.. _intro_proc_setup:

Setup
=====

.. toctree::
   :hidden:

   sh_gamit
   sh_glred

The first step in running the scripts is to create a project directory (e.g. :file:`emed18/` or :file:`emed/2018/` for data from 2018 for the eastern Mediterranean) with two subdirectories:
:file:`rinex/` and :file:`tables/`.

Copy into the :file:`rinex/` directory all of the local RINEX files you plan to use in your processing.
GAMIT will handle either RINEX 2 or RINEX 3 formats, but the RINEX 3 files must be renamed to the 10-character RINEX 2 naming scheme (lowercase :file:`{<ssss>}{<ddd>}{<s>}.{<yy>}o` and :file:`brdc{<ddd>}{<s>}.{<yy>}n`;
this happens automatically in :program:`sh_gamit`).
RINEX files for IGS directories to be downloaded automatically during the processing are specified using entries in a control file (:file:`sites.defaults`) (see :numref:`intro_proc_control` and Section 6.3 of the `GAMIT Reference Manual <http://geoweb.mit.edu/gg/docs/GAMIT_Ref.pdf>`_).

Then run :program:`sh_setup` to link or copy into the project :file:`tables/` directory the appropriate control and data files.
All of the required templates and tables reside in :file:`~/gg/tables/`, where :file:`~/gg/` is a required alias pointing to the highest level of the GAMIT/GLOBK installation.
Executing :program:`sh_setup` will invoke :program:`sh_links.tables` to *link* the standard data tables described in :numref:`intro_proc_flow`) and will *copy* the eight control and data files listed below:

:file:`process.defaults`
   Edit this file to specify your computation environment, sources for internal and external data and orbit files, start time and sampling interval, instructions for archiving the results, and an email address to receive a summary of the run.

:file:`sites.defaults`
   Edit this file to specify which local and IGS stations are to be used and how station meta-data are to be handled.

:file:`station.info`
   This file contains the receiver and antenna type and height of instrument (HI) values as a function of time for all occupations of the stations you will use.
   Although it can be generated during processing by :program:`sh_gamit`, the best approach is usually to construct the file prior to processing using the tools described in :numref:`intro_proc_example`.

Coordinate files
   :program:`sh_gamit` maintains in the experiment :file:`tables/` directory two files of *a priori* coordinates.
   The file ending in :file:`.apr` (set as :content:`aprf = igb14_comb.apr` in the current :file:`~/gg/tables/process.defaults` template) contains the Cartesian coordinates (position and velocity) of stations you wish to have unchanged throughout the processing.
   The L-file (:file:`lfile.`), which can contain either Cartesian position and velocity (default, same as :file:`.apr` file) or spherical position (GAMIT old-style, use the :option:`-oldfmt_lfile` option in :program:`sh_setup`), is updated after each day is processed if the adjustments exceed a specified value (0.3 m by default).
   If you have good coordinates for stations not in the :file:`.apr` file, you should append these to the :file:`.apr` file if you want them to be unchanged.
   For any station that does not have coordinates in :file:`lfile.`, :program:`sh_gamit` will attempt to calculate coordinates via a pseudorange solution, or (if :content:`use_rxc = Y` in :file:`process.defaults`) use the coordinates in the RINEX header.
   When GAMIT runs, these coordinates will be updated in the project :file:`tables/lfile.` from the phase solution so that for successive days on which the same station is observed, the accurate coordinates will be used.

:file:`sestbl.` and :file:`sittbl.`
   Edit these files to set the appropriate options for your analysis.
   Make sure that any station for which you specify tight constraints in :file:`sittbl.` has accurate coordinates in the :file:`.apr` file.

:file:`autcln.cmd`
   Controls for cleaning the data in program :program:`autcln`.
   This file will usually not require editing unless you encounter unusual data during the processing.