> ![](media/image1.jpeg){width="7.0in" height="0.7923611111111111in"}
>
> **Using the AquaMap System**
>
> **at a Study Site**
>
> **\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~**

![](media/image2.png){width="0.6201388888888889in" height="0.79375in"}

> **Using the AquaMap System**
>
> **at a Study Site**
>
> Prepared by:
>
> **Jeff Miller**
>
> **National Park Service**
>
> **Virgin Islands National Park**
>
> **St. John, USVI**
>
> June 2002
>
> ***\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~\~***
>
> One of a series of monitoring protocols prepared for the Florida
> Caribbean Science Center
>
> under the auspices of the Caribbean Field Station, St. John, USVI
>
> **U.S. Department of the Interior**
>
> **U.S. Geological Survey**

#  {#section .unnumbered}

#  {#section-1 .unnumbered}

# Acknowledgements {#acknowledgements .unnumbered}

> We'd like to acknowledge and thank the many people that helped bring
> this protocol alive: Rich Aronson, Elena Astilleros, Winnie Batch, Ed
> Beaty, Don Catanzaro, Ries Collier, Marcia Creary, Bob Dorazio, Steve
> Hertzberg, Dennis Hubbard, Karla Hubbard, Marco Flagg, Maryann Franke,
> Nick Funicelli, Ginger Garrison, Andy Goldstein, Walt Jaap, Judy Lang,
> Ellen Link, Dulcie Linton, Steve Miller, Thad Murdock, Matt Patterson,
> Jim Petterson, Brendalee Phillips, Laura Plaut, Kaf Smith, William
> Stelzer, Rob Waara, Leslie Walling, and Jeremy Woodley.

######### Using AquaMap at a Study Site {#using-aquamap-at-a-study-site .unnumbered}

I.  Overview

```{=html}
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```
A.  Materials and Equipment [1](#materials-and-equipment)

B.  System Components [2](#system-components)

C.  Summary of AquaMap Protocol
    [3](#summary-of-aquamap-protocol-and-time-requirements)

```{=html}
<!-- -->
```
II. System Preparations

```{=html}
<!-- -->
```
A.  Site Reconnaissance [4](#site-reconnaissance)

Goal: to have a knowledge of the physical characteristics (i.e.,
habitat, boundaries, depths, etc) of the potential study site.

### Aerial photos {#aerial-photos .TOC-3}

### Snorkeling {#snorkeling .TOC-3}

### Preliminary dives {#preliminary-dives .TOC-3}

### Previous reports {#previous-reports .TOC-3}

By the end of this you should know if this is a site you want to study.

D.  System Readiness [4](#system-readiness)

Goal: this is what needs to be done before using the equipment in the
field.

### Charge the diver and baseline stations {#charge-the-diver-and-baseline-stations .TOC-3}

### Attach flotation collars and connecting lines  {#attach-flotation-collars-and-connecting-lines .TOC-3}

### Configure the stations  {#configure-the-stations .TOC-3}

### --- Load the proper operating system in stations {#load-the-proper-operating-system-in-stations .TOC-3 .unnumbered}

### --- Load the proper configuration file in stations {#load-the-proper-configuration-file-in-stations .TOC-3 .unnumbered}

### Prepare the diver station  {#prepare-the-diver-station .TOC-3}

### Install "dummy" plugs after charging {#install-dummy-plugs-after-charging .TOC-3}

### Consult checklist to evaluate need for lines, floats, etc.  {#consult-checklist-to-evaluate-need-for-lines-floats-etc. .TOC-3}

By the end of this section you should be ready to use the system in the
field.

III. AquaMap Basics

