MB-System Announcements

MB-System 5.8.1 Now Available (22 March 2024)

MB-System 5.8.0 Now Available (22 January 2024)

MB-System 5.7.8 Now Available (17 January 2021)

Not So Recent: Announcements Archive

  • This version requires GMT 5.4 or later.
  • For more information read the MB-System 5.7.6 ChangeLog file
  • The MB-System 5.7.6 source distribution is available for download
  • The MB-System GitHub source code repository can also be accessed directly at:
  • Changes since the 5.7.5 release include:
    • Many bug fixes to programs and data format i/o modules.
    • New programs in optional photomosaicing section:
      • mbgrd2obj
      • mbphotomosaic
      • mbgetphotocorrection
      • mbphotogrammetry
      • mbgrd2octree
      • mbm_makeimagelist
    • New program in optional Terrain Relative Navigation section:
      • mbtrnpp
    • Continuous Integration testing:
      Continuous integration testing has been implemented using the Travis CI service integrated with Github. The tests are performed by running ‘make check’ and are executed automatically whenever commits are made to the Github repository.
    • Partial migration to C++:
      The source code for programs in the src/utilities directory has been migrated to C++. Also, much of the C and C++ code has been updated to be consistent with the C11 and C++11 standards.
    • Deprecated programs:
      Several programs that are no longer part of the current data
      processing approach have been declared deprecated and have been moved from src/utilities to a new directory src/deprecated. The deprecated programs have also been converted to C++ and are still built and installed as part of MB-System. We tentatively plan to remove these programs entirely from MB-System distributions at the time of the 6.0 release. These programs are:
      • mb7k2jstar
      • mb7k2ss
      • mb7kpreprocess
      • mbauvnavusbl
      • mbhsdump
      • mbhysweeppreprocess
      • mbinsreprocess
      • mbkongsbergpreprocess
      • mbneptune2esf
      • mbrollbias
      • mbrphsbias
      • mbstripnan
      • mbswplspreprocess 

 

MB-System Source Code Repository Moved to GitHub (17 December 2018)

 

MB-System packaging in Homebrew for MacOs updated (31 October 2017)

