ChangeLog.md

## MB-System ChangeLog File:

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.

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.

---
### MB-System Version 5.8 Releases and Release Notes:
---
- Version 5.8.3beta16    July 26, 2026
- Version 5.8.3beta15    July 26, 2026
- Version 5.8.3beta14    July 6, 2026
- Version 5.8.3beta13    June 18, 2026
- Version 5.8.3beta12    January 7, 2026
- Version 5.8.3beta11    December 27, 2025
- Version 5.8.3beta10    December 22, 2025
- Version 5.8.3beta09    December 4, 2025
- Version 5.8.3beta08    November 16, 2025
- Version 5.8.3beta07    October 22, 2025
- Version 5.8.3beta06    October 1, 2025
- Version 5.8.3beta05    September 30, 2025
- Version 5.8.3beta04    September 18, 2025
- Version 5.8.3beta03    August 31, 2025
- Version 5.8.3beta02    August 29, 2025
- Version 5.8.3beta01    August 27, 2025
- **Version 5.8.2          August 19, 2025**
- Version 5.8.2beta24    July 19, 2025
- Version 5.8.2beta23    June 25, 2025
- Version 5.8.2beta22    June 16, 2025
- Version 5.8.2beta21    March 15, 2025
- Version 5.8.2beta20    February 22, 2025
- Version 5.8.2beta19    January 19, 2025
- Version 5.8.2beta18    December 8, 2024
- Version 5.8.2beta17    November 7, 2024
- Version 5.8.2beta16    November 6, 2024
- Version 5.8.2beta15    October 1, 2024
- Version 5.8.2beta14    September 6, 2024
- Version 5.8.2beta13    August 23, 2024
- Version 5.8.2beta12    August 22, 2024
- Version 5.8.2beta11    August 19, 2024
- Version 5.8.2beta10    August 16, 2024
- Version 5.8.2beta09    August 4, 2024
- Version 5.8.2beta08    July 27, 2024
- Version 5.8.2beta07    June 27, 2024
- Version 5.8.2beta06    June 13, 2024
- Version 5.8.2beta05    May 19, 2024
- Version 5.8.2beta04    May 13, 2024
- Version 5.8.2beta02    May 1, 2024
- Version 5.8.2beta01    April 29, 2024
- **Version 5.8.1          March 22, 2024**
- Version 5.8.1beta09    March 22, 2024
- Version 5.8.1beta08    March 10, 2024
- Version 5.8.1beta07    February 24, 2024
- Version 5.8.1beta04    February 16, 2024
- Version 5.8.1beta03    February 8, 2024
- Version 5.8.1beta02    February 7, 2024
- Version 5.8.1beta01    February 1, 2024
- **Version 5.8.0          January 22, 2024**

---

#### 5.8.3beta16 (July 26, 2026)

Program mbusbl2fnv: New program that converts a USBL (ultra-short baseline) ROV
tracking CSV file to an MB-System fast navigation (fnv) text file. The input CSV
format has one header line followed by data lines giving epoch time, latitude,
longitude, and ROV depth; heading, speed, roll, pitch, and heave are not present
in USBL tracking data and are output as 0.0.

Program mbswath2las: New program that exports swath bathymetry soundings to LAS 1.4
point cloud files, one point per valid (unflagged) beam, allowing swath bathymetry to
be loaded directly into LAS/LIDAR-oriented point cloud viewers, GIS packages, and
processing pipelines (e.g. CloudCompare, QGIS, PDAL) that do not otherwise read MBIO
formats. By default sounding positions are written as geographic longitude/latitude
in decimal degrees (WGS84); a projected coordinate system may instead be specified so
that positions are written as easting/northing in meters.

Build system: Continued work to allow MB-System to build on Windows, extending fixes
made previously to the CMake configuration and to src/mbtrn and src/mbtrnav. This
round of changes covers the non-TRN libraries and programs: src/gsf (CMakeLists.txt
changes only, no code changes required), src/mbio (mb_defaults.c, mb_mem.c, and
mbsys_kmbes.c), src/gmt, and src/mbaux, src/bsio, and src/surf, where the Windows
shim for XDR is now built as its own library, libmb_xdr_win32, within src/mbaux.
Also updated src/mbgrd2ltf, src/mbmesh, src/otps, and src/photo to build consistently
on MacOs, Linux, and Windows, along with a number of general CMake project-structure
fixes.

