Oceanic SAMM User manual

SAMM
Stand Alone Mosaicking Module
User Manual
Oceanic Imaging Consultants, Inc.
1144 10th Avenue • Suite 200
Honolulu, Hawai‘i 96816-2442
Phone [phone] • Fax [phone]
Email [email protected]m • Web www.oicinc.com

Copyright © 2017 Oceanic Imaging Consultants, Inc. - Printed in the United States of America (USA). All
rights reserved.
This manual and all other related documentation are protected by copyright and distributed under
licenses restricting its use, duplication, distribution, and recompilation. No part of this Manual or related
documentation covered by copyright herein may be reproduced in any form or by means -- graphic,
electronic, or mechanical -- including photocopying, recording, taping, or storage in an information
retrieval system, without the prior written authorization of Oceanic Imaging Consultants, Inc.
The products described in this manual may be protected by one or more U.S. or foreign patents, and
pending applications.
Oceanic Imaging Consultants, Inc. retains the right to make changes to the contents of this Manual at any
time, without notice. Oceanic Imaging Consultants, Inc. makes no warranty for the use of its products
and assumes no responsibility for any errors that may appear in this document, nor does it make a
commitment to update the information contained herein.
 Oceanic Imaging Consultants, Inc.
1144 10th Avenue • Suite 200
Honolulu, Hawai‘i 96816-2442
www.oicinc.com
Telephone: [phone]
Fax: [phone]
Email: sup[email protected]om
TRADEMARKS
SAMM is a trademark of Oceanic Imaging Consultants, Inc., in the U.S.A. and other countries.
Third party trademarks are the property of their respective owners and should be treated as such.
WARNING AND DISCLAIMER
Every effort has been made to make this manual as complete and as accurate as possible, but no
warranty or fitness is implied. The information provided is on an “as is” basis. The authors and the
publisher shall have neither liability nor responsibility to any person or entity with respect to any loss or
damages arising from the information contained in this book or from the use of the CD or programs
accompanying it.
Rev. 2/17/2017

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Table of Contents
1 WELCOME TO SAMM ...................................................................................................... 6
2 SYSTEM REQUIREMENTS AND SETUP......................................................................... 8
2.1 Sensor and Input Requirements ................................................................................................ 8
2.2 System Requirements ............................................................................................................... 9
2.3 Installing SAMM ....................................................................................................................... 10
2.4 Launch SAMM ......................................................................................................................... 11
2.5 Create or Open a Project ......................................................................................................... 12
3 THE GRAPHICAL USER INTERFACE ............................................................................14
3.1 Mosaic Window ....................................................................................................................... 14
3.2 Toolbar ..................................................................................................................................... 15
3.3 Sidebar .................................................................................................................................... 16
3.3.1 Swath List ...................................................................................................... 17
3.3.2 Live Info ......................................................................................................... 17
3.3.3 Playback Controls .......................................................................................... 17
3.3.4 Sonar Controls ............................................................................................... 18
3.3.5 Processing Controls ...................................................................................... 18
3.4 Forward Look Window ............................................................................................................. 19
3.5 SLS Oscilloscope Window ....................................................................................................... 19
3.6 Meta Data Properties ............................................................................................................... 20
3.7 Status Bar ................................................................................................................................ 20
4 CONFIGURE SAMM ........................................................................................................22
4.1 Project Tab .............................................................................................................................. 23
4.1.1 Projected Coordinate System ........................................................................ 23
4.1.2 Sensor Offsets ............................................................................................... 23
4.2 Display Tab .............................................................................................................................. 24
4.2.1 General .......................................................................................................... 24
4.2.2 Swath Colormap ............................................................................................ 25
4.2.3 Units of measure ........................................................................................... 25
4.3 Mosaic Tab .............................................................................................................................. 26
4.3.1 General .......................................................................................................... 26
4.3.2 MSK output (connected/live sonars) ............................................................. 27
4.4 Contacts tab............................................................................................................................. 27
4.5 About ....................................................................................................................................... 28
4.6 Rendering Method ................................................................................................................... 28
4.7 Reset Button ............................................................................................................................ 29
4.8 Configuration Tutorial .............................................................................................................. 29
5 CHARTS AND BACKGROUND IMAGES ........................................................................31
5.1 Basic vs. Advanced Interface .................................................................................................. 31
5.2 Raster vs. Vector File Types ................................................................................................... 31
5.3 Retrieve NOAA Electronic Navigational Charts ....................................................................... 31
5.4 Elements of the Basic Chart Display Options Window ............................................................ 32
5.4.1 Basic Chart Display Popup Windows ............................................................ 33
5.4.2 Using the Basic Chart Loader ....................................................................... 34
5.5 Elements of the Advanced Chart Display Options Window .................................................... 35
5.5.1 Buttons .......................................................................................................... 36
5.5.2 The Folders Tab ............................................................................................ 37
Populating the Charts Database ................................................................... 37
5.5.3 The Chart Preview Tab.................................................................................. 38
5.5.4 The Charts Tab .............................................................................................. 39
5.5.4.1 Color Coding .................................................................................................. 39
Green ............................................................................................................. 40

