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ChangeLog.html
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<body>
<hr>
<h2 id="toc_0">MB-System ChangeLog File:</h2>
<p>This file lists changes to the source code of the MB-System open
source software package for the processing and display of swath sonar data.
This file is located at the top of the MB-System source code distribution
directory structure.</p>
<p>In the list below, releases shown in bold type are major, announced releases.
The other entries are test or "beta" releases that were not announced and generally
not widely distributed. Prior to 5.7.1, the MB-System source code repository was
a privately hosted Subversion archive. In that era, announced source distribution
releases were made available for download by ftp. Starting with 5.7.1 the
MB-System source code repository is hosted by Github at
https://github.com/dwcaress/MB-System/
and each distribution corresponds to a discrete Github release tag. Releases that
include "beta" in the tag name are preliminary and generally not announced.
Distributions that do not include "beta" in the tag name correspond to the major,
announced releases. The source distributions associated with all releases, major
or beta, are equally accessible as tarballs through the Github interface.</p>
<hr>
<h3 id="toc_1">MB-System Version 5.8 Releases and Release Notes:</h3>
<hr>
<ul>
<li>Version 5.8.1beta08 March 10, 2024</li>
<li>Version 5.8.1beta07 February 24, 2024</li>
<li>Version 5.8.1beta04 February 16, 2024</li>
<li>Version 5.8.1beta03 February 8, 2024</li>
<li>Version 5.8.1beta02 February 7, 2024</li>
<li>Version 5.8.1beta01 February 1, 2024</li>
<li><strong>Version 5.8.0 January 22, 2024</strong></li>
</ul>
<hr>
<h4 id="toc_2">5.8.1beta08 (March 10, 2024)</h4>
<p>Mbm_grdplot: Added colortable 10, which runs from blue to red and can be used for
plots of seismic reflection or subbottom profiler data when the trace signals are
both positive or negative.</p>
<p>SEGY format data: Changed MB-System SEGY traceheader to include a sensordepthtime
float value in bytes 216-219. This will be used to hold the two-way traveltime in
seconds corresponding to the source depth assuming a 1500 m/sec water sound speed.
This value can be used as a trace start delay time in plotting to account for the
source location of subbottom profiler data collected from submerged platforms like
AUVs and ROVs. The MB-System programs mbsegygrid and mbm_grdplot use the source
depth value in meters, but some external packages need the delay time.</p>
<p>SEGY format data: MB-System now recognizes file suffixes *.sgy and *.SGY in addition
to *.segy *.SEGY *.seg and *.SEG</p>
<p>Mbsegyinfo: Fixed calculation and reporting of trace minimum and maximum values.</p>
<p>Mbextractsegy: Now allows output of subbottom analytic data as well as envelope data.
Use of the -S4 command will output three separate segy files, one with the envelope
function, one with the subbottom correlate, and one with the correlate conjugant
(i.e. the Hilbert transform of the correlate). The section plot script generated now
will create plots of all three trace types.</p>
<p>Mbpreprocess and mbprocess: Now support merging navigation and attitude from Schmidt
Ocean Institute RVDAS format ROV navigation.</p>
<p>Mbpreprocess and format MBF<em>EM710RAW (58): The command --kluge-auv-sentry-sensordepth
now works for format 58 files (3rd generation Kongsberg multibeam data in *.all files)
such that available sensordepth values are embedded in the output format MBF</em>EM710MBA
(59) files.</p>
<h4 id="toc_3">5.8.1beta07 (February 24, 2024)</h4>
<p>CMake build system: Fixed ability to set OTPS location in cmake build system.</p>
<p>CMake build system: Added installation of header files required for external programs to
utilize MB-System libraries.</p>
<h4 id="toc_4">5.8.1beta04 (February 16, 2024)</h4>
<p>Format 261 (MBF_KEMKMALL): Updated support for Kongsberg Kmall format to match updated specification J.</p>
<h4 id="toc_5">5.8.1beta03 (February 8, 2024)</h4>