```{=html}
<!-- -->
```
A.  Deploying the Baseline Stations
    [6](#deploying-the-baseline-stations)

Goal: this section will tell you how to deploy the baseline stations and
suggestions on where to deploy them.

### General information {#general-information .TOC-3}

### Station deep or shallow? {#station-deep-or-shallow .TOC-3}

### Transducer up or down? {#transducer-up-or-down .TOC-3}

### Suggestions on where to locate the stations around the site. {#suggestions-on-where-to-locate-the-stations-around-the-site. .TOC-3}

By the end of this section you will know how to deploy the baseline
stations and have suggestions on where to deploy them around your study
site.

E.  Avoiding SONAR Communication Troubles
    [9](#avoiding-sonar-communication-troubles)

Goal: this section will help you understand how to optimize SONAR signal
propagation and reception while using conventional [scuba]{.smallcaps}
equipment.

### Sound waves vs. air spaces {#sound-waves-vs.-air-spaces .TOC-3}

### Avoiding exhalation bubbles {#avoiding-exhalation-bubbles .TOC-3}

### Avoiding other blockages {#avoiding-other-blockages .TOC-3}

By the end of this section you will know how to position the AquaMap
equipment, especially the diver station and transducer, to ensure the
best SONAR communications.

F.  Baseline Configuration Data [9](#baseline-configuration-data)

Goal: this section defines the baseline configuration and describes how
it is derived, where it is applied and where to go in this protocol for
additional information

### Definition {#definition .TOC-3}

### Bearing of baselines {#bearing-of-baselines .TOC-3}

### Depth and range of baselines {#depth-and-range-of-baselines .TOC-3}

### Angle between baseline 1 and baseline 2 {#angle-between-baseline-1-and-baseline-2 .TOC-3}

By the end of this section you will know how the baseline configuration
is defined, derived and applied; and where to go for additional
instructions.

G.  The Configuration File [10](#the-configuration-file)

Goal: this section will introduce you to the configuration file,
describe how to create or edit it, how to download it to the diver and
baseline stations, and where to go for configuration file contents and
recommended settings.

### Introduction to the configuration file {#introduction-to-the-configuration-file .TOC-3}

### Contents and recommended settings for the configuration file  {#contents-and-recommended-settings-for-the-configuration-file .TOC-3}

### Create and/or edit the configuration file {#create-andor-edit-the-configuration-file .TOC-3}

### Download the file to the diver and baseline stations {#download-the-file-to-the-diver-and-baseline-stations .TOC-3}

By the end of this section you will know about configuration files, how
to make and modify them, where to go within this protocol to find
information defined within the configuration file, and how to download
the configuration file.

H.  Recording Position and Observation Data

    with the Diver Station [13](#recording-data-at-the-site)

Goal: this section will define position and observation recordings,
describe how and when to perform each, and where to go in this protocol
for additional information.

### Definitions  {#definitions .TOC-3}

### Download the recorded data {#download-the-recorded-data .TOC-3}

### Modify the configuration file to record observations {#modify-the-configuration-file-to-record-observations .TOC-3}

### Delete the recording {#delete-the-recording .TOC-3}

By the end of this section you will know the two types of record­ings,
how to make them and what to do with the recorded data.

I.  The Convert Program [14](#the-convert-program)

Goal: this section will introduce Convert™ program, and describe its use
and where to go in this protocol for instructions.

### Definition and use {#definition-and-use .TOC-3}

### File management {#file-management .TOC-3}

### How do I use Convert? {#how-do-i-use-convert .TOC-3}

By the end of this section you will know when to use Convert and that
the instructions for use are in Appendix B.

J.  The AREA Program [15](#the-area-program)

Goal: this section introduces features of the AREA™ program, and
describes where to go in the protocol for instructions.

### Definition {#definition-1 .TOC-3}

### Features of AREA {#features-of-area .TOC-3}

### How do I use it? {#how-do-i-use-it .TOC-3}

By the end of this section you will know when and how to use AREA, and
that the instructions for use are in Appendix C.

IV. Using AquaMap in the Field [15](#using-aquamap-in-the-field)

Goal: this section outlines some of the uses and objectives for diving
with the AquaMap system and will tell you where to go in this protocol
to get more information.

A.  The Range and Noise Tests -- diagnostic tests conducted before any
    tracking is done (see Section A below).

B.  Initial Tracking -- preliminary tracking to identify the right
    placement of the baseline stations and conduct the initial perimeter
    trace (see Section B below).

C.  Definitive Baseline Survey -- conducted after placement of the
    baseline stations has confirmed to collect information that is
    entered into the configuration file for this site and conduct the
    definitive perimeter trace (see Section C below).

D.  Navigating to Sample Points -- initial tracking to, identification,
    and sampling of randomly selected sample points (see Section D
    below).

E.  Relocate Sample Points -- subsequent tracking to, identification,
    and sampling of previously randomly selected points (see Section E
    below).

By the end of this section you will know where to go in this protocol to
get details on the procedure you are using the AquaMap for.

A.  The Range and Noise Tests

Goal: this section will tell you when and why to perform these tests,
how to set up the stations, conduct the tests, and evaluate the results.

### Set up the diver station [16](#set-up-the-diver-station.) {#set-up-the-diver-station-16 .TOC-3}

### Set up the baseline station [17](#set-up-the-baseline-station.) {#set-up-the-baseline-station-17 .TOC-3}

### Conduct the range test [18](#conduct-the-range-test.) {#conduct-the-range-test-18 .TOC-3}

### Conduct the noise test [18](#conduct-the-noise-test.) {#conduct-the-noise-test-18 .TOC-3}

### Evaluate the test results . [19](#evaluate-the-test-results.) {#evaluate-the-test-results-.-19 .TOC-3}

By the end of this section you will know how to set up and conduct the
range/ noise tests, and how to evaluate and apply the results.

K.  Initial Tracking

Goal: This section will define and describe how to conduct an initial
baseline survey, evaluate the placement of the baseline stations, and
define and describe how to perform an initial perimeter recording.

### Set up for tracking [20](#setting-up-for-tracking.) {#set-up-for-tracking-20 .TOC-3}

### Measure the bearing of baseline #1 [20](#measure-the-bearing-of-baseline-1.) {#measure-the-bearing-of-baseline-1-20 .TOC-3}

### Conduct an initial baseline survey [21](#conduct-an-initial-baseline-survey.) {#conduct-an-initial-baseline-survey-21 .TOC-3}

### Navigate around in the area. [22](#navigate-around-in-the-area.) {#navigate-around-in-the-area.-22 .TOC-3}

### Evaluate the [sonar]{.smallcaps} signal quality [23](#evaluate-the-sonar-signal-quality.) {#evaluate-the-sonar-signal-quality-23 .TOC-3}

### Record the site perimeter [23](#_Ref7927055) {#record-the-site-perimeter-23 .TOC-3}

### Download and convert the recorded data [24](#download-and-convert-the-recorded-data.) {#download-and-convert-the-recorded-data-24 .TOC-3}

### Finalize the baseline station positions. [24](#finalize-the-baseline-station-positions.) {#finalize-the-baseline-station-positions.-24 .TOC-3}

### Mark and document the station positions [25](#mark-and-document-the-baseline-station-positions.) {#mark-and-document-the-station-positions-25 .TOC-3}

By the end of this section, you will know how to conduct an initial
baseline survey, track around the area evaluating the SONAR signal
quality, make a perimeter recording and evaluate those results to help
in the determination of the final position of the baseline stations.
This section is repeated until you are satisfied with the quality of
SONAR signal you are receiving and you have marked the positions of the
baseline stations.

L.  The Definitive Baseline Survey

Goal: this section will describe how to perform, the definitive baseline
survey, evaluate and enter the result into the configuration file. It
will also describe how to perform the definitive perimeter trace.

### Conduct the survey [27](#conduct-the-survey.) {#conduct-the-survey-27 .TOC-3}

### Analyze the recorded data [27](#analyze-the-recorded-data.) {#analyze-the-recorded-data-27 .TOC-3}

### Edit and reload the configuration file [31](#edit-and-reload-the-configuration-file.) {#edit-and-reload-the-configuration-file-31 .TOC-3}

### Make the definitive perimeter recording [32](#make-the-definitive-perimeter-recording.) {#make-the-definitive-perimeter-recording-32 .TOC-3}

By the end of this section you will be able conduct a definitive
baseline survey, and obtain and use the results to conduct the
definitive perimeter trace.

M.  Navigating to Waypoints

Goal: this section will describe AquaMap system preparations and
techniques to navigate to sample points for the first time.

### Locating Waypoints [33](#locating-waypoints.) {#locating-waypoints-33 .TOC-3}

### Understanding RMS error [34](#understanding-rms-error.) {#understanding-rms-error-34 .TOC-3}

### How do you know when you're there?  {#how-do-you-know-when-youre-there .TOC-3}

### Making observation recordings [35](#making-observation-recordings.) {#making-observation-recordings-35 .TOC-3}

By the end of this section you will know how to track to and find
waypoints that have been loaded into the diver station.

N.  Relocating Waypoints

Goal: this section will describe how to track to and relocate sample
Waypoints that were previously defined.

### Retrieve information from the configuration file [36](#retrieve-information-from-the-configuration-files-and-other-metadata-sources.) {#retrieve-information-from-the-configuration-file-36 .TOC-3}

### Prepare the equipment. [36](#prepare-the-equipment.) {#prepare-the-equipment.-36 .TOC-3}

### Set up at the site. [36](#set-up-at-the-study-site.) {#set-up-at-the-site.-36 .TOC-3}

### Save the recorded data [36](#set-up-at-the-study-site.) {#save-the-recorded-data-36 .TOC-3}

By the end of this section you will know how to use the AquaMap system
to relocate and resample points that were selected and sampled at an
earlier date

V.  Data Management and Summary Chart

Goal: In this section you will find options for the storage and display
of data obtained when tracking with the AquaMap system.

A.  File and Data Management [37](#file-and-data-management)

### Import the converted data recording files in MS Excel {#import-the-converted-data-recording-files-in-ms-excel .TOC-3}

### Save the recording data spreadsheet {#save-the-recording-data-spreadsheet .TOC-3}

### Generate the summary chart  {#generate-the-summary-chart .TOC-3}

### Add the transect origin and terminus point. {#add-the-transect-origin-and-terminus-point. .TOC-3}

O.  Creating a Data Summary Chart [37](#creating-a-data-summary-chart)

By the end of this section you will know how to create a text and data
summary chart to store and display AquaMap data.

> **[Appendices]{.smallcaps}**

A.  Recommended Configuration File Settings

Goal: in this section you will find details regarding the contents and
settings for parameters contained within the configuration file.

### Configuration screen 1 [40](#config1) {#configuration-screen-1-40 .TOC-3}

### Configuration screen 2 [40](#config2) {#configuration-screen-2-40 .TOC-3}

### Configuration screen 3 [40](#config3) {#configuration-screen-3-40 .TOC-3}

### Configuration screen 4 [41](#config4) {#configuration-screen-4-41 .TOC-3}

### Configuration screen 5 [41](#config5) {#configuration-screen-5-41 .TOC-3}

### Edit Waypoints [42](#editways) {#edit-waypoints-42 .TOC-3}

### Create Search Pattern [42](#editways) {#create-search-pattern-42 .TOC-3}

### Edit Diver Observation Recordings [42](#editways) {#edit-diver-observation-recordings-42 .TOC-3}

By the end of this section you will know the commonly modified
parameters contained within the configuration file, and their
recommended settings.

P.  Using the Convert Program

Goal: in this section you will find the instructions for using the
Convert™ program to perform specific tasks.

### Load the file [43](#load-the-file.) {#load-the-file-43 .TOC-3}

### Select the settings [43](#select-the-settings.) {#select-the-settings-43 .TOC-3}

> (e.g., to display a perimeter trace recording, evaluate SONAR quality,
> or display observation recordings)

### Save the converted data [44](#save-the-converted-data.) {#save-the-converted-data-44 .TOC-3}

By the end of this section, you should know when and how to use Convert.

Q.  Using the AREA Program

Goal: n this section you will find the instructions for using the AREA™
program to perform specific tasks.

### View the perimeter data as a graph [45](#view-the-perimeter-data-as-a-graph.) {#view-the-perimeter-data-as-a-graph-45 .TOC-3}

### Evaluate SONAR communication [45](#evaluate-the-plot-for-sonar-communication-effectiveness.) {#evaluate-sonar-communication-45 .TOC-3}

### Calculate the size of your study area [45](#determine-the-size-of-your-study-area.) {#calculate-the-size-of-your-study-area-45 .TOC-3}

### Generate sample points [46](#generate-sample-points.) {#generate-sample-points-46 .TOC-3}

### --- Create the total sample population {#create-the-total-sample-population .TOC-3 .unnumbered}

### --- Create a randomized sample population  {#create-a-randomized-sample-population .TOC-3 .unnumbered}

### --- Select a subset of random sample population  {#select-a-subset-of-random-sample-population .TOC-3 .unnumbered}

### --- Create a path to sample points  {#create-a-path-to-sample-points .TOC-3 .unnumbered}

### --- Create a subset of additional sample points {#create-a-subset-of-additional-sample-points .TOC-3 .unnumbered}

### Load the sample points into the diver station [49](#load-the-sample-points-into-the-diver-station.) {#load-the-sample-points-into-the-diver-station-49 .TOC-3}

### Check the Waypoint coordinates [50](#check-the-waypoint-coordinates.) {#check-the-waypoint-coordinates-50 .TOC-3}

By the end of this section, you should know when and how to use the AREA
program.

> **D. Glossary of Terms** [52](#_Ref9236033)

# Overview

AquaMap is similar in concept to the Global Position System (GPS),
except that it operates underwater, on a much smaller scale, and uses a
[sonar]{.smallcaps} (sound navigation and ranging) system to emit and
receive high frequency sound. Although light and most radio waves travel
more slowly and shorter distances in water than in air, sound propagates
significantly faster and much fur­ther in water, and is therefore used in
fish finders and depth sounders, as well as by marine mam­mals to
navigate and communicate.

When using AquaMap to fix a position, the diver station emits a signal
that is received by two or three baseline stations at established
locations which then send a signal back to the diver station. The diver
station uses the defined locations of the baseline stations and the time
it takes to receive each return signal to calculate its own location. To
use this system to navigate accurately and relo­­cate the same points over
time, each baseline station must be returned each time at exactly the
same depth and location, and the diver station must have the correct
information regarding their positions.

We use the AquaMap system to:

-   map the perimeter of a study,

-   calculate the site area in square meters,

-   define the population of sample points within that site,

-   randomly select a number of points from that population, and then

-   locate those points during initial and subsequent surveys.

## Materials and Equipment

(in addition to standard dive equipment)

-   AquaMap hardware

    -   1 diver station with [sonar]{.smallcaps} transducer, magnetic
        pointer, battery charger with power cord, and two dummy plugs
        (to seal ports while not in use)

    -   3 baseline stations, each with a dummy plug, battery charger
        with power cord, and a flotation collar with associated nuts,
        bolts, and washers

    -   Data exchange cables and connector adapters for connecting the
        AquaMap components to your PC

-   Computer software

-   AquaMap applications (SmartDive and DT-test) and utilities (DiveTerm
    and Convert)

    -   Microsoft Excel

    -   AREA plug-in or program

-   Miscellaneous underwater equipment

    -   Compass

    -   Narwhal to hold the diver station and transducer

    -   Rope

    -   Miscellaneous floats, pins, sand screws

    -   Lift bags, if needed to add positive buoyancy to the baseline
        stations in order to stabilize them in the current

## System Components

Our use of AquaMap requires three baseline stations that are deployed at
the study site and one mobile diver station.

-   **The baseline stations** are cylinders that house batteries,
    electrical circuitry, and a transducer (the end of the baseline
    station or cable from which the [sonar]{.smallcaps} pulse is
    released and received).

-   **The diver station** is a hand-held device used to compute
    positions relative to the base­line sta­tions. Unlike GPS devices,
    which indicate location using latitude and longitude, the "fixes"
    computed by the diver station are "Waypoints" in an X:Y coordinate
    system refer­enced to the location of the baseline stations. However,
    baseline station positions can be marked using GPS. So that you can
    create a site map and relocate selected Way­points, the diver
    station's features include position recording (tracing your track)
    and storage of Way­point coordinates. The diver sta­tion keypad is
    operated by using a magnetic pointer. For details about diver
    station features, see the AquaMap Operators Manual, and DiveTracker
    Users Man­ual.

> Throughout this protocol, these icons are used:

-   Signifies activities generally done on land, and usually requiring a
    computer.

> ![](media/image3.png){width="1.0in" height="0.27708333333333335in"}
> Signifies activities done at the study site, mostly underwater.
>
>  Indicates a specific step in carrying out the protocol.

-   Tips to keep you on track.

> ![](media/image4.jpeg){width="0.24375in"
> height="0.24375in"}Precautions to help safeguard your life, your
> equipment, or your data.

## Summary of AquaMap Protocol and Time Requirements

+-------------------+-------------------------+------------------------+
| **Procedure **   | #####                   | ![](media/ima          |
|                   | # In the Office  {#in- | ge3.png){width="1.0in" |
|                   | the-office .unnumbered} | height="0.27           |
|                   |                         | 77777777777778in"}**In |
|                   |                         | the Field**            |
+-------------------+-------------------------+------------------------+
| **System          | -   Charge station      |                        |
| preparations**    |     batteries           |                        |
|                   |                         |                        |
| *(\~ 2-4 hours)*  | -   Create and download |                        |
|                   |     the configuration   |                        |
|                   |     file when           |                        |
|                   |     applicable          |                        |
|                   |                         |                        |
|                   | -   Plan where you'll   |                        |
|                   |     locate the baseline |                        |
|                   |     stations            |                        |
+-------------------+-------------------------+------------------------+
| **Range and noise | -   Set up DT-test on   | -   Conduct the range  |
| tests**           |     diver and baseline  |     and noise tests    |
|                   |     stations            |                        |
| *(1 or possibly 2 |                         |                        |
| dives; total time |                         |                        |
| \~1 day)*         |                         |                        |
+-------------------+-------------------------+------------------------+
|                   | -   Evaluate the test   |                        |
|                   |     results             |                        |
+-------------------+-------------------------+------------------------+
| **Initial         |                         | -   Determine baseline |
| baseline survey   |                         |     compass bearing    |
| and perimeter     |                         |                        |
| recording**       |                         | -   Conduct initial    |
|                   |                         |     baseline survey    |
| *(2 dives are     |                         |                        |
| best)*            |                         | -   Trace and record   |
|                   |                         |     site perimeter     |
+-------------------+-------------------------+------------------------+
| **Evaluating      | -   Download and        |                        |
| recorded data**   |     convert data from   |                        |
|                   |     the diver station   |                        |
| *(\~2-4 hours)*   |                         |                        |
|                   | -   View the data as a  |                        |
|                   |     graph               |                        |
|                   |                         |                        |
|                   | ```{=html}              |                        |
|                   | <!-- -->                |                        |
|                   | ```                     |                        |
|                   | -   Estimate the size   |                        |
|                   |     of your study site  |                        |
|                   |                         |                        |
|                   | -   Review raw range    |                        |
|                   |     recording           |                        |
+-------------------+-------------------------+------------------------+
|                   |                         | If necessary based on  |
|                   |                         | results of track­ing    |
|                   |                         | and recording, adjust  |
|                   |                         | place­ment of baseline  |
|                   |                         | stations. This will    |
|                   |                         | require repeating the  |
|                   |                         | initial baseline       |
|                   |                         | survey and perimeter   |
|                   |                         | recording.             |
+-------------------+-------------------------+------------------------+
| **Definitive      |                         | -   Permanently        |
| baseline survey** |                         |     benchmark the      |
|                   |                         |     locations of the   |
| *(1 dive plus 1   |                         |     baseline stations  |
| hour pre-dive and |                         |                        |
| 1-2 hours         |                         | -   Collect the        |
| post-dive)*       |                         |     baseline survey    |
|                   |                         |     data               |
+-------------------+-------------------------+------------------------+
|                   | -   Download and        |                        |
|                   |     convert the data    |                        |
|                   |                         |                        |
|                   | -   Determine the       |                        |
|                   |     baseline ranges     |                        |
|                   |                         |                        |
|                   | -   Edit and reload     |                        |
|                   |     configuration file  |                        |
+-------------------+-------------------------+------------------------+
| **Definitive      |                         | -   Conduct the        |
| perimeter         |                         |     definitive tracing |
| tracing**         |                         |     of the site        |
|                   |                         |     perimeter          |
| *(1 dive plus 1-2 |                         |                        |
| office hours)*    |                         |                        |
+-------------------+-------------------------+------------------------+
|                   | -   Download and        |                        |
|                   |     convert the data    |                        |
|                   |                         |                        |
|                   | -   Edit and reload     |                        |
|                   |     configuration file  |                        |
+-------------------+-------------------------+------------------------+
| **Defining        | -   Identify a          |                        |
| Waypoints and     |     population of       |                        |
| transects**       |     sam­pling points in  |                        |
|                   |     the site and order  |                        |
| *(1-3 hours)*     |     them randomly       |                        |
|                   |                         |                        |
|                   | -   Select a sample of  |                        |
|                   |     random points that  |                        |
|                   |     will define your    |                        |
|                   |     transects and       |                        |
|                   |     create a path to    |                        |
|                   |     connect them        |                        |
|                   |                         |                        |
|                   | -   Load path into the  |                        |
|                   |     diver station       |                        |
+-------------------+-------------------------+------------------------+

# System Preparations 

## Site Reconnaissance

The establishment of a long term monitoring site should be done only
after a thorough evaluation of the site, and possible comparison with
other candidate sites. Using tools such as aerial photos, maps, charts,
and any previous reports you should become famil­iar with the general
orientation of your potential study site. This may involve general
observation snorkel trips or dives at the site so that you can define
your study area in terms of:

-   general layout;

-   orientation (to compass headings or land based-features);

-   habitat type(s);

-   approximate size;

-   features for delineating boundaries, e.g., depth gradients, sloping
    fore reef, sand channels, rocky outcroppings; and

-   potential hazards as a work site, e.g., in ship channel.

This process can take days to weeks, with the result being a site that
you have chosen based on knowledge and information, both historical and
actual field data.

## System Readiness

In addition to familiarizing yourself with how to use the DiveTracker
soft­ware you've installed on your PC, there are many steps to get
through before you can begin using AquaMap to locate sample points on
your study site. However, before you go into the field to use the
equipment, you'll need to do the following.

### Charge the station batteries.

Before diving, you'll need to charge the diver station and the three
baseline stations. The diver station window will show a charging graph.
When charging is complete, the mes­sage \"[done]{.smallcaps}\" will
appear. On the baseline stations, the indicator light patterns will show
whether the units are charging or fully charged.

When you connect the diver station to charge, observe the graph in the
display window and keep track of how long the charge is taking and the
voltage level when it is complete. The dis­played information will
accurately reflect the charging level after about one minute, and
updates are displayed every 15 seconds.

> If the battery charge does not reach 12 volts in ≈90 minutes, consider
> the following:

-   If it takes ≤45 minutes to reach 12 volts, the battery may not have
    been low when charging began. Consi­der charging the battery again.
    If it does the same, assume the station is fully charged. However,
    if you're certain the battery was low and it still shows fully
    charged in much less than 90 minutes, consider replacing the
    battery. (Send it back to the company.) The batteries will need to
    be replaced about every three years, depend­ing on storage
    temperature, use, number of charging cycles, etc.

-   If the charge time was ≤90 minutes, and the voltage = 10 or 11, it
    may be a false full charge reading. Sometimes the voltage "curve"
    flattens out, simulating a fully charged battery. Consider
    re-starting the charge. You may see a shorter charge time since you
    are starting with a partially charged battery, but the voltage
    should reach 12.

-   If the charge time was \< 10 minutes and the voltage reading is
    "Temp Trig," this indicates the Temperature Trigger has been
    activated. Consi­der this a system error, and re-charge the station.

**The baseline stations must be using the SmartDive application to be
charged.**

> ![](media/image4.jpeg){width="0.24375in" height="0.24375in"}There is
> no way to monitor battery strength in the baseline station. If you've
> been running the DT-test (page [16](#the-range-and-noise-tests)) and
> the battery gets too low, you may not be able to connect the station
> to the computer in order to switch to the SmartDive application. The
> light flash patterns are similar, so you may not be certain which
> program is running. If the station will not initialize and proceed to
> the flash pattern after you've attempted to charge it, the problem may
> be that it was in the DT-test application. Therefore, you should
> reattach the baseline stations to the com­puter and switch to Smart­Dive
> as soon as possible after you're through with the DT-test so the
> battery can be charged.
>
> **If you cannot initiate the charge program** on either the diver or
> the baseline sta­tions you may need to use a three-way adapter plug
> that will enable you to connect the stations to an outside power
> source while they are connected to your PC. This will permit you to
> load the SmartDive application, thus allowing the battery-charg­ing
> program to run.

### Attach flotation collars and connecting lines.

Fasten a flotation collar snugly around each baseline station. To ensure
that the same baseline station is deployed at the same location for each
dive, each station should be labeled (BS1, BS2, BS3) and have a matching
label on its collar.

These syntactic foam collars provide enough flotation for installation
in low-surge, low-current conditions, but in surgy waters, you may find
it necessary to add a liftbag or other flotation device to stabilize the
baseline station in the water column. To facilitate this, weave a small,
strong line through the flotation collar bolts that can fasten the
lifting device.

### Configure the stations.

-   Run the appropriate operating system on the diver and baseline
    stations.

    -   SmartDive for normal tracking

    -   DT-test for the Range and Noise tests

-   Load the right configuration file (see page
    [11](#download-the-configuration-file-to-the-diver-and-baseline-stations.)).

### Prepare the diver station.

-   Install the diver station into the Narwhal. Connect the mobile
    transducer to the diver station so that it can communicate with the
    baseline stations.

-   Make sure you have the magnetic pointer that oper­ates the diver
    station and keep a spare one in your [bcd]{.smallcaps} pocket.

### Install plugs to protect the communications ports from salt water.

> After charging and configuring the diver and baseline stations, make
> sure that the data exchange ports have each been sealed with a dummy
> plug. These ports are used only when connecting the stations to your
> PC. The connections are watertight to a depth of \>100m, but saltwater
> will corrode the internal connections, causing errors in signal
> transmission. Since there's generally no reason to take the diver
> station under­water without its transducer, that dummy plug may never
> actually be used underwater. How­ever, it's a good idea to use it while
> the diver station is out of water and doesn\'t need to be connected to
> the transducer.

### Check your equipment list.

Especially while you're getting used to this system, we recommend making
a list so that you can check that you have the equipment necessary for
your field work. Such a list is not included here, as it will vary among
sites. See "Materials and Equip­ment," page
[1](#materials-and-equipment).

#  AquaMap Basics

## Deploying the Baseline Stations

### 1. General Information {#general-information-1 .unnumbered}

-   **Station buoyancy**. With its flotation collar, each baseline
    station is ∼7 lbs. positively buoy­ant in salt water, so temporary
    holding devices (e.g., weight belts or concrete blocks) are needed
    during the initial stages of mapping and tracking. Lay the weights
    carefully on the bottom so as not to harm any fragile component.
    Later on, sand screws or pins can be installed to more per­ma­nently
    mark where the baseline stations are to be located, and lines can be
    cut and/or spliced to use at a specific site (see page
    [25](#mark-and-document-the-baseline-station-positions.)).

-   **Finding the baseline stations.** To make sure that divers who are
    not carrying the diver station can easily find the baseline
    stations, run a fiberglass measuring tape between them. This is
    especially helpful in the early stages of site set-up, but can be
    used throughout tracking.

-   **Unobstructed signal path.** The signal path from the diver and
    baseline station transducer is similar to the light emitted by a
    street lamp in that the energy is radiated down and away from the
    trans­ducer. The base­line stations need clear signal paths to each
    other and the diver station.

    -   Make sure that terrain features such as boulders or a slop­ing
        sea floor do not obstruct the signal path.

    -   Any fastener, clip, knot, float, excess line, tie wrap, lift
        bag, or marine growth on sub­merged lines and floats may
        interfere with signal transmis­sion.

    -   Currents, surge, and wave action can loosen objects that are not
        securely fastened and cause problems during tracking. Do not
        take the chance that a "tucked in" line will remain so during
        the entire day of track­ing.

    -   You must take the same precau­tions in regard to the attachment
        of the float to the diver station trans­ducer.

### 2. Baseline station depth.  {#baseline-station-depth. .unnumbered}

For best results, the baseline stations should be at least 2m above the
sea floor and no less than 2m below the sur­face. They should not be so
shallow as to be severely affected by wave energy or endan­gered by boat
traffic. They are generally deployed at \~3m. Reels, tapes, and/or lines
may be used to raise the stations to the right depth. Brass or stainless
clips can be tied to the transducer cage to simplify attachment to
lines, reels, or tapes. But at some shallow sites, SONAR communication
is better if the stations are posi­tioned near the bottom.

### 3. Transducer up or down? {#transducer-up-or-down-1 .unnumbered}

When the baseline stations are placed near the surface, the transducer
is generally posi­tioned pointing down. When the baseline station is
placed near the bottom, the transducer is generally placed pointing up,
but experiment to see what works best at your site.

### 4. Where to locate the baseline stations. {#where-to-locate-the-baseline-stations. .unnumbered}

Using maps, charts, photographs and/or notes taken while conducting
recon­naissance snor­kels or dives, make a pre-dive approximation of the
best places to put the baseline stations in or around the study site. As
shown in Example A, the line connecting Baseline Stations 1 and 2 is
referred to as Baseline #1; it will cor­re­spond to the X-axis on a
plotted graph of your site. Here are some points to keep in mind.

-   When you are positioned at Station 1 and facing Station 2, Station 3
    must be located to the your right.

-   We have found that an L-shaped arrangement like that shown in
    Example A, with the three stations placed near the peri­me­­ter of the
    site, often works well. When Station 3 forms a 90° angle with
    Stations 1 and 2, Baseline #2 will correspond to the negative Y-axis
    on a plotted graph of your site.

    ![](media/image5.wmf){width="5.0in" height="3.2777777777777777in"}

    -   You may find it best to orient Baseline #1 on the long axis of
        the site, if there is one, and slightly beyond the site
        perimeter. For example, if the deep side of the site boundary is
        a forereef slope to a sandy plain, Stations 1 and 2 could be
        posi­tioned 10m to 15m from the forereef slope in the sandy
        plain. This will permit better sonar signal reception when
        tracking along the forereef slope.

    -   ![](media/image6.png){width="1.5in"
        height="1.1770833333333333in"}

    -   AquaMap works best if the baseline stations are 50m to 150m
        apart, and no closer than 30m.

    -   Signals from only two baseline stations are needed to "fix" a
        posi­tion with the diver sta­tion. However, if the system has been
        con­fig­ured for three baseline stations, then AquaMap has to
        receive signals from all three sta­tions in order to determine
        which two baseline stations provide the best geometry for
        cal­cu­lat­ing the position; the signal from the third station is
        then used to determine which side of the baseline for the fix.
        You therefore need to arrange the stations so that at any point
        within the study site, the maximum distance from the diver
        station to the farthest baseline station is within the
        operational range established by the [tx-]{.smallcaps}test.

## Avoiding SONAR Communication Troubles

### Sound waves vs. air spaces. 

The AquaMap [sonar]{.smallcaps} signals do not travel effectively
through air spaces. As re-breathers are impractical and exhalation
bubbles will always be present, they may reduce [sonar]{.smallcaps}
communication by blocking the signals or creating noise that causes
interference. We attempt to calibrate for this noise by performing the
range and noise tests (page [16](#the-range-and-noise-tests)), but other
steps can be taken to minimize bubble trouble.

### Avoiding exhalation bubbles. 

![](media/image7.png){width="1.4701388888888889in"
height="1.1104166666666666in"}Our tests have shown that signal reception
improves more than 50% if we can keep the diver station transducer out
of the exhalation bubble stream. Desert Star, the developers of AquaMap,
suggest having the diver station transducer cord travel behind the tank
and through a [bdc]{.smallcaps} fastener clamp that is held buoyant
above you by a small peanut-type float, but this places the transducer
in or near the bubble stream. Instead, we have developed a holder to
securely cradle the diver station and position the transducer, allowing
flexibility in different environments. Because of its resemblance to the
long-tusked Arctic whale, we call the holder \"the Narwhal.\"

### Avoiding other blockages. 

With the Narwhal, the diver station transducer can be hard-mounted in
the end of a PVC pipe or suspended by a peanut float. In either case, it
is posi­tioned about 0.5m in front of the diver's body and exhaled
bubbles. The diver must remain aware of the trans­ducer location so that
other objects, divers, or reef features do not block the sonar signal.
To keep the transducer vertical, attach a peanut-type float to the top
of the frame around the trans­ducer.

## Baseline Configuration Data

To use the AquaMap system to relocate precisely the same points
underwater over time, you need to:

-   position the baseline stations in exactly the same place (location
    and depth) each time; and

-   load the diver station with a configuration file that contains
    accurate data about where the stations are located.

To obtain this baseline configuration data, you need to determine four
aspects of the baseline stations\' positions.

+------------------------------+---------------------------------+----+
| **Baseline configuration     | **How it is determined**        | ** |
| component**                  |                                 | Pa |
|                              |                                 | ge |
|                              |                                 | ** |
+------------------------------+---------------------------------+----+
| -   Bearing of baseline 1    | Measured by divers with a       | [  |
|     (the line from BS1 to    | com­pass achieving accuracy      | 20 |
|     BS2)                     | within 5º-10º of actual         | ]( |
|                              | bearing.                        | #m |
|                              |                                 | ea |
|                              |                                 | su |
|                              |                                 | re |
|                              |                                 | -t |
|                              |                                 | he |
|                              |                                 | -b |
|                              |                                 | ea |
|                              |                                 | ri |
|                              |                                 | ng |
|                              |                                 | -o |
|                              |                                 | f- |
|                              |                                 | ba |
|                              |                                 | se |
|                              |                                 | li |
|                              |                                 | ne |
|                              |                                 | -1 |
|                              |                                 | .) |
+------------------------------+---------------------------------+----+
| -   Depth of each baseline   | Measured by the stations during | [2 |
|     station                  | in-water tests (baseline        | 1] |
|                              | surveys).                       | (# |
| -   Length/range of each     |                                 | co |
|     baseline                 |                                 | nd |
|                              |                                 | uc |
|                              |                                 | t- |
|                              |                                 | an |
|                              |                                 | -i |
|                              |                                 | ni |
|                              |                                 | ti |
|                              |                                 | al |
|                              |                                 | -b |
|                              |                                 | as |
|                              |                                 | el |
|                              |                                 | in |
|                              |                                 | e- |
|                              |                                 | su |
|                              |                                 | rv |
|                              |                                 | ey |
|                              |                                 | .) |
+------------------------------+---------------------------------+----+
| -   Angle between baselines  | Automatically during initial    | [2 |
|     1 and 2 (the line from   | baseline survey.                | 1] |
|     BS1 to BS3)              |                                 | (# |
|                              | Manually when you evaluate the  | co |
|                              | baseline survey data.           | nd |
|                              |                                 | uc |
|                              |                                 | t- |
|                              |                                 | an |
|                              |                                 | -i |
|                              |                                 | ni |
|                              |                                 | ti |
|                              |                                 | al |
|                              |                                 | -b |
|                              |                                 | as |
|                              |                                 | el |
|                              |                                 | in |
|                              |                                 | e- |
|                              |                                 | su |
|                              |                                 | rv |
|                              |                                 | ey |
|                              |                                 | .) |
|                              |                                 |    |
|                              |                                 | [  |
|                              |                                 | 27 |
|                              |                                 | ]( |
|                              |                                 | #a |
|                              |                                 | na |
|                              |                                 | ly |
|                              |                                 | ze |
|                              |                                 | -t |
|                              |                                 | he |
|                              |                                 | -r |
|                              |                                 | ec |
|                              |                                 | or |
|                              |                                 | de |
|                              |                                 | d- |
|                              |                                 | da |
|                              |                                 | ta |
|                              |                                 | .) |
+------------------------------+---------------------------------+----+

## The Configuration File

### 1. Introduction {#introduction .unnumbered}

To use AquaMap to navigate accurately and relocate the same points over
time, each baseline station must be returned to exactly the same depth
and location each time, and the diver station must have the correct
information regarding their positions. This information is provided by
soft­ware, referred to as a configuration file, that is downloaded into
each station. The configura­tion file defines the operational para­meters
and working environment during Aqua­Map use at a parti­cular site and
tells the diver station and the baseline stations how to com­muni­cate
with each other. Later on, you can also store the Waypoints used for
data sampling in the configura­tion file.

You will need to keep a metadata file log (a "readme" text file) in a
central location that lists the names and storage locations of all the
files that you create. Make written notes of the names of all files used
such as config­uration, Waypoint, recordings, and con­verted files. Try­ing
to remember which file con­tains which information can be difficult after
you've moved on to another site.

As listed in the following table, the user is respon­sible for entering
and editing 10 key com­po­nents of this file. You create an initial
configuration file after completing the range and noise tests at your
study site. As you gain more informa­tion about the site and the location
of your base­line stations, you will need to go back and edit this file
and reload it into the stations. Once you have created an initial
configuration file, you may also edit that file for use at another study
site in a sim­i­lar environment rather than create a new file from
scratch.

### 2. Contents and Recommended Settings {#contents-and-recommended-settings .unnumbered}

+------------------------------------+---------------------------+----+
| **Configuration file component**   | **How it is determined**  | ** |
|                                    |                           | Pa |
|                                    |                           | ge |
|                                    |                           | ** |
+====================================+===========================+====+
| -   The number of baseline         | Depends on your study     | [  |
|     stations being used            | site and which AquaMap    | 1] |
|                                    | equipment you're using    | (# |
| ```{=html}                         |                           | ma |
| <!-- -->                           |                           | te |
| ```                                |                           | ri |
| -   The number of mobile stations  |                           | al |
|     being used                     |                           | s- |
|                                    |                           | an |
| -   If any surface stations are    |                           | d- |
|     being used                     |                           | eq |
|                                    |                           | ui |
| -   The water temperature          |                           | pm |
|                                    |                           | en |
|                                    |                           | t) |
+------------------------------------+---------------------------+----+
| -   Threshold for background noise | Derived from range and    | [1 |
|     levels                         | noise tests               | 6] |
|                                    |                           | (# |
|                                    |                           | th |
|                                    |                           | e- |
|                                    |                           | ra |
|                                    |                           | ng |
|                                    |                           | e- |
|                                    |                           | an |
|                                    |                           | d- |
|                                    |                           | no |
|                                    |                           | is |
|                                    |                           | e- |
|                                    |                           | te |
|                                    |                           | st |
|                                    |                           | s) |
+------------------------------------+---------------------------+----+
| -   The baseline configuration     | Entered automatically     | [  |
|                                    | into the diver station    | 19 |
|                                    | during initial test dives | ]( |
|                                    |                           | #i |
|                                    | Entered manually after    | ni |
|                                    | the definitive baseline   | ti |
|                                    | survey                    | al |
|                                    |                           | -t |
|                                    |                           | ra |
|                                    |                           | ck |
|                                    |                           | in |
|                                    |                           | g) |
|                                    |                           |    |
|                                    |                           | [  |
|                                    |                           | 27 |
|                                    |                           | ]( |
|                                    |                           | #a |
|                                    |                           | na |
|                                    |                           | ly |
|                                    |                           | ze |
|                                    |                           | -t |
|                                    |                           | he |
|                                    |                           | -r |
|                                    |                           | ec |
|                                    |                           | or |
|                                    |                           | de |
|                                    |                           | d- |
|                                    |                           | da |
|                                    |                           | ta |
|                                    |                           | .) |
+------------------------------------+---------------------------+----+
| -   Automatic Gain Control         | Standard settings that    | [4 |
|     operation                      | are used in all           | 1] |
|                                    | configuration files       | (# |
| -   Length of RMS error queue      |                           | co |
|                                    |                           | nf |
| -   Data to be recorded during     |                           | ad |
|     observation recordings         |                           | v) |
|                                    |                           |    |
|                                    |                           | [4 |
|                                    |                           | 1] |
|                                    |                           | (# |
|                                    |                           | co |
|                                    |                           | nf |
|                                    |                           | ad |
|                                    |                           | v) |
|                                    |                           |    |
|                                    |                           | [  |
|                                    |                           | 42 |
|                                    |                           | ]( |
|                                    |                           | #c |
|                                    |                           | on |
|                                    |                           | fo |
|                                    |                           | bs |
|                                    |                           | er |
|                                    |                           | v) |
+------------------------------------+---------------------------+----+
| -   A data file containing         | After doing the           | [4 |
|     Waypoint coordinates           | definitive baseline       | 6] |
|                                    | survey and perimeter      | (# |
|                                    | recording                 | ge |
|                                    |                           | ne |
|                                    |                           | ra |
|                                    |                           | te |
|                                    |                           | -s |
|                                    |                           | am |
|                                    |                           | pl |
|                                    |                           | e- |
|                                    |                           | po |
|                                    |                           | in |
|                                    |                           | ts |
|                                    |                           | .) |
+------------------------------------+---------------------------+----+

### 3. Create and/or edit the configuration file. {#create-andor-edit-the-configuration-file. .unnumbered}

You can either create a new configuration file or modify an existing one
by editing it. When you create or edit a configuration file, you can
choose from two options:

-   With the *simple* create or edit, the settings and values used in
    the config­u­ration file are determined for you based on your answers
    to some general questions about the study site.

-   With the *advanced* create or edit, you enter the settings and
    values into the con­fig­uration file your­self.

The advanced mode includes more setting options, but we suggest you use
it because it seems to produce more reliable results than does the
simple mode. In both modes, any settings that you do not specify are
left at the default setting if you are creating a file, or at whatever
the prior setting was if you are editing a file. **The default and
recommended settings are shown in Appendix A.**

-   On your PC, go to [start]{.smallcaps} and choose: [programs
    divetracker diveterm]{.smallcaps}.