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Orange ........................................................................................................... 40
Yellow ............................................................................................................ 40
Gray ............................................................................................................... 40
Manually Loaded vs. Folder Added Chart Behavior ...................................... 40
5.5.5 The Log Tab .................................................................................................. 41
5.6 Advanced Chart Loader Tutorial ............................................................................................. 41
5.7 Chart Customization Commands............................................................................................. 41
6 ADD FILES OR BEGIN ACQUISITION ............................................................................43
6.1 Add Files in Playback or Post-Processing Mode ..................................................................... 43
6.1.1 Load Files ...................................................................................................... 43
6.1.2 Advanced Load Files ..................................................................................... 44
6.1.3 Playback Files ............................................................................................... 45
6.1.4 Advanced Playback Files .............................................................................. 45
6.2 Load Files from Directory ........................................................................................................ 47
6.3 Interface with Metadata Sensors ............................................................................................. 49
6.4 Connect To…........................................................................................................................... 50
6.4.1 Kongsberg Mesotech M3 .............................................................................. 50
6.4.2 Kongsberg Mesotech MS1000 ...................................................................... 51
6.4.3 Teledyne BlueView 2D Multibeam Imaging Sonar ........................................ 52
6.4.4 Tritech Gemini 720i/is, Marine Electronics Dolphin, Blueprint Oculus, or
R2Sonic ...................................................................................................................... 54
Troubleshooting ............................................................................................. 54
Gemini Sonar Controls .................................................................................. 55
R2Sonic Sonar Controls ................................................................................ 56
Marine Electronics Dolphin Sea View ........................................................... 57
6.4.5 Edgetech Discover, Klein SonarPro and GeoDAS ........................................ 59
Edgetech Discover ........................................................................................ 59
Klein SonarPro .............................................................................................. 60
GeoDAS ........................................................................................................ 61
7 DISPLAY AND PROCESSING SETTINGS ......................................................................63
7.1 Adjust the Mosaic Window Display.......................................................................................... 63
7.2 Manage Swaths ....................................................................................................................... 64
7.2.1 Swath Management and Playback Tutorial ................................................... 64
7.3 Toggle Display Units ................................................................................................................ 65
7.3.1 Display Units Tutorial ..................................................................................... 65
7.4 Apply Imagery Processing Options ......................................................................................... 66
7.4.1 Processing Controls ...................................................................................... 66
7.4.2 Swath Properties ........................................................................................... 67
7.4.3 Playback of *.son files ................................................................................... 67
7.5 Other Display Options ............................................................................................................. 68
7.6 Imagery Processing Tutorials .................................................................................................. 69
Trimming Tutorial ........................................................................................... 69
Rendering Tutorial ......................................................................................... 69
8 WORKING WITH CONTACTS .........................................................................................72
8.1 Mark Contacts.......................................................................................................................... 72
8.2 Elements of the Contacts Window........................................................................................... 73
8.2.1 Thumbnails List ............................................................................................. 74
8.2.2 Contacts Toolbar ........................................................................................... 74
8.2.3 Contact Display ............................................................................................. 75
8.2.4 Properties Table ............................................................................................ 75
8.2.5 Staging Table ................................................................................................ 75
8.2.6 Contact Display Commands .......................................................................... 76
8.3 Attribute Contacts .................................................................................................................... 77
8.3.1 Classify Contacts ........................................................................................... 78