  • This is now the current release of MB-System.
  • This version requires GMT 5.4 or later.
  • For more information read the MB-System 5.7.5 ChangeLog file
  • The MB-System 5.7.5 source distribution is available for download
  • The MB-System GitHub source code repository can also be accessed directly at: https://github.com/dwcaress/MB-System
  • The MB-System  5.7.5 release includes support for two major new multibeam data formats: Teledyne s7k version 3 and Kongsberg kmall.
  • The Teledyne s7k version 3 format is supported with format id 89. These data are produced by recent and current Reson, Hydrosweep, and Blueview multibeam sonars. R2sonic multibeams can also output data in s7k format.
  • The Kongsberg kmall format is output by the current generation of Kongsberg multibeam sonars, including the EM2040, EM712, EM304, and EM124. Bathymetry recalculation by raytracing is not fully functional yet, but all other aspects of processing (bathymetry editing, navigation editing or adjustment, backscatter correction and filtering) are functional.
  • At MBARI we have experienced instances in which bathymetry editing done in mbeditviz failed to show up in the processed files after mbprocess was run. In all cases this problem involved new editing done on previously edited data.
  • There have been recent changes to the edit save files (*.esf suffix) used by mbedit, mbeditviz, mbclean, and mbareaclean to hold bathymetry editing events and applied by mbprocess when producing processed files. In particular, the timestamps used to associated edit events with individual sonar pings (or lidar scans) are now handled with a precision exceeding 1 microsecond. This follows less recent changes to the fast bathymetry files (*.fbt suffix) in which timestamps also started being handled to microsecond precision.
  • These changes to increase the precision to which time in handled internally in MB-System derive from some of the current generation acoustic and optical seafloor mapping sensors that can have separate data records with ping or scan time stamps separated by 10 milliseconds or less.
  • The problem arises from having timestamps in *.esf files and/or *.fbt files that differ from the original timestamps by more than the amount now used to associate edit events with particular pings or scans (0.11 milliseconds). Logic has been embedded to identify and correct these problems on the fly, but that logic clearly fails in some instances. However, these problems can be corrected using a combination of mbdatalist and mbclean.
  • If one finds that interactive edits are not reflected in grids produced after processing with mbprocess, do the following:
    • First remake the *.fbt files using mbdatalist using the -N option to force creating new ancillary files:
        mbdatalist -I datalist.mb-1 -N -V
    • Reset the edit event timestamps in the *.esf files using mbclean:
        mbclean -I datalist.mb-1 -T0.0011
    • The -T tolerance option sets the maximum time difference between the edit event timestamp and the ping or scan timestamp allowed. Since the maximum time difference that should have been produced by rounding errors in previous versions is about 1 millisecond = 0.001 second, I recommend using a tolerance of 0.0011 seconds (works for me…).
    • Finally, reprocess the data using mbprocess:
        mbprocess -I datalist.mb-1
    • As always, if you follow the convention of naming the primary datalist file “datalist.mb-1”, then the “-I datalist.mb-1” arguments can be omitted from the mbdatalist, mbclean, and mbprocess calls. If you use some other name for the datalist file, then you must specify it in the commands.
  • The Monterey Bay Marine GIS User Group will be holding its annual meeting at MBARI on Wednesday March 30, 2016.
  • In conjunction with this meeting, David Caress will present a one-day MB-System workshop the next day (Thursday March 31).
  • The primary focus will be on processing surveys done with submerged platforms such as AUVs and ROVs, including optimizing imperfect subsea navigation so that features match in overlapping and crossing swaths.
  • If you plan to attend the MB-System workshop, please RSVP.
  • If you plan to attend the Monterey Bay Marine GIS User Group meeting, please register on their site.
  • GMT 4
  • No further changes or fixes will be made to MB-System 5.4 releases.
  • We recommend that users migrate to GMT 5.1 (or later) and MB-System 5.5 (or later)
  • The MB-System 5.4.2220 source distribution will remain available for download through the end of 2015, but will not be maintained or supported by the MB-System team
  • Documentation of the file format used for “fast bathymetry” or fbt files in MB-System has been improved with the incorporation of C source code for a working program to read fbt files.
  • The updated documentation and source code example can be found here.
  • The sample source code is licensed under the Lesser GNU Public license, or LGPL and so can be used in the integration of a third-party, commercial bathymetry editor with MB-System
  • This format is also known as MBF_MBLDEOIH, or format 71.
  • An MB-System Developer’s Workshop was held at MBARI on February 18-20, 2014.
  • The agenda, participant list, notes, and a group photo are available here.
  • One outcome of our 2012 MB-System Planning Meeting was a request for yearly workshops, alternating between meetings for developers and for users. This was the first such workshop, attended primarily by active MB-System developers.
  • A consequence of this meeting is a new Developer’s Guide to Writing an MB-System I/O Module describing how to support a new data format in MB-System.
  • We are considering holding a user’s workshop early in 2015. Feel free to express interest in attending such an event on the MB-System User’s Discussion List.
  • For several years we have used the MB-System Discussion List as the primary means for communication within the MB-System community.
  • We have recently begun using a separate but similar email list for discussions regarding MB-System development, leaving the original list for all other sorts of discussions.
  • Effectively, we now have two lists:
  • Both lists require membership for posting, and have publically viewable message archives.
  • If you want to follow everything that is happening with MB-System, subscribe to both lists. If you don’t want to see lengthy threads on coding details, just subscribe to the MB-System User’s Discussion List.
  • MB-System has been packaged for MacOs X as part of Homebrew.
  • If you have Homebrew installed, then MB-System and its prerequisites can be installed using these two commands:brew tap homebrew/sciencebrew install mbsystem