<p>Mbphotomosaic: Fixed priority-heading option that allows image prioritization on
the basis of camera heading.</p>
<h4 id="toc_6">5.8.1beta02 (February 7, 2024)</h4>
<p>Mbphotomosaic: Added options to detect and correct dark images (for when strobe lights
partially drop out), to ignore dark images, and to allow image prioritization on
the basis of camera heading.</p>
<h4 id="toc_7">5.8.1beta01 (February 1, 2024)</h4>
<p>Mbpreprocess: Now checks for successive pings/scans with the same timestamp, and
adds enough time to the second timestamp (0.0000033 seconds) that these pings/scans
are seen as different by the beam edit flag handling code. For dual head sensors
this logic only compares timestamps for the same subsensor, so simultaneous operation
of the two subsensors (sonar or lidar heads) is allowed.</p>
<p>Mbvoxelclean: Fixed bug in which previously beamflags from previously existing esf
files were ignored. Also fixed a non-initialized pointer bug that produced occasional
crashes.</p>
<h4 id="toc_8">5.8.0 (January 22, 2024)</h4>
<p><strong>Version 5.8.0</strong> is now the current release of MB-System. </p>
<p>The source code distribution can be downloaded from the MB-System Github repository at:<br>
<a href="">https://github.com/dwcaress/MB-System/archive/refs/tags/5.8.0.tar.gz</a></p>
<p>In addition to many bug fixes, the changes of 5.8.0 relative to the prior major release (5.7.8) include:</p>
<p><strong>New build system:</strong><br>
MB-System is now built and installed using the CMake package, rather than GNU Autotools. The old build system is still present and can be used to install MB-System on old operating systems (e.g. Ubuntu 18.04), but all support for building on recent, current and future operating systems will be for use of CMake. See the Download and Install (https://www.mbari.org/technology/mb-system/installation/) instructions page for details.</p>
<p><strong>Global ties to reference grids in MBnavadjust:</strong><br>
MBnavadjust is a toolset used adjust navigation of submerged platform (e.g. AUV or ROV) surveys so that features match where swaths overlap and cross. The primary information comes from measuring the navigation offsets required to match features using cross correlation of the bathymetry data. MBnavadjust now also allows the survey navigation to be tied to reference bathymetry models, typically from GPS-navigated hull mounted surveys, so that the navigation can be tied to the world frame of reference.</p>
<p><strong>Realtime Terrain Relative Navigation:</strong><br>
MB-System now includes a Terrain Relative Navigation (TRN) codebase developed at Stanford and MBARI that uses realtime topography information to where a platform is located on a pre-existing topography map. The MB-System tool mbtrnpp implements TRN in the case of an AUV or ROV equipped with a multibeam sonar. </p>
<p><strong>Photomosaicing tools available:</strong><br>
Tools for generating photomosaics from sets of still seafloor photographs are now built as part of MB-System. Documentation and examples are being developed but are not available at the time of this release.</p>
<hr>
<h3 id="toc_9">MB-System Version 5.7 Releases and Release Notes:</h3>
<hr>
<ul>
<li>Version 5.7.9beta72 January 14, 2024</li>
<li>Version 5.7.9beta71 January 3, 2024</li>
<li>Version 5.7.9beta70 January 2, 2024</li>
<li>Version 5.7.9beta69 December 17, 2023</li>
<li>Version 5.7.9beta68 November 30, 2023</li>
<li>Version 5.7.9beta66 November 18, 2023</li>
<li>Version 5.7.9beta65 November 17, 2023</li>
<li>Version 5.7.9beta64 November 16, 2023</li>
<li>Version 5.7.9beta63 November 10, 2023</li>
<li>Version 5.7.9beta62 November 3, 2023</li>
<li>Version 5.7.9beta61 November 2, 2023</li>
<li>Version 5.7.9beta60 October 22, 2023</li>
<li>Version 5.7.9beta59 September 19, 2023</li>
<li>Version 5.7.9beta58 August 30, 2023</li>
<li>Version 5.7.9beta57 June 27, 2023</li>
<li>Version 5.7.9beta53 June 15, 2023</li>
<li>Version 5.7.9beta52 March 9, 2023</li>
<li>Version 5.7.9beta51 February 14, 2023</li>
