user name.
43   - Don't type the ``$`` symbol. It indicates that a command should be typed
44   - on the command line of your terminal.
45   -
46   -.. note::
47   - You may need to add the ``--no-check-certificate`` option to download the
48   - files using ``wget``.
49   -
50   -.. note::
51   - In case you encounter the following error message
52   -
53   - .. code-block:: bash
54   -
55   - HTTP request sent, awaiting response... 401 Unauthorized
56   - Authentication selected: Basic realm="ownCloud"
57   - Reusing existing connection to owncloud.cta-observatory.org:443.
58   - HTTP request sent, awaiting response... 404 Not Found
59   - 2017-06-06 14:43:33 ERROR 404: Not Found.
60   -
61   - or any other problems with the download, please contact
62   - sstober@cta-observatory.org.
63   -
64   -To make sure that you have the relevant files you may check the MD5 checksums
65   -after downloading by typing for example
66   -
67   -.. code-block:: bash
68   -
69   - $ md5 gps.tar.gz
70   -
71   -on Mac OS X or
72   -
73   -.. code-block:: bash
74   -
75   - $ md5sum gps.tar.gz
76   -
77   -on Linux. Below the expected results:
78   -
79   -.. code-block:: bash
80   -
81   - gps.tar.gz c7129c71e911920f82273270c9d7c818
82   - gc.tar.gz 07aa46bb2d67cd64fa4685078643b043
83   - egal.tar.gz 4ea5f2ff8312b700dcc133a89d9fd096
84   - agn.wobble.tar.gz df8fc4f9de22ac36a86023ccbfd0cf89
85   - caldb.tar.gz ce718128e1b2fe19c4b8dc79b688d113
86   - models.tar.gz 87662cf53a2988522f485cad984d8810
87   -
88   -Now uncompress the files at any place by typing
  13 +Once downloaded, uncompress the files at any place by typing
89 14  
90 15 .. code-block:: bash
91 16  
... ...