From 3f06f605ba0f4cd95f4ef6f89ce83a6dbb168c13 Mon Sep 17 00:00:00 2001 From: Jürgen Knödlseder Date: Wed, 24 Jan 2018 19:27:09 +0100 Subject: [PATCH] Fix some documentation bugs --- doc/source/users/reference_manual/cstsdist.rst | 2 +- doc/source/users/tutorials/1dc/first_fitting.rst | 2 +- doc/source/users/tutorials/1dc/first_improving.rst | 2 +- doc/source/users/tutorials/1dc/first_stacked.rst | 5 ++--- doc/source/users/tutorials/howto/comptel/howto_comptel_fitting.rst | 2 +- doc/source/users/tutorials/howto/fermi/howto_fermi_fitting.rst | 6 +++--- doc/source/users/tutorials/howto/howto_display.rst | 2 +- doc/source/users/tutorials/howto/howto_edisp.rst | 2 +- doc/source/users/tutorials/howto/howto_exclude.rst | 2 +- doc/source/users/tutorials/howto/howto_extent.rst | 6 +++--- doc/source/users/tutorials/howto/howto_lightcurve.rst | 2 +- doc/source/users/tutorials/howto/howto_phasecurve.rst | 2 +- doc/source/users/tutorials/howto/howto_ts.rst | 2 +- doc/source/users/tutorials/howto/howto_tsmap.rst | 2 +- doc/source/users/tutorials/howto/howto_ulimit.rst | 2 +- doc/source/users/tutorials/howto/howto_vo.rst | 2 +- doc/source/users/tutorials/howto/index.rst | 2 +- doc/source/users/tutorials/quickstart/butterfly.rst | 4 ++-- doc/source/users/tutorials/quickstart/onoff.rst | 2 +- doc/source/users/tutorials/quickstart/residual_map.rst | 2 +- doc/source/users/user_manual/introduction.rst | 4 ++-- doc/source/users/user_manual/models_spatial_src.rst | 2 +- 22 files changed, 29 insertions(+), 30 deletions(-) diff --git a/doc/source/users/reference_manual/cstsdist.rst b/doc/source/users/reference_manual/cstsdist.rst index 8262415..e7f26c2 100644 --- a/doc/source/users/reference_manual/cstsdist.rst +++ b/doc/source/users/reference_manual/cstsdist.rst @@ -15,7 +15,7 @@ sets. The Test Statistics is defined as twice the log-likelihood difference that is obtained when fitting simulated data with and without a given source model component. -:red:`cstsdist` will create an ASCII file in comma-separated value (CSV) format, +:ref:`cstsdist` will create an ASCII file in comma-separated value (CSV) format, containing one row per TS computation. The first row is a header row providing the column names. The following rows give the TS value, the log-likelihood values of the fit with or without the source, the number of observed and diff --git a/doc/source/users/tutorials/1dc/first_fitting.rst b/doc/source/users/tutorials/1dc/first_fitting.rst index e29fcb6..954a841 100644 --- a/doc/source/users/tutorials/1dc/first_fitting.rst +++ b/doc/source/users/tutorials/1dc/first_fitting.rst @@ -16,7 +16,7 @@ Fitting the model components to the counts cube scripts for result display that use the ``matplotlib`` Python module can be found in the ``$CTOOLS/share/examples/python`` - folder (see :ref:`how to display results<1dc_howto_display>`). + folder (see :ref:`how to display results`). Now you are ready to fit the model to the counts cube and to determine its maximum likelihood parameters. diff --git a/doc/source/users/tutorials/1dc/first_improving.rst b/doc/source/users/tutorials/1dc/first_improving.rst index 5702254..2ddec06 100644 --- a/doc/source/users/tutorials/1dc/first_improving.rst +++ b/doc/source/users/tutorials/1dc/first_improving.rst @@ -96,7 +96,7 @@ components for these additional sources in the :ref:`model definition file ` in order to reduce the fit residuals. An example for such an exercise is shown -:ref:`here <1dc_howto_extent>`. +:ref:`here `. .. figure:: first_skymap_residual_iem.png :width: 400px diff --git a/doc/source/users/tutorials/1dc/first_stacked.rst b/doc/source/users/tutorials/1dc/first_stacked.rst index 9074873..6d94c1c 100644 --- a/doc/source/users/tutorials/1dc/first_stacked.rst +++ b/doc/source/users/tutorials/1dc/first_stacked.rst @@ -14,7 +14,7 @@ Stacking the data since for many cases the effect of the energy dispersion is negligible, and taking energy dispersion into account is computationally intensive. If you want to learn how to take the energy dispersion into account please - read :ref:`this section<1dc_howto_edisp>`. + read :ref:`this section `. To analyse the selected observations, we recommend to stack the events into a counts cube. You do this using the :ref:`ctbin` tool: @@ -70,13 +70,12 @@ the counts cube, which considerably reduces the number of User parameters that are queried by the tool. .. note:: - The binning of the exposure cube does not need to correspond to the binning of the counts cube. In any case, exposure values will be determined by interpolation from the values stored in the exposure cube file. The same is true for the point spread function and background cubes that are described below, or the energy dispersion cube that is described - :ref:`here<1dc_howto_edisp>`. + :ref:`here `. Next, :ref:`ctpsfcube` computes the weighted Point Spread Function of the stacked counts cube. diff --git a/doc/source/users/tutorials/howto/comptel/howto_comptel_fitting.rst b/doc/source/users/tutorials/howto/comptel/howto_comptel_fitting.rst index 2c8ebf9..07d56b3 100644 --- a/doc/source/users/tutorials/howto/comptel/howto_comptel_fitting.rst +++ b/doc/source/users/tutorials/howto/comptel/howto_comptel_fitting.rst @@ -185,7 +185,7 @@ fitted values, and where the statistical uncertainties were added using the ``error`` attribute. To investigate how the fit went you should inspect the log file ``ctlike.log`` that was also created by :ref:`ctlike`: -.. code-block:: bash +.. code-block:: none 2017-08-26T22:05:05: +=================================+ 2017-08-26T22:05:05: | Maximum likelihood optimisation | diff --git a/doc/source/users/tutorials/howto/fermi/howto_fermi_fitting.rst b/doc/source/users/tutorials/howto/fermi/howto_fermi_fitting.rst index 6ea3869..a3278d0 100644 --- a/doc/source/users/tutorials/howto/fermi/howto_fermi_fitting.rst +++ b/doc/source/users/tutorials/howto/fermi/howto_fermi_fitting.rst @@ -90,7 +90,7 @@ fitted values, and where the statistical uncertainties were added using the ``error`` attribute. To investigate how the fit went you should inspect the log file ``ctlike.log`` that was also created by :ref:`ctlike`: -.. code-block:: bash +.. code-block:: none 2017-08-26T10:35:10: +=================================+ 2017-08-26T10:35:10: | Maximum likelihood optimisation | @@ -193,7 +193,7 @@ using the Fermi-LAT Science Tools. when the tool is applied to the same test data. As you will see below, the fitted model parameters are basically identical. - .. code-block:: bash + .. code-block:: none Extragalactic_diffuse: Normalization: 1 @@ -240,7 +240,7 @@ using the Fermi-LAT Science Tools. This results in - .. code-block:: bash + .. code-block:: none 2017-08-26T13:05:12: === GModelSky === 2017-08-26T13:05:12: Name ......................: Vela diff --git a/doc/source/users/tutorials/howto/howto_display.rst b/doc/source/users/tutorials/howto/howto_display.rst index 1e4aa1e..fb78eaf 100644 --- a/doc/source/users/tutorials/howto/howto_display.rst +++ b/doc/source/users/tutorials/howto/howto_display.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_display: +.. _howto_display: How to display the results? --------------------------- diff --git a/doc/source/users/tutorials/howto/howto_edisp.rst b/doc/source/users/tutorials/howto/howto_edisp.rst index 1d3784f..ec2791f 100644 --- a/doc/source/users/tutorials/howto/howto_edisp.rst +++ b/doc/source/users/tutorials/howto/howto_edisp.