diff --git a/doc/source/_templates/index.html b/doc/source/_templates/index.html index 266b7d0..c3ee5c9 100644 --- a/doc/source/_templates/index.html +++ b/doc/source/_templates/index.html @@ -34,35 +34,4 @@ and next steps, and advance with the coding of the software. {%endtrans%}

{%trans%} ctools is free software distributed under the GNU GPL license version 3 {%endtrans%}

-

{%trans%}Getting started{%endtrans%}

- - - -

{%trans%}Documentation{%endtrans%}

- - - -

{%trans%}Links{%endtrans%}

- - +{% endblock %} diff --git a/doc/source/_themes/sphinx13/layout.html b/doc/source/_themes/sphinx13/layout.html index 2031c03..07b2716 100644 --- a/doc/source/_themes/sphinx13/layout.html +++ b/doc/source/_themes/sphinx13/layout.html @@ -69,10 +69,10 @@
diff --git a/doc/source/download.rst b/doc/source/admin/download.rst index d07c3f3..753e310 100644 --- a/doc/source/download.rst +++ b/doc/source/admin/download.rst @@ -1,4 +1,4 @@ -.. _download: +.. _sec_download: Download ======== @@ -15,11 +15,14 @@ Releases The latest ctools release is ``ctools-1.2.1`` (30 May 2017). -Below a table of ctools releases. Please note that at this stage of the -project there is a strict link between the ctools and gammalib versions. -Please make sure that you have the corresponding gammalib version installed -before installing ctools. The Mac OS X packages comprise both ctools and -gammalib. +Below a table of ctools releases. Please read the :ref:`sec_release` to +learn more about new features and corrected bugs in a given release. + +.. warning:: + At this stage of the project there is a strict link between the ctools and + gammalib versions. Please make sure that you have the corresponding gammalib + version installed before installing ctools. The Mac OS X packages comprise + both ctools and gammalib. .. list-table:: :header-rows: 1 @@ -155,7 +158,7 @@ the following command sequence (the code will be installed into the $ export CTOOLS=/usr/local/gamma $ source $CTOOLS/bin/ctools-init.sh -Please read the :ref:`sec_getting` section if you need more information on +Please read the :ref:`sec_install` section if you need more information on how to install ctools. .. note:: diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst new file mode 100644 index 0000000..2facfdf --- /dev/null +++ b/doc/source/admin/index.rst @@ -0,0 +1,11 @@ +.. _sec_admin: + +Getting ctools +============== + +.. toctree:: + :maxdepth: 1 + + download + install + release_history/index diff --git a/doc/source/users/user_manual/getting.rst b/doc/source/admin/install.rst index ba02298..5ef5394 100644 --- a/doc/source/users/user_manual/getting.rst +++ b/doc/source/admin/install.rst @@ -1,7 +1,7 @@ -.. _sec_getting: +.. _sec_install: -Getting the ctools -================== +Installing ctools +================= Before you start ---------------- @@ -58,7 +58,7 @@ You will need the following to build the GammaLib: Furthermore it is recommended to have readline and ncurses installed (including the developer packages). -After downloading the GammaLib tarball (see :ref:`download`), save it +After downloading the GammaLib tarball (see :ref:`sec_download`), save it in an appropriate location (for example ``$HOME/builds``), and type .. code-block:: bash @@ -130,7 +130,7 @@ If you use C shell or a variant then add the following to your Building ctools --------------- -After downloading the ctools tarball (see :ref:`download`), save it in +After downloading the ctools tarball (see :ref:`sec_download`), save it in an appropriate location (for example ``$HOME/builds``), and type .. code-block:: bash diff --git a/doc/source/users/release_history/1.0.1.rst b/doc/source/admin/release_history/1.0.1.rst index b1753f3..b1753f3 100644 --- a/doc/source/users/release_history/1.0.1.rst +++ b/doc/source/admin/release_history/1.0.1.rst diff --git a/doc/source/users/release_history/1.0.rst b/doc/source/admin/release_history/1.0.rst index cc36d08..cc36d08 100644 --- a/doc/source/users/release_history/1.0.rst +++ b/doc/source/admin/release_history/1.0.rst diff --git a/doc/source/users/release_history/1.1.rst b/doc/source/admin/release_history/1.1.rst index 