diff --git a/docs/source/experiment.rst b/docs/source/experiment.rst index 9ab8283..9c68471 100644 --- a/docs/source/experiment.rst +++ b/docs/source/experiment.rst @@ -118,8 +118,8 @@ Experiment Sub-Directories NeXus files (described below). The files don't have to be stored in this sub-directory, but if they are in another location, it is recommended to copy them here for completeness. If the calibrations - have been performed by external processes, the PONI parameters can - be imported directly. + have been performed by another package, the PONI parameters can be + imported directly from a PONI file. **configurations** The ``configurations`` sub-directory contains NeXus files that act diff --git a/docs/source/images/server_settings.png b/docs/source/images/server_settings.png new file mode 100644 index 0000000..3956006 Binary files /dev/null and b/docs/source/images/server_settings.png differ diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 12359fc..0a55c75 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -160,66 +160,68 @@ Here is the structure of the ``nxserver`` directory:: Settings`` dialog, both of which are located in the ``Server`` menu added as a NeXpy plugin when NXRefine is installed. -Server Settings -^^^^^^^^^^^^^^^ -The file, ``settings.ini`` in the server directory contains settings for -the server, the beamline, and the workflow. These values can be changed, -either by opening the "Edit Settings" dialog in the NeXpy "Server" menu -or at the command line using ``nxsettings -i``. Hitting the [Return] key -keeps the current value. Here are the parameters:: - - $ nxsettings -i - - Default settings stored in /path/to/parent/nxserver - - - server Parameters - ------------------- - type [multicore]: - cores [4]: - concurrent [True]: - run_command [None]: - template [None]: - cctw [cctw]: - - instrument Parameters - ------------------- - source [None]: - instrument [None]: - raw_home [None]: - raw_path [None]: - analysis_home [None]: - analysis_path [None]: - - NXRefine Parameters - ------------------- - wavelength [0.2]: - distance [500]: - geometry [default]: - phi [-5]: - phi_end [360]: - phi_step [-0.1]: - chi [-90]: - omega [0]: - gonpitch [0]: - x [0]: - y [0]: - nsteps [3]: - frame_rate [10]: - - NXReduce Parameters - ------------------- - threshold [50000]: - min_pixels [10]: - first [10]: - last [3640]: - polar_max [10]: - hkl_tolerance [0.05]: - monitor [monitor1]: - norm [10000]: - polarization [0.99]: - qmin [5]: - qmax [10]: - radius [0.2]: - -These parameters will be described later. \ No newline at end of file +Default Settings +^^^^^^^^^^^^^^^^ +The file, ``settings.ini`` in the server directory contains the default +settings for the server, the beamline, and the workflow. These values +can be changed, either by opening the "Edit Settings" dialog in the +NeXpy "Server" menu or at the command line using ``nxsettings -i``. +Hitting the [Return] key keeps the current value. + +.. figure:: /images/server_settings.png + :align: right + :width: 90% + :figwidth: 40% + + *Example server settings.* + +The right-hand figure shows an example of the first two sections of the +``settings.ini``. The other sections contain default values of the data +reduction parameters that can be customized for each experiment (see the +next section). + +**Server Settings** +The server settings are used by the workflow server, which is described +in a later section. + +* **type** + The server type can either be ``multicore`` or ``multinode``. The only + difference is that multinode servers have a list of defined nodes, to + which jobs may be submitted, so their names will also be stored in + the settings file. If jobs are submitted to a job server, without + needing to specify the node, or if all the jobs are performed on the + local machine, then the server type should be ``multicore``. + +* **cores** + This sets the number of jobs that can be run simultaneously by the + server. Once reaching the limit, new jobs will only start as old ones + are finished. + +* **concurrent** + This determines whether parallelized processes should be used in the + workflow. These speed up the computation, but can be disabled if they + cause issues with the server. Note that this refers to whether + multiple processes can be run simultaneously, *e.g.*, in peaks + searches, not whether multiple jobs can be submitted to the server. + Valid values are ``True`` or ``False``. + +* **run_command** + This is a string that is prepended to any jobs that are submitted to + the server. It can contain a set of switches in addition to the + job submission command itself. + +* **template** + In some systems, it is necessary to wrap the command that is submitted + to the server in a shell script. This is the name of the script, which + should be stored in the ``nxserver`` directory. It should contain the + string ````, which is replaced by the job command. + +* **cctw** + This is the path to the CCTW executable used to transform data from + instrumental coordinates to reciprocal space. + +**Instrument Settings** +The instrument settings are used to define the name of the instrument, +which is used to import a customized plugin for importing metadata, +and a set of paths defining the location of the raw and reduced data +locations.