<li>Version 5.7.9beta50 February 12, 2023</li>
<li>Version 5.7.9beta49 January 22, 2023</li>
<li>Version 5.7.9beta48 December 16, 2022</li>
<li>Version 5.7.9beta47 November 15, 2022</li>
<li>Version 5.7.9beta46 November 11, 2022</li>
<li>Version 5.7.9beta45 November 6, 2022</li>
<li>Version 5.7.9beta44 August 9, 2022</li>
<li>Version 5.7.9beta43 July 29, 2022</li>
<li>Version 5.7.9beta42 June 26, 2022</li>
<li>Version 5.7.9beta41 June 22, 2022</li>
<li>Version 5.7.9beta40 June 18, 2022</li>
<li>Version 5.7.9beta38 June 18, 2022</li>
<li>Version 5.7.9beta37 June 17, 2022</li>
<li>Version 5.7.9beta36 June 15, 2022</li>
<li>Version 5.7.9beta35 June 13, 2022</li>
<li>Version 5.7.9beta34 June 5, 2022</li>
<li>Version 5.7.9beta33 June 5, 2022</li>
<li>Version 5.7.9beta32 June 4, 2022</li>
<li>Version 5.7.9beta30 June 4, 2022</li>
<li>Version 5.7.9beta29 May 13, 2022</li>
<li>Version 5.7.9beta28 March 21, 2022</li>
<li>Version 5.7.9beta27 February 28, 2022</li>
<li>Version 5.7.9beta26 January 2, 2022</li>
<li>Version 5.7.9beta25 December 29, 2021</li>
<li>Version 5.7.9beta24 December 27, 2021</li>
<li>Version 5.7.9beta23 December 18, 2021</li>
<li>Version 5.7.9beta22 December 5, 2021</li>
<li>Version 5.7.9beta21 December 4, 2021</li>
<li>Version 5.7.9beta20 December 1, 2021</li>
<li>Version 5.7.9beta19 November 6, 2021</li>
<li>Version 5.7.9beta18 October 31, 2021</li>
<li>Version 5.7.9beta17 October 16, 2021</li>
<li>Version 5.7.9beta16 August 27, 2021</li>
<li>Version 5.7.9beta15 August 26, 2021</li>
<li>Version 5.7.9beta14 July 25, 2021</li>
<li>Version 5.7.9beta13 July 18, 2021</li>
<li>Version 5.7.9beta12 July 4, 2021</li>
<li>Version 5.7.9beta11 June 26, 2021</li>
<li>Version 5.7.9beta10 June 16, 2021</li>
<li>Version 5.7.9beta09 June 8, 2021</li>
<li>Version 5.7.9beta07 May 7, 2021</li>
<li>Version 5.7.9beta06 March 24, 2021</li>
<li>Version 5.7.9beta05 March 8, 2021</li>
<li>Version 5.7.9beta04 February 21, 2021</li>
<li>Version 5.7.9beta03 February 7, 2021</li>
<li>Version 5.7.9beta02 January 27, 2021</li>
<li>Version 5.7.9beta01 January 18, 2021</li>
<li><strong>Version 5.7.8 January 17, 2021</strong></li>
<li>Version 5.7.7 January 17, 2021 (flawed, quickly superceded)</li>
<li>Version 5.7.7beta09 January 17, 2021</li>
<li>Version 5.7.7beta08 January 6, 2021</li>
<li>Version 5.7.7beta06 December 30, 2020</li>
<li>Version 5.7.7beta05 December 28, 2020</li>
<li>Version 5.7.7beta04 October 28, 2020</li>
<li>Version 5.7.7beta03 October 27, 2020</li>
<li>Version 5.7.7beta02 October 8, 2020</li>
<li>Version 5.7.7beta01 October 7, 2020</li>
<li><strong>Version 5.7.6 October 5, 2020</strong></li>
<li>Version 5.7.6beta56 September 28, 2020</li>
<li>Version 5.7.6beta55 September 16, 2020</li>
<li>Version 5.7.6beta54 September 14, 2020</li>
<li>Version 5.7.6beta53 September 13, 2020</li>
<li>Version 5.7.6beta52 September 9, 2020</li>
<li>Version 5.7.6beta51 September 4, 2020</li>
<li>Version 5.7.6beta50 September 2, 2020</li>
<li>Version 5.7.6beta49 September 2, 2020</li>
<li>Version 5.7.6beta48 September 1, 2020</li>
<li>Version 5.7.6beta47 September 1, 2020</li>
<li>Version 5.7.6beta46 August 31, 2020</li>
<li>Version 5.7.6beta45 August 26, 2020</li>
<li>Version 5.7.6beta44 August 24, 2020</li>
<li>Version 5.7.6beta43 July 23, 2020</li>
<li>Version 5.7.6beta42 July 21, 2020</li>
<li>Version 5.7.6beta41 July 12, 2020</li>
<li>Version 5.7.6beta40 July 7, 2020</li>
<li>Version 5.7.6beta38 June 8, 2020</li>
<li>Version 5.7.6beta37 May 26, 2020</li>
<li>Version 5.7.6beta36 May 17, 2020</li>
<li>Version 5.7.6beta34 May 14, 2020</li>
<li>Version 5.7.6beta33 May 5, 2020</li>
<li>Version 5.7.6beta32 April 22, 2020</li>
<li>Version 5.7.6beta31 March 2, 2020</li>
<li>Version 5.7.6beta30 February 20, 2020</li>
<li>Version 5.7.6beta29 February 17, 2020</li>
<li>Version 5.7.6beta28 February 13, 2020</li>
<li>Version 5.7.6beta27 February 3, 2020</li>
<li>Version 5.7.6beta26 February 2, 2020</li>
<li>Version 5.7.6beta25 January 20, 2020</li>
<li>Version 5.7.6beta24 January 16, 2020</li>
<li>Version 5.7.6beta23 January 11, 2020</li>
