What's New in MB-System Version 5

The version 5.1.x releases of MB-System includes a number of changes and improvements relative to the version 4 releases. The most significant changes include:

A new approach to managing data processing.

Many tools - one output file. In previous versions of MB-System, each processing program read an input swath data file and produced an output swath data file. This "serial" processing scheme generally produced a large number of intermediate data files. MB-System version 5.0 features the integration of the editing and analysis tools with a single program, mbprocess, that outputs processed data files. The new "parallel" processing scheme covers bathymetry data processing, but does not yet incorporate the sidescan processing capabilities. All of the old tools and capabilities are still part of the distribution.
Recursive datalists. The lists of data files used by gridding and plotting programs can now be recursive, making it simpler to manage data from many different surveys.
Automatic format identification. MB-System programs will now attempt to automatically identify the swath data format based on the filename suffix.
Extended inf files. Users can generate inf files by directing the output of mbinfo to a file named by adding an ".inf" suffix to the swath data file name. Several programs can parse inf files, if they exist, to quickly obtain data locations or ranges. This feature speeds operations such as gridding, mosaicing, and automated plotting.

New command line tools.

MBprocess. This new tool performs a variety of processing tasks and produces a single output processed swath data file. The program mbprocess can apply bathymetry edits from mbedit and mbclean, navigation edits from mbnavedit, sound velocity profile changes from mbvelocitytool, and a variety of other corrections.
MBset. This new tool allows users to create and modify the parameter files used to control the operation of mbprocess.
MBdatalist. This new tool allows users to list the files referenced by a recursive datalist structure. It can also be used to create the ancillary ".inf", ".fbt", and ".fnv" files for all of the data files referenced in a recursive datalist structure.
MBsvplist. This new tool lists water sound velocity profiles embedded in swath data files, creating secondary files that can be read into MBvelocitytool.
MBareaclean. This new tool identifies and flags artifacts in swath sonar bathymetry data within a specified area of interest. The area is divided into a grid with square cells or bins, and the data are grouped according to these bins. Once all of data are read, statistical tests are applied to the soundings within each bin.
MBotps. This new tool uses the Oregon State Tidal Prediction Software (OTPSnc) package to calculate open ocean tidal models for bathymetry correction.
MBextractsegy. This new tool extracts subbottom profiler data from swath files to SEGY format files.
MBsegyinfo. This new tool extracts SEGY data file information and statistics.
MBsegylist. This new tool produces arbitrary ascii tables from SEGY data files.
MBsegygrid. This new tool grids seismic and subbottom data from SEGY data files.
MBsegypsd. This new tool calculates sonograms from SEGY data files.

Improved bathymetry and navigation editors.

MBedit and MBnavedit now swallow data files whole rather than reading in limited size buffers.
MBedit now outputs beam edit events rather than an entire swath file. The edits are applied by MBprocess.
MBnavedit now outputs the edited navigation rather than an entire swath file. The edited navigation is merged using MBprocess.
Both editors show the position of the currently displayed data within the entire data file.
MBnavedit has two navigation modeling modes relevant to swath data collected using poorly navigated ROVs and towfishes. One mode applies a dead reckoning model with interactively set drifts, and the other involves inverting for an optimally smooth navigation by penalizing speed and acceleration.
MBnavadjust. This new tool allows users to adjust poorly navigated surveys by matching features in overlapping swathes. It is particularly useful for processing surveys conducted from submerged platforms.

New Visualization Based Tools

MBgrdviz is a GMT grid 2D/3D visualization utility. MBgrdviz also allows the display of sonar navigation, sites, and routes, and interactive survey planning.

MBeditviz is an interactive 3D visualization bathymetry editor and patch test tool.

Support for Projected Coordinate Systems

MB-System now incorporates the source code for the PROJ.4 Cartographic Projections library, providing support for (apparently) all commonly used geodetic coordinate systems. PROJ.4 was developed by Gerald Evenden (then of the USGS), and was obtained from the www.remotesensing.org website.