```{=html}
<!-- -->
```
-   A message will appear: "No link, please reset station." Ignore this.
    The diver station does not have to be attached to your PC in order
    for you to create or edit a configuration file.

```{=html}
<!-- -->
```
-   You will need to set DiveTerm to use metric units. Go to [file 
    options]{.smallcaps} and select [use metric units.]{.smallcaps}

-   Go to the [file]{.smallcaps} drop-down menu and choose [create a
    configuration]{.smallcaps} [file]{.smallcaps} or [edit a
    configuration]{.smallcaps} [file,]{.smallcaps} and then
    [advanced]{.smallcaps} or [simple,]{.smallcaps} depending on what
    you need to do. If you are editing an existing file, open it in the
    Select Configuration File window.

-   As shown in Appendix A, you will pass through five screens for
    [advanced create]{.smallcaps} or [advanced edit]{.smallcaps} (three
    for [simple]{.smallcaps}), but you need to concern yourself with
    only some of the settings at this point. The table above lists some
    of the more common entries you may need to check. Click on
    [next]{.smallcaps} when you are ready to go to the next screen.

-   When you are at the last configuration screen click on
    [ok]{.smallcaps} if you are satisfied with your choices. If not,
    choose [back]{.smallcaps} to return to a previous screen and change
    what needs chang­ing.

-   When you click on [ok]{.smallcaps}, you will be prompted to save the
    file with a name and location. Use a name (with a \*.par extension)
    that corresponds to the site where you will be track­ing and the
    default file location, then click on [save]{.smallcaps}.

### Download the configuration file to the diver and baseline stations.

After the configuration file has been saved, you need to download it
into the diver and base­line stations.

-   Make sure the diver station is not powered on (= [off]{.smallcaps}).

-   Connect the diver station to your PC using the gray data exchange
    cable (a gen­der adapter may be necessary) and the adapter connector.

-   Open DiveTerm on your PC (if it isn't open yet) and turn on the
    diver sta­tion.

-   Within a few seconds, you should see a message on your PC that the
    link has been established. If you do not, turn off the station,
    close DiveTerm, and start over.

-   When a link has been established, click on [run]{.smallcaps} (the
    small button on the lower left side of the display). When the
    application window appears, choose [smtdive]{.smallcaps} (the most
    recent version, if more than one is listed). Pause to allow
    SmartDive to load (5-10 seconds).

```{=html}
<!-- -->
```
-   When SmartDive loads, it automatically tests the [sonar]{.smallcaps}
    com­muni­cation. Since the stations do not operate well in air, the
    message [test fail]{.smallcaps} will appear, followed by some
    numbers and binary code. That's okay, and you can proceed with these
    steps.