<li>Version 5.7.6beta21 December 12, 2019</li>
<li>Version 5.7.6beta20 November 26, 2019</li>
<li>Version 5.7.6beta19 November 22, 2019</li>
<li>Version 5.7.6beta18 November 21, 2019</li>
<li>Version 5.7.6beta17 November 15, 2019</li>
<li>Version 5.7.6beta16 October 29, 2019</li>
<li>Version 5.7.6beta15 October 21, 2019</li>
<li>Version 5.7.6beta14 October 8, 2019</li>
<li>Version 5.7.6beta12 September 20, 2019</li>
<li>Version 5.7.6beta10 September 18, 2019</li>
<li>Version 5.7.6beta8 September 9, 2019</li>
<li>Version 5.7.6beta6 August 26, 2019</li>
<li>Version 5.7.6beta5 August 6, 2019</li>
<li>Version 5.7.6beta4 August 2, 2019</li>
<li>Version 5.7.6beta2 July 25, 2019</li>
<li>Version 5.7.6beta1 July 6, 2019</li>
<li><strong>Version 5.7.5 June 26, 2019</strong></li>
<li>Version 5.7.5beta12 June 24, 2019</li>
<li>Version 5.7.5beta11 June 16, 2019</li>
<li>Version 5.7.5beta10 June 9, 2019</li>
<li>Version 5.7.5beta9 June 8, 2019</li>
<li>Version 5.7.5beta8 April 11, 2019</li>
<li>Version 5.7.5beta7 March 28, 2019</li>
<li>Version 5.7.5beta6 March 26, 2019</li>
<li>Version 5.7.5beta5 March 22, 2019</li>
<li>Version 5.7.5beta4 March 21, 2019</li>
<li>Version 5.7.5beta3 March 14, 2019</li>
<li>Version 5.7.5beta2 March 4, 2019</li>
<li>Version 5.7.5beta1 February 26, 2019</li>
<li>Version 5.7.5beta0 February 25, 2019</li>
<li><strong>Version 5.7.4 February 12, 2019</strong></li>
<li><strong>Version 5.7.3 February 8, 2019</strong></li>
<li>Version 5.7.2 February 4, 2019</li>
<li><strong>Version 5.7.1 December 19, 2018</strong></li>
</ul>
<hr>
<h4 id="toc_10">5.7.9beta72 (January 13, 2024)</h4>
<p>Build Systems: Made building and installing deprecated programs optional for both
the CMake and Autoconf build systems.</p>
<p>Man pages: Restructured the web page versions of the manual pages installed with
MB-System. Recast the postscript versions of the manual pages into Pdf files.</p>
<p>Mbgrdviz: Generated a new version of the MB-System Route files.</p>
<p>Mbm_route2mission: Now works with both old and new format route files.</p>
<h4 id="toc_11">5.7.9beta71 (January 3, 2024)</h4>
<p>CMake build system: Fixed creating the levitus.h header file used by mblevitus
and mbconfig to define the location of the Levitus database and the OTPS
installation, thereby making mblevitus and mbconfig work properly.</p>
<h4 id="toc_12">5.7.9beta70 (January 2, 2024)</h4>
<p>Mblist: Added capability to output beam travel times, angles and other values
needed to recaclulate bathymetry by raytracing.</p>
<p>Format 261 (MBF_KEMKMALL): Fixed recalculation of bathymetry by raytracing - the
problem was that the interpolation of attitude data onto the beam receive time
was faulty, so an incorrect roll value was used in calculating the beam raytracing
takeoff angles.</p>
<h4 id="toc_13">5.7.9beta69 (December 17, 2023)</h4>
<p>Format 192 (MBF_IMAGEMBA): Fixed correction of beam amplitude values (previously
corrected values were not successfully inserted into the data structure).</p>
<p>Mbauvloglist: Program altered so that time and utcTime fields are printed by
default in format %17.6f and %12.6f, respectively, even though the MBARI Dorado AUV
log files have default formats of %8.8e instead. Now by default the timestamps are
printed usefully with precision to microseconds.</p>
<p>Mbbackangle: Fixed bug in which mbbackangle did not process sidescan or amplitude
data from files in formats that support variable numbers of beams and pixels.</p>
<p>Mbsslayout: Fixed bug in which a command to swap the starboard and port sidescan
channels was ignored.</p>
<h4 id="toc_14">5.7.9beta68 (November 30, 2023)</h4>
<p>CMake build system: It turns out that the GSF i/o module was not getting built and
used by default. The build system has been fixed so that the GSF format i/o module
is built and linked unless the cmake command includes -DbuildGSF=OFF, as in:
cmake -DbuildGSF=OFF ..</p>
<p>Mbnavadjustmerge: Added options to shift global ties singly or all together.</p>
<p>Mbtrnpp: Fixed use of covariances from TRN: to get x y z covariances use covariance[2],