288940e..288940e 100644 --- a/doc/source/users/release_history/1.1.rst +++ b/doc/source/admin/release_history/1.1.rst diff --git a/doc/source/users/release_history/1.2.1.rst b/doc/source/admin/release_history/1.2.1.rst index 65562d5..65562d5 100644 --- a/doc/source/users/release_history/1.2.1.rst +++ b/doc/source/admin/release_history/1.2.1.rst diff --git a/doc/source/users/release_history/1.2.rst b/doc/source/admin/release_history/1.2.rst index b0e3f66..b0e3f66 100644 --- a/doc/source/users/release_history/1.2.rst +++ b/doc/source/admin/release_history/1.2.rst diff --git a/doc/source/users/release_history/1.3.rst b/doc/source/admin/release_history/1.3.rst index 154d317..154d317 100644 --- a/doc/source/users/release_history/1.3.rst +++ b/doc/source/admin/release_history/1.3.rst diff --git a/doc/source/users/release_history/index.rst b/doc/source/admin/release_history/index.rst index b1b07fa..7a64c36 100644 --- a/doc/source/users/release_history/index.rst +++ b/doc/source/admin/release_history/index.rst @@ -1,4 +1,4 @@ -.. _release: +.. _sec_release: Release History =============== diff --git a/doc/source/conf.py b/doc/source/conf.py index 040fba5..b98c1b4 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -59,7 +59,7 @@ master_doc = 'contents' # General information about the project. project = u'ctools' -copyright = u'2014-2016, ctools developers' +copyright = u'2014-2017, ctools developers' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff --git a/doc/source/contents.rst b/doc/source/contents.rst index 6a6141a..21d94ce 100644 --- a/doc/source/contents.rst +++ b/doc/source/contents.rst @@ -1,3 +1,5 @@ +.. _sec_contents: + Documentation ============= @@ -5,7 +7,7 @@ Documentation :maxdepth: 1 about - download + admin/index users/index develop/index - users/help + help/index diff --git a/doc/source/develop/index.rst b/doc/source/develop/index.rst index becc863..436ecd4 100644 --- a/doc/source/develop/index.rst +++ b/doc/source/develop/index.rst @@ -1,4 +1,4 @@ -.. _develop: +.. _sec_develop: Developer documentation ======================= @@ -39,6 +39,14 @@ Below some reasources to learn how to contribute to ctools: profiling/index releasing/index +Links: + +* `GitLab `_ +* `GitHub `_ +* `Redmine `_ +* `Open HUB `_ +* `Source code documentation (Doxygen) `_ + And here some status shields: .. image:: https://cta-jenkins.irap.omp.eu/buildStatus/icon?job=ctools-integrate-os diff --git a/doc/source/develop/releasing/devel.rst b/doc/source/develop/releasing/devel.rst index 907e670..ba7086a 100644 --- a/doc/source/develop/releasing/devel.rst +++ b/doc/source/develop/releasing/devel.rst @@ -1,4 +1,4 @@ -.. _dev_releasing_merge: +.. _dev_releasing_devel: Incrementing the development version ==================================== diff --git a/doc/source/users/faq.rst b/doc/source/help/faq.rst index 78c690d..c775af1 100644 --- a/doc/source/users/faq.rst +++ b/doc/source/help/faq.rst @@ -77,7 +77,7 @@ asked. The GammaLib interface is still not fully stabilised, hence ctools is continuously adapted to match the interface evolution - (see the :ref:`download` section for a correspondance of versions). + (see the :ref:`sec_download` section for a correspondance of versions). We plan however to put the GammaLib interface under change control. ctools should then become more independent from GammaLib. diff --git a/doc/source/users/help.rst b/doc/source/help/index.rst index 1571a9d..2b6cce8 100644 --- a/doc/source/users/help.rst +++ b/doc/source/help/index.rst @@ -1,11 +1,16 @@ -.. _help: +.. _sec_help: Getting Help ============ -If you need help you should first check the -:ref:`Frequently Asked Questions ` and the list of -:ref:`Known Issues `. +If you need help you should first check + +.. toctree:: + :maxdepth: 1 + + faq + issues + In case that you do not find an answer to your question you may post your question on the ctools@irap.omp.eu mailing list. To subscribe to this list you simply need to send an e-mail to @@ -43,4 +48,4 @@ Also explain the motivation for your request and provide some hint on how urgently you need the new feature. You may click on ``Watch`` in the top-right corner of the