=====================================================
 Strait of Georgia  Initialization Data for SOG Code
=====================================================

This directory contains initialization data files for the SOG code for runs
in the Strait of Georgia.  The files are of 3 types, stored in
separate sub-directories:

* ctd - CTD profiles with SOG code readable headers
* stratogem_nuts - Interpolated data from STRATOGEM cruise bottle
  casts with SOG code readable headers
* bottle_data - IOS bottle data  with SOG code readable headers


File Name Conventions
=====================

The CTD data files are named according to the pattern:

``SG-ss-yyyy-mm-dd.sog``

where

* ``SG`` indicates that the file is from Strait of Georgia
* ``ss`` is the station id at which the data was collected; e.g. S3
* ``yyyy`` is the year part of the date on which the data was collected
* ``mm`` is the month part of the date on which the data was collected
* ``dd`` is the day part of the date on which the data was collected
* ``.sog`` indicates that the file has been formatted with a SOG code
  readable header

So, the CTD data file used to intialize the R4 run is
``ctd/SG-S3-2004-10-19.sog``.  Data in ``SG-*.sog`` files can come
from STRATOGEM cruise CTD casts, or from IOS cruises. 

The STRATOGEM cruise bottle data files are named according to the
pattern:

``Nuts-ss-yyyy-mm-dd.sog``

where

* ``Nuts`` indicates that the data is interpolated from STRATOGEM
cruise bottle casts
* ``ss`` is the station id at which the data was collected; e.g. S3
* ``yyyy`` is the year part of the date on which the data was collected
* ``mm`` is the month part of the date on which the data was collected
* ``dd`` is the day part of the date on which the data was collected
* ``.sog`` indicates that the file has been formatted with a SOG code
  readable header

So, the Nuts data file used to intialize the R4 run is
``stratogem_nuts/Nuts-S3-2004-10-19.sog``.  Data in ``Nuts-*.sog``
files is produced by processing STRATOGEM bottle data files with the
``bottle.m`` and ``nuts_profile.m`` MATLAB scripts (see below).

The IOS bottle data files are named according to the pattern:

``btl-ss-yyyy-mm-dd.sog``

where

* ``btl`` indicates that the data is from IOS cruise bottle casts
* ``ss`` is the station id at which the data was collected; e.g. S3
* ``yyyy`` is the year part of the date on which the data was collected
* ``mm`` is the month part of the date on which the data was collected
* ``dd`` is the day part of the date on which the data was collected
* ``.sog`` indicates that the file has been formatted with a SOG code
  readable header

IOS bottle data is used to initialize runs from before and after the
STRATOGEM project data collection period, i.e. before 2002 and after 2004.

So, the bottle data file used to intialize the R1 run is
``bottle_data/btl-S3-2001-mm-dd.sog``.


SOG Code Readable Header Format
===============================

The SOG code readable header is 12 lines long.

The first 11 lines start with an ``!`` character and are intended for
human consumption:

* Line 1 gives the column numbers and their widths in the form
  ``---n---`` where the total number of characters is the column
  width, and ``n`` is the column number
* Lines 2 through 9 hold text descriptions of the column contents
* Line 10 indicates the column widths again as groups of ``-`
  characters, separated by spaces
* Line 11 is `` ! Depth Temp Sal Chlor Fluores Nitrate Phyto Silicon``
  where the words are data identifiers that must be in the order shown
* Line 12 is a list of integers indicating in which column the data
  items listed in line 11 appear.  If the data item is not included in
  the file, or is not to be used from the file its index is set to
  ``-1``.

Here is an example of a header from a STRATOGEM CTD profile file::

  !--2--- ---3---- --4--- ---5--- --6--- ---7---- --8---  ---9---  ---10---
  !Pressu Temperat Conduc Fluores Beam	PAR	Oxygen: Salinity Density
  !re     ure:     tivity cence:  Transm		Dissolv :T0:C0   
  !       Primary         URU:    		ed:SBE           
  !                       Seapoin                  
  !                       t                        
  !
  !
  !
  !------ -------- ------ ------- ------- -------- ----
  ! Depth Temp Sal Chlor Fluores Nitrate Phyto Silicon
     2	   3    9   -1    5       -1      -1    -1


Data File Processing Scripts
============================

The following MATLAB scripts process data files into into the formats
found in this directory.

``bottle.m``
------------

``bottle.m`` reads the bottle data files in the shared directory
``/ocean/shared`` and saves the S3 data in ``nuts.mat``

``nuts_profile.m``
------------------

``nuts_profile.m`` reads nuts.mat and interpolates the values onto a
0-40 m depth interval at 0.5 m increments.  It writes out the ascii
files ``Nuts_cruiseid.txt`` which include three columns

depth nitrate silicon
(m)    (uM)    (uM)