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_edisp: +.. _howto_edisp: How to take the energy dispersion into account? ----------------------------------------------- diff --git a/doc/source/users/tutorials/howto/howto_exclude.rst b/doc/source/users/tutorials/howto/howto_exclude.rst index 6a57154..6d165e6 100644 --- a/doc/source/users/tutorials/howto/howto_exclude.rst +++ b/doc/source/users/tutorials/howto/howto_exclude.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_exclude: +.. _howto_exclude: How to exclude bins from a counts cube? --------------------------------------- diff --git a/doc/source/users/tutorials/howto/howto_extent.rst b/doc/source/users/tutorials/howto/howto_extent.rst index 384a2f7..0ec8db2 100644 --- a/doc/source/users/tutorials/howto/howto_extent.rst +++ b/doc/source/users/tutorials/howto/howto_extent.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_extent: +.. _howto_extent: How to determine the extension of a source? ------------------------------------------- @@ -55,7 +55,7 @@ For illustration, an excerpt of the :ref:`ctlike` log file is shown below. The disk with of ``Src003`` has been fitted to 0.335 +/- 0.003 degrees. The source is detected with a TS value of 5393.8. -.. code-block:: bash +.. code-block:: none 2017-08-25T19:37:47: === GModelSky === 2017-08-25T19:37:47: Name ......................: Src003 @@ -121,7 +121,7 @@ of 5665.7 which is considerably larger than the TS value of 5393.8 that is found above for the radial disk model. Below an excerpt of the :ref:`ctlike` log file: -.. code-block:: bash +.. code-block:: none 2017-08-25T20:32:55: === GModelSky === 2017-08-25T20:32:55: Name ......................: Src003 diff --git a/doc/source/users/tutorials/howto/howto_lightcurve.rst b/doc/source/users/tutorials/howto/howto_lightcurve.rst index d45f456..3252555 100644 --- a/doc/source/users/tutorials/howto/howto_lightcurve.rst +++ b/doc/source/users/tutorials/howto/howto_lightcurve.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_ligthcurve: +.. _howto_ligthcurve: How to generate a light curve? ------------------------------ diff --git a/doc/source/users/tutorials/howto/howto_phasecurve.rst b/doc/source/users/tutorials/howto/howto_phasecurve.rst index 4501612..29e3208 100644 --- a/doc/source/users/tutorials/howto/howto_phasecurve.rst +++ b/doc/source/users/tutorials/howto/howto_phasecurve.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_phasecurve: +.. _howto_phasecurve: How to generate a phase curve of a pulsar? ------------------------------------------ diff --git a/doc/source/users/tutorials/howto/howto_ts.rst b/doc/source/users/tutorials/howto/howto_ts.rst index 7acc568..d228470 100644 --- a/doc/source/users/tutorials/howto/howto_ts.rst +++ b/doc/source/users/tutorials/howto/howto_ts.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_ts: +.. _howto_ts: How to compute the signifiance of a source? ------------------------------------------- diff --git a/doc/source/users/tutorials/howto/howto_tsmap.rst b/doc/source/users/tutorials/howto/howto_tsmap.rst index 427b921..5dff9a3 100644 --- a/doc/source/users/tutorials/howto/howto_tsmap.rst +++ b/doc/source/users/tutorials/howto/howto_tsmap.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_tsmap: +.. _howto_tsmap: How to generate a Test Statistic map? ------------------------------------- diff --git a/doc/source/users/tutorials/howto/howto_ulimit.rst b/doc/source/users/tutorials/howto/howto_ulimit.rst index ec24475..bfe7762 100644 --- a/doc/source/users/tutorials/howto/howto_ulimit.rst +++ b/doc/source/users/tutorials/howto/howto_ulimit.