covariance[0], covariance[5] rather than 0, 1, and 2.</p>
<h4 id="toc_15">5.7.9beta66 (November 18, 2023)</h4>
<p>Mbdatalist: Fixed an unitialized string causing intermittent failure.</p>
<h4 id="toc_16">5.7.9beta65 (November 17, 2023)</h4>
<p>Mbinfo and mblist: Fixed bug introduced with the alternate navigation capability that
caused mbinfo and mblist to fail when running on single files rather than through datalists.</p>
<p>Mbnavadjust: Improved handling of reference grids. The list of reference grids now starts
with an option "<Previously Selected Reference Grid>" that will cause loading a section
with a global tie set to also load the reference grid (if any) loaded when the tie was
created. If a specific reference grid is selected from the reference grid list, then that
reference grid will be loaded when any section is loaded, regardless of whether a prior
global tie already exists. </p>
<p>Mbtrnpp: Fixed bug identified by Kent Headley that caused divide by zeros when calculating swath
width filtering of soundings.</p>
<p>CMake build system: Fixed the unit testing, and enabled building unit tests by default.
After "make all" is run, the unit tests can be run with "make test".</p>
<h4 id="toc_17">5.7.9beta64 (November 16, 2023)</h4>
<p>Reading GMT grids: Fixed a very significant bug that caused GMT grids to be read into
memory incorrectly by mb<em>read</em>gmt<em>grd() in src/mbaux/mb</em>readwritegrd.c. The problem was
that the GMT default padding of grids by 2 grid cells around all edges was applied
incorrectly, with a result that the topography (or other data) in the grid was shifted
two grid cell widths north. The creation of grids by mbgrid or mbmosaic was correct;
the problem came when the grids were read in by mbgrdviz, mbanglecorrect, mbprocess,
and mbnavadjust.</p>
<h4 id="toc_18">5.7.9beta63 (November 10, 2023)</h4>
<p>Further fixes to the CMake build system, which now actually builds all components of
MB-System on MacOs Ventura, Debian 11 and 12, and Ubuntu 20 and 22.</p>
<p>Moved the MB-System version tag and version date variables from the build system
files CMakeLists.txt and configure.ac into src/mbio/mb_define.h so that there is only
one place to edit the versioning.</p>
<h4 id="toc_19">5.7.9beta62 (November 3, 2023)</h4>
<p>Fixed the Cmake build system so that all components of the current MB-System source can be
built, installed, and run on MacOs using CMake.</p>
<p>Updated the copyright notices in the several hundred source files.</p>
<h4 id="toc_20">5.7.9beta61 (November 2, 2023)</h4>
<p>Read functions mb<em>get</em>all(), mb<em>get(), mb</em>read(): Fixed bug in handling the vertical dimension
while applying alternate navigation. Bathymetry were being corrected wrongly for changes
in the sensordepth.</p>
<p>Datalists: Fixed problem in which processed files would not be read when the raw files do
not conform to MB-System suffix conventions.</p>
<p>Mbbackangle: Changed to not set parameter files when the swath files do not contain the
expected amplitude and/or sidescan data. </p>
<p>Mbgrd2gltf: Added "#include <cmath>" to src/mbgrd2gltf/bathymetry.cpp to enable compiling on CentOs 7.</p>
<p>Configure.ac and Configure: Modified to find Proj on CentOs 7 systems.</p>
<h4 id="toc_21">5.7.9beta60 (October 22, 2023)</h4>
<p>Mbnavadjust: Added an application or use mode to MBnavadjust projects. Projects can now be primary,
secondary, or tertiary, with the setting found in the Controls diaglog brought up
via the Options menu. A primary project behaves as MBnavadjust projects have always
behaved, so that applying the navigation model writes the adjusted navigation model to *.na0
files parallel to the swath files and sets the *.par parameter files so that mbprocess merges
the adjusted navigation as it generates the processed swath files. In a secondary project,
applying the adjusted navigation model writes *.na1 files parallel to the processed swath
files (not the raw swath files), and in a tertiary project the output is in *.na2 files.