Library mbview: Fixed a memory-management bug in route handling in which deleting the
last point of a route (removing the whole route) shifted the internal route array down
without first freeing the deleted route's own point/segment arrays and without clearing
the vacated array slot afterward. This leaked memory, silently caused two routes to alias
the same underlying arrays, and could crash mbgrdviz and other mbview-based programs with
a double free when routes were deleted and new routes subsequently added. A broader audit
of the mbview route, navigation, site, and vector handling code found and fixed several
related problems: an inverted bounds check in mbview_getrouteinfo() that allowed
out-of-bounds array reads; a memory leak on navigation-line deletion (per-segment drape
buffers were never freed); dead code in the route list widget that silently disabled
selection highlighting; uninitialized segment endpoint data when adding vectors; and
list-selection and list-deletion callbacks for the route and navigation list dialogs
that could act on the wrong entry if a list item were ever marked inactive. Also fixed
the title bars of the 2D Parameters, 3D Parameters, Shading Parameters, Profile Display,
About, and "please wait" message dialogs, which previously displayed internal Motif
widget names (e.g. "mbview_dialogShell_2dparms") instead of readable titles.

Program mbgrdviz: Fixed a bug in the Generate Survey Route feature in which a cached
route index could go stale if the user deleted an unrelated route via the 3D view while
the Area Route dialog remained open, causing the next "Generate Survey" click to delete
the wrong route. Also fixed the title bar of the Area Route dialog, which previously
displayed the internal widget name "dialogShell_arearoute" instead of "Generate Survey
Route for Selected Area...".

Program mbeditviz: Fixed a crash on opening a swath file that MBIO cannot actually read,
caused by a missing status check before dereferencing the file handle. Fixed a
memory-management bug in file deletion analogous to the mbview route bug above, in
which removing a file from the loaded-files list left a stale duplicate array slot that
could later alias data between two loaded files. Fixed several file-record fields
(including processed-file-info and sensordepth navigation arrays) that were left
uninitialized on newly imported files. Added a bounds check to the ping-reading loop to
prevent a heap buffer overflow when a swath file's *.inf index file undercounts its
actual number of pings. Fixed a bug in which dismissing the 3D soundings window
overwrote the global verbosity setting rather than the intended error-code variable.
Fixed a bug in which a single navigation-loading failure for one file silently skipped
loading navigation for every subsequent file in the same session. Fixed a leak and
potential crash on the (rare) memory allocation failure path when importing files. Fixed
the title bar of the Error dialog (previously showed "dialogShell_error") and corrected
a garbled status message ("Reading data list...").

Program mbnavadjust (and the mbnavadjustmerge and mbnavadjustfine tools that share its
project I/O and data structures): Fixed a bug in which deleting a tie point used a
stale, unrelated global variable instead of the tie actually being deleted, corrupting
which tie was removed and, in one call path, capable of an out-of-bounds write into the
crossings array. Fixed a wide-ranging set of missing bounds checks in the project file
reader, which previously trusted the file's own record counts and array indices to size
loops and index fixed-size per-crossing and per-section arrays, and used unbounded string
conversions into fixed-size path buffers - a corrupted or hand-edited project file could
overflow multiple buffers. Fixed a bug in which removing a file from a project (via
mbnavadjustmerge) left remaining sections' file/section identity fields stale, able to
silently misattribute sections to the wrong file. Fixed a memory leak in which a file's
section array was allocated with the standard C library and freed with an MB-System
function that only recognizes memory it allocated itself, so the free silently did
nothing. Fixed three sites in mbnavadjustmerge where a newly grown crossing's file
references were read before being assigned, an out-of-range crossing could be added
with no validation, and a failed allocation was not checked before the new crossing was
used. Fixed four missing-brace bugs that caused a visualization update function to run
unconditionally regardless of whether a visualization window was ever open. Fixed a
command-line tool (mbnavadjustfine) build break caused by a call with the wrong number
of arguments, a numeric option that corrupted adjacent settings and always aborted the
program, an uninitialized pointer used in an error message, a per-crossing memory leak,
continuing an alignment computation after detecting invalid input, and a divide-by-zero
when every sounding in a section was flagged. Fixed a project-merging command that
validated and updated the wrong internal counter, and a project list display that never
showed survey-vs-survey "block" comparisons. Also fixed a missing dialog title, a
silent failure to write cached triangulation data, an unchecked allocation before use,
several unbounded command-line path arguments, a dead duplicate-crossing check, an
undefined-behavior fclose() on a failed file open (7 sites), and a display counter that
was always zero.