```{=html}
<!-- -->
```
-   When the Terminal window appears, go to the [command]{.smallcaps}
    drop-down menu and choose [configure station]{.smallcaps}.

-   When the Location window is displayed, select the appropriate
    configuration file and click on [open]{.smallcaps}.

-   When the Download Configuration File window appears, select the
    station that's con­nected to your PC and choose
    [download]{.smallcaps}. A numeric display will show the progress of
    the download.

If you get an error message or the scrolling numbers indicate no
progress, close Dive­Term and turn off the station. Re-launch DiveTerm
and, when it is open, turn on the diver station and repeat the steps
above.

![](media/image4.jpeg){width="0.24375in" height="0.24375in"}When the
download to a station is complete, first disconnect the station and then
turn it off. Do *not* choose [done]{.smallcaps} on your PC until you
have con­­figured all of the stations.

-   After the configuration file had been downloaded to the diver
    station, you will be prompted to download the file to BS1. After
    making sure it is turned off, connect BS1 to your PC using the data
    exchange cable and connector adapter.

-   Turn on BS1 and repeat the downloading proce­dure for it and the
    other baseline sta­tions. Although the diver station displays a
    message that a link has been established, with the baseline stations
    you will need to watch the flash patterns. When you see one rapid
    flash per second (this may take about a minute), the link has been
    established.

![](media/image4.jpeg){width="0.24375in" height="0.24375in"}Check the
label on the baseline station to make sure that you\'re down­load­ing the
configuration file to the station selected in the display win­dow. If you
select BS2 from the display window when you have BS3 con­nected to the
computer and you then position BS3 in the BS3 site position, you would
be unable to track successfully.

-   When all of the stations have been configured, choose
    [done]{.smallcaps}. Turn off the last sta­tion and insert dummy plugs
    into all the cable connection ports.

## Recording Data at the Site

> The digital data generated by the diver station at your study site can
> be saved as either of two types of record­ings.

### Definitions.

-   ***Position recordings*** are used to make a continuous recording of
    sequential posi­tions, e.g., to trace the perimeter of a study site
    or the line of a transect. They are also serve as a diagnostic tool
    for assessing SONAR signal effectiveness. You press F4 once from
    within the precision navigation screen, and the diver sta­tion will
    record every signal to and from the diver station position until you
    press F4 again or the memory is full (after 60 to 90 minutes,
    depending on how frequently posi­­tion fixes are received).

-   ***Observation recordings*** are made at specific points, such as at
    the transect origin and termi­nus. Before the dive, you use the
    configuration file to define which data are to be recorded, and this
    recording will be made each time you press F3 from within the
    precision navigation screen. If you want to relocate a point later
    on, this is the most accurate way to save the posi­tion. The
    [rms]{.smallcaps} error is also displayed and recorded, so you know
    the accu­­racy and precision of the location where the observation was
    made.

### Download the recorded data.

You need to download the position and observation data from the diver
station as "record" files (\*.rec) in order to view them on your PC and
make room on the diver station for other recordings.

-   Connect the diver station to your PC and go to
    [diveterm.]{.smallcaps}

-   Turn on the diver station.

-   When a link has been established, go to [run]{.smallcaps} 
    [smtdive]{.smallcaps}.

-   When the terminal window appears, go to the [command]{.smallcaps}
    drop-down menu and choose [read "tape" memory
    (smartdive/microtrack)]{.smallcaps}.

-   When the Select File window is displayed, select a name and location
    for the record file. We recommend using the default location.

-   Click on [save]{.smallcaps}. A percent display will indicate the
    progress of the data down­load.

-   When the download is complete, turn off the diver station,
    disconnect it from the com­puter, and close DiveTerm.

### Modify the configuration file to record observations.

Within the configuration file is an option that allows for default data
to be recorded as observation recordings. Put a check mark next to that
option in the Edit Diver Observation Records section of the Config-5
screen of Advanced Edit/Create. See Appendix A for more details.

### Delete the recording.

Depending on how frequently position fixes are received, the diver
sta­­tion memory will eventually fill up. For example, if fixes are
received once per second, the memory will be full in about two hours
(SmartDive refers to it as a "tape.") After you have downloaded the file
to a [pc]{.smallcaps}, you can erase the tape so that it can be filled
again. To do this:

-   Press the [mode]{.smallcaps} button on the diver station to call up
    the main menu.

-   Use the 0/ key to move to select [erase tape]{.smallcaps}.

-   Press [enter]{.smallcaps} to execute the erasure.

## The Convert™ Program

### 1. Definition and use. {#definition-and-use. .unnumbered}

Convert is the program that modifies recorded data into a useable
format. It will convert both position and observation recordings
relative to either:

-   Raw Auto-position (distance from the diver station to each baseline
    station), or

-   X and Y Auto-position (location of the diver station relative to the
    X and Y axes).

You need to know what you want to do with the data before you convert
it. Common examples are:

-   Position recording (initial or definitive perimeter) for graphic
    display: save **for** **import**, converted with respect to **X and
    Y** axes.

-   Position recording for evaluating SONAR communication effectiveness:
    saved **for** **import**, convert with respect to **raw** ranges.

-   Observation recordings for graphic display: saved **for import**,
    converted with respect to **X and Y** axes.

-   Observation recordings for written report: saved **as text**,
    converted with respect to **X and Y** axes.

Since Convert displays locations and ranges, it needs to know the
baseline configur­a­tion that existed when the recording was made.
Therefore, when converting a record­ing, you will have to know and have
on your computer's hard-drive the con­fig­­uration file that was used
during the recording.

### 2. File management. {#file-management. .unnumbered}

When the data has been converted, a split window will appear, with the
observa­tion data displayed in the top portion of the window, and the
position data in the lower portion. Which type of file is created (and
what data are displayed) from those record­ings depends on which settings
you select for the conversion program. (See Appendix B for setting
details.)

> Observation recordings = \*.rec file
>
> Converted observation recordings saved as text = \*.obs file
>
> Converted observation recordings saved for import = \*.dbi file
>
> Position recordings = \*.rec file
>
> Converted position recording saved as text = \*.dat file
>
> Converted position recording saved for import = \*.dbi file

### 3. How to use convert.  {#how-to-use-convert. .unnumbered}

The detailed instructions for CONVERT are found in Appendix B.

## The AREA Program

### 1. Definition.  {#definition. .unnumbered}

Desert Star programmer Andy Goldstein wrote the AREA program for the
purpose of displaying a sample area and creating sample waypoints within
that display. Since it displays the points recorded in a perimeter
trace, it can also be used to visually eval­u­ate the effectiveness of
SONAR communications. For example, major gaps in the perimeter trace
would represent a loss of or blocked signal.

### 2. Features.  {#features. .unnumbered}

The AREA program will calculate the size of the displayed area, plot the
total num­ber of sample points, randomize those points, find the best
path through the points, and save them as a waypoint file (\*.wpt) for
easy loading into the diver stations.

### 3. How to use the AREA program. {#how-to-use-the-area-program. .unnumbered}

Detailed instructions for this program are found in Appendix C.

#  Using AquaMap in the Field

There are five major activities in which AquaMap is used in the field.

-   **Range and noise tests.**

    -   The Range test helps you determine how far apart you can
        position the baseline stations and how large an area you can
        "map" as a perimeter.

    -   The Noise test provides data about the ambient noise level in
        your study site so that you can enter the "threshold" value into
        the configuration file.

        See section A, page [16](#the-range-and-noise-tests).

-   **Initial tracking.** During this activity, sonar communications and
    placement of the base­line stations are evaluated by:

    -   Positioning the baseline stations

    -   Measuring the bearing between B1 and B2.

    -   Performing an initial baseline configuration *in situ.*

    -   Performing an initial perimeter recording/trace.

    -   Downloading the recordings for analysis.

        You have completed this activity when you have determined
        permanent locations for the baseline stations. See section B,
        page [19](#initial-tracking).

-   **Definitive baseline survey.** To acoustically measure the distance
    between the baseline sta­tions, you make a position recording at each
    station. This recording is downloaded into a [pc]{.smallcaps} and
    brought into a spreadsheet for analysis. Eventually the data are
    used to modify the con­fig­uration file, which is downloaded into the
    diver and base­line stations. Then the definitive perimeter recording
    is made to provide the tracing that will be used to identify the
    sample pop­ulation and select random points. See section C, page
    [26](#the-definitive-baseline-survey).

-   **Navigating to Waypoints.** This involves tracking through the site
    using only the AquaMap system to locate sample points for the first
    time that you identified by the AREA program. See section D, page
    [33](#navigating-to-waypoints).

-   **Relocating sample points.** This involves:

    -   Locating the correct configuration file on your computer hard
        drive,

    -   Downloading it into the diver and baseline stations,

    -   Deploying the baseline stations at the right depth and
        orientation, and

    -   Tracking to the original sample points using the AquaMap system,
        possibly using laminated photos taken at the site on a prior
        occasion.

        See section E, page [36](#relocating-waypoints).

## The Range and Noise Tests

Our experience has shown effective tracking within a 200-meter range.
However, the propaga­tion of [sonar]{.smallcaps} signals at a given site
may be affected by a combination of bay configura­tions, biologi­cal
noise, bubble interference, and substrate composition, and may vary from
day to day. When selecting a study site, you will therefore need to
determine the effective operational range of AquaMap within the area and
consider the site's acoustical qualities. For the range test, you use
the diver station to measure the signal strength from a baseline station
over a known distance, which means measuring how far from the baseline
station its pulse can be "heard" by the diver sta­tion. For the noise
test, you turn off the baseline station and use the diver station to
measure the ambient noise of the study area.

To do this, download DT-test from your PC to one of the baseline
stations (set up to transmit continuously) and to the diver station (set
up to receive). DT-test is a software program that contains the
operational commands for both the range/transmit (TX) and noise (RX)
tests. The more locations within your study site at which you perform
these tests, the better your model of signal propagation characteristics
will be. But spending even one dive to conduct a range test along a
transect and collect noise data at 10 to 15 points will provide a fairly
accurate esti­mate of AquaMap's operational range in a given locale.

### 1. Set up the diver station.

-   Connect the diver station to the serial port of your PC via the gray
    data exchange cable and the connector adapter.

-   After you\'ve made sure the diver station is turned off, on your PC,
    go to [start]{.smallcaps} and choose: [programs  divetracker 
    diveterm]{.smallcaps}.

-   When DiveTerm is open, touch the magnetic pointer to the small
    indentation on the left lateral side of the diver station to turn it
    on.

-   When a link is established, in the DiveTerm window choose: [run 
    dt-test.]{.smallcaps}

If a link is not established, shut down DiveTerm[,]{.smallcaps} turn off
the diver station, then reboot both.

-   Press #6 on the diver station keypad or your [pc]{.smallcaps} keypad
    to select the [receive]{.smallcaps} function. This station will now
    be listening for the signal from the transmitting baseline station.

-   You can adjust the gain and the frequency by using the magnetic
    pointer on the diver station function keys.

    -   The gain controls the amplification of [sonar]{.smallcaps}
        signals. Pressing F1 will change the gain sequentially through
        four settings (0,1,2,3). Each increase in gain doubles the
        sensitivity (see "gain" in the glossary in Appendix D). Use the
        Gain 2 setting for the noise test.

    -   Pressing F2 will change the frequency in units of 1 kHz. The
        frequency should be the same as that of the baseline station (29
        kHz).

### 2. Set up the baseline station.

-   Connect the gray data exchange cable to the serial port of your PC
    (a gender adapter may be necessary).

-   Connect the other end of the cable to the appropriate connector
    adapter (8-pin, box end) and attach the adapter to one of the
    baseline stations.

-   On your [pc]{.smallcaps}, go to [start]{.smallcaps} and choose:
    [programsdivetracker diveterm.]{.smallcaps}

-   When DiveTerm is open, turn the baseline station on by rotating the
    round on-off knob at the end of the station 180°.

-   When a link is established, in the DiveTerm window choose: [run 
    dt-test.]{.smallcaps}

-   Press #7 on your PC keypad to choose "7 ([tx]{.smallcaps})". This
    will start the baseline station transmitting. You can adjust the
    fre­quency and speed, but these settings should be left on the
    defaults for these tests.

The frequency should be set to the frequency of interest minus 5 kHz.
The default set­ting is 29 kHz, which monitors 34 to 41 kHz. You can
adjust the fre­quency in 1 kHz increments by pressing the F1 function key
on your computer keypad. The default speed is "slow." Pressing F2 will
alternate between slow and fast speed.

-   When the baseline station is clicking (you may hear it, or feel it
    by putting your finger on the transducer), which indicates that it
    is transmitting a signal, you can disconnect the station and close
    DiveTerm.

    ![](media/image4.jpeg){width="0.24375in" height="0.24375in"}**Do not
    turn off the baseline station** until after the range test has been
    com­pleted. If it gets turned off, you\'ll have to repeat the entire
    setup pro­cess to enable the station to transmit, which requires use
    of a com­puter.

### ![](media/image3.png){width="1.0in" height="0.27708333333333335in"}3. Conduct the range test. {#conduct-the-range-test. .unnumbered}

The purpose of the range ([tx)]{.smallcaps} test is to measure the
actual operational range of AquaMap at your intended study site by
finding out the maximum signal strength at known distances from one
transmitting baseline station.

-   Place a baseline station in your study area, preferably at the
    approximate location of where you plan to put BS1 or BS2.

-   Use the diver station to record the noise level at a known distance
    (e.g., 5 meters) from the baseline station. Remain in this position
    for approximately one minute and record the maximum signal received.
    Example of diver station display:

    Gain (F1): 2

    Frequency (F2): 29000

    min/max: 006/084

    *Below the line under "min/max" is a graphic display of
    transmissions received. The "min/ max" will update every 10
    seconds.*

-   Moving along a straight line, record the noise level each time you
    have approxi­mately doubled your distance from the baseline station.
    (e.g., at 10 m from the baseline station, then 25 m, 50 m, 100 m,
    and 200 m). The effec­tive opera­tional range generally ends at about
    200 meters from the baseline station.

-   Although the signal propagation should be similar in all directions
    from the baseline station, if time and patience permit, noise levels
    may also be recorded for evaluation in other quadrants in the study
    area.

-   When this test is finished, turn off the baseline station but leave
    the diver station on.

### ![](media/image3.png){width="1.0in" height="0.27708333333333335in"}4. Conduct the noise test. {#conduct-the-noise-test. .unnumbered}

The purpose of the noise ([rx)]{.smallcaps} test is to determine the
general noise characteristics of your study site, with an emphasis on
broadband noise, the most common type you will encoun­­ter. Broadband
noise, which may be caused by biological sources (e.g., snapping
shrimp), has frequency compo­nents across a wide range. However, you may
encounter noise on a specific fre­quency, such as from a depth sounder or
other piece of under­water acoustic equipment. This test will pick up
noise from scuba regu­lators and impacts on the trans­ducer, so try to
mini­mize them. The baseline sta­tion should be turned off after the range
test to eliminate the "pings" it emits.

During the [rx]{.smallcaps} test, the diver station listens on the
selected frequency and measures the mini­mum and maximum signal detected
in a five-second period. These signals are dis­played numer­ically and
graphically on the diver station screen.

-   You will need to have the diver station configured in the receive
    mode, as it was for the range test, so that it will detect ambient
    noise on the specified frequency range. Use Gain 2 and a frequency
    of 29 kHz.

-   Swim with the diver station to various locations in the study area,
    including the peri­meter, near tall coral colonies and in both deep
    and shallow areas. After remaining in a location for at least a
    minute, record the maximum value you have seen on the diver station
    display while there. Also note if many signals are con­si­d­erably
    below the maxi­mum. (Since the maximum value is determined over a
    15-second period, if many or most of the signals are lower than the
    maximum, your range may not be well repre­sented by the maximum level
    indication.) Make sure you also record the gain and fre­quency that
    were used during the test. Perform the test in as many locations
    around your site as time and patience permit.

-   To end the test, press [enter]{.smallcaps} on the diver station,
    then F4 ([off]{.smallcaps}). You should now have a reasonable
    approximation of the noise characteristics in the study area.

### 5. Evaluate the test results.

Compare the signal received at known distances in the range test with
the ambient noise levels as mea­sured in the noise test. When the maximum
signal received is equal to the average noise level, you have reached
the maximum operational range. It\'s pru­dent to have the actual distance
between the stations remain somewhat less than the average operational
range measured (∼75%).

In addition, in order for the system to reliably derive a position,
signals must be above the maxi­mum noise level you determined for the
site. A good rule of thumb is to set the thres­hold level so that signals
will be received at 1.5 times the average of the maxi­mum values you
recorded. For example: assume the maximum values for the 20 mea­sure­ments
taken during the noise test ranged from 0 and 15, with an average of 10.
The AquaMap default setting for the threshold value, which is 12, could
be used because it's close to 1.5 times the average noise level for the
area. If the average value was more than 10, you could increase the
threshold value when you create or edit the con­figuration file for the
sta­tions, as explained on page
[11](#create-andor-edit-the-configuration-file.).

You may use this information to modify the settings for "threshold" in
the configuration file. Our experience in tropical waters has shown them
to be fairly noisy environments and, as explained on page 8, a diver's
bubbles can cause inter­fer­ence with the SONAR signal. We generally use a
threshold value of 15 on Gain 2, and have had success tracking with
ranges to 200 meters, sometimes more.

## ![](media/image3.png){width="1.0in" height="0.27708333333333335in"} Initial Tracking

After you know how to deploy the baseline stations (page
[6](#deploying-the-baseline-stations)) and load the right configuration
file into the stations (page [10](#the-configuration-file)), you can
begin tracking in your study site. The steps described in this section
are repeated until you are satisfied with the quality of the SONAR
signal you are receiving and you have marked the final locations of the
baseline stations.

A baseline survey is a test or series of tests that provide critical
data regarding the positions of the baseline stations. Before the system
can map or track, it must have data from a baseline survey entered into
the configuration file. There are two ways to accomplish this:

-   In an initial baseline survey, the positions are automatically
    calculated and entered by the diver station underwater, as described
    in this section.

-   In a definitive baseline survey, data obtained at the site are
    manually entered into the configuration file and then downloaded
    into the stations before returning to the site. This procedure is
    described in the section C, page
    [26](#the-definitive-baseline-survey).

### Setting up for tracking.

You'll need to do the following before you undertake tracking for any
purpose, including either an the initial or defin­itive base line survey.

-   **Anchor the boat.** If the longest distance is between BS1 and BS2,
    you may want to anchor the boat midway between these locations as
    defined in your pre-dive planning. In that case, one diver would
    take the stations for BS1 and BS3, and a second diver the station
    for BS2.

-   **Turn on the baseline and diver stations before entering the
    water.** Leave the base­line stations on while they are in the water.
    Check the flashing light near the on-off switch.

    -   One blink per second means the baseline station is standing by,
        waiting for an interrogate, i.e., waiting to be surveyed.

    -   A fast double blink means an interrogate has been received.

    -   Continuous rapid blinking means the battery is low.

> ![](media/image4.jpeg){width="0.24375in" height="0.24375in"}Caution:
> This is a strenuous technical dive with risks of entangle­ment and
> over-exertion. Divers are carrying both extra weight and flo­ta­tion
> while swimming long distances. All divers must be familiar and
> com­fortable with the dive plan and aware of emergency contingencies
> before starting.

-   **Position the baseline stations** in the locations you have
    selected. (See page [6](#deploying-the-baseline-stations).)

### Measure the bearing of baseline #1. 

You'll need to determine the compass orientation of baseline #1 so that
when you've decided on permanent locations for the baseline stations you
can enter the data into the configuration file. We do this by
temporarily marking the loca­tions with surface floats, then maneuver the
boat so that we can get a compass bearing from the float on the line
from BS1 to BS2. An alternative is to run a transect tape at depth
between the sand screws or pins securing the stations, pull the tape
taut, and measure the bearing along that line. If you later reposition
the BS1 or BS2, you'll have to determine the new compass bearing and
revise the configuration file accord­ingly.

 When considering the use of surface floats, keep in mind that wave
action may be transmitted through a surface float and line to a base­line
station, moving the station and decreasing position accur­acy. Although
helpful when determining the baseline orientation, floats are gen­er­­ally
not a good idea during routine tracking and mapping. They make it easier
to locate the stations, but increase the risk that the sta­tions will be
jostled during tracking.

### Conduct an initial baseline survey.

In an initial baseline survey of your study site, you establish where
the baseline sta­tions are located by simply pressing a button on the
diver station. This process is used to determine the depths of the
baseline stations, and it is sufficient for accurate tracking and
mapping during a single dive. However, because of the variability of
measurements taken in moving water, position fixes obtained during an
initial baseline survey way *may not* be repeatable at a later date,
even if the baseline stations are deployed in the same place. (They
could be used for future dives if the stations were not removed from the
site, but the sta­tions are too expen­sive to leave behind.)

**Limitations.** It's a matter of sample size. An initial baseline
survey determines the loca­tion of the stations based on the reception of
a single signal from each baseline station. The "error" in the data
obtained in a single survey may be significant enough to affect the
accuracy of mapping, tracking, and point relocation on sub­sequent dives.
The data obtained in repeat baseline surveys are inevitably variable;
two initial baseline surveys done during two dif­ferent dives may pro­duce
slightly differ­ent positions for the base­line stations even if you
deploy them in exactly the same locations. For example, if BS1 sways 35
cm to the east, BS2 sways 35 cm to the west, and BS3 sways 35 cm to the
north, that can provide enough variation in the survey to create a
position relocation error of more than one meter.

Because we use AquaMap to help relocate positions with sub-meter
accuracy repeat­edly over time, the position data must draw from a larger
sample, increasing the reliability of the data by increasing the number
of signals on which the data are based. To establish these dis­tances
precisely requires the reception of repeated signals, as is done in the
definitive baseline survey, as described on page
[26](#the-definitive-baseline-survey).

**What the diver does.** The diver should hover motion­less in an area
\~5m away from both baselines while the diver station is recording data.
The diver should not change depth or loca­tion during this process, which
takes about one minute.

-   Press the [mode]{.smallcaps} button on the diver station to call up
    the main menu.

-   Use the 0/ key to move to select [baseline]{.smallcaps}.

-   Press [enter]{.smallcaps} to display the [baseline
    define]{.smallcaps} screen.

-   Press F4 ([ok]{.smallcaps}) to display the [baseline
    config]{.smallcaps} screen.

-   Press [enter]{.smallcaps} to clear any previous data from the
    [allign]{.smallcaps} field.

-   Press the numeric keys to enter the compass bearing for Baseline #1
    in the [allign]{.smallcaps} field, then press [enter]{.smallcaps}.
    If a wrong number is entered, press F3 ([del]{.smallcaps}) to delete
    the mistaken entry and enter the correct number.

-   The cursor is now placed to enter data in the S-Depth field. But
    this is for the depth of the surface station, which we do not use,
    so just press [enter]{.smallcaps}. Although you do not see the data,
    the diver station is also noting the depths of the baseline
    stations.

-   The display will fill with zeros. Confirm this configuration by
    pressing F4 ([ok]{.smallcaps}). The diver station will beep and
    return to the [diver status]{.smallcaps} screen.

**What the diver station does.** The diver station will display "[now
survey­ing...,]{.smallcaps}" send interrogates to each baseline station
in turn, and listen for a return signal.

-   **If the diver station receives a reply,** it will send another
    interrogate, listen for a reply, then compare that value with the
    previous reply. If the two values are within a tolerance margin, the
    diver station will display what values it has accepted, send an
    interrogate to BS2 and repeat the process.

-   **If the diver station does not receive a reply,** it will make
    eight more attempts to interrogate that baseline station. The number
    of the current attempt will be displayed on the screen. If a return
    signal is not received after nine attempts to interrogate a baseline
    station, the diver station will display the range data as
    [n/a]{.smallcaps} and the bearing data as 0.0 or [n/a]{.smallcaps}.
    The diver station will then proceed to inter­rogate any remaining
    baseline stations.

After all three baseline stations have been interrogated:

-   If data values within the tolerance margin have been obtained for
    all three baseline sta­tions, a **[survey ok]{.smallcaps}** message
    will appear.

-   If the diver station cannot communicate with one or more of the
    baseline stations, or if the data values obtained from any of the
    baseline stations do not fall within the toler­ance margin, a **[no
    survey data!]{.smallcaps}** mes­sage will appear.

**If you get the [no survey data]{.smallcaps} message,** you'll have to
reposition one or more of the baseline stations and try again. Although
base­line data are entered into the configura­tion file during the initial
baseline survey, they can be over-written or replaced in a sub­se­quent
sur­vey on the same dive, unlike the data that are "hard-coded" into the
config­ur­ation file during a defini­tive baseline survey.

### Navigate around in the area.

After completing the initial baseline survey, you can practice using the
diver station at your study site and evaluate the quality of your SONAR
communications. You'll want to swim through the area several times at
differ­ent depths while watching the diver station display to determine
if communi­cation is good within the entire site.

![](media/image8.png){width="2.2in"
height="2.0506944444444444in"}**Using the diver station.** To press a
key on the diver station keypad, use the magnetic pointer. A feedback
beep indicates that the key has been triggered. Most of the display
screens have four labels across the bot­tom, posi­tioned over the four
func­tion keys. These indi­cate the command that will be triggered by
pressing that func­tion key, e.g., pressing F1 when it appears under
[nxt]{.smallcaps} on the screen will move you to the next screen. Most
other keys on the keypad have multiple func­tions. The arrow keys are
used to select entries from a list or to move around a data field. Refer
to the Aqua­Map manual to learn about the informa­tion that is displayed
on the diver station and how to get to the different screens. You will
primarily be using the two nav­i­­­gation screens: general and precision.

### Evaluate the SONAR signal quality. 

The key indicators of the quality of [sonar]{.smallcaps} communication
within the site are:

-   **Time since last fix.** This is displayed in the upper left of the
    general navigation screen, and lower right of the precision
    navi­gation screen, next to the label "l". During good signal
    com­mu­ni­cations, the diver station may be able to fix its loca­tion
    every 2 to 3 seconds. If you are moving and the time since last fix
    exceeds 30 sec­onds, your position may not be accurately reflected by
    the diver station. Try chang­ing your depth and check to make sure
    that the transducer is not blocked by your dive buddy or your
    exhaled air bubbles.

-   **Baseline signal indicator**. This is displayed on the lower left
    of the precision navigation screen, next to [base.]{.smallcaps}

    -   An "l" means that a pulse was received during the last
        positioning attempt.

    -   You should also see three "+" signs, one for each baseline
        station. If a "--" sign appears, it means that that signal is
        not getting through (e.g., if there's a minus sign in the second
        space, it means BS2 is not com­mu­nicating).

    -   An "i" means idle, i.e., no signal was received.

    -   An \"s\" indicates that a signal has been received but its
        location could not be calculated, e.g., the baseline sta­tion is
        out of range.