The purpose for this change is to allow the existence of multiple navigation adjustment models
for the same swath data, generally because there may be reasons to have different vertical
adjustments. The secondary and tertiary navigation models are termed alternative navigation
models. A specific example is for repeated surveys of an active volcano experiencing
deformation - one may want to adjust surveys so that vertical offsets over time are removed
to allow a seamless topographic map, and to also adjust surveys so that the vertical changes
betweeen surveys are revealed by differencing the topographic models.
The MBnavadjust project file version has been updated to 3.15 with the addition of the
USEMODE parameters (primary=0, secondary=1, tertiary=2). MBnavadjust will read all old format
projects but only write out the current format.</p>
<p>Mbgrid, mbmosaic, and mblist: These programs are now capable of accessing alternative
navigation for processed swath data if such files exist and a datalist structure is set
to enable use of the alternative navigation, as described above. The internal changes
made to enable this capability are described below.</p>
<p>Datalists and a mechanism for alternative navigation:
A new specialized datalist tag has been implemented to allow use of the alternative
navigations files (*.na1 and *.na2) introduced above. Adding this tag to a datalist is the
only way to access alternative navigation when reading swath files. If the following line appears
in a datalist:
$ALTNAVSUFFIX:.na1
then following this tag the new datalist parsing function will look for a *.na1 file parallel
to each processed file, and return a flag and the path to that file. This functionality works
recursively, as all things do in datalist structures - a top level use of this tag sets the
behavior for all datalist parsing down through a recursive datalist file structure. To use this
functionality, a program must use a new function mb<em>datalist</em>read3() in place of mb<em>datalist</em>read()
or mb<em>datalist</em>read2():</p>
<div><pre><code class="language-none">int mb_datalist_read(int verbose, void *datalist_ptr, char *path, char *dpath,
int *format, double *weight, int *error);
int mb_datalist_read2(int verbose, void *datalist_ptr, int *pstatus, char *path,
char *ppath, char *dpath, int *format,
double *weight, int *error);
int mb_datalist_read3(int verbose, void *datalist_ptr, int *pstatus, char *path,
char *ppath, int *astatus, char *apath,
char *dpath, int *format, double *weight, int *error);</code></pre></div>
<p>Here the new astatus is a boolean indicating that an alternative navigation file exists for
this swath file, and apath is a string containing the path for that alternative navigation file.
In order to have the MBIO library calls actually use the alternative navigation in place of the
navigation embedded in processed swath files, the program must use another new function
mb<em>read</em>init<em>altnav() to initialize reading (instead of mb</em>read<em>init()) - here the change is
to pass in the astatus and apath values obtained from mb</em>datalist_read3(). </p>
<div><pre><code class="language-none">int mb_read_init(int verbose, char *file, int format, int pings, int lonflip,
double bounds[4], int btime_i[7], int etime_i[7],
double speedmin, double timegap, void **mbio_ptr,
double *btime_d, double *etime_d, int *beams_bath,
int *beams_amp, int *pixels_ss, int *error);
int mb_read_init_altnav(int verbose, char *file, int format, int pings,
int lonflip, double bounds[4], int btime_i[7], int etime_i[7],
double speedmin, double timegap, int astatus, char *apath,
void **mbio_ptr, double *btime_d, double *etime_d,
int *beams_bath, int *beams_amp, int *pixels_ss, int *error);</code></pre></div>
<p>If mb<em>read</em>init<em>altnav() is used, astatus is true, and apath is a valid alternative
navigation file, then calls to mb</em>get<em>all(), mb</em>get(), and mb_read() will return survey
records with the alternative navigation merged in place of the embedded navigation.</p>
<p>The only programs utilizing this capability are mbgrid, mbmosaic, and mblist - this allows
generating data products utilizing the alternative navigation.</p>
<p>We have chosen to implement these features using new MBIO functions rather than the simpler
approach of modifying the original functions. This choice is to avoid breaking the MBIO API for
existing other programs at this time. We will likely simplify the API at some point in
the future when the consequences of an API change are understood and manageable.</p>
<h4 id="toc_22">5.7.9beta59 (September 19, 2023)</h4>
<p>Mbnavadjustmerge: Made copying of mbnavadjust projects more efficient.</p>
<p>Mbnavadjustmerge: Add --remove-short-sections option to eliminate undesirably
short sections by merging them with their prior section.</p>
<p>Mbnavadjustmerge: Add --remove-file option to remove a file from an mbnavadjust project.</p>
<p>Mbcontour: Fixed drawing of survey tracklines - restored to generate thin lines.</p>
<h4 id="toc_23">5.7.9beta58 (August 30, 2023)</h4>
<p>Mbm_route2mission: Modifications to accomodate changes to Dorado AUV vehicle software.</p>
<p>Mbinfo: Added -Q option which causes mbinfo to read statistics from existing *.inf
files rather than to read the actual swath files. Variances, record types, nonfatal error messages
and mask output cannot be generated with this option.</p>
<p>Mbnavadjustmerge: Fixed bug in merging projects.</p>
<p>Docker: Added a lightweight (945 MB) MB-System Dockerfile build based on alpine
Linux distribution. The image contains full MB-System, including TRN and graphical tools.