issue page to make sure -that you will receive an e-mail notification when the issue is updated. \ No newline at end of file +that you will receive an e-mail notification when the issue is updated. diff --git a/doc/source/users/issues.rst b/doc/source/help/issues.rst index ac3f41f..ac3f41f 100644 --- a/doc/source/users/issues.rst +++ b/doc/source/help/issues.rst diff --git a/doc/source/users/glossary.rst b/doc/source/users/glossary.rst index e798b08..8c22e04 100644 --- a/doc/source/users/glossary.rst +++ b/doc/source/users/glossary.rst @@ -1,3 +1,5 @@ +.. _sec_glossary: + Glossary ======== diff --git a/doc/source/users/index.rst b/doc/source/users/index.rst index d8bba2a..0252e1a 100644 --- a/doc/source/users/index.rst +++ b/doc/source/users/index.rst @@ -1,4 +1,4 @@ -.. _users: +.. _sec_users: User Documentation ================== @@ -9,8 +9,4 @@ User Documentation tutorials/index user_manual/index reference_manual/index - faq - issues glossary - release_history/index - help diff --git a/doc/source/users/tutorials/1dc/getting_tools.rst b/doc/source/users/tutorials/1dc/getting_tools.rst index 4d53b1a..0bca36d 100644 --- a/doc/source/users/tutorials/1dc/getting_tools.rst +++ b/doc/source/users/tutorials/1dc/getting_tools.rst @@ -24,7 +24,7 @@ After downloading, configure GammaLib and ctools as follows: $ export CTOOLS=/usr/local/gamma $ source $CTOOLS/bin/ctools-init.sh -Have a look at :ref:`getting the ctools ` if you need more +Have a look at :ref:`getting the ctools ` if you need more information about the installation and configuration process. .. note:: diff --git a/doc/source/users/tutorials/1dc/index.rst b/doc/source/users/tutorials/1dc/index.rst index a6162bd..2c99a73 100644 --- a/doc/source/users/tutorials/1dc/index.rst +++ b/doc/source/users/tutorials/1dc/index.rst @@ -11,5 +11,4 @@ First CTA Data Challenge getting_data data_organisation first - howto diff --git a/doc/source/users/user_manual/getting_started/beyond_combine.rst b/doc/source/users/tutorials/beyond/beyond_combine.rst index 611cda6..611cda6 100644 --- a/doc/source/users/user_manual/getting_started/beyond_combine.rst +++ b/doc/source/users/tutorials/beyond/beyond_combine.rst diff --git a/doc/source/users/user_manual/getting_started/beyond_irf.rst b/doc/source/users/tutorials/beyond/beyond_irf.rst index 7bdb4ca..7bdb4ca 100644 --- a/doc/source/users/user_manual/getting_started/beyond_irf.rst +++ b/doc/source/users/tutorials/beyond/beyond_irf.rst diff --git a/doc/source/users/user_manual/getting_started/beyond_model.rst b/doc/source/users/tutorials/beyond/beyond_model.rst index 54388ac..54388ac 100644 --- a/doc/source/users/user_manual/getting_started/beyond_model.rst +++ b/doc/source/users/tutorials/beyond/beyond_model.rst diff --git a/doc/source/users/user_manual/getting_started/beyond_residual.rst b/doc/source/users/tutorials/beyond/beyond_residual.rst index 22d96a0..4c42a47 100644 --- a/doc/source/users/user_manual/getting_started/beyond_residual.rst +++ b/doc/source/users/tutorials/beyond/beyond_residual.rst @@ -49,7 +49,7 @@ The :ref:`csresmap` script is then used as follows: Residual map computation algorithm (SUB|SUBDIV|SUBDIVSQRT) [SUBDIV] In our example, the map will cover a field of 4° x 4° centred on the -Crab nebula at a pixel scale of 0.02° per pixel. +Crab nebula at a pixel scale of 0.02 degrees per pixel. The resulting residual map ``resmap.fits``, smoothed with a Gaussian kernel of 3 pixels to enhance features, is shown in the following figure. Obviously, the map is free from any significant residuals. diff --git a/doc/source/users/user_manual/getting_started/beyond_stacked.rst b/doc/source/users/tutorials/beyond/beyond_stacked.rst index b6c8236..b6c8236 100644 --- a/doc/source/users/user_manual/getting_started/beyond_stacked.rst +++ b/doc/source/users/tutorials/beyond/beyond_stacked.rst diff --git a/doc/source/users/user_manual/getting_started/beyond_tsmap.rst b/doc/source/users/tutorials/beyond/beyond_tsmap.rst index 02ff853..02ff853 100644 --- a/doc/source/users/user_manual/getting_started/beyond_tsmap.rst +++ b/doc/source/users/tutorials/beyond/beyond_tsmap.rst diff --git a/doc/source/users/user_manual/getting_started/beyond.rst b/doc/source/users/tutorials/beyond/index.rst index 92225ab..37dcaa2 100644 --- a/doc/source/users/user_manual/getting_started/beyond.rst +++ b/doc/source/users/tutorials/beyond/index.rst @@ -1,4 +1,4 @@ -.. _beyond: +.. _sec_beyond: Beyond the first steps ---------------------- @@ -11,7 +11,7 @@ And you should be ready for doing your own cutting edge CTA science data analyses. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 beyond_combine beyond_stacked diff --git a/doc/source/users/user_manual/getting_started/resmap-bkg.png b/doc/source/users/tutorials/beyond/resmap-bkg.png index bb5d85e..bb5d85e 100644 --- a/doc/source/users/user_manual/getting_started/resmap-bkg.png +++ b/doc/source/users/tutorials/beyond/resmap-bkg.png diff --git a/doc/source/users/user_manual/getting_started/resmap-crab.png b/doc/source/users/tutorials/beyond/resmap-crab.png index a5840fb..a5840fb 100644 --- a/doc/source/users/user_manual/getting_started/resmap-crab.png +++ b/doc/source/users/tutorials/beyond/resmap-crab.png diff --git a/doc/source/users/user_manual/getting_started/tsmap-crab.png b/doc/source/users/tutorials/beyond/tsmap-crab.png index 5af71f6..5af71f6 100644 --- a/doc/source/users/user_manual/getting_started/tsmap-crab.png +++ b/doc/source/users/tutorials/beyond/tsmap-crab.png diff --git 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a/doc/source/users/tutorials/1dc/howto_phasecurve_prob.png +++ b/doc/source/users/tutorials/howto/howto_phasecurve_prob.png diff --git a/doc/source/users/tutorials/1dc/howto_phasecurve_probphases.png b/doc/source/users/tutorials/howto/howto_phasecurve_probphases.png index 6eb974d..6eb974d 100644 --- a/doc/source/users/tutorials/1dc/howto_phasecurve_probphases.png +++ b/doc/source/users/tutorials/howto/howto_phasecurve_probphases.png diff --git a/doc/source/users/tutorials/1dc/howto_ts.rst b/doc/source/users/tutorials/howto/howto_ts.rst index 1bb2077..1bb2077 100644 --- a/doc/source/users/tutorials/1dc/howto_ts.rst +++ b/doc/source/users/tutorials/howto/howto_ts.rst diff --git a/doc/source/users/tutorials/1dc/first_tsmap.png b/doc/source/users/tutorials/howto/howto_tsmap.png index 4bd4fd0..4bd4fd0 100644 --- a/doc/source/users/tutorials/1dc/first_tsmap.png +++ b/doc/source/users/tutorials/howto/howto_tsmap.png diff --git a/doc/source/users/tutorials/1dc/howto_tsmap.rst b/doc/source/users/tutorials/howto/howto_tsmap.rst index f221530..40fbf35 100644 --- a/doc/source/users/tutorials/1dc/howto_tsmap.rst +++ b/doc/source/users/tutorials/howto/howto_tsmap.rst @@ -39,7 +39,7 @@ The :ref:`cttsmap` tool creates a FITS file containing for each pixel the Test Statistic value as well as the fit parameters for the test source. The figure below shows the resulting Test Statistic map. -.. figure:: first_tsmap.png +.. figure:: howto_tsmap.png :width: 400px :align: center diff --git a/doc/source/users/tutorials/1dc/howto_ulimit.rst b/doc/source/users/tutorials/howto/howto_ulimit.rst index 0534de4..0534de4 100644 --- a/doc/source/users/tutorials/1dc/howto_ulimit.rst +++ b/doc/source/users/tutorials/howto/howto_ulimit.rst diff --git a/doc/source/users/tutorials/1dc/howto_vo.rst b/doc/source/users/tutorials/howto/howto_vo.rst index f17effd..f17effd 100644 --- a/doc/source/users/tutorials/1dc/howto_vo.rst +++ b/doc/source/users/tutorials/howto/howto_vo.rst diff --git a/doc/source/users/tutorials/1dc/howto_vo_aladin_after.png b/doc/source/users/tutorials/howto/howto_vo_aladin_after.png index 8611126..8611126 100644 --- a/doc/source/users/tutorials/1dc/howto_vo_aladin_after.png +++ b/doc/source/users/tutorials/howto/howto_vo_aladin_after.png diff --git a/doc/source/users/tutorials/1dc/howto_vo_aladin_before.png b/doc/source/users/tutorials/howto/howto_vo_aladin_before.png index 453c104..453c104 100644 --- a/doc/source/users/tutorials/1dc/howto_vo_aladin_before.png +++ b/doc/source/users/tutorials/howto/howto_vo_aladin_before.png diff --git a/doc/source/users/tutorials/1dc/howto_vo_aladin_catalog.png b/doc/source/users/tutorials/howto/howto_vo_aladin_catalog.png index 9fdbf75..9fdbf75 100644 --- a/doc/source/users/tutorials/1dc/howto_vo_aladin_catalog.png +++ b/doc/source/users/tutorials/howto/howto_vo_aladin_catalog.png diff --git a/doc/source/users/tutorials/1dc/howto_vo_topcat_after.png b/doc/source/users/tutorials/howto/howto_vo_topcat_after.png index 62cb9fb..62cb9fb 100644 --- a/doc/source/users/tutorials/1dc/howto_vo_topcat_after.png +++ b/doc/source/users/tutorials/howto/howto_vo_topcat_after.png diff --git a/doc/source/users/tutorials/1dc/howto_vo_topcat_before.png b/doc/source/users/tutorials/howto/howto_vo_topcat_before.png index 7dbfcef..7dbfcef 100644 --- a/doc/source/users/tutorials/1dc/howto_vo_topcat_before.png +++ b/doc/source/users/tutorials/howto/howto_vo_topcat_before.png diff --git a/doc/source/users/tutorials/1dc/howto_vo_topcat_scatter.png b/doc/source/users/tutorials/howto/howto_vo_topcat_scatter.png index 07aac72..07aac72 100644 --- a/doc/source/users/tutorials/1dc/howto_vo_topcat_scatter.png +++ b/doc/source/users/tutorials/howto/howto_vo_topcat_scatter.png diff --git a/doc/source/users/tutorials/1dc/howto.rst b/doc/source/users/tutorials/howto/index.rst index fe2c2f7..0af03fb 100644 --- a/doc/source/users/tutorials/1dc/howto.rst +++ b/doc/source/users/tutorials/howto/index.rst @@ -3,8 +3,11 @@ Analysis cookbook ================= -The following sections explain how you can address some specific analysis -issues. +The following sections teach you how to use ctools to address some typical +science analysis. The sections provide examples that are based on the data +distributed within the CTA Consortium for the +:ref:`first CTA Data Challenge `. +These examples can be easily adapted to any data you have at your disposal. .. toctree:: :maxdepth: 1 @@ -18,17 +21,4 @@ issues. howto_lightcurve howto_phasecurve howto_exclude - howto_vo - -If you cannot find the answer to your question, have a look at the -:ref:`first steps with ctools ` -and the -:ref:`beyond the first steps ` -sections of the User Manual. You may also consult the -:ref:`Reference Manual ` -as well as the -:ref:`frequently asked questions `. -If after this you still need some help, please create a -`support ticket `_. -Specify ``Support`` as Tracker, choose a short and meaningful subject, -and add an exhaustive description of your request. + howto_vo \ No newline at end of file diff --git a/doc/source/users/user_manual/iact_analysis/analysis.rst b/doc/source/users/tutorials/iact_analysis/analysis.rst index e38d0e0..3438468 100644 --- a/doc/source/users/user_manual/iact_analysis/analysis.rst +++ b/doc/source/users/tutorials/iact_analysis/analysis.rst @@ -1,10 +1,10 @@ -.. _sec_analysis: +.. _sec_iact_analysis: Analysing IACT data =================== In order to analyse data from current IACTs, you first have to retrieve the -data. Information on how to do that can be found in the section :ref:`sec_copy`. +data. Information on how to do that can be found in the section :ref:`sec_iact_copy`. Check available FITS production ------------------------------- @@ -174,7 +174,7 @@ Alternatively, you can merged models using the :ref:`csmodelmerge` script: A list of available sky models can be found `here `_. If you are not familiar with creating sky models you should read the section -about :ref:`modelling CTA data `. +about :ref:`modelling CTA data `. Example XML files diff --git a/doc/source/users/user_manual/iact_analysis/copy.rst b/doc/source/users/tutorials/iact_analysis/copy.rst index e8e3dd8..5ac7365 100644 --- a/doc/source/users/user_manual/iact_analysis/copy.rst +++ b/doc/source/users/tutorials/iact_analysis/copy.rst @@ -1,4 +1,4 @@ -.. _sec_copy: +.. _sec_iact_copy: Copying IACT data ================== diff --git a/doc/source/users/user_manual/iact_analysis/high_level.rst b/doc/source/users/tutorials/iact_analysis/high_level.rst index 66abd58..c4d6d31 100644 --- a/doc/source/users/user_manual/iact_analysis/high_level.rst +++ b/doc/source/users/tutorials/iact_analysis/high_level.rst @@ -1,4 +1,4 @@ -.. _sec_high_level: +.. _sec_iact_high_level: High level analysis tools for IACT data ======================================= @@ -291,7 +291,7 @@ value is added to the output file. For instance a map of the prefactor can be vi $ ds9 