  • Thanks to Anthony Lukach for creating and maintaining the Homebrew MB-System package.
  • The Marine Geology and Geophysics Program of the NSF has approved our request for another five years of funding for MB-System development and support.
  • We thank all of the MB-System users who provided letters of collaboration or support for this proposal. Your time and effort are appreciated!!
  • We also thank our NSF program manager Donna Blackman for shepharding this project through the system at a very difficult time.
  • The proposal can be read here
  • Our proposal was mostly funded intact. Requested effort to develop and maintain the software are fully funded. The documentation effort was cut by 25%, and funds to support annual workshops were also cut.
  • OSGeo-Live Version 6.5 was released on February 26, 2013.
  • OSGeo-Live is a self-contained bootable DVD, USB thumb drive or Virtual Machine based on Xubuntu, that allows you to try a wide variety of open source geospatial software without installing anything.
  • This distribution includes over 50 open source geospatial software packages, including MB-System 5.3.1982.
  • Hamish Bowman is responsible for packaging and including MB-System into OSGeo-Live.
  • The distribution is found at: http://live.osgeo.org/
  • The MB-System quick start description is at: http://live.osgeo.org/en/overview/mb-system_overview.html
  • The article reference is: Rembert, J. Ryan (2012), “MB-System: An Open Source Bathymetric Processing Solution”, LIDAR, Volume 2 Issue 6, pp. 52-56.
  • You can find the issue of LIDAR at: http://lidarmag.com/emag/2016/vol6no4/index.html
  • The article is available separately at: http://www.lidarmag.com/PDF/LiDARMagazine_Rembert-MBSystem_Vol2No6.pdf
  • Thanks to J. Ryan Rembert for publishing a very nice review of MB-System.
  • Thanks to Alejandro Hinojosa of CICESE for letting us know about this review.
  • Our program manager at the Marine Geology and Geophysics Program, Ocean Sciences Division, U.S. National Science Foundation has indicated that the MB-System renewal proposal reviewed well and is on the list of projects that are high priority for funding.
  • However, no funding decisions will be made until the 2013 and 2014 NSF budgets are settled, a process that may very well take another few months.
  • On August 15, 2012, we submitted a proposal to the Marine Geology and Geophysics Program, Ocean Sciences Division, U.S. National Science Foundation requesting a five-year renewal of funding for MB-System support and development.
  • This was structured as two linked, collaborative proposals from MBARI (Principle Investigator David Caress) and Lamont-Doherty (Principle Investigator Dale Chayes).
  • The proposal title is: “Collaborative Research: Development and Support of the MB-System Software Package for Processing and Display of Swath Mapping Sonar Data”.
  • The proposal text is here: 2012 MB-System NSF Proposal
  • Supplementary information supporting the proposal is here: Supplementary Information for the 2012 MB-System NSF Proposal., and includes:
    • Collaboration letters.
    • MB-System user community size estimate.
    • Publications citing MB-System
  • For a variety of reasons, we need to document the existence of a significant MB-System user community.
  • In February we estimated the number of organizations using MB-System during 2011 through a combination of Discussion List membership and source distribution download statistics.
  • As part of resubmitting our NSF proposal, we have updated our estimate using current Discussion List membership.
  • We currently identify 197 user organizations, including 41 academic institutions in the U.S. and 68 elsewhere in the world, 11 U.S. government agencies and 40 government agencies in other countries, and 37 commercial organizations.
  • The details are here: MB-System User Community Estimate from Downloads.
  • As of release 5.3.1955, the file format used for “fast bathymetry” or fbt files in MB-System has changed.
  • In particular, the navigation, sonar depth, and related parameters are now stored as binary double rather than scaled binary short integer values, with the result that cm-scale surveys can now be usefully processed with MB-System.
  • This format is also known as MBF_MBLDEOIH, or format 71.
  • Documentation of both the new and old format, along with directions and source code to enable the integration of a third-party bathymetry editor with MB-System, can be found in this updated document.
  • On February 9, Christian Ferreira established an MB-System page on Facebook.
  • As of leap day, 35 Facebook users “like” this page.
  • On January 17-18, 2012, we held an MB-System Planning Meeting at Lamont-Doherty Earth Observatory to develop the priorities for our NSF proposal (to be submitted on February 15, 2012.
  • This was a small meeting involving the core MB-System development team, users that have substantially contributed to the project in recent years, and representatives of organizations that have expressed interest in parallel development efforts contributing to MB-System
  • The goals were to:
    1. Define priorities and tasks for the next five year MB-System project to be proposed to NSF-OCE in February by Caress and Chayes.
    2. Define priorities and tasks for MB-System related development efforts by other groups.
  • The details are here: Notes of and results from the MB-System planning meeting.
  • Ocean Floor Geophysics of Vancouver, Canada, has funded the development of an MB-System i/o module for multibeam data in the HYSWEEP HSX format.
  • This capability is available beginning with the 5.3.1917 release distribution. HYSWEEP HSX has an MBIO format id of 201.
  • Also included is a new preprocessing utility for data in the HSX format, named mbhysweeppreprocess.
  • At this time, the new code has only been tested with respect to data collected using the combination of an R2Sonic multibeam and an Octans gyro/MRU. There will undoubtably be fixes and future development required to successfully support HSX data generally.
  • The Scripps Institution of Oceanography’s Shipboard Technical Support group maintains a repository of open source software RPM distributions for Red Hat Enterprise Linux and CentOS Linux.
  • This repository includes both source and binary distributions of MB-System, GMT, and netCDF that can be accessed using the yum utility. The MB-System RPMs require the GMT and netCDF RPMs, but have no other external dependencies.
  • Thanks to Frank Delahoyde for pointing us at these repositories.