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Add Comments .............................................................................................. 78
Add Tags ....................................................................................................... 78
8.3.2 Measure Contacts ......................................................................................... 79
8.3.3 Calculate Contact Height ............................................................................... 79
8.3.4 Change Position ............................................................................................ 79
8.3.5 Rename Contacts .......................................................................................... 79
8.3.6 Contact Attribution Commands ..................................................................... 80
8.4 Group Contacts ....................................................................................................................... 81
8.5 Export Contacts ....................................................................................................................... 82
8.5.1 Send contacts to the staging table ................................................................ 82
8.5.2 Prep the Staging Table .................................................................................. 83
8.5.3 Export a Report ............................................................................................. 83
8.5.4 Delete Contacts ............................................................................................. 84
8.5.5 Contact Organization Commands ................................................................. 84
8.6 Contacts Tutorial ..................................................................................................................... 85
9 ADDITIONAL FEATURES ...............................................................................................88
9.1 Meta data properties ................................................................................................................ 88
9.2 Select tool ................................................................................................................................ 88
9.3 Measure tool ............................................................................................................................ 88
9.4 Export Tool .............................................................................................................................. 89
9.4.1 File Type ........................................................................................................ 90
9.4.2 Extents ........................................................................................................... 91
9.4.3 Resolution ...................................................................................................... 91
9.4.4 Background color ........................................................................................... 91
9.4.5 Export Tutorial ............................................................................................... 91
10 END ACQUISITION AND CLOSE PROJECT ..................................................................92
Figures
Figure 1. SAMM installation process and dialogs ....................................................................................... 10
Figure 2. SAMM opening dialog, allowing creation of new project, opening existing or mission import. ... 12
Figure 3. Graphical User Interface .............................................................................................................. 14
Figure 4. Swath List .................................................................................................................................... 17
Figure 5. Live Info ....................................................................................................................................... 17
Figure 6. Playback Controls ........................................................................................................................ 17
Figure 7. Sonar Controls ............................................................................................................................. 18
Figure 8. FLS Controls ................................................................................................................................ 18
Figure 9. SLS Controls ................................................................................................................................ 18
Figure 10. Forward Look Window ............................................................................................................... 19
Figure 11. SLS Oscilloscope Window ......................................................................................................... 19
Figure 12. Meta Data Properties ................................................................................................................. 20
Figure 13. Configuration Dialog .................................................................................................................. 22
Figure 14. Projection Tab ............................................................................................................................ 22
Figure 15. Survey Setup Panel ................................................................................................................... 24
Figure 16. General Panel ............................................................................................................................ 25
Figure 17. Swath Colormap Panel .............................................................................................................. 25
Figure 18. Units of Measure Panel ............................................................................................................ 25
Figure 19. General Panel ............................................................................................................................ 26
Figure 20. MSK output Panel ...................................................................................................................... 27
Figure 21. Contacts Tab ............................................................................................................................. 27
Figure 22. About Panel ............................................................................................................................... 28
Figure 23. Update Panel ............................................................................................................................. 28
Figure 24. Crash Detection Prompt ............................................................................................................ 28