```{=html}
<!-- -->
```
-   Even in tropical waters, differences in temperature may affect
    signal pro­­paga­tion, so the diver station transducer should be in the
    same water tempera­ture as the baseline station transducers. You can
    use your own sense of temperature to determine this; you don\'t need
    a ther­­mom­eter. If you feel a significant thermoclyne (as often
    occurs near the water sur­face under intense sun), the signal may
    have diffi­culty passing through.

**What if the [sonar]{.smallcaps} quality is unsatisfactory?** Although
there may be times when one or more stations are not receiving signals,
such a lapse should not continue for more than 90 seconds. If it does,
check to make sure nothing is blocking the diver station transducer
(e.g., a dive buddy, a school of fish, or the float on the diver station
transducer). If you cannot locate any other source of the problem,
you'll need to move one or more of the baseline stations and conduct
another ini­tial baseline survey, which can be done by over-writing the
configuration file data in the diver sta­tion (see page
[21](#conduct-an-initial-baseline-survey.)).

### Record the site perimeter.

As explained on page [13](#recording-data-at-the-site), the diver
station can make two types of recordings, position and observation. You
can use a position recording that you make as you trace your study site
perimeter to test how well [sonar]{.smallcaps} signals are received
through­out the site and begin the process of iden­ti­fying a sample
population. Like the initial baseline survey, this step will need to be
repeated after you've collected more data.

-   Go to the site boundary and choose an identifiable point from which
    to start.

-   At the [diver status]{.smallcaps} screen, press F2 to go to the
    [general navigation]{.smallcaps} screen[.]{.smallcaps}

-   Press [enter]{.smallcaps} to display the [precision
    navigation]{.smallcaps} screen.

-   Press F4 to change from standby to [record]{.smallcaps} mode.

-   Circumnavigate the study site, swimming at a comfortable speed and
    making sure your dive partner does not block the SONAR signal path.

-   During this swim, monitor the \"time since last fix\" and the
    \"baseline signal indi­cator\" to check the [sonar]{.smallcaps}
    signal reception in the study site.

-   When you are back at your starting point, press F4 to return to
    [standby]{.smallcaps} mode.

-   If you are done tracking for the day, you can retrieve and turn off
    all stations.

Or, if you are working with a laptop in the field, you can leave the
stations *in situ* and immediately download and convert the recorded
data as described below.

### Download and convert the recorded data.

-   Connect the diver station to your [pc]{.smallcaps} and go to
    [diveterm.]{.smallcaps}

-   Turn on the diver station.

-   When a link has been established, go to [run]{.smallcaps} 
    [smtdive]{.smallcaps}.

-   When the terminal window appears, go to the [command]{.smallcaps}
    drop-down menu and choose [read "tape" memory
    (smartdive/microtrack)]{.smallcaps}.

-   When the Select File window is displayed, select a name and location
    for the record file. We recommend using the default location.

-   Click on [save]{.smallcaps}. A percent display will indicate the
    progress of the data down­load.

-   When the download is complete, turn off the diver station,
    disconnect it from the com­puter, and close DiveTerm.

-   Convert the data to display the position recording as a graph (see
    Appendix B).

After you've downloaded the file to your [pc]{.smallcaps}, you can clear
the diver station memory so it will have space for your next recording
(see page [14](#delete-the-recording.)).

### Finalize the baseline station positions.

Here are the considerations to keep in mind as you decide whether you're
ready to finalize the locations for the baseline stations.

**You'll want to reposition one or more of the baseline stations if:**

-   The diver station had to make many attempts to interrogate one or
    more baseline stations during the initial baseline configuration; or

-   The baseline station indicator sporadically displayed "─"
    (indicating that a baseline signal is not getting through) during
    the site swims or perimeter tracing, especially there was no
    consistent pattern of blockage, i.e., the "─" bounced from station
    to station; or

-   The position recording graph showed several large gaps between
    positions.

The baseline stations can be moved in all directions, depths, and
orientation (transducer up or down), and each move can be considered for
each station. If you reposition a baseline sta­tion, however, you will
need to repeat:

-   the initial baseline survey;

-   the preliminary site swim watching the baseline station indicator on
    the precision navigation screen; and

-   the perimeter tracing and position recording, and display the new
    data as a graph in the [area]{.smallcaps} program.

**You can leave the baseline stations where they are if:**

-   You had fairly rapid communications between the stations during the
    initial base­line survey. If the diver station received a reply from
    each baseline station after only a few attempts, this may indicate
    good sonar communication.

-   While you were swimming in the study site, the baseline signal
    indicator display showed "+ + +" most of the time, you encountered
    only a few places where signals dropped out, and that was for less
    than 30 seconds. Even with good sonar comm­un­ication, the number of
    times the signal drops out will vary depending on the size of the
    site. For example, in a large site which takes 10 to 15 minutes to
    circumnavi­gate while swimming, 10 to 15 dropouts would not be
    unusual.

-   Evaluation of the position data graph displayed by the area program
    reveals no significant gaps between positions, or no more than a
    very few small gaps.

### Mark and document the baseline station positions.

After you've decided where you want to locate the baseline stations, the
locations should be marked at the site in a non-destructive manner and
identified by GPS coor­dinates as accur­ately as possible.

-   In sandy bottom, sand screws work well; in hard bottom environments,
    survey stakes or pins that have been modified to have a
    rust-resistant attachment "eye" at the top work well.

    -   With its flotation collar, each baseline station is ∼7 lbs.
        positively buoyant in salt water, but since minimal holding
        power is necessary, sand screws only need to be installed
        halfway into the sand, and the portion of the screw remaining
        above the sand will help during relocation.

    -   To make it easier to relocate the sand screws or pins later on,
        connect them to submerged floats by 3 to 5 feet of line, and
        make detailed field notes and drawings.

-   The lines used to attach the stations to the sand screws or survey
    stakes can be left at the bottom between dives or deployed only when
    using the stations.

    -   Permanent lines allow for easy positioning of the stations at
        the correct depth during each use, but they will become
        bio-fouled, may sink to the bottom causing damage, and may be a
        navigation hazard if very shallow.

    -   Temporary lines avoid the problems associated with permanent
        lines, but accurate notes must be taken regarding the depth of
        the stations. If you are scheduled to use AquaMap at the same
        site for several days, temporary lines can be left there until
        the work has been completed.

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```
-   Measure the depth of each station from the [on-off]{.smallcaps} knob
    end of the sta­tion where the depth sensor is located, not from the
    transducer end.

Information on the locations of the baseline stations should be
documented in the metadata file and stored with the site information
(see page [37](#data-management-and-summary-chart)).

**Integration with GIS.** To provide another means of relocating the
baseline sta­tions over time and make it possible to integrate AquaMap
with GIS data, you will want to get the GPS coordinates for the
stations. This can be done with a portable or boat-mounted unit: get as
close as possible to each base­line station, position yourself dir­ectly
over it, steady the boat and/or GPS unit, and record the position.
Software is being developed that will link the GPS coordinates to the
sample positions and con­vert the X:Y coor­dinates to GPS.

##  The Definitive Baseline Survey

After you've settled on where you want to locate the baseline stations
and you're satisfied with your ability to track and receive SONAR
signals throughout the study area, you need to do a definitive baseline
survey. This procedure uses the system's abil­ity to measure "raw
ranges," or the actual distance between the stations.

-   **The diver swims to each baseline station**, turns on the
    position-recording feature, and remains at the station for 3 to 5
    minutes while the system serves essentially as an acoustical
    measuring tape. The signals received by the diver station every 1 to
    3 seconds measure the distance between it and each of the baseline
    stations. By increasing the number of mea­sure­ments taken of the
    distance between baseline stations, we dramatically increase the
    sample size ("N = 80 to 120") from that used in the initial baseline
    survey ("N = 1").

-   **After data have been recorded at all three baseline stations**,
    the recording is down­loaded to a field laptop or office computer and
    used to deter­mine:

    -   the range of Baseline #1 (the distance between BS1 and BS2) and
        Baseline #2 (the dis­tance between BS1 and BS3);

    -   the angle between Baseline #1 and #2; and

    -   the depth of each baseline station.

-   **The depth of the baseline stations can be measured** using a depth
    gauge, but a more accurate measurement can be obtained from the data
    recorded by the diver station when you made the position recording.
    The first three lines in the converted recording (lower display in
    the Con­vert window) are the baseline configuration data used when
    the recording was made, including the station depth.

> These num­bers, along with the bearing of Baseline #1 that you obtained
> on the initial base­line survey, are manually entered into a
> configuration file and loaded into each station. As long as the same
> configuration file is used at the same site with the baseline sta­tions
> in the same place, posi­tion fixes obtained with data using the
> definitive baseline survey are repeat­able and precise.
>
> So you'll have enough space in the diver station memory, make sure
> you've erase the tape of any previous records before conducting
> another survey (see page [14](#delete-the-recording.)).

### Conduct the survey.

-   Position yourself with the diver station at BS1 and hold the
    transducers of the two sta­tions approximately 0.3m apart without
    altering the loca­tion of the baseline station or blocking the signal
    path.

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-   Depending on current, surge, and wave action, positioning the diver
    station transducer can be difficult. Don't let your body block the
    signal path.

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```
-   Press F2 and then [enter]{.smallcaps} to get to the [precision
    navigation]{.smallcaps} screen.

-   Press F4 to change from standby to record mode. Keep the diver
    station at the base­line station for as long as possible while in
    record mode (at least 2 minutes, but more ideally 5 minutes). Using
    signals received every few seconds, the diver station will
    repeatedly record the horizontal distance measured between it and
    the three baseline stations. The vertical component of the distance
    (the result of any difference in the depth of the sta­tions) is
    automatically removed.

```{=html}
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```
-   Be careful not to move the baseline station during the survey and to
    mini­mize the motion of the diver station transducer, which serves as
    the reference point for multiple range calculations**.** Any
    movement will degrade the accuracy of the survey.

```{=html}
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```
-   When you're done at BS1, press F4 to turn off the recording feature
    and remain in standby mode while swimming to BS2. This will make it
    easier to extract the base­line survey ranges that are needed.

-   Repeat the transducer positioning and recording process at BS2 and
    BS3. This will give you the distance between the three stations.

### Analyze the recorded data.

**a. *Download and convert the data.*** You need to download the
recording from the diver sta­tion to your PC (page
[13](#recording-data-at-the-site)) and convert the data as summarized
below (see Appendix B for more details). This converted file will be
imported into an Excel spread­sheet for data anal­ysis.

-   When the download is complete, go to [start]{.smallcaps} and choose:
    [programs divetracker  convert]{.smallcaps}.

-   Go to the [file]{.smallcaps} drop-down menu and choose [load a new
    record]{.smallcaps}.

-   You will be prompted to choose the file that you want to convert
    (the one you just downloaded and saved), and the configuration file
    that was being used when the recorded file was created.

-   When prompted to confirm that the download was created from a mobile
    station, click on [yes]{.smallcaps}.

-   At the Settings window, in order to view only station depths and raw
    baseline lengths, do not check either [show raw auto-position
    data]{.smallcaps} or [show x/y auto-posi­tion data]{.smallcaps}.

-   Click on [ok]{.smallcaps} to convert the data.

**b. *Determine the baseline station depths.*** After data is converted,
the lower part of the screen will display a single line of data for each
baseline station. The depth of the baseline stations can be found in the
far right column, mea­sured in meters.

-   Copy the baseline station depths to the metadata file (see page
    [37](#data-management-and-summary-chart)). You will need this
    information when you edit the configura­tion file in order to add the
    baseline station range data. Although the depths are entered into
    the configuration file in meters, most depth gauges read in feet, so
    it is useful to convert the meters to feet (multiply by 3.281) and
    have both numbers available.

```{=html}
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```
-   In the Convert utility, B0 = Baseline Station 1, B1 = Baseline
    Station 2, and B2 = Baseline Station 3. B3 does not contain data
    because we only use three baseline stations.

**c. *Display the baseline range data on a spreadsheet.*** To get the
baseline ranges, you will reload the same file of recorded data, choose
the configuration file that you used when the recorded file was created,
and confirm that the download was created from a mobile station.

-   But this time in the Settings window, place a check next to [show
    raw auto-position data]{.smallcaps}.

-   When the data has been converted, which will takes less than one
    minute, go to [file  save position data for import]{.smallcaps}.

-   In the [observation]{.smallcaps} fields, place a check in all four
    boxes for [round trip lengths:]{.smallcaps} 1, 2, 3, and 3 (3
    appears twice). Leave the [delimiter]{.smallcaps} as a semicolon.
    Click on [ok]{.smallcaps}.

-   You will be prompted to save this as a \*.dbi file; do so with a
    unique name to the default location (C:/Program
    Files/DiveTracker/Records), then close Convert.

-   Open a blank worksheet in MS Excel.

-   Go to [fileopen]{.smallcaps}. Select the \*.dbi file you just saved
    (usually in (C:/Program Files/ DiveTracker/Records).

```{=html}
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```
-   If you don\'t see any \*.dbi files listed, make sure you\'ve
    selected all files on the \"Files of type\" menu in the Open file
    dialog box.

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```
-   The Text Import Wizard will appear. Within the field for [choose
    original data type]{.smallcaps}, select [delimited,]{.smallcaps}
    which is usually the default. Click on [next.]{.smallcaps}

-   In the [delimiter]{.smallcaps} field, remove the checkmark next to
    [tab]{.smallcaps} and place one next to [semi­colon]{.smallcaps}.

-   Click on [finish.]{.smallcaps} The converted data will be displayed
    on the spreadsheet.

A B C D A B C D

![](media/image9.png){width="5.99375in" height="2.7131944444444445in"}

The spreadsheet will display the data in sets of four columns. The
values in columns A, B, and C indi­­cate the distance in meters from the
diver station to each of the three baseline stations (BS1, BS2, and
BS3), as recorded by the diver station every few seconds while you were
receiving signals at the site. Column D is all null data because it is
for a channel that looks for data from a surface station or a fourth
baseline station, neither of which we use.

The values in Column A, which indicate the distance between the diver
station and BS1, should start out close to zero and generally be less
than 1 meter because you were position­ing the diver station transducer
as close as possible to the BS1 trans­ducer. (Ignore any nega­tive values,
i.e., -1, -2, -3, as these indicate errant signals.) When you reach a
certain roll as you scroll down, the values in Column A will abruptly
increase and the values in Column B drop close to zero. This row is the
first data you recorded after moving to BS2. Consequently, the distance
from the diver station to BS2 (shown in Column B) is very small, while
the distance indicated to BS1 (Column A) is now similar to that in
Column B in the preceding rows.

**d. *Separate the range data into three sets.*** To determine the
distance between the baseline stations, you will need to separate the
spread­­sheet data into three sets according to which of the three
baseline stations the signals were recorded at.

-   To separate the data recorded at the BS1 position from that recorded
    at the BS2 posi­tion, scroll down until you reach the row where the
    values in Columns A and B abruptly change. [highlight]{.smallcaps}
    the four cells in that row and the rest of those four columns down
    to the end of the data.

-   [cut]{.smallcaps} that data and [paste]{.smallcaps} it at the top of
    Column F.

-   Scroll down until the values in Column F abruptly increase while
    those in Column H drop close to zero. This indicates the first row
    of data that you recorded after moving to BS3.
    [highlight]{.smallcaps} the four cells in that row and the rest of
    those four columns down to the end of the data.

-   [cut]{.smallcaps} that data and [paste]{.smallcaps} it at the top of
    Column K.

-   You have now divided the data into three sets according to the
    baseline station at which it was recorded. You can label these data
    sets by inserting a row above the data and entering the label, "B1
    Data Series" in cell A1, "B2 Data Series" in cell F1, and "B3 Data
    Series" in cell K1.

**e*. Determine the average and median values.*** Use the average and
median of the data to make a best estimate as to the distance between
the three baseline stations.

-   When calculating average and median values, be sure to exclude the
    negative values in the Excel formula cell range.

```{=html}
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-   To calculate the average and median range for Baseline #1 (the
    distance from BS1 to BS2), take the average and median of the values
    of Columns B and F.

-   To calculate the average and median range for Baseline #2 (the
    distance from BS1 to BS3), take the average and median of the values
    of Columns C and K.

-   To calculate the average and median range for Baseline #3 (the
    distance from BS2 to BS3), take the average and median of the values
    of Columns H and L. Although Base­line #3 is not used in the field,
    the value is used in the Law of Cosines to find the angle between
    Baseline #1 and Baseline #2, as explained below. It is necessary to
    include this angle in the con­figuration file to complete the
    definitive baseline survey.

**f. *Evaluate the results.***

-   Look at the differences between the average and the median for each
    range. Keep in mind that although negative numbers should be
    excluded, the average values do include any noise or poor signals.
    The median value represents the "middle" of the list of numbers, and
    may be the better option. Choose one value to use for the length of
    Base­line #1 and one for Baseline #2.

-   In addition to using these values to edit the configuration file as
    described in the next step, these data and the depths of the
    baseline stations should be stored permanently somewhere safe so
    that you do not have to repeat this process if the electronic
    con­fig­uration file becomes corrupted, deleted or lost.

```{=html}
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```
-   The main purpose of this data analysis is so you can be consis­tent
    in posi­tioning the baseline stations and in the range and angle data
    entered in the configuration file. If you always position the
    base­line sta­tions in the same place and always use the appropriate
    data in the con­fig­uration file, AquaMap will attempt to locate the
    points in the same place. The accuracy of the baseline ranges
    becomes signi­ficant only if you want to geo-reference sam­ple points
    using GPS.

**g. *Determine the angle between baselines #1 and #2.*** The easiest
way to calculate the angle is to use the diagram on the spreadsheet,
where the formula has been incorporated.

-   Go to the bottom part of the spreadsheet, below the sections for
    calculat­ing the average and median baseline ranges, where it reads:
    "Now Calculate the Angle between baseline-1 and baseline-2". The
    exact location of this depends on how many rows of data you imported
    to do the range calculations.

  ------------------ ---------- ------- --------- ------------- ---------- --------- ---------
  **Sample                                                                           
  Spreadsheet                                                                        
  Baseline Diagram**                                                                 

                                                                                     

                                        **BS2**                 107.8127             

                                                                                     

                                        64.0842                                      **BS3**

                                        **a**                                        

                                        **BS1**                 87.0458              

  c\^2=a\^2+b\^2-2 a                                                                 
  b cos(a)                                                                           

  a=                 89.69095                                                        
  ------------------ ---------- ------- --------- ------------- ---------- --------- ---------

-   The values shown in the triangle diagram for the length of each
    baseline and angle \"a\" between baseline #1 and #2 are the numbers
    that were in the spread­sheet when it was last saved. The proportions
    of the diagram may not fit your site, but you need to assign the
    correct values to baselines #1 and #2 as they exist at your site.
    (Baseline #1 is the vertical line, baseline #2 is the nearly
    horizontal line to the right of baseline #1, and baseline #3 is the
    longest line.)

-   Enter the values you have determined for the baseline lengths in
    step 7 in the same cells as the current values. If you input the
    data in another cell, it will not be read by the formula and the
    calculation will be in error.

-   As you change the baseline values, the value calculated for angle
    "a" will auto­matically change where it appears just below and to the
    left of the triangle display. This is the value you will enter into
    the configuration file.

-   Save this worksheet with a name unique to the site.

If you\'d like to work through the law of cosines yourself, you can use
the following:

> **The Law of Cosines**
>
> c^2^=a^2^+b^2^-2 a b (cos\[a\])
>
> "a" = the angle between Baseline #1 and Baseline #2.

#### OR {#or .unnumbered}

> "a" = inverse cosine of [(Baseline #1)2 + (Baseline #2)2 -- (Baseline
> #3)2]{.underline}
>
> 2 x (Baseline #1 x Baseline #2)
>
> all divided by (180x Pi)

### Edit and reload the configuration file.

The baseline survey data that you have calculated in the preceding steps
must be manually added to the configura­tion file you are using at the
site. This file editing procedure is summarized below; see page
[11](#create-andor-edit-the-configuration-file.) for more details.

-   On your [pc]{.smallcaps}, go to start and choose: [programs
    divetracker diveterm]{.smallcaps}.

-   Go to [file  options]{.smallcaps} and select [use metric
    units.]{.smallcaps}

-   On your [pc]{.smallcaps}, open DiveTracker and go to [diveterm 
    file  edit]{.smallcaps} [a]{.smallcaps} [config­ur­a­t­ion file 
    advanced edit.]{.smallcaps}

-   In the Select Configuration File window, open the same configuration
    file that you used to do the definitive baseline survey.

-   In [config-3]{.smallcaps}, you will need to enter the data from the
    definitive baseline survey.

    -   Enter the baseline station depths in meters as determined in
        step 2-b.

    -   Enter the range (length) for baseline #1 as determined in step
        2-f above.

    -   Enter the bearing of baseline #1 as determined on page
        [20](#measure-the-bearing-of-baseline-1.).

    -   Enter the range (length) for baseline #2 as determined in step
        2-f above.

    -   Enter the angle between baselines #1 and #2 as determined in
        step 2-g. This entry is confusing because the cell label is
        similar to that for the bearing of baseline #1, but the correct
        entry is for the angle between baselines #1 and #2.

-   Click on [next]{.smallcaps} twice to get to [config-5.]{.smallcaps}
    When you click on [ok]{.smallcaps}, you will be prompted to enter a
    file name and location. Then click on [save.]{.smallcaps}

-   Note the file name in the metadata file for this site.