  • This repository can be found at:
    http://sts.ucsd.edu/repos/centos-5/local
  • The SIO-STS gpg signing key is
    http://sts.ucsd.edu/repos/centos-5/local/RPM-GPG-KEY-ST
  • The MB-System source code repository is now publically accessible through a web interface.
  • Users can download individual files or the entire MB-System development structure.
  • This repository always reflects the current state of MB-System development.
  • This updated document addresses the issue of integrating a third-party, proprietary source bathymetry editor with the GPL-licensed MB-System processing environment.
  • In particular, the edit event definition and related source code have been augmented to handle data from multiple head sonars that produce multiple pings with identical timestamps.
  • For the most part, integration of a bathymetry editor with MB-System can be accomplished using executable programs that are part of the MB-System distribution, and therefore freely available to be installed by users independent of any proprietary software.
  • However, we also include some code derived from the MB-System distribution that we will separately release under the Lessor GNU Public License (LGPL), allowing those functions to be linked with proprietary software.
  • On April 18, 2009, Marcel Croon posted instructions for installing GMT and MB-System on Ubuntu systems to the MB-System Discussion List.
  • A slightly edited version of these instructions are available here.
  • Thanks Marcel!
  • This isn’t really new, but we haven’t previously highlighted these efforts to package MB-System for easy installation.
  • Since 2004, Kurt Schwehr of CCOM/JHC has maintained a Fink Project MB-System package for MacOs X. Users must specify use of “unstable” packages to make the MB-System package available.
  • Since July 2008, MB-System has been included in Poseidon Linux, the “Scientific GNU/Linux”. Poseidon is an Ubuntu Linux based distribution including a selection of open source software packages intended to support scientific research. In particular, it offers several specific tools in the areas of GIS, 3D Visualization, Mathematics, Statistics and several other fields of research.
  • As of May 11, MBARI changed the list server hardware and software that hosts the MB-System Discussion List
  • The MB-System Discussion List URL has changed to http://listserver.mbari.org/sympa/info/mbsystem
  • Anyone can read the list archives. Click on “Archives” in the web interface linked above.
  • Only members can post to the list. Join the list via the web interface linked above.
  • List members can post via the web interface or by emailing to mbsystem@mbari.org
  • Beta Distributions of MB-System are generated much more frequently than “official” releases, mostly because we have difficulty keeping the documentation concurrent with the code development.
  • The sections of these web pages relating to downloads now note that beta distributions are frequently updated, and include a link to the most recent beta distribution.
  • Version 5.1.1 will be released as soon as reasonable documentation is completed for the new tools mbgrdviz and mbeditviz.
  • The Marine Geology and Geophysics Program of the NSF has approved our request for another five years of funding for MB-System development and support.
  • We thank all of the MB-System users who provided letters of support for inclusion in this proposal. Your time and effort are appreciated!!
  • The proposal can be read here
  • We are developing an MB-System Cookbook to provide tutorial style documentation for MB-System Version 5. An updated draft of this cookbook by Val Schmidt, Dale Chayes, and David Caress is being made available here along with the data samples used to illustrate the use of our software.
  • MB-System version 6 is already under development. Our intent is to embed a 3D vizualization capability into tools used for tasks such as project management, bathymetry editing, and patch tests. The first tool using this capability is part of the 5.0.6 release. This program is called MBgrdviz, and allows simple 2D and 3D vizualization of GMT grids. Some screen dumps are available here.
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  • This document addresses the issue of integrating a third-party bathymetry editor with the MB-System processing environment.
  • Since some editors may have licensing and distribution schemes (e.g. commercial with source held proprietary) that are inconsistent with the GNU Public License (GPL) applied to MB-System, the suggestions presented here do not involve direct use of GPL licensed MB-System source code.
  • For the most part, this can be accomplished using executable programs that are part of the MB-System distribution, and therefore freely available to be installed (but not sold) by third parties.
  • However, we also include some code derived from the MB-System distribution that we will separately release under the Lessor GNU Public License (LGPL), allowing those functions to be linked with commercial software.
  • We are developing an MB-System Cookbook to provide tutorial-style documentation for MB-System Version 5. A preliminary (incomplete) draft of this cookbook by Val Schmidt, Dale Chayes, and David Caress is being made available here along with the data samples used to illustrate the use of our software.
  • We have established an MB-System discussion email list to facilitate communication among MB-System developers and users see links below.
  • ATLAS Hydrographics GmbH of Bremen, Germany, has released the source code used to read and write swath mapping sonar data in the SURF format as open source under the GNU Public License (GPL).
  • ATLAS markets a number of widely used multibeam sonars, including the Fansweep 15 and Fansweep 20 multibeams for shallow water surveying and the Hydrosweep MD-2 and Hydrosweep DS-2 multibeams for mid- to deep-water surveying.
  • The ATLAS HYDROMAP processing package stores Fansweep and Hydrosweep data in the SURF format. A large amount of seafloor mapping data worldwide is archived in this format.
  • We will be adding support for the SURF format in MB-System soon (as time and resources allow).
  • The Marine Geology and Geophysics Program of the NSF has approved our request for another five years of funding for MB-System development and support.
  • We thank all of the MB-System users who provided letters of support for inclusion in this proposal. Your time and effort are appreciated!!
  • We also thank Dr. David Epp, our NSF Program Manager, and the mail reviewers and panel members who reviewed our latest proposal.