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Figure 25. Configuration Window for Demo Data ....................................................................................... 30
Figure 26. Empty Basic Chart Display Options Window ............................................................................. 32
Figure 27. Select Overlay Type Error Message .......................................................................................... 33
Figure 28. ASCII Text Import Options ......................................................................................................... 34
Figure 29. Charts Loaded in Basic Window, with Context Menu................................................................ 34
Figure 30. Chart Display Options Window upon Launch ............................................................................ 36
Figure 31. Add/Scan Charts Panel ............................................................................................................. 37
Figure 32. Populated Chart Database ........................................................................................................ 38
Figure 33. Charts Tab ................................................................................................................................. 39
Figure 34. Add Data Dropdown Menu ........................................................................................................ 43
Figure 35. Advanced Load Dialog .............................................................................................................. 44
Figure 36. Advanced Playback Dialog ........................................................................................................ 46
Figure 37. GUI in Playback Mode ............................................................................................................... 47
Figure 38. Load from directory dialog ......................................................................................................... 48
Figure 39. Navigation Interfacing ................................................................................................................ 49
Figure 40. M3 Interfacing ............................................................................................................................ 50
Figure 41. MS1000 Interfacing.................................................................................................................... 51
Figure 42. ProViewer NMEA Panel ............................................................................................................ 52
Figure 43. ProViewer Data Streaming Configuration ................................................................................. 52
Figure 44. BlueView Interfacing .................................................................................................................. 53
Figure 45. Gemini Interfacing...................................................................................................................... 54
Figure 46. Gemini Sonar Controls .............................................................................................................. 55
Figure 47. Black banding artifacts with high gain and the same data with lower gain. .............................. 56
Figure 48. R2Sonic Sonar Controls ............................................................................................................ 56
Figure 49. Dolphin Sea View Interfacing .................................................................................................... 57
Figure 50. Dolphin Sea View Controls ........................................................................................................ 57
Figure 51. Blueprint Oculus Interfacing ...................................................................................................... 58
Figure 52. Blueprint Oculus Controls .......................................................................................................... 58
Figure 53. SAMM interface to Edgetech Discover ..................................................................................... 59
Figure 54. SAMM interface to Klein SonarPro ............................................................................................ 60
Figure 55. GeoDAS UDP Broadcast Settings ............................................................................................. 61
Figure 56. SAMM Interface to GeoDAS ...................................................................................................... 61
Figure 57. Status Bar Position Units ........................................................................................................... 66
Figure 58. Imagery Processing Options ..................................................................................................... 66
Figure 59. SLS Processing Options ............................................................................................................ 67
Figure 60. Swath Properties Window ......................................................................................................... 67
Figure 61. Display Options Dialog With Navigation Track Options ............................................................ 68
Figure 62. Brightness and Gamma Rendering Effects ............................................................................... 70
Figure 63. Feathering Effect ....................................................................................................................... 70
Figure 64. Contacts in Mosaic Window ...................................................................................................... 72
Figure 65. Contacts Window ....................................................................................................................... 73
Figure 66. Assigning Tags .......................................................................................................................... 79
Figure 67. Grouped Contacts and Context Menu ....................................................................................... 82
Figure 68. Filtering by Tag .......................................................................................................................... 83
Figure 69. Create Report Success Window ................................................................................................ 84
Figure 70. Meta data properties window ..................................................................................................... 88
Figure 71. Measure Tool ............................................................................................................................. 89
Figure 72. Export dialog .............................................................................................................................. 89
Figure 73. Single GeoTIFF export vs Tiled GeoTIFFs export .................................................................... 90
Figure 74. Exported data displayed in GoogleEarth ................................................................................... 90

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Tables
Table 1. System Requirements ................................................................................................................ 9
Table 2. Create or Open Project ................................................................................................................. 13
Table 3. Toolbar Icons ................................................................................................................................ 15
Table 4. Status bar ...................................................................................................................................... 20
Table 5. Parameters and Units ................................................................................................................... 26
Table 6. Change the Rendering Method ..................................................................................................... 29
Table 7. Configure Project .......................................................................................................................... 29
Table 8. Load and Display Charts............................................................................................................... 41
Table 9. Chart Customization Commands .................................................................................................. 41
Table 10. Mosaic Window Extent Commands ............................................................................................ 63
Table 11. Swath Management Commands ................................................................................................ 64
Table 12. Contacts Toolbar Icons ............................................................................................................... 74
Table 13. Contact Display Commands ....................................................................................................... 76
Table 14. Contact Attribution Commands ................................................................................................... 80
Table 15. Contact Organization Commands ............................................................................................... 84
Acronyms and Abbreviations
cm centimeter
CPU central processing unit
ENC Electronic Navigational Chart
FLS forward-looking sonar
GIS geographic information system
GPU graphics processing unit
GUI graphical user interface
NMEA National Marine Electronics Association
NOAA National Oceanic and Atmospheric Administration
OIC Oceanic Imaging Consultants, Inc.
PPI plan position indicator
SAMM Stand Alone Mosaicking Module
SLS
TIFF
side-looking sonar
Tagged-Image File Format
UTM Universal Transverse Mercator

