Hawaiian Ocean Mixing Experiment (HOME)--Processing of mooring A2 SBE-16 data 
Kevin Bartlett,
Last modified September 2 2004

The contents of this directory's sub-directories are explained below: 

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# 0) The "OSUmatfiles" directory:
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The "OSUmatfiles" directory contains .mat files sent to us by
OSU. These files are missing some of the information we like to have
in our .mat files, and there seem to be some problems with timestamps
(see the readme files in OSUmatfiles for details). Unfortunately, we
don't yet have the raw .hex and .con files we would need to extract
data and create our own .mat files, so this is all we have at the
moment. 

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# 1) The "orig" directory:
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The "orig" directory contains the original data files copied from the
data-acquisition computer. These files are completely unmodified.

The .hex files have names incorporating their upload dates and
instrument names. For example, 20030612_0800.hex contains binary data
uploaded from SBE-16 #0800 on June 12, 2003.

The Seabird Electronics communications software sometimes generated
error messages indicating that a particular binary upload had
failed. In other cases, the uploaded data file was much smaller than
it should have been, given the length of the deployment. The .hex
files resulting from these failed upload attempts have been placed in
the orig/faileduploads directory.

SBE-16s do not store their calibration constants internally. Instead,
the constants are stored in configuration files on the processing
computer. The configuration files for the SBE-16s used on mooring A2
can be found in the orig/SBE16configfiles directory. The coefficients
in these .con files were obtained from calibration sheets provided by
Seabird Electronics. The coefficients were entered manually using
Seabird's "SBE Data Processing" software. All coefficients were double
checked before processing commenced.

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# 2) The "step01" directory:
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Ran Seabird's datcnv program to convert the .hex files and their
respective .con files to ascii .cnv files. When first generated, these
.cnv files had the same basenames as their .hex precursors, but they
were renamed to reflect both the mooring name and the instrument type,
in addition to the instrument's serial number. For example,
20030612_0800.cnv was renamed a2_sbe16_0800.cnv.

The .cnv files output by the datcnv program have a header section
followed by five columns of numerical data. These columns are:

   scan: Scan Count
   timeS: Time, Elapsed [seconds]
   t090C: Temperature [ITS-90, deg C]
   c0S/m: Conductivity [S/m]
   flag:  (-9.990e-29 for bad points)

In processing the SBE-16 data files from mooring C1, it was found that
the "timeS: Time, Elapsed [seconds]" data column was incorrect, so it
should not be trusted here, either. The problem was corrected when the
ascii .cnv files were read into Matlab .mat files (see below).

The ascii .cnv files were read into Matlab and saved as .mat files
using the sbe2mat.m program. Each .mat file contains a structured variable
named "SBEdata" with 21 fields.

The field "SBEtype" is 16 (for SBE-16) in all the .mat files in this
directory.

The field "filename" gives the name of the .cnv file from which the
data for this .mat file were extracted.

SBEdata.header contains the entire header portion of the .cnv file,
saved as a character array. The following fields contain information
extracted from the file header:

  SerialNumStr: String containing the serial number of the SBE-16;
  HeaderNumSamples: Number of samples in file;
  HeaderNumFree: Free space remaining in memory (in terms of samples);
  ShipStr: Ship's name, entered by user;
  CruiseStr: Cruise name, entered by user;
  StationStr: Station name, entered by user;
  LatStr: Latitude, entered by user;
  LonStr: Longitude, entered by user;
  LogStatus: 1 if SBE-16 was still logging at time of upload. 0 otherwise.
  TimeStamps: Timestamps from header.
  TimeStampsSampleRangeStart: Start of sample range associated with timestamp.
  TimeStampsSampleRangeEnd: End of sample range associated with timestamp.
  TimeStampsSampleInterval: Sample interval (seconds) for this timestamp range.

The remaining five fields in SBEdata contain the time series data from
the .cnv file. There are fields for temperature in degrees C
(SBEdata.temp) and conductivity in S/m (SBEdata.cond). There is also
the field SBEdata.flag, which is SeaBird's data-quality indicator for
the data points (0 for good, -9.990e-29 for bad).

The time vector for the time series is found in two different
fields. SBEdata.ElapsedSeconds contains the elapsed seconds since the
instrument began logging. This elapsed seconds vector is not the same
as the bogus elapsed seconds column in the .cnv file. Rather, it was
calculated by sbe2mat.m, using the known start time and sample
interval and the intermittent timestamps from the header section of
the .cnv files (this is what SeaBird Electronics' software is supposed
to do).

The SBEdata.time vector was calculated from the SBEdata.ElapsedSeconds
field, but is in the Matlab time format, UTC (see help datenum).

Notes: 

 * The optional fields StationStr, LatStr and LonStr were intended for
use in non-moored applications; they are all empty in these data
files.

 * Fields like TimeStampsSampleRangeStart and TimeStampsSampleInterval
were useful for creating and checking time vectors, etc.,  but
SerialNumStr is probably the only useful field extracted from the
header for anyone using these .mat files. 

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# 3) The "step02" directory:
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Ran the Matlab routine correct_timestamps.m to correct the time
vectors in the .mat files for clock drift. The clock drift information
was read from the ascii file SBE16ClockDrift.txt.

The .mat files output by correct_timestamps.m were of the same format
of those in the step01 directory, with the exception that the
ElapsedSeconds field has been stripped from the SBEdata structured
variable (the elapsed seconds field had previously been useful because
time in the original data always incremented in an integer number of
seconds. After correcting for clock drift, this was no longer the
case).

Plotted the temperature from each instrument to determine the apparent 
time of anchor release at deployment and recovery. Times are given as
a range, indicating that the anchor release occurred between the two
given data points:

                      Deployment
0800:    16-Nov-2002 02:05:48    16-Nov-2002 02:15:48
1087:    16-Nov-2002 02:11:30    16-Nov-2002 02:21:30
1090:    16-Nov-2002 02:06:50    16-Nov-2002 02:16:50
1099:    16-Nov-2002 02:10:45    16-Nov-2002 02:20:45

                      Recovery
0800:    11-Jun-2003 22:07:37    11-Jun-2003 22:17:37
1087:    11-Jun-2003 22:14:04    11-Jun-2003 22:24:04
1090:    11-Jun-2003 22:09:29    11-Jun-2003 22:19:29
1099:    11-Jun-2003 22:14:30    11-Jun-2003 22:24:30