tsmap.fits[Prefactor] Since :ref:`cttsmap` has to run a parameter optimisation in each skymap bin, it is very time comsuming to -compute a fine-granulated TS sky map. Read here how to split up the :ref:`computation into several jobs `. +compute a fine-granulated TS sky map. Read here how to split up the :ref:`computation into several jobs `. Similar as many other tools :ref:`cttsmap` can also work on binned observation input: .. code-block:: bash diff --git a/doc/source/users/user_manual/iact_analysis/index.rst b/doc/source/users/tutorials/iact_analysis/index.rst index 5c98063..a06cccf 100644 --- a/doc/source/users/user_manual/iact_analysis/index.rst +++ b/doc/source/users/tutorials/iact_analysis/index.rst @@ -1,8 +1,10 @@ +.. _sec_iact: + Analysing current IACT data =========================== .. toctree:: - :maxdepth: 2 + :maxdepth: 1 copy analysis diff --git a/doc/source/users/user_manual/iact_analysis/simulation.rst b/doc/source/users/tutorials/iact_analysis/simulation.rst index de9e16c..9e2ac45 100644 --- a/doc/source/users/user_manual/iact_analysis/simulation.rst +++ b/doc/source/users/tutorials/iact_analysis/simulation.rst @@ -1,4 +1,4 @@ -.. _sec_simulation: +.. _sec_iact_simulation: Simulating IACT data ==================== @@ -10,7 +10,7 @@ Simulations for a specific observation container ------------------------------------------------ On default, :ref:`ctobssim` builds a new observation container by querying relevant user parameters. In case an observation XML container is already in place, the hidden parameter ``inobs`` can be specified (:ref:`see here how to create an -observation container `). It might be useful to run :ref:`ctselect` beforehand to ensure that the simulation knows about +observation container `). It might be useful to run :ref:`ctselect` beforehand to ensure that the simulation knows about energy thresholds, field of view, etc. If an unselected observation container is used, the simulation tool will query for global energy boundaries and a global RoI radius. The following example illustrates the usage of an already selected observation container. @@ -59,7 +59,7 @@ observations with at a certain zenith angle range (20-25 degrees) and azimuth an Runlist outfile [zen20_az90.lis] Of course, further details could be specified, e.g. one might want to check for a certain range of muon efficieny, or any other parameter which impacts IRFs. -The output runlist subsequently has to be converted to an observation XML file using :ref:`csiactobs` (:ref:`see here how to execute this tool `). +The output runlist subsequently has to be converted to an observation XML file using :ref:`csiactobs` (:ref:`see here how to execute this tool `). In the following it is assumed that the observation XML file of the selected representative observations is produced and called ``myobs.xml``. Create caldb entry diff --git a/doc/source/users/user_manual/iact_analysis/tips.rst b/doc/source/users/tutorials/iact_analysis/tips.rst index 38326c7..1f09b91 100644 --- a/doc/source/users/user_manual/iact_analysis/tips.rst +++ b/doc/source/users/tutorials/iact_analysis/tips.rst @@ -1,4 +1,4 @@ -.. _sec_tips: +.. _sec_iact_tips: Tips, Tricks and FAQs ===================== @@ -260,7 +260,7 @@ parameter: Compute flux maps ----------------- The creation of a flux map is much more expensive in terms of computing than an -excess map. In the section about :ref:`high level analysis tools `, +excess map. In the section about :ref:`high level analysis tools `, the usage of :ref:`cttsmap` was demonstrated. This tool can also be used to generate flux maps. For this, the user has to incorporate a test source in the XML model file. This source should consist of a spectral component using a @@ -500,4 +500,4 @@ script and for example ds9: $ python $CTOOLS/examples/show_spectrum.py spectrum.fits $ ds9 excessmap.fits - \ No newline at end of file + diff --git a/doc/source/users/tutorials/index.rst b/doc/source/users/tutorials/index.rst index 602a85c..f675ae1 100644 --- a/doc/source/users/tutorials/index.rst +++ b/doc/source/users/tutorials/index.rst @@ -6,4 +6,8 @@ Tutorials .. toctree:: :maxdepth: 1 + quickstart/index + beyond/index + howto/index 1dc/index + iact_analysis/index \ No newline at end of file diff --git a/doc/source/users/user_manual/getting_started/binning.rst b/doc/source/users/tutorials/quickstart/binning.rst index b0ac1f5..b0ac1f5 100644 --- a/doc/source/users/user_manual/getting_started/binning.rst +++ b/doc/source/users/tutorials/quickstart/binning.rst diff --git a/doc/source/users/user_manual/getting_started/butterfly.jpg b/doc/source/users/tutorials/quickstart/butterfly.jpg index 814edc1..814edc1 100644 --- a/doc/source/users/user_manual/getting_started/butterfly.jpg +++ b/doc/source/users/tutorials/quickstart/butterfly.jpg diff --git a/doc/source/users/user_manual/getting_started/butterfly.rst b/doc/source/users/tutorials/quickstart/butterfly.rst index 4e1b664..4e1b664 100644 --- a/doc/source/users/user_manual/getting_started/butterfly.rst +++ b/doc/source/users/tutorials/quickstart/butterfly.rst diff --git a/doc/source/users/user_manual/getting_started/cntmap-fits.jpg b/doc/source/users/tutorials/quickstart/cntmap-fits.jpg index 265cf59..265cf59 100644 --- a/doc/source/users/user_manual/getting_started/cntmap-fits.jpg +++ b/doc/source/users/tutorials/quickstart/cntmap-fits.jpg diff --git a/doc/source/users/user_manual/getting_started/cntmap-map.jpg b/doc/source/users/tutorials/quickstart/cntmap-map.jpg index b22de89..b22de89 100644 --- a/doc/source/users/user_manual/getting_started/cntmap-map.jpg +++ b/doc/source/users/tutorials/quickstart/cntmap-map.jpg diff --git a/doc/source/users/user_manual/getting_started/dskeys.jpg b/doc/source/users/tutorials/quickstart/dskeys.jpg index 0185466..0185466 100644 --- a/doc/source/users/user_manual/getting_started/dskeys.jpg +++ b/doc/source/users/tutorials/quickstart/dskeys.jpg diff --git a/doc/source/users/user_manual/getting_started/energy_dispersion.rst b/doc/source/users/tutorials/quickstart/energy_dispersion.rst index 60da875..60da875 100644 --- a/doc/source/users/user_manual/getting_started/energy_dispersion.rst +++ b/doc/source/users/tutorials/quickstart/energy_dispersion.rst diff --git a/doc/source/users/user_manual/getting_started/fitting.rst b/doc/source/users/tutorials/quickstart/fitting.rst index dd0994e..dd0994e 100644 --- a/doc/source/users/user_manual/getting_started/fitting.rst +++ b/doc/source/users/tutorials/quickstart/fitting.rst diff --git a/doc/source/users/user_manual/getting_started/quickstart.rst b/doc/source/users/tutorials/quickstart/index.rst index 8a297f7..ec01bce 100644 --- a/doc/source/users/user_manual/getting_started/quickstart.rst +++ b/doc/source/users/tutorials/quickstart/index.rst @@ -15,7 +15,7 @@ fitted spectral model. And you will learn how to take energy dispersion into account. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 simulating binning diff --git a/doc/source/users/user_manual/getting_started/simulating.rst b/doc/source/users/tutorials/quickstart/simulating.rst index 42076a0..42076a0 100644 --- a/doc/source/users/user_manual/getting_started/simulating.rst +++ b/doc/source/users/tutorials/quickstart/simulating.rst diff --git a/doc/source/users/user_manual/getting_started/unbinned.rst b/doc/source/users/tutorials/quickstart/unbinned.rst index b2a5452..b2a5452 100644 --- a/doc/source/users/user_manual/getting_started/unbinned.rst +++ b/doc/source/users/tutorials/quickstart/unbinned.rst diff --git a/doc/source/users/user_manual/getting_started/index.rst b/doc/source/users/user_manual/getting_started/index.rst index 57b6851..2ce9cfd 100644 --- a/doc/source/users/user_manual/getting_started/index.rst +++ b/doc/source/users/user_manual/getting_started/index.rst @@ -1,12 +1,12 @@ -Getting started -=============== +.. _sec_using: + +Using ctools +============ .. toctree:: - :maxdepth: 2 + :maxdepth: 1 - quickstart - beyond + python models response - python diff --git a/doc/source/users/user_manual/getting_started/models.rst b/doc/source/users/user_manual/getting_started/models.rst index b023cbd..f9ebdd2 100644 --- a/doc/source/users/user_manual/getting_started/models.rst +++ b/doc/source/users/user_manual/getting_started/models.rst @@ -1,4 +1,4 @@ -.. _models: +.. _sec_models: Modelling CTA data ------------------ @@ -14,7 +14,7 @@ Generally, the measured events can be separated into two distinct classes: events being attributed to gamma rays of celestial origin (the "source" events) or events being attributed to any other kind of trigger (the "background" events). -In the first case, the :ref:`Instrument Response Functions (IRFs) ` +In the first case, the :ref:`Instrument Response Functions (IRFs) ` describe how an incident gamma-ray converts into a measured event. In the second case there is often no general prescription, and the distribution of background events is commonly modeled directly in the data @@ -33,10 +33,10 @@ Model components are generally parametric, and model parameters can be adjusted through a maximum likelihood procedure to find the set of parameters that represent best the measured data. Model components representing celestial sources are convolved with the -:ref:`IRFs ` to predict the expected number of source events in +:ref:`IRFs ` to predict the expected number of source events in the data. Background model components will be directly expressed as expected number -of background events without any :ref:`IRF ` convolution. +of background events without any :ref:`IRF ` convolution. .. _sec_model_implementation: diff --git a/doc/source/users/user_manual/getting_started/python.rst b/doc/source/users/user_manual/getting_started/python.rst index 1761650..8263211 100644 --- a/doc/source/users/user_manual/getting_started/python.rst +++ b/doc/source/users/user_manual/getting_started/python.rst @@ -1,4 +1,4 @@ -.. _python: +.. _sec_python: Using ctools from Python ------------------------ diff --git a/doc/source/users/user_manual/getting_started/response.rst b/doc/source/users/user_manual/getting_started/response.rst index 4fe09f7..599cd09 100644 --- a/doc/source/users/user_manual/getting_started/response.rst +++ b/doc/source/users/user_manual/getting_started/response.rst @@ -1,4 +1,4 @@ -.. _response: +.. _sec_response: CTA Instrument Response Functions --------------------------------- diff --git a/doc/source/users/user_manual/glossary.rst b/doc/source/users/user_manual/glossary.rst deleted file mode 100644 index 2a10e51..0000000 --- a/doc/source/users/user_manual/glossary.rst +++ /dev/null @@ -1,35 +0,0 @@ -Glossary -======== - -- **GammaLib** (``_) - - A versatile toolbox for scientific analysis of astronomical - gamma-ray data. - -- **cfitsio** (``_) - - Library of C and Fortran subroutines for reading and writing data - files in FITS data format. - -- **FITS** (``_) - - Flexible Image Transport System. - -- **FTOOLS** (``_) - - Collection of utility programs to create, examine, or modify data - files in the FITS data format. - -- **GNU** (``_) - - A free Unix-like operating system. - -- **HEASARC** (``_) - - High Energy Astrophysics Science Archive Research Centre. - -- **Python** (``_) - - Dynamic programming language that is used in a wide variety of - application domains. - diff --git a/doc/source/users/user_manual/index.rst b/doc/source/users/user_manual/index.rst index 5d97ec0..243ca69 100644 --- a/doc/source/users/user_manual/index.rst +++ b/doc/source/users/user_manual/index.rst @@ -3,12 +3,9 @@ User Manual =========== .. toctree:: - :maxdepth: 2 + :maxdepth: 1 introduction - getting getting_started/index - iact_analysis/index plotting - glossary diff --git a/doc/source/users/user_manual/introduction.rst b/doc/source/users/user_manual/introduction.rst index cf05565..52515ab 100644 --- a/doc/source/users/user_manual/introduction.rst +++ b/doc/source/users/user_manual/introduction.rst @@ -55,7 +55,6 @@ command line or used as Python classes, as illustrated below: In this User Manual you will now learn how to install and use the ctools package. -If you encounter any problems, please read the :ref:`faq` and :ref:`issues` -sections. If you're desperate, you may need :ref:`help`. -And you should read the :ref:`develop` section if you would like to +If you encounter any problems, please read the :ref:`sec_help` section. +And you should read the :ref:`sec_develop` section if you would like to contribute to the ctools developments.