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1 Welcome to SAMM
There was a time not too long ago when the interface to a sonar was a printer. The sonar would
ping, echoes would return, be converted to voltage, and a stylus on a moving belt would cross a
scroll of paper, burning images proportional to the echo strength. Now many sonars come with
perfectly adequate graphical user interfaces that create a waterfall or PPI (plan-position
indicator) view of the data. These are fine, but often lack context, i.e. they don’t show the data
in reference to each other, or the world. SAMM changes all this.
SAMM (Stand Alone Mosaicking Module) is Oceanic Imaging Consultants Inc.’s (OIC) software
program for real-time mosaicking of underwater imagery. SAMM automatically creates mosaics
of your sidescan, forward-look (FLS) and mechanical scanning sonar data in real time over your
co-registered charts or imagery, while logging the raw data for playback and post-processing.
Whether in real-time or playback, SAMM will show where you’ve been and what you saw.
This manual documents SAMM’s features and functions. Information is presented in the order
that you need it for out-of-the-box playback or data acquisition. It discusses each process in the
SAMM workflow and how to accomplish it. Selected sections conclude with a table of
commands relevant to the workflow process described in that section, which serves as a review
of the commands available in SAMM and how to execute them. Selected sections also include
an interactive tutorial for demonstrating some of the features. Test data are provided with the
software for use with the tutorial instructions. The sections are as follows:
 System Requirements and Setup
 The Graphical User Interface (GUI)
 Configure SAMM
 Load Charts
 Add Files or Begin Acquisition
 Display and Processing Settings
 Work with Contacts
 Additional Features
 End Acquisition and Close Project.
We use the following typographical rules throughout this manual for emphasis and clarity:
 Boldface indicates onscreen buttons, commands, fields, or icons from a toolbar, menu
or window.
 Courier New indicates user input or SAMM output. This includes all of the text in the
SAMM interface that your actions can change.
 Grey shading of text or columns in a table indicates specific tutorial instructions. Follow
these directions to check your work against the figures in this manual.
 Key names are written as they appear on the keyboard. Key combinations are indicated
with a plus sign between them, e.g., to press Alt+F, press Alt and F simultaneously.
 Click means to press the left mouse button. Double-click means to quickly press the left
mouse button twice. Right-click means to press the right mouse button.
For further assistance using the SAMM program, we encourage you to contact us.
Phone [phone] Fax: [phone]
e-mail [email protected]m Web: www.oicinc.com

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2 System Requirements and Setup
This section describes the sensor and system requirements for computers hosting SAMM, and
how to install, launch, and create/open a project in the software.
2.1 Sensor and Input Requirements
SAMM is designed to read sonar data, position and sensor heading, and produce a mosaic.
SAMM can do this for forward-look, sector-scan and side-look (sidescan) sonars. SAMM can
read this data in real-time from the sensor, or from files in playback mode. In forward-look
mode, SAMM is compatible with Kongsberg Mesotech M3, Teledyne BlueView 2D imaging,
Tritech Gemini, Marine Electronics Dolphin SeaView, Blueprint Subsea Oculus, Haiying Marine
HY1645 and the R2Sonic 202x in forward-looking mode. SAMM can also interface with
Kongsberg Mesotech MS1000 single-beam scanning sonar and Imagenex 881L-GS/882L gyro
stabilized scanning sonar. In sidescan mode, SAMM is compatible with Edgetech Discover (and
all supported sonars), Klein SonarPro (and all supported sonars) and OIC’s GeoDAS (and all
supported sonars), SAMM also supports reading of Starfish .logdoc, Triton .xtf, C-Max .cm2,
and Humminbird .dat data. Contact OIC for other sonar formats. SAMM requires input of
sensor position (longitude/latitude) as well as true heading. SAMM assumes your GPS receiver
is set to the WGS 1984 reference datum, but supports user configuration of datum.
SAMM directly interfaces to the Tritech Gemini 720, the R2Sonic 202x, the Marine Electronics
Dolphin SeaView and the Blueprint Subsea Oculus FLS, effectively replacing any native sonar
software and providing all control, display and logging functions. For these sonars, SAMM
requires:
 the sonar software not be run concurrently with SAMM; and
 navigation and heading sensors must be supplied to SAMM directly, as they will not be
included with the sonar data
For the sidescan systems (Edgetech, Klein, OIC) and the Kongsberg M3/MS1000, BlueView,
Imagenex 881L-GS/882L and HY1645 sonars, SAMM interfaces with the manufacture's
software, leaving all control and processing to the native sonar software, and providing display,
target marking and mosaicking capabilities. For these sonars, SAMM requires:
 the sonar software must be run concurrently with and connected to SAMM; and
 navigation and heading sensors or must be supplied to the sonar software, so that
SAMM can receive position and heading included with the sonar data
At the time of this writing, SAMM does not interface in real-time to Sound Metrics ARIS/DIDSON
sonar, Reson 7128/7130 and Norbit forward-looking sonar systems. However, their recorded
data files (.aris/.dds and .s7k) can be loaded or played back in SAMM to generate mosaic
imagery if they are logged with position and heading data.