Runs on MacOS 12 (Monterey) and Ubuntu 22.04.</p>
<p>TRN tools: Minor changes to .gitignore (add binaries) and mbtrn/utils/tbinx.cpp (add signal
handler, reconnect timing, bug fix).</p>
<p>Mblist: Added option to merge data from a secondary file and allow printing those
secondary data values. The secondary file is columnar text in which the first column
holds the time stamp in epoch or unix time (seconds since 1/1/1970), and up to 19
following columns hold other data collected during the survey (e.g. temperature or
salinity measured on a CTD sensor).</p>
<p>Mbeditviz: The scale widget controlling grid cell size now changes it's range if either
the minimum or maximum values are selected (halving or doubling, respectively).</p>
<p>Mbnavadjustmerge: Copying mbnavadjust projects is much more efficient due to use of
a fast file copy function replacing a shell call of the program cp.</p>
<h4 id="toc_24">5.7.9beta57 (June 27, 2023)</h4>
<p>Mbm_route2mission: Added -T option to embed use of Terrain Relative Navigation in
MBARI Mapping AUV missions.</p>
<p>Format 89 (MBF_RESON7K3): Fixed too small buffer size for broadcast Teledyne s7k
data records, which caused mbtrnpp to crash by seg fault. This was 32K and is now 600K.</p>
<p>Mbnavadjust: Fixed bug in the inversion algorithm.</p>
<h4 id="toc_25">5.7.9beta53 (June 15, 2023)</h4>
<p>Rewrote the CMake build system based on the work of both Tom O'Reilly and Josch. This
build system now works on MacOs Ventura. We will continue to augment and test using
cmake so that this build system also works on Ubuntu and Debian Linux.</p>
<p>Mbtrnpp and related TRN code: Many updates and improvements from Kent Headley</p>
<p>Mbcontour: The navigation line width and color can now be set using the -W argument</p>
<p>Format SOIUSBLN (275): Supports USBL tracking data from R/V Falkor (too) as format 275.</p>
<p>Format SOIROVN (276): Supports ROV SuBastian INS navigation data as format 276.</p>
<p>Mbm_route2mission: Added a depth limit parameter to the -D argument.</p>
<p>Mbgrdviz: Fixed display of vector data.</p>
<p>General: Fixed automated handling of asynchronous nav and attitude data when reading
Kongsberg or Teledyne multibeam data that have not been preprocessed. Changes are in
mbio/mb_navint.c</p>
<p>Format RESON7K3 (89): Fixed counting of valid records in the file catalog.</p>
<p>Mbgetphotocorrection, mbphotomosaic, mbphotogrammetry: Fixed to properly handle embedding
of parameters within recursive imagelist structures, allowing mixing of photographs taken
with difference camera systems or perhaps different camera calibrations.</p>
<p>Mbgetphotocorrection, mbphotogrammetry: enabled multi-threading.</p>
<p>Mbauvloglist: Allow merging attitude data from a separate file. Allow decimation of input.</p>
<p>Mbmosaic: Augmented azimuth priority mode so that the azimuth alone can be specified, in which
case the azimuth priority factor is one.</p>
<p>Mbpreprocess: Now outputs integrated navigation for all sensors producing mapping data.</p>
<p>Formats 56 (MBF<em>EM300RAW) and 57 (MBF</em>EM300MBA): Fixed catastrophic bug introduced in
5.7.9beta50 that treated many signed values (like acrosstrack distance) as unsigned.</p>
<h4 id="toc_26">5.7.9beta52 (March 9, 2023)</h4>
<p>Formats 56 (MBF<em>EM300RAW) and 57 (MBF</em>EM300MBA): Fixed catastrophic bug introduced in
5.7.9beta50 that treated many signed values (like acrosstrack distance) as unsigned.</p>
<p>MBgrdviz: Added ability to export routes as TECDIS LST files for display in a variety of
marine chart display software. </p>
<p>Autotools build system: Altered Makefile.am files in third<em>party/googlemock and
third</em>party/googletest to eliminate benign but alarming error messages during make install
and make clean commands.</p>
<p>Mbm_route2mission: Added ability to insert a magnetometer calibration maneuver into an
AUV mission spiral descent using the -Naltitude/mode command, where altitude is the
spiral descent termination altitude and mode = 0 for no start survey behavior, 1 for