A large number of commonly used projected coordinate systems (e.g. UTM) are defined in a file (mbsystem/share/projections.dat) distributed with MB-System. These include all of the standard UTM zones, all of the standard state plate coordinate systems, and most of the European Petroleum Survey Group (EPSG) coordinate systems (also including UTM).
MB-System can now handle swath data that is navigated in a supported projected coordinate system. In particular, data files that are navigated with UTM eastings and northings instead of longitude and latitude can now be plotted and processed with MB-System.
The programs mbgrid and mbmosaic can now output grids and mosaics in any of the projected coordinate systems specified in mbsystem/share/projections.dat.
The TIFF images generated with mbm_grdtiff and mbgrdtiff now fully conform to the GeoTIFF standard, providing that the source grids or mosaics were generated using mbgrid or mbmosaic in either Geographic coordinates, UTM coordinates, or any of the EPSG coordinate systems specified in the projections.dat file. This means, for instance, that GeoTIFF images generated with mbgrdtiff will be properly georeferenced when they are imported into ESRI ArcGIS or other GIS packages.

Restructuring the code.

All of the C code now conforms to the ANSI C standard.
The underlying input/output library (MBIO) has been substantially rewritten. The structure has been streamlined, simplifying both future development and support of the existing code. The MBIO API has been greatly modified.

Handling of old Simrad multibeam data.

Vendor format data from the old Simrad multibeams (pre-1997 sonars) are now supported by a single format id (51) rather than a separate format id for each sonar model. The old format id's are automatically aliased to 51, so existing shellscripts will continue to work.
MB-System no longer supports beam flagging in format 51 data. The use of mbedit and mbclean on format 51 data will cause the flagged beams to be irrevocably nulled. Previous versions of MB-System used the highest bit in the depth values to represent beam flags because no Simrad data seemed to use that bit. We have not obtained data with depth values using the full bit-range, conflicting with the old beam flagging scheme. We recommend that old Simrad data be translated to the extended processing format (57) which contains proper beam flags and supports all processing functions. Format 57 is also used for processing data from the current Simrad multibeam sonars.
Sidescan data from old Simrad multibeams (pre-1997 sonars) are now handled in the same manner as data from the newer sonars (e.g. EM3000, EM3000, EM120). The raw samples in the vendor data format are binned, averaged, and interpolated into a 1024 pixel sidescan swath. This binned sidescan is not saved in the vendor format, so (as above) it is recommended that the data be translated to an extended format (57) that stores both bathymetry beam flags and processed sidescan.

Streamlining of MB-System Default Parameters.

Prior to version 5.0, the MB-System defaults set by mbdefaults included the format id, a control for ping averaging, longitude and latitude bounds for windowing by area, and begin and end times for windowing in time. These values are no longer set in the .mbio_defaults file or controlled by mbdefaults. As noted above, the format id is automatically identified from the filename when possible. When filenames do not match one of the recognized structures, users must specify the format using the relevant programs -Fformat option. The controls for ping averaging and windowing in time and space are rarely used, and must now be explicitly set in command line arguments.

New Data Formats

Furuno HS10 multibeam bathymetry is supported as format 171.
SeaBeam 2120 multibeam data in the L3 Communications XSE format are supported as format 94 (already used to support Elac Bottomchart MkII XSE data).
Raw STN Atlas multibeam data generated by the upgraded Hydrosweep DS2 multibeam on the R/V Ewing are supported by read-only format 182. Processing is supported using the augmented read-write format 183.
The IFREMER netCDF multibeam archiving data format is supported as format 75. Similarly, the IFREMER netCDF navigation archiving data format is supported as format 167.
The STN Atlas processing data format SURF is supported as format 181. At present, SURF is supported as a read-only format. This allows plotting and gridding of the SURF data, but not processing. Writing or translating the SURF data to allow processing will be supported in a later version.
The Hawaii Mapping Research Group's MR1 format is supported as format 64. This format is used to disseminate data from both the HMRG interferometric sonars (e.g. MR1) and the WHOI DSL 120 deep-towed inteferometric sonar. This format has been supported by including the code for the HMRG library libmr1pr in the MB-System library. Thanks to Roger Davis and HMRG for making the code available under the GPL.
The Reson 7k format produced by the 7000 series Reson SeaBat multibeams and the Reson 6046 datalogger is now supported as format 88. This format can incoporate sidescan sonar and subbottom profiler data as well as the multibeam data.
Third generation Simrad multibeams (EM122, EM302, EM710) are supported by formats 58 and 59.
Imagenex and Odom DeltaT multibeams are supported by formats 191 and 192.

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