```{=html}
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```
-   Always use this configuration file when surveying this particular
    site unless you relocate the baseline stations. If you must move the
    base­line stations, you'll need to repeat the definitive baseline
    sur­vey and re-edit the configuration file.

```{=html}
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```
-   After the configuration file has been edited, you need to reload it
    into the diver and baseline stations as explained on page
    [11](#download-the-configuration-file-to-the-diver-and-baseline-stations.).

When the revised configuration file had been downloaded into all of the
stations, they are ready to be used at the study site. At this point,
you will want to conduct a definitive perimeter swim and recording.

-   If the diver station is loaded with a configuration file in which
    the baseline configuration data has been manually entered, a
    baseline survey cannot be conducted because the hard-coded data will
    over­­-ride the system's ability to store new con­figuration data.

### Make the definitive perimeter recording.

This is the same as the initial perimeter recording, except that the
stations now have the definitive baseline survey loaded, and this
recording will be used to define your sample area and create ran­dom
sample points.

As explained starting on page [23](#_Ref7927055), after you\'ve erased
the tape to clear the diver station mem­ory, you can repeat the steps to:

-   Record the site perimeter;

-   Download and convert the recorded data; and

-   Save the data as a \*.dbi file.

This file is then loaded into the [area]{.smallcaps} program (see
Appendix C) so that you can:

-   define the sample population,

-   randomize that population,

-   select the number of sample points you need, and

-   download the points to the diver station.

## Navigating to Waypoints

As described the preceding section, by this point you should have:

-   downloaded the definitive perimeter recording;

-   used the AREA program to generate random sample points;

-   modified the site configuration file by adding the sample point
    coordinates; and

-   loaded the configuration file into the diver and baseline stations.

For information on how to use the AREA program and load the Waypoints
into the diver station, see Appendix C. The X:Y coordinates are
displayed on the precision navigation screen, but some­times you want to
refer to them when you\'re at a different screen. To keep them in sight,
we put a piece of duct tape on the diver station above the display
window and write 10 to 15 coor­­di­nates on the tape with a permanent
marker. These should all be double-checked for accuracy before going
into the field.

### Locating Waypoints.

To navigate to a particular point, you moni­tor the general and precision
navi­gation screens. To move between the two screens, press
[enter]{.smallcaps}.

-   To go to the [general navigation]{.smallcaps} screen from the [diver
    status]{.smallcaps} screen, press F2. In this screen, you call up
    the destinations for navigation. The system will scroll through
    Home, B1, B2, B3, then the Waypoints. ((B1, B2, and B3 are the three
    baseline stations and if you are not using a surface station, Home
    and B1 are the same location.)

-   To get to the next Waypoint, press F2 again, or you can press #2
    ([inc)]{.smallcaps} on the diver sta­tion keypad to go "up" the queue
    (i.e., Home, B1, B2, B3, then Way­points 1, 2, 3, 4, etc.) Pressing
    #4 ([dec)]{.smallcaps} will take you "down" the queue, revers­ing the
    order of Waypoints.

-   To navigate to a selected Waypoint, use a hand-held or hose-mounted
    compass posi­tioned at least six inches away from the diver station.
    Use the "bearing to destination" on the upper right of the general
    navi­ga­tion screen as a guide. While moving on that bearing, the
    "range to desti­na­tion" (upper left of screen) should decrease. The
    "cross track error" number below the "range to destination" tells
    you how far you are from the line that connects two consecutive
    Waypoints. This is useful if you are proceeding up the queue from
    one consecutive Waypoint to another, but not if you are navigating
    to non-con­se­cu­tive Waypoints or selecting a Waypoint "down the
    queue" of saved points.

```{=html}
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```
-   To prevent needle deflection, hold the compass as far away as
    pos­si­ble from the diver station, which is metal and contains
    batteries.

```{=html}
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```
-   Use the X:Y coordinates stored on right side of the general
    navigation screen or written on the diver station to find out where
    you're supposed to be heading. As the range decreases to \<10m, slow
    your swimming speed. The bearing will fluctuate around the saved
    Waypoint, trying to home you in on the exact spot.

-   When the range reads \<3m, press [enter]{.smallcaps} to switch to
    the [precision naviga­tion]{.smallcaps} screen. This will display
    your X:Y position and the [rms]{.smallcaps} error
    ("[e]{.smallcaps}") so that you can fine-tune your position and
    determine the quality of the posi­tion fix. The larger the error
    number, the lower the data confidence. (See box on page
    [34](#understanding-rms-error.).)

-   Also monitor the "time since last fix" shown after the label
    "[l,]{.smallcaps}" which is located in the upper left of general
    navigation screen and the lower right of the precision navigation
    screen. This will tell you the time interval since the last
    successful communications between the transducers.

-   Use your mental image of the reef and the axis system to guide you
    in the proper direction, modifying the X:Y coordinates of your
    actual location so that they match as close as reasonably possible
    those of the location you are trying to track. This may take several
    minutes of adjustment and slight movements. Use good buoyancy
    control to avoid contact with the reef and having the transducer
    signals blocked by the reef or your dive partner.

### Understanding RMS error.

The diver station saves its recent position fixes in a queue file. The
root mean square ([rms)]{.smallcaps} error indicates the reliability of
your current X:Y position as shown on the diver station by calculating
the average distance between the positions in the queue. While you are
sta­tion­ary, the positions in the queue should be very similar and the
[rms]{.smallcaps} error therefore relatively low. As you start mov­ing
and the positions in the queue become farther apart, the
[rms]{.smallcaps} error becomes higher.

The number of fixes used to determine the [rms]{.smallcaps} error is
displayed on the lower right of the pre­cision navigation screen, next to
label [c]{.smallcaps} (between [d]{.smallcaps} = depth and
[l]{.smallcaps} = time since last fix). The default is 10. This means
that when you first reach a point you wish to record, the position queue
will contains a string of 10 position fixes tracking your previous path,
resulting in a high [rms]{.smallcaps} error. You can wait a few moments
for the [rms]{.smallcaps} error to decrease as additional fixes are
taken where you have stopped, or you can immediately lower the
[rms]{.smallcaps} error by pressing F3 ([clr]{.smallcaps}), which will
to reduce the queue to 2. Pressing F3 again will return the queue to 10
position fixes.

When you create or edit the configuration file, you can change the
default 10-position queue. We recommend using 5 positions, which gives
you relatively high accur­acy without having to wait for 10 clear
consistent positions. Pressing F3 will still reduce the queue to 2, a
number that cannot be modified.

For example, the display next to "C" may read 02/02. The top number is
the number of points being used to calculate the [rms]{.smallcaps} error
and the bottom number is the number of points in the queue position
string (as defined in the configuration file). C: 03/05 would mean that
the last 3 positions are being used but 5 are being sought to calcu­late
the [rms]{.smallcaps} error. As another position is fixed, the display
will change to C:04/05. C:05/05 would mean the last five positions are
being used to cal­cu­late the [rms]{.smallcaps} error.

### How do you know when you\'re there? 

When tracking to a Waypoint, you\'ll find that you\'re swim­ming to a
point that is defined only by X:Y coordinates and looking at a \"general
naviga­tion screen\" with a fluctuating \"range to destination\" and a
\"precision navigation screen\" with a fluc­tu­ating [rms]{.smallcaps}
error. How do you decide when you\'ve reached the designated Waypoint? A
rea­sonable answer is: you can consider yourself at the Waypoint when:

-   you\'re within 0.5m of the X:Y coordinates; and

-   your [rms]{.smallcaps} error is less than 0.5m.

At that point you can tie off the transect tape if you are laying one,
or make an observation recording, if you are collecting data on random
sample points as described in the next section.

### Making observation recordings.

Observation recordings differ from position recording in that:

-   Instead of recording a series of sequential positions, observation
    recordings are made at specific points. They can be used to record
    the transect origin and termi­nus, for example, and the location of
    specific features of interest.

-   Instead of recording only the location of a point, observation
    record­ings can be used to collect other information by specifying
    this in the configuration file.

-   The [rms]{.smallcaps} error is displayed and recorded during
    observation recordings, so you know the accu­racy and precision of
    the location where the observation was made.

-   To modify the configuration file to record observations, apply a
    check mark to that option in the \"Edit Diver Observation Records\"
    in the Config-5 screen of Advanced Edit/Create. As shown in the
    configuration settings list in Appendix A, we recom­mend these data
    be included in all obser­va­tion recordings: Automatic Depth, X, Y,
    RMS Error, and Tem­perature.

When the config­ur­a­tion file is loaded in the diver and baseline
stations, this informa­tion will be recorded each time you press F2 from
within the precision naviga­tion screen. Once the observation recordings
have been made and the sample taken, you are ready to navigate to the
next Waypoint. This continues till the sam­pling is complete, or your
bottom-time or air pres­sure indicates that you need to surface.

The procedure for downloading and converting observation recordings is
the same as for position recordings, as explained on page
[13](#recording-data-at-the-site) and in Appendix C. Data are typi­cally
imported to an MS Excel spreadsheet or saved for display as text. To
save observation data for import when the conversion is complete:

-   Go to [file  save position data for import.]{.smallcaps} (There is
    no option to save observa­tion data for import, so select this menu
    item.)

-   In the Save for Import dialog box, put a check in each of the seven
    boxes next to: [depth, x, y, rms error, temp, northing]{.smallcaps}
    and [easting]{.smallcaps}. Make a mental or written note that you
    are saving these categories from the observation recording for use
    when the data are displayed in the Excel spreadsheet. In the
    Delimiter box, put a semi­colon (;). Then click on [ok]{.smallcaps}.

-   In the Save Import box, select a name and loca­tion for this new
    \*.dbi file. (We use the default, C:/Program
    Files/Dive­Tracker/Record/.dbi.) Then click on [save]{.smallcaps}.