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_ulimit: +.. _howto_ulimit: How to compute upper limits? ---------------------------- diff --git a/doc/source/users/tutorials/howto/howto_vo.rst b/doc/source/users/tutorials/howto/howto_vo.rst index f17effd..af4d0f4 100644 --- a/doc/source/users/tutorials/howto/howto_vo.rst +++ b/doc/source/users/tutorials/howto/howto_vo.rst @@ -1,4 +1,4 @@ -.. _1dc_howto_vo: +.. _howto_vo: How to use Virtual Observatory tools with ctools? ------------------------------------------------- diff --git a/doc/source/users/tutorials/howto/index.rst b/doc/source/users/tutorials/howto/index.rst index 7b9a09d..891d908 100644 --- a/doc/source/users/tutorials/howto/index.rst +++ b/doc/source/users/tutorials/howto/index.rst @@ -1,4 +1,4 @@ -.. _1dc_howto: +.. _howto: Analysis cookbook ================= diff --git a/doc/source/users/tutorials/quickstart/butterfly.rst b/doc/source/users/tutorials/quickstart/butterfly.rst index 955e804..928b2b0 100644 --- a/doc/source/users/tutorials/quickstart/butterfly.rst +++ b/doc/source/users/tutorials/quickstart/butterfly.rst @@ -63,8 +63,8 @@ A graphical display of the results is shown below: Python module. You can find these scripts in the ``$CTOOLS/share/examples/python`` folder. - Read the section about :ref:`sec_plotting` to learn more about the - available scripts. The plot above was generated using: + Read :ref:`howto_display` to learn more about the available scripts. The + plot above was generated using: .. code-block:: bash diff --git a/doc/source/users/tutorials/quickstart/onoff.rst b/doc/source/users/tutorials/quickstart/onoff.rst index 1cefd83..8e11279 100644 --- a/doc/source/users/tutorials/quickstart/onoff.rst +++ b/doc/source/users/tutorials/quickstart/onoff.rst @@ -127,7 +127,7 @@ the On region and the Off regions, ``onoff_on.reg`` and a skymap where you can see the pointing direction along with the position of the On and Off regions. -.. figure:: onoff.png +.. figure:: onoff.jpg :width: 400px :align: center diff --git a/doc/source/users/tutorials/quickstart/residual_map.rst b/doc/source/users/tutorials/quickstart/residual_map.rst index 7f6c6aa..d28e5f0 100644 --- a/doc/source/users/tutorials/quickstart/residual_map.rst +++ b/doc/source/users/tutorials/quickstart/residual_map.rst @@ -38,7 +38,7 @@ the residual counts map. The image is displayed below using kernel smoothing applied. Obviously, there are no significant residuals, which indicates that the model fit was satisfactory. -.. figure:: residuals.jpg +.. figure:: residual_map.jpg :width: 400px :align: center diff --git a/doc/source/users/user_manual/introduction.rst b/doc/source/users/user_manual/introduction.rst index 1c55081..6a19cca 100644 --- a/doc/source/users/user_manual/introduction.rst +++ b/doc/source/users/user_manual/introduction.rst @@ -43,7 +43,7 @@ the ctool or cscript followed by the ``--help`` option: ctools includes also a Python module that declares every ctool as a Python class. The following example illustrates the usage: -.. code-block:: python +.. code-block:: bash $ python >>> import ctools @@ -57,7 +57,7 @@ ctools comprise also cscripts, which are Python scripts that have the same user interface as the ctools binaries. cscripts can be started from the command line or used as Python classes, as illustrated below: -.. code-block:: python +.. code-block:: bash $ python >>> import cscripts diff --git a/doc/source/users/user_manual/models_spatial_src.rst b/doc/source/users/user_manual/models_spatial_src.rst index 8fb2e8e..1c9b2b8 100644 --- a/doc/source/users/user_manual/models_spatial_src.rst +++ b/doc/source/users/user_manual/models_spatial_src.rst @@ -281,7 +281,7 @@ Diffuse source ``Normalization`` can be replaced by ``Prefactor``. .. note:: - You may add the ``normalize="0"``to the spatial model tag to avoid the + You may add the ``normalize="0"`` to the spatial model tag to avoid the normalization of the diffuse map to an integral of unity .. code-block:: xml -- libgit2 0.21.4