start survey behavior alone, and 2 for start survey plus a magnetometer calibration
maneuver.</p>
<h4 id="toc_27">5.7.9beta51 (February 14, 2023)</h4>
<p>Format 89 (MBF_RESON7k3): Removed debug message inadvertently left active in 5.7.9beta50.</p>
<h4 id="toc_28">5.7.9beta50 (February 12, 2023)</h4>
<p>General: Changed many sprintf() calls to snprintf() calls. </p>
<p>General: Fixed many compiler warnings having to do with unused variables, unitialized
variables, and possible string overflows.</p>
<p>MBnavadjust: Fixed interface issues for importing multiple reference grids and
selecting those while makeing global ties.</p>
<p>Format 261 (MBF_KEMKMALL): Added code to detect and handle gracefully some
instances of corruption of MRZ datagrams, particularly due to missing bytes.</p>
<p>Format 201 (MBF_HYSWEEP1): Fixed reading of Hysweep multibeam in which beam angles are
stored in spherical coordinates but are not corrected for roll and pitch. Updated
support to handle multibeam data with angles in spherical coordinates that have not
been corrected for roll and pitch, and to be consistent with the most recent Hypack
users manual released February 2023.</p>
<h4 id="toc_29">5.7.9beta49 (January 22, 2023)</h4>
<p>Mbm<em>grdplot, mbm</em>grd3dplot, mbm<em>histplot, mbm</em>plot, mbm_xyplot: Made evince one
of the default Postscript viewers because it is commonly installed on Ubuntu
machines.</p>
<p>General: Addressed compiler warnings due to uninitialized variables, inconsistent
variable typing, and other minor issues.</p>
<p>MBnavadjust: Changed the solution algorithm so that the final stage of LSQR
matrix inversion is done in several steps. As before, the first three stages are
to construct an initial model by interpolating any global ties, then solve for
and apply average offsets for each survey, then conduct an iterative relaxation
towards an additional perturbation solution. Each stage produces a perturbation
solution, that is, a solution to fit the navigation offsets remaining after
applying the existing navigation model. Each perturbation is added to the
navigation model, which is then the starting point for the next stage. These
three stages build up an approximate navigation solution that solves most of the
original mismatch between overlapping and crossing swathes. The final stage is
to build and solve an overdetermined least squares matrix problem constrained by
all crossing and global times, by any surveys with fixed navigation, and also
constrained by a penalty against first and second derivatives of the perturbation.
Now, for multi-survey projects the matrix solution stage consists of first
solving the full matrix problem, then solving for a perturbation to satisfy
the remaining misfit for each of the individual surveys in turn, and finally
redoing the full matrix problem. Again, after each solution step the resulting
perturbation is added to the navigation solution.</p>
<p>Mbnavadjust: Added two new list options for sorted crossing ties. Now the sorted
crossing tie list can be limited to the top 5% or 1% of ties.</p>
<p>Format MBF_MBARIROV (165): Added recognition for new filenaming conventions for
MBARI ROV navigation files.</p>
<h4 id="toc_30">5.7.9beta48 (December 16, 2022)</h4>
<p>Mbmosaic: Fixed parsing of the -Ypriority<em>source option when priority</em>source is
a filename.</p>
<p>Mbm<em>grdplot: Fixed handling of image file min max when color</em>mode == 6.</p>
<p>Mbnavadjust: Added controls allowing the mode of global ties to be changed
interactively.</p>
<p>Mbnavadjust: Changed project file format, adding the the id of the source
reference grid used for each global tie.</p>
<p>Mbview library: Fixed problem where mbview did not render the last row and
column of a grid (the easternmost and northernmost data). Also attempted to
make picking more robust.</p>
<p>Mbnavadjust: Fixed interpolation of global ties to create the starting navigation
model during inversions. Fixed several actions in section and reference grid mode.</p>