```{=html}
<!-- -->
```
-   **Recovering the baseline stations:** Remember to save both air and
    bot­tom time for retrieving the baseline sta­tions at the end of the
    last dive. They may be some distance from where you are tracking and
    take considerable bottom-time, air, and energy to retrieve, unless
    they can be retrieved by snorkeling.

## Relocating Waypoints

So, a year has gone by, and it\'s time to go out and sample the random
sites you selected last year. What do you we need to do to resample the
points?

### Retrieve information from the configuration files and other metadata sources.

-   Review any notes or charts from the previous sampling.

-   Verify the presence of all necessary files on the computer and/or
    field laptop.

-   If using the videotaping protocol, consider capturing swim-back
    photos that show the transect placement. The videotaping protocol
    explains how you can put these photos on a single laminated page for
    each transect.

### Prepare the equipment.

-   Locate the depths of the baseline stations from the configuration
    file, and find lines appro­priate to secure their positions.

-   Charge system batteries (yours and AquaMap\'s).

-   Write the depths of the baseline stations on a slate to accompany
    deployment of the baseline stations.

-   Load the configuration file into the diver and baseline stations.

-   Write the X:Y coordinates for the Waypoints on duct tape that has
    been put on the diver station.

-   Carefully review the dive plan, contingencies and steps for finding
    baseline stations posi­­tions at the site. With the passage of time,
    any submerged lines will be bio-fouled and pins that were once easy
    to locate will be camouflaged.

### Set up at the study site.

-   Position the baseline stations.

-   Use the General and Precision Navigations screens to re-locate the
    sample (e.g., transects).

-   If using the video method, use the laminated photos to aid in the
    exact placement of the transect.

-   Use the observation recording feature to save the coordinates for
    the sample position, i.e., the origin and terminus of the transect.

### Save the recorded data.

-   After a day of re-sampling, download and save the recorded data to a
    computer.

-   Erase the recording tape.

Repeat steps 3 and 4 until all samples have been revisited.

# Data Management and Summary Chart

## File and Data Management

Following these AquaMap protocols will result in the creation of many
files in a variety of formats (e.g., \*.rec, \*.dbi, \*.wpt, \*.par),
some of them vital to the data's ongoing value. Therefore it\'s
essential that you track and document the file names and storage
loca­tions so that others can use the files in the future. Among other
tasks, this means that you need to:

-   Compile all data files into a central computer location (directory
    or folder).

-   If you are using more than one computer, be sure to consolidate
    files. Using a laptop computer in the field is helpful, but make
    certain that you also save or transfer the files to a desk­top
    computer.

-   Keep a metadata file log (a "readme" text file) in a central
    location that lists the names and storage locations of all files
    created. Make written notes of the names of all files used such as
    config­uration, Waypoint, recordings, and con­verted files. Try­ing to
    remember which file con­tains which information can be difficult
    after you've moved on to another site.

## Creating a Data Summary Chart

You may want to display data in a MS Excel chart to display various data
positions and text information, including: name of the site; perimeter
trace (position recording data); baseline sta­tion locations and
coordinates, sample point positions and coordinates, baseline bearings
and station depths, and locations of any permanent sample positions or
transects.

The summary chart can also be used to:

-   Display the difference between the target sample coordinate points
    and the actual sample positions as documented in the observation
    recording. This can be summarized in a statement such as: "average
    difference X direction = *0.4*m, average difference Y direction =
    *0.38*m."

-   Compare sample position precision on subsequent years. For example,
    if random samples were established in 2001and re-sampled in 2002,
    one set of points can be used to dis­play the 2001 sample positions
    and another set to display the actual sample positions as documented
    in the observation recordings for 2002. From these coordinate
    values, you can also evaluate the average absolute difference
    between the two points.

To create a summary chart, you will need to run the recorded data
through the Convert program (see Appendix B), import the data into an
Excel workbook, and create text boxes within the chart.

### Import the converted data recording files into MS Excel. 

-   Open MS Excel and go to [file]{.smallcaps} [ open]{.smallcaps}. At
    the bottom of the dialog box and select [all files]{.smallcaps} as
    the file type.

-   Open the \*.dbi file of the recorded data you want to display.

-   The dialog box for the Text Import Wizard should open. Click on
    [ok]{.smallcaps} to proceed to the second wizard box.

-   Select semicolon (;) or other delimiter as necessary to separate the
    data into columns. You can see the results of your selections in the
    data preview.

-   Click on [finish.]{.smallcaps} (If you select [next]{.smallcaps}
    instead of finish, leave the default for column data format as
    [general]{.smallcaps}.)

-   The data will appear in spreadsheet columns, but it is imported
    without headers so you will need to label the columns. (You have to
    remember which components were included when the position data was
    converted to create the \*.dbi file.)

    -   Insert a row above the data set. (Click on the number 1 that
        identifies the first row of the spreadsheet to highlight it,
        then go to the Insert drop-down menu and select
        [row]{.smallcaps}.)

    -   Label the columns of data you have just imported as described
        below.

> **For position data:**

-   Position data are imported to two columns headed
    [northing]{.smallcaps} and [easting]{.smallcaps}.

-   Label the next two columns X and Y.

-   The Northing and Easting values must be converted into X:Y
    coordinates. The formulae are: **X = Easting** and **Y = -1 x
    (Northing)**. This means that:

    -   For the X coordinates, you can copy the data from the Easting
        column into the X column.

    -   For the Y coordinates, multiply the cells containing the
        Northing values by --1, i.e., in the first cell under the header
        Y, enter: "**= --1\***\" followed by the label of the cell
        containing the first Northing value.

> **For observation data:**

-   If you followed the suggested protocol for making observation
    recordings, these data will be imported to seven columns on a
    separate spreadsheet. They should be headed [depth, x, y, rms error,
    temp, northing]{.smallcaps} and [easting]{.smallcaps}.

-   Select the headers and all data from the observation recording
    spreadsheet.

-   Go to [edit]{.smallcaps} and choose [copy.]{.smallcaps}

-   Switch to the window containing the spreadsheet with the imported
    position data.

-   Paste the observation data in the next available columns to the
    right of the position data.)

The spreadsheet from which the observation data was copied can be closed
without saving it, as these data have been added to the initial position
data spreadsheet.

### Save the recording data spreadsheet.

-   Go to [file]{.smallcaps} [ save as]{.smallcaps}. At the top of the
    dialog box, browse to the appropriate [save in]{.smallcaps}
    location.

-   At the bottom of the dialog box, select [microsoft excel
    wookbook]{.smallcaps} as the file type.

-   Type in the appropriate file name. The ".xls" extension will
    automatically be added and should not be entered as part of the
    name.

-   Click on [save]{.smallcaps}.

### Generate the summary chart.

-   Select the two columns containing only the position X-Y data, not
    the header.

-   Press the Chart Wizard button to open the Chart Wizard.

-   For Step 1 of 4, Chart Type, select [x y (scatter)]{.smallcaps} as
    chart type. For the chart sub-type, select the top one, which has
    points without lines and is described as \"Compares values of
    pairs.\" Click on [next.]{.smallcaps}

-   Step 2, Chart Source Data: no changes are necessary. Click on
    [next.]{.smallcaps}

-   Step 3, Chart Options: you can enter a chart title at this point if
    you wish. Do not label the X or Y axis. Click on [next]{.smallcaps}.

-   Step 4, Chart Location: under [place chart]{.smallcaps}, select [as
    a new sheet]{.smallcaps} and either rename the chart at this time or
    use the default name. Click on [finish]{.smallcaps}. The chart
    containing the position data will be displayed in a separate
    spreadsheet within the workbook labeled [chart]{.smallcaps}.

### Add the transect origin and terminus point.

-   Position the mouse on the chart background (not on an axis gridline
    or sample point), press the right mouse button and select [source
    data]{.smallcaps}.

-   In the Source Data window, select the [series]{.smallcaps} tab and
    click on [add]{.smallcaps}.

-   For Name, enter "transect positions."

-   For the X and Y Values, you need to reference the location in the
    spreadsheet that contains the data you want to add. Start by
    clicking on the spreadsheet icon to the right of the X Values box.
    This will open the Excel spreadsheet and the Source Data -- X Values
    window.

-   Click on the appropriate tab in the spreadsheet, and then select the
    data containing the X coordinates for the transect positions. This
    will link the data to the Source Data -- X Values window. Close that
    window by pressing the [x]{.smallcaps} at the upper right corner.
    That will return you to the Source Data window.

-   Repeat the same procedure for the Y values, except select the Y
    coordinates for the transect positions.

This chart will help summarize the work done at a study site. It can be
modified to meet the needs of the target audience. It may be helpful to
laminate this plot for use underwater during subse­quent year samplings.

# [Appendix A]{.smallcaps}  {#appendix-a .unnumbered}

**Recommended Configuration File Settings**

+-----+----------------------+-----------------------------------------+
| *   | **Simple**           | **Advanced**                            |
| *Sc |                      |                                         |
| ree |                      |                                         |
| n** |                      |                                         |
+-----+----------------------+-----------------------------------------+
| []  | We use the defaults: | Use defaults for all settings. They     |
| {#c |                      | are:                                    |
| onf | -   Environment      |                                         |
| ig1 |     Type: Open       | -   Depth Compensation (cm): 76.200.    |
| .an |     Ocean.           |                                         |
| cho |                      | -   Max. Operating Depth (meters):      |
| r}* | -   Number of        |     76.200.                             |
| *[c |     Surface          |                                         |
| onf |     Transducers: 0.  | -   Max. Baseline Range (meters):       |
| ig] |                      |     350.000.                            |
| {.s |                      |                                         |
| mal |                      | -   Max. Mobile Slant Range (meters):   |
| lca |                      |     350.000.                            |
| ps} |                      |                                         |
| 1** |                      | -   Origin Northing (meters): 0.000.    |
|     |                      |                                         |
|     |                      | -   Easting (meters): 0.000.            |
+-----+----------------------+-----------------------------------------+
| []  | -   Number of        | -   Network type: Mobile Station, 3     |
| {#c |     Baseline         |     baseline, Mobile interrogated.      |
| onf |     Stations: The    |                                         |
| ig2 |     default is 2; we | -   Communication Speed: 8.9            |
| .an |     use 3.           |     nibbles/sec (35.7 baud).            |
| cho |                      |                                         |
| r}* | -   Number of Mobile | -   Address Mode: double ping, address  |
| *[c |     Stations: We use |     code interrogated.                  |
| onf |     the default, 1   |                                         |
| ig] |     (for the diver   |                                         |
| {.s |     station).        |                                         |
| mal |                      |                                         |
| lca |                      |                                         |
| ps} |                      |                                         |
| 2** |                      |                                         |
+-----+----------------------+-----------------------------------------+
| []  | Water Temperature:   | The baseline station depths and the     |
| {#c | The default is 10ºC; | baseline ranges and bearings are all    |
| onf | we use 28°-30°C in   | set initially at 0. You'll enter the    |
| ig3 | the Caribbean.       | actual settings after you conduct the   |
| .an |                      | baseline survey.                        |
| cho | This screen also     |                                         |
| r}* | provides access to   | Do not modify the following default     |
| *[c | the "Edit Waypoints" | settings for turn around time and       |
| onf | screen (see page     | channel frequency:                      |
| ig] | [42](#editways))     |                                         |
| {.s |                      | -   Turn Around Time (uSec): 100000.    |
| mal |                      |                                         |
| lca |                      | -   Channel 1 Freq (Hz): 33898.         |
| ps} |                      |                                         |
| 3** |                      | -   Channel 2 Freq (Hz): 36364.         |
|     |                      |                                         |
|     |                      | -   Channel 3 Freq (Hz): 38462.         |
|     |                      |                                         |
|     |                      | -   Channel 4 Freq (Hz): 40816.         |
|     |                      |                                         |
|     |                      | -   Water Salinity (ppt): 35. Adjust as |
|     |                      |     necessary for fresh or salt water.  |
|     |                      |                                         |
|     |                      | -   Default Water Temp: Because it is   |
|     |                      |     needed in order to accurately       |
|     |                      |     calculate the speed of sound in the |
|     |                      |     water and therefore distance, you   |
|     |                      |     should estimate or measure the      |
|     |                      |     water temperature for the site in   |
|     |                      |     which you are working as precisely  |
|     |                      |     as possible. The diver station      |
|     |                      |     measures the water temperature      |
|     |                      |     where it is located, but the value  |
|     |                      |     entered here will be used if the    |
|     |                      |     temperature-sensing device fails.   |
|     |                      |     The default is 10ºC; we use         |
|     |                      |     28°-30°C in the Caribbean.          |
|     |                      |                                         |
|     |                      | -   Pos. Avg. Sample Size: This is the  |
|     |                      |     number of values stored to          |
|     |                      |     calculate the RMS (root mean        |
|     |                      |     square) error displayed in the      |
|     |                      |     precision navigation screen. The    |
|     |                      |     default is 10 posi­tions. We prefer  |
|     |                      |     to use 5 positions, which provides  |
|     |                      |     a reasonable trade-off between      |
|     |                      |     preci­sion and the time it takes to  |
|     |                      |     get a reading.                      |
|     |                      |                                         |
|     |                      | -   Max RMS error (m): 0.914. Do not    |
|     |                      |     modify this default setting.        |
|     |                      |                                         |
|     |                      | -   Distance Between Auto Search Lines  |
|     |                      |     (cm): 0.000. Use this default       |
|     |                      |     initially. It can be modified if    |
|     |                      |     you want to do a programmed search  |
|     |                      |     pattern.                            |
+-----+----------------------+-----------------------------------------+

# Recommended Configuration File Settings {#recommended-configuration-file-settings .unnumbered}

*(continued)*

+--------+-------------------------------------------------------------+
| **Sc   | []{#confadv .anchor}**Advanced Create or Edit Configuration |
| reen** | File Settings**                                             |
+--------+-------------------------------------------------------------+
| []{#c  | We recommend that you leave all of the following settings   |
| onfig4 | at the default values.                                      |
| .ancho |                                                             |
| r}**[c | -   Gain: 2.                                                |
| onfig] |                                                             |
| {.smal | -   Detection Threshold Level: 12. Change if necessary as a |
| lcaps} |     result of your noise test or subsequent experience at   |
| 4**    |     the site.                                               |
|        |                                                             |
|        | -   Transmit Power: 127.                                    |
|        |                                                             |
|        | -   Pulse Length (uSec): 4000.                              |
|        |                                                             |
|        | -   AGC (Automatic Gain Control): If this box is checked,   |
|        |     the AGC is enabled, which means the AGC will do a gain  |
|        |     adjust every 3 to 5 minutes. If the diver station       |
|        |     transducer is affected by bubbles when the gain         |
|        |     adjustment is made, the AGC may be set too high,        |
|        |     eliminating signals. You may wish to disable the AGC    |
|        |     (remove the checkmark) to avoid this.                   |
|        |                                                             |
|        | -   AGC Activation Interval (Sec): 120.                     |
|        |                                                             |
|        | -   AGC Min 'No Positions' Interval (Sec): 15.              |
|        |                                                             |
|        | -   AGC/Noise Test Duration (Sec): 5.                       |
|        |                                                             |
|        | -   AGC Max Number of Noise Events: 1.                      |
|        |                                                             |
|        | -   Baseline no-activity shutdown period (seconds): 120.    |
|        |                                                             |
|        | -   Baseline Station sleep periods (seconds): 120.          |
|        |                                                             |
|        | -   Baseline Station post-sleep listening periods           |
|        |     (seconds): 15.                                          |
|        |                                                             |
|        | -   Mobile Station no-activity shutdown periods (seconds):  |
|        |     0.                                                      |
|        |                                                             |
|        | -   Mobile Station sleep periods (seconds): 0.              |
|        |                                                             |
|        | -   Mobile Station post-sleep listening periods (seconds):  |
|        |     0.                                                      |
+--------+-------------------------------------------------------------+
| []{#c  | -   Telemetry Type: 2-channel telemetry (default).          |
| onfig5 |                                                             |
| .ancho | -   Data availability: Surface Station only (default).      |
| r}**[c |                                                             |
| onfig] | Do not select any of these three boxes: Serial Transfer Raw |
| {.smal | Position Data, Serial Transfer X-Y Depth Position Data, or  |
| lcaps} | Serial Transfer Message Data.                               |
| 5**    |                                                             |
|        | -   Number of Mobile Stations: 1.                           |
|        |                                                             |
|        | The remaining six boxes represent buttons that allow you to |
|        | modify the contents they describe. Eventually you may want  |
|        | to modify the contents of the [edit waypoints]{.smallcaps}  |
|        | or [edit diver observation records]{.smallcaps} screens, as |
|        | shown next.                                                 |
+--------+-------------------------------------------------------------+

# Recommended Configuration File Settings {#recommended-configuration-file-settings-1 .unnumbered}

*(continued)*

+------------+---------------------------------------------------------+
| Optional   |                                                         |
| screens    |                                                         |
| for        |                                                         |
| additional |                                                         |
| con        |                                                         |
| figuration |                                                         |
| file       |                                                         |
| functions: |                                                         |
+------------+---------------------------------------------------------+
| []         | This screen is used to load Waypoint files or modify a  |
| {#editways | Waypoint.                                               |
| .anch      |                                                         |
| or}**[edit | -   The bottom of the display should read that all the  |
| wayp       |     coordinates are in meters.                          |
| oints]{.sm |                                                         |
| allcaps}** | -   The "Do Not Use Baseline Relative Coordinates" box  |
|            |     should not be checked.                              |
| [(]{.sma   |                                                         |
| llcaps}see | -   When closing this window, if you want to save your  |
| page       |     changes, select [ok]{.smallcaps}, then follow the   |
| [49]       |     directions to save the file under a different name. |
| (#load-the |     If you do *not* want to save the changes, select    |
| -sample-po |     [cancel]{.smallcaps}.                               |
| ints-into- |                                                         |
| the-diver- | -   To create the Waypoints for a search pattern,       |
| station.)) |     select [create search pattern]{.smallcaps}.         |
+------------+---------------------------------------------------------+
| **[create  | This screen enables you to define the parameters of the |
| search     | search pattern.                                         |
| pa         |                                                         |
| ttern]{.sm | -   Define Start Position X and Y.                      |
| allcaps}** |                                                         |
|            | -   Define the compass bearing *relative to the bearing |
|            |     of the baseline* of the first leg of the search     |
|            |     pattern. For example, if your direction of travel   |
|            |     will be parallel to the bearing of the baseline,    |
|            |     this value should be "0" degrees.                   |
|            |                                                         |
|            | -   Check or un-check the box for [first turn           |
|            |     right]{.smallcaps} as appropriate.                  |
|            |                                                         |
|            | -   Fill in the appropriate values for [leg length,     |
|            |     separation]{.smallcaps} & [search area              |
|            |     width.]{.smallcaps}                                 |
+------------+---------------------------------------------------------+
| **[edit    | This screen designates which data are recorded when the |
| diver]{.sm | observation but­ton is pressed from within the precision |
| allcaps}** | naviga­tion screen. If you want to relocate a point      |
| []{#       | later on, this is the most accurate way to save the     |
| confobserv | position, and it also records the RMS error value. We   |
| .a         | suggest checking the boxes for [automatic depth, x, y,  |
| nchor}**[o | rms error,]{.smallcaps} and [temp.]{.smallcaps} These   |
| bservation | data will be dis­played in columns when the tape is      |
| re         | downloaded.                                             |
| cords]{.sm |                                                         |
| allcaps}** |                                                         |
|            |                                                         |
| (see page  |                                                         |
| [35](#ma   |                                                         |
| king-obser |                                                         |
| vation-rec |                                                         |
| ordings.)) |                                                         |
+------------+---------------------------------------------------------+

# [Appendix B]{.smallcaps} {#appendix-b .unnumbered}

**Using the Convert Program**

Convert™ is a utility program developed by Desert Star Systems that can
be used to convert posi­tion and obser­­va­tion recordings to a useable
format. To use it, you need to have both the con­fig­ur­a­tion file that was
being used when the data was recorded and the downloaded recording (a
\*.rec file) on your computer hard drive.

### Load the file.

-   Go to [start]{.smallcaps} and choose: [programs  divetracker 
    convert.]{.smallcaps}

-   Go to the [file]{.smallcaps} drop-down menu and choose [load a new
    record]{.smallcaps}.

-   ![](media/image10.png){width="1.75in" height="3.16875in"}You will be
    prompted to select the \*.rec file that you wish to plot.

-   You will be prompted to select the configuration file (\*.par) that
    was being used when the record file was being created.

-   When prompted to confirm that the download was cre­ated from a mobile
    diver station (rather than a surface station), click on
    [yes]{.smallcaps}.

### Select the settings.

-   When the Settings dialog box appears, make sure that a "0" is
    entered in all five fields: Northing (meters), Easting (meters),
    Depths offset (meters), Baseline orientation (degrees), and Serial
    Number Offset. The default set­tings are all "0" except for Baseline
    orientation, which will show whatever value you entered for the
    compass bearing in the con­figuration file used during the record­ing.

-   At the bottom of the dialog box, you can check off one or neither of
    the two options ([show raw auto-position data]{.smallcaps} and [show
    x/y auto-position data)]{.smallcaps} depending on what are going to
    do with the data and how you want it displayed. Some common examples
    are:

+---------------------------+-----------+-----------------------------+
| **Use of data**           | **Re      | **Choose**                  |
|                           | cording** |                             |
+===========================+===========+=============================+
| -   Display perimeter     | Position  | [show x/y auto-position     |
|     trace in the Area     |           | data]{.smallcaps}           |
|     program               |           |                             |
+---------------------------+-----------+-----------------------------+
| -   Evaluate SONAR        | Position  | [show raw auto-position     |
|     effec­tive­ness by      |           | data]{.smallcaps}           |
|     looking at tracking   |           |                             |
|     data to see from      |           |                             |
|     which station missed  |           |                             |
|     signals were recorded |           |                             |
+---------------------------+-----------+-----------------------------+
| -   Plot transect origins | Ob        | [show x/y auto-position     |
|     and ter­mi­nuses on MS  | servation | data]{.smallcaps}           |
|     Excel graph           |           |                             |
+---------------------------+-----------+-----------------------------+
| -   Note transect origins | Ob        | [show x/y auto-position     |
|     and ter­mi­nuses in     | servation | data]{.smallcaps}           |
|     metadata file         |           |                             |
+---------------------------+-----------+-----------------------------+
| -   Enter station depths  | Position  | Neither option              |
|     as mea­sured by the    |           |                             |
|     pressure sensor into  |           |                             |
|     the configuration     |           |                             |
|     file                  |           |                             |
+---------------------------+-----------+-----------------------------+

-   After you have made any necessary adjustments to the settings, click
    on [ok]{.smallcaps} to convert the data.

When the recording has been converted, a split window will appear, with
the observa­tion data displayed in the top portion of the window, and the
position data in the lower portion. Which data are displayed from those
recordings depends on the settings you selected for the conversion
program.

### Save the converted data.

Both position and observation recordings (\*.rec file format) can be
saved in a text format, or in a format for import into other software
programs.

> Observation recordings = \*.rec file
>
> Converted observation recordings saved as text = \*.obs file
>
> Converted observation recordings saved for import = \*.dbi file
>
> Position recordings = \*.rec file
>
> Converted position recording saved as text = \*.dat file
>
> Converted position recording saved for import = \*.dbi file

Converted recordings saved as text files can be opened within any text
reading program such as Notepad or MS Word.

# A converted recording saved with a \*.dbi extension can be displayed in a chart by importing it into a software program like MS Excel or AREA, a utility program developed by Desert Star Systems. For more information about creating a chart in MS Excel, see page [37](#import-the-converted-data-recording-files-into-ms-excel.). For more information about using AREA, see [Appendix C]{.smallcaps} 

# [Appendix C]{.smallcaps} {#appendix-c .unnumbered}

**Using the AREA Program**

### View the perimeter data as a graph.

Displaying the position data you recorded during a perimeter swim as a
graph will help you visual­ize the SONAR communications throughout the
study site. To do this, you will need to view the converted recording as
a \*.dbi file.

-   On your PC, go to [start]{.smallcaps} and right click to get to
    [explorer]{.smallcaps}. Go to the C drive, and choose: [program
    files  divetracker  area.exe.]{.smallcaps} (You may find it easier
    to cre­­ate a shortcut on your desktop.)

-   When the [area]{.smallcaps} program opens, you will see a Graph
    window and a Waypoints win­dow. By moving the Waypoints window to the
    right, you\'ll be able to see the Com­mands window located beneath
    it. Go to [file]{.smallcaps} []{.smallcaps} [load file]{.smallcaps}
    and select the applicable \*.dbi file. (Default location =
    C:/Program Files/ Dive­Tracker/Records)

The plot of recorded points will be displayed on the graph. Some points
may appear as "out­liers;" these usually indicate noise received during
the recording.

To adjust the size of the graph:

-   Go to the [windows]{.smallcaps} drop-down menu and choose [display
    parameters.]{.smallcaps}

-   Enter the numbers you choose in the spaces provided for the X and Y
    Origin[.]{.smallcaps}

-   Enter the numbers for the desired length of each axis in the X and Y
    Extent.

The graph will change as you enter the numbers.

### Evaluate the plot for SONAR communication effectiveness.

Look for gaps between points. This may coincide with blocked SONAR
signals due to large coral heads, other benthic features, or other site
anomalies.

### Determine the size of your study area.

To calculate the area within the perimeter you have recorded (to
approximate your study area), use the mouse to trace a line that
connects the position recording points.

-   Open the \*.dbi file of the perimeter recording in the
    [area]{.smallcaps} program to display the main plot of your study
    site. Adjust the size of the graph so that it is large and easy to
    outline with your mouse. Don\'t worry about missing the display of
    outlying points; they are not relevant to the study site.

-   In the Commands window, choose [draw poly.]{.smallcaps}

-   Starting at any point on the perimeter, hold the right mouse button
    down while you trace the perimeter of your site as defined by the
    position recording points. Stop when you return to the place where
    you began.

```{=html}
<!-- -->
```
-   **Do not overlap the beginning and ending points.** If you make a
    mis­take in the tracing, release the mouse button. If incomplete, the
    peri­meter drawing will auto­matically enclose. Click on
    [unset]{.smallcaps} in the Commands win­dow to erase the tracing and
    you can start over.

```{=html}
<!-- -->
```
-   When you are satisfied with the perimeter tracing, choose [calculate
    area]{.smallcaps} in the Com­mands window. The size, expressed in
    square meters, will appear in a message dialog box. Copy this number
    for use in your metadata.

-   Clicking on [ok]{.smallcaps} will remove the message box. Close the
    Commands window by clicking on the [x]{.smallcaps} at the upper
    right corner.

### Generate sample points.

After you have completed the definitive baseline and perimeter survey,
you can use the data to create the sample population, randomize that
population, and select randomized sets from within that population.
During this process, you will create the following files containing
Waypoints:

-   **Total sample population.** These sample points are numbered
    sequentially in a serpen­tine pattern.

-   **Randomized sample population.** This file contains the same points
    as the total popu­lation, but they have been renumbered randomly.

-   **Subset of randomized sample population.** You select the minimum
    number of sample points that you will need to analyze a particular
    study site.

-   **Additional subset** from the randomized sample population. You
    select an addi­tional number of points that may be needed if any of
    those in the initial subset are found to be in a unac­ceptable or
    undesired sample habitat. These "spare" points are also loaded into
    the diver sta­tion to be used if necessary.

To simplify loading Waypoints into the sta­tions, you can include these
spare points in the same file as the initial subset. How­ever, the AREA
program includes a feature that will re-se­quence a set of points into a
more efficient path in order to minimize the dis­tance you must swim. To
preserve the sta­tistical validity of the random sam­p­­ling pro­cess, you
cannot take advantage of this feature unless you keep the spare points
in a separate file. If you create a single set of Waypoints that
includes the potential spares, you must track to the points in their
random sequence until you have found the needed num­ber in accept­able
habitat.

The total sample population file is needed only to create the randomized
popu­la­tion and does not have to be saved, but the other three files
listed above must be saved for future use.

> **a. Create the total sample population.**

-   On your PC, go to [program files  divetracker 
    area.exe.]{.smallcaps} This will open the Waypoints window and the
    Commands window directly beneath it.

-   Open the \*.dbi file of the perimeter recording in the
    [area]{.smallcaps} program and trace the site perimeter as described
    in the preceding section.

-   In the Waypoints window, use the grid divisions to enter the X
    spacing and Y spac­ing (i.e., the number of meters) between the
    sample points. For our videotap­ing protocol, we are using 10-meter
    separation on both the X and Y axes.

-   Choose [make]{.smallcaps} to see the total population of possible
    points within the perimeter of your outlined study area, given the
    spacing interval you have defined. The points are numbered
    sequentially in a serpentine pattern, beginning in the lower left.

This file does not have to be saved; it will be modified in the next
step to create a ran­dom­ized sample population.

> **b. Create a randomized sample population.**

-   Choose [select and randomize all]{.smallcaps}. The numbers will turn
    red, and their order will be scrambled.

-   For reasons of statistical validity, you will only do this scramble
    once; that is why this file must be saved. Click on
    [save]{.smallcaps} at the bottom of the Waypoints window.

-   Select the name and location for this \*.wpt file. (We use the
    default location, C:/Pro­gram Files/DiveTracker/Config...) Click on
    [save]{.smallcaps} again.

-   When prompted to con­­firm whether the points are in meters, click on
    [yes]{.smallcaps}.

-   The [area]{.smallcaps} program will confirm that the points are in
    meters and how many points were saved in the file. Click on
    [ok.]{.smallcaps} Do not close the [area]{.smallcaps} program.

> []{#_Ref495558640 .anchor}**c. Select a subset of random sample
> points.**

From the randomized sample population, you will select a subset of
Waypoints based on the number of samples necessary for the site
analysis. For example, this protocol calls for the use of twenty
10-meter transects within the study site, so it will require creating a
file con­tain­ing the coordinates for 20 Waypoints, each of which will
indicate the starting point for a 10-meter transect.

-   Choose [select range]{.smallcaps} to bring up the Input Text
    **Start** Index window.

-   Enter the number of the first Waypoint (i.e., "1") in the
    permutation that you want to find, then click on [ok.]{.smallcaps}

-   The Input Text **End** Index window will open. Enter the number of
    the last Waypoint you want to include in this sub-sample (i.e., 20),
    then click on [ok.]{.smallcaps}

-   The subset of the random population will be displayed in red; the
    other sample points are in black. To conceal the black Waypoints and
    view only those in the subset, choose [only show selected
    waypoints]{.smallcaps}.

-   Click on [save]{.smallcaps} at the bottom of the Waypoints window.

-   In the Save Waypoints window, you will be prompted for a name and
    location for this \*.wpt file. (We use the default location,
    C:/Program Files/Dive­Tracker/ Config...). Click on
    [save]{.smallcaps} again.

> **d. Create a path to connect the points.**

The sequence in which the Waypoints appear may not provide the most
efficient path for tra­veling from one point to the next. If you are
certain that you will need to use *all* of the sam­ple points in this
subset, the Waypoints window offers two ways to create a more effi­cient
path. These alternate paths include the same Waypoints; only the numbers
indicating their sequence change.

-   If you choose [make path serp,]{.smallcaps} the Waypoints will be
    rear­ranged in a ser­pen­tine pat­tern beginning in the lower left,
    progressing to the right[.]{.smallcaps}

-   If you choose [make path greedy,]{.smallcaps} the Waypoints will be
    rearranged using the "greedy" algorithm.

In both cases, a message will indicate the distance you would travel if
using that particular path. Click on [ok]{.smallcaps} to close the
message box.

-   Remember: To adhere to statistical principles of random samp­ling,
    you can only re-sequence points that you will defin­itely use for
    sample analysis. This means that if your subset of ran­domized subset
    contains 20 Waypoints and you re-sequence them to create a more
    effi­­cient path, you must use *at least* 20 sampling points in your
    data analysis. That's because if you re-sequence 20 points and then
    use only the first 10 in the analysis, those 10 points are no longer
    considered randomly selected; their selection is biased toward the
    points at the beginning of the most efficient path.

To use one of the two alternate paths:

-   Click on [make path serp]{.smallcaps} or [make path
    greedy]{.smallcaps} to display each option. Click [ok]{.smallcaps}
    when the distance is displayed.

-   Click on [save]{.smallcaps} at the bottom of the Waypoints window
    when the path you want is displayed in it.

-   In the Save Waypoints window, you will be prompted for a name and
    location for this \*.wpt file. (We use the default location,
    C:/Program Files/Dive­Tracker/ Config...) Click on [save]{.smallcaps}
    again. Do not close the [area]{.smallcaps} program.

> **e. Create a subset of additional sample points.**

Study sites inevitably contain some locations that are unsuitable for
sampling. For example, in a spur and groove reef zone, a transect may
fall in a sand groove. If more than 5 meters of a transect are in sand,
the sample point should be discarded. If you must discard any Waypoints
from your initial subset because they are in unacceptable locations, you
will need additional points in order to sample the desired number of
Waypoints.

For example, we select 1-20 as our initial subset of random sample
points, then select an additional ten points to be used in case any of
the original 20 points are found in unac­cept­able habitats. If all 20 of
the original subset are found to be acceptable, none of the addi­tional
points are used. If the videotape for a transect filmed from the initial
subset of Waypoints turns out blurry, you cannot replace it with a
transect filmed from the additional sub­set, as this would violate
statistical principles of random sampling.

-   To create this file of additional Waypoints, deselect (un-check) the
    box next to [only show selected waypoints]{.smallcaps}.

-   Then repeat the steps under "Select a subset of random sample
    points" (see page [47](#_Ref495558640)). However, the [start
    index]{.smallcaps} and [end index]{.smallcaps} numbers will change.
    For example, if the initial subset of Waypoints had a start index of
    1 and an end index of 20, then a subset for 10 alternate Waypoints
    will have a [start index]{.smallcaps} of 21 and an [end
    index]{.smallcaps} of 30.

-   To display these additional points, choose [only show selected
    way­points]{.smallcaps}.

-   Click on [save]{.smallcaps} at the bottom of the Waypoints window.

As explained in step 4 above, you cannot use the [make path
serp]{.smallcaps} or [make path greedy]{.smallcaps} option to create a
more efficient path for a set of points unless you're certain that
you'll use all of the points in the set. Since you don't know how many
spares you'll need, these additional sample points must remain in the
sequence in which they were chosen.

-   In the Save Waypoints window, you will be prompted for a name and
    location for this \*.wpt file. (We recommend using the default
    location, C:/Program Files/Dive­Tracker/Config...) Click on
    [save]{.smallcaps} again.

-   Close the [area]{.smallcaps} program.

### Load the sample points into the diver station.

You will need to load the files containing the initial subset of random
sample points and the additional Waypoints into the configuration file
so that they can be trans­ferred to the Aqua­Map stations. The transfer is
a two-step process: the \*.wpt file is loaded into the configura­tion
file and then the edited configuration file is loaded into the diver
station. (See Appendix A for infor­ma­tion about editing and downloading
the configuration file.) Although the initial subset can be
automatically transferred to the configuration file, which prevents
transcription errors, the addi­tional subset must be manually entered.

-   Open DiveTerm and go to [file ]{.smallcaps} [edit a
    configuration]{.smallcaps} [file  advanced edit]{.smallcaps}.

-   In the Select Configuration File window, open the appropriate \*.
    par file.

-   Click on [next]{.smallcaps} until you get to [config-5]{.smallcaps}
    of the configuration file.

-   Choose [edit waypoints]{.smallcaps} near the bottom on the left of
    the screen. A Waypoints win­dow will be displayed into which you can
    either manually or automatically enter the coor­dinates.

> **Automatic transfer:**

-   To enter the coordinates for the first subset of random sam­ple
    points automatically, choose [load file]{.smallcaps}.

-   In the Save Waypoints window, select the \*.wpt file that you
    created earlier.

-   Click on [open]{.smallcaps}. This will automatically load the
    coordinates into the config­ur­a­­tion file.

```{=html}
<!-- -->
```
-   Given the recommended arrangement of the baseline stations (see page
    [7](#where-to-locate-the-baseline-stations.)), the coordinates
    should be in a *positive X, negative Y* for­mat. This may not be the
    case if the sample area encompasses both sides of the Y axis, but it
    is a good thing to check.

> **Manual entry:**

-   To manually enter the additional set of Waypoint coordinates,
    you\'ll need to see them in the \*.wpt file. Go to
    [start]{.smallcaps} and choose: [programs  accessories
    notepad]{.smallcaps}.

-   Go to the [file]{.smallcaps} drop-down menu and open the \*.wpt file
    containing the 10 Way­points you saved.

-   Before entering the coordinates manually to the diver station, you
    must convert them to meters. Multiply by 0.3048. Write down the
    converted values and close the \*.wpt file.

-   Enter the coordinates in the Waypoints window in sequen­tial order,
    e.g., starting with 21. Click in the appro­priate cell or use the tab
    key to move through the cells.

```{=html}
<!-- -->
```
-   Check the values and units for Waypoints carefully!

> **Saving and loading the edited configuration file:**

-   Click on [ok]{.smallcaps} in the Waypoints window and in the
    [config-5]{.smallcaps} screen.

-   You will be prompted to save the configuration file, since it has
    now been modified with the newly saved Waypoint coordinates. Select
    a name and location. (We use the default location, C:/Program
    Files/DiveTracker/ Config...) Click on [save]{.smallcaps}.

-   Download the edited configuration file into the diver station and
    baseline stations (see page
    [11](#download-the-configuration-file-to-the-diver-and-baseline-stations.))
    so you can track to the Waypoints on each path.

```{=html}
<!-- -->
```
-   AquaMap uses both Waypoints and Saved Points. Waypoints, which are
    the points entered into the configuration file, begin with "W".
    Saved Points, which are saved through the diver station (typi­cally
    in the field), begin with "S".

### Check the Waypoint coordinates.

It is a good idea to confirm that the Waypoints have been correctly
entered into the diver sta­tion before going out in the field. To do
this:

-   Turn on the diver station.

-   Select the [mode]{.smallcaps} key.

-   Select "0"/ ↓ four times to select [waypoint]{.smallcaps}.

-   Press [enter]{.smallcaps}. This will display the View Waypoint
    screen. Use the function keys to move through each of the Waypoints
    so you can verify their X , Y coordinates.

```{=html}
<!-- -->
```
-   If you hit the F3 (DEL) key, you will delete a Waypoint from the
    list. To reinstall it, you would have to edit the configuration
    file.

> When you are done checking all the Waypoints, select F4/OK to return
> to the diver status screen.

# [Appendix D]{.smallcaps} {#appendix-d .unnumbered}

[]{#_Ref9236033 .anchor}**Glossary of Terms**

**AquaMap System:** A SONAR-based survey and mapping system used for
the mapping, and sample point location/re-location components. The
system consists of three principle components, Diver Station, Baseline
Station, PC software.

**Baseline configuration** (physical setup): Use of AquaMap requires
that the baseline stations be placed in a rectangular coordinate system.
A line starting a Baseline Station 1 and extend­ing through Baseline
Station 2 defines the X-axis. Baseline Station 3 *must* be located
within 180º clockwise of the X-axis. Ideally, it will be placed at \~
90°.

(Data): Baseline configuration may also refer to the data entered into
the diver station to define the orientation from Baseline Station 1 to
Baseline Station 2. The alignment will be used by the diver station to
compute and display the bearing to a selected destination. The accuracy
of the measurement does not affect the accuracy of surveying. It is
there­fore usually adequate to use a regular dive compass to determine
the orientation of the baseline.

**Baseline station:** A cylinder housing batteries, electrical
circuitry, and SONAR transducer that is deployed near the corners of a
rectangular survey site to serve as the reference points for the
baseline survey.

**Baseline survey:** When this command is selected in the diver station,
SONAR signals are sent from and received by all stations to "locate"
their positions, from which all positions during the subsequent tracking
will be referenced.

**Configure:** To download the configuration file from your PC to the
baseline and diver stations, e.g., "The next step is configuring the
baseline stations."

**Configuration file:** A computer file created by the user to defines
the operational parameters and working environment during AquaMap use.
This is a two-step process of creating/ editing a configuration file,
and downloading that file. All stations must be configured using the
same configuration file.

**Connector adapter:** AquaMap device with black round wires with brass
pins at one end for insert­ing into the baseline or diver station and a
plug for connecting to the data exchange cable on the other end.

**Convert™:** This utility program is used to transform data recorded in
the diver station into a usable format, such as perimeter tracking
outlines.

**Cross-track error:** This display indicates your distance from a
direct course between the previ­ous sample point and the next selected
point, e.g., \<-100 means that the course line is 100 meters/feet to
your left; \>-100 means it is to your right. When the display reads
--000-, you are on the most direct line between the two points. This
value is only accurate when you are tracking between sequential points
in ascending order, e.g., when you are going from point 10 to 11 or from
point 23 to 24. It is not accurate in other sequences, e.g., from point
7 to 9 or point 11 to 10.

**DT-test™:** A program loaded in the diver station that contains the
operational commands for the noise and range test.

**Data exchange cables:** The flat wires with a fitting that connect the
PC serial port either the com­­mun­ication cable of the baseline station or
diver station.

**Delimiter:** A character such as a semicolon that separates two data
fields.

**DiveTerm:** This small program is used to perform several utility
functions such as downloading configuration files to stations and
downloading tape memory.

**DiveTracker:** This folder contains the programs Convert and Dive
Tracker.

**Diver station:** This hand-held device computes and displays the SONAR
tracking data. The key­pad is activated by a magnetic pointer to operate
the station.

**Diver status screen:** This screen is displayed on the diver station
to provide dive-related data when using the SmartDive operating system.

**File types:**

> **\*.dat** AquaMap text file created by converting position recorded
> data.
>
> **\*.dbi** AquaMap files that are created after recording data has
> been run through "Con­vert." A \*.dbi file is loaded into the area
> program for mapping and plotting purposes.
>
> **\*.obs** AquaMap text file created by converting observation
> recorded data.
>
> **\*.par** AquaMap configuration files that are loaded into the
> baseline and diver stations.
>
> **\*.rec** AquaMap files that are created after downloading the
> recorded fixes during perimeter tracking.
>
> **\*.wpt** AquaMap waypoint files that are loaded into the Edit
> Waypoint option of the Edit/Create Configuration file.
>
> **\*.xls** Spreadsheet format for Microsoft Excel.

**Frequency:** When using AquaMap, the frequency is expressed in Hertz
and should generally be set to the frequency of interest minus 5000 Hz.
For example, when doing a noise test, it should be set to the default
29000 Hz (34000-5000=29000).

**Gain:** This is used in AquaMap to control the amplification of SONAR
signals. The four gain settings (0,1,2,3) each represent a doubling in
sensitivity, similar to the volume control on a stereo.

**Gender adapter:** This device is fitted between the serial port of the
PC and a cable connector; also known as "male/female connectors".

**General navigation screen:** Template screen displayed on the diver
station and used for navig­at­ing to a destination. It displays the
distance, bearing and cross-track error to the next waypoint or
destination.

**Metadata:** As used in this protocol, metadata refers to details about
the data collection dive and may include depth, time, divers, dive
conditions, etc.

**Mobile station:** Another name for the diver station.

**Noise test:** This function of the AquaMap system that listens for and
then plots (graphically and numerically) the ambient noise on a defined
frequency.

**Precision navigation screen:** Template screen displayed on the diver
station and used to fine-tune the diver's position and measure the
quality of the position fix. It displays the X:Y posi­tion, typical
position error, baseline signal indicator, position queue status and
time since last fix.

**Queue:** This is the file of position coordinates that are used to
resolve the quality of a position fix (RMS error). It can be set to
contain the last two or the last ten coordinates.

**RMS error** (root mean squared): This typical position error reflects
the average distance between each position in the queue and the average
position of all position fixes. A large error indi­cates that positions
are widely scattered, and thus there is little data confidence. A small
error shows that the positions in the queue are closely tracking each
other, thus the data confidence is high.

**Range test:** This is a test of the AquaMap system's ability to hear a
discrete SONAR signal over measured distances.

**Readme file:** This computer file is created in a word processing
application in order to enter meta­data.

**Record:** This command is used in the Precision Navigation Screen to
save the position fixes to the diver station memory. To clear the
memory, the position fixes must be downloaded to a PC and/or deleted.

**SmartDive**: A program that operates within the diver station used for
tracking.

**Standby:** When this command issued in the precision navigation
screen, none of the position fixes are being saved in the diver station
memory.

**SONAR transducer cable:** A \~6 foot cable with a SONAR transducer on
one end and a connec­tor to the diver station on the other. It is
attached to the diver station, and calculates the position of the diver
(with the diver station) relative to the baseline stations. A float is
attached to the hook at the transducer end to keep the transducer
floating above the diver.

**Threshold**: This feature is set in the Advanced Configuration File of
the AquaMap system after conducting the noise and range tests.

**Transducer:** This is the end of the baseline station or SONAR cable
from which the pulse is released and received.

**Waypoint coordinates:** These are pairs of numbers that correspond to
the X:Y points used by the AquaMap system to locate a position in
reference to the baseline stations. They are entered into the diver
station as a file, or manually entered into the configuration file.