Program mbnavadjust (and mbnavadjustmerge): A follow-up round of fixes targeting crashes
reported when displaying and selecting global ties. Fixed invalid qsort() comparator
functions for the sorted global-tie and sorted crossing-tie list displays that never
returned zero for equal or incomparable elements, violating the strict-weak-ordering
contract required by qsort() and able to crash on quicksort-family implementations
(including those used by both Linux glibc and macOS/BSD libc). Fixed a heap buffer
overflow in the sparse inversion matrix built for the preliminary per-block offset
solution (used by both the main navigation inversion and the "Autoset Z Offsets"
feature): the matrix's row stride was set to 3 times the number of survey blocks, but
the backing array was only ever allocated for a fixed stride of 6, overflowing on any
project combining more than two surveys - an entirely ordinary case - during exactly the
step that folds global tie offsets into the solution. Fixed a stale-variable bug in the
"Autoset Z Offsets" feature where the per-block averaged global tie offset was indexed
with a leftover loop variable from an unrelated, already-finished loop instead of the
current block index, an out-of-bounds heap read. Fixed a bug in mbnavadjustmerge where
merging additional files into a project unconditionally renumbered every copied
section's reference-grid ID, corrupting the "no reference grid assigned" sentinel value
into a bogus but plausible-looking grid index for any section without a global tie or
reference grid; a section thus corrupted could cause mbnavadjust to load and display the
wrong reference grid when its global tie was later selected. Also fixed a missing bounds
check (and a related debug-only variable mixup) in the reference grid loader that could
read the reference-grid name array out of bounds given a negative grid index, and fixed
the project's global-tie counters not being decremented when mbnavadjustmerge removes a
file that held global ties, which left the "ties analyzed" status display overcounted.

Program mbdatalist: Fixed a bug in which the long option --report incorrectly triggered
the same behavior as --copy instead of generating a datalist report, due to a copy-paste
error in the option-parsing code.

Program mbinfo: Fixed a bug in which the long option --ping-variances accepted but
silently ignored its argument; only the equivalent short option -P worked correctly.

Program mbmakeplatform: Fixed a typo (--platform-documenation-url) that made the
correctly-spelled --platform-documentation-url option unrecognized. Fixed a bug in which
--sensor-source-camera1/2/3 and --set-source-camera1/2/3 were all registered under the
same un-numbered option name, making the numbered variants unreachable.

Program mbpreprocess: Fixed missing option-table entries for --time-latency-apply-altitude
and --filter-apply-altitude, which had working handlers but were never recognized by the
command-line parser. Also fixed both handlers, which incorrectly applied the correction
to attitude data instead of altitude data due to using the wrong internal flag bit.

Program mbvoxelclean: Fixed a bug in which --count-flagged was declared as requiring an
argument even though it is a boolean flag, causing the documented bare-flag usage to be
rejected by the command-line parser.

Program mbsslayout: Fixed several option-parsing and ancillary-data-correction bugs found
during a documentation audit. --line-route had a working handler but was never registered
with the option parser, making it unusable. --line-range-threshold was accepted but
silently discarded, so the survey-line range threshold was always hardcoded to 50 meters
regardless of what was specified on the command line. --time-latency-apply-altitude
applied its time latency correction to attitude data instead of altitude data (the same
bit-flag bug as in mbpreprocess), and a soundspeed time-latency correction was gated on
that same wrong (attitude) flag bit, causing it to fire whenever --time-latency-apply-attitude
was used alone. The entire --filter/--filter-apply-* family of options, intended to apply
a Gaussian time-domain filter to ancillary data (navigation, sensordepth, heading,
attitude, altitude), was never registered with the option parser and had no
implementation; this has now been implemented using the existing mb_apply_time_filter()
library function, mirroring the equivalent feature in mbpreprocess. Added a new
--line-position-list option that defines survey lines from a simple ASCII file of
waypoint longitude/latitude pairs, as a lighter-weight alternative to --line-route's full
MB-System route file format.

Man pages: Audited the man pages for all 46 programs in src/utilities against their
actual command-line option implementations, finding and fixing documentation
discrepancies in 24 of them, including missing options (mb7k2jstar, mbareaclean,
mbauvloglist, mbbackangle, mbgetesf, mbrolltimelag, mbroutetime, mbsegygrid, mbsegypsd,
mbset, mbsvplist, mbsslayout, mbvoxelclean, mbmakeplatform), stale options describing
command-line flags that no longer exist (mbclean, mbhistogram, mbsegylist, mbsegypsd,
mbsslayout, mbsvpselect), and incorrect descriptions or default values (mb7k2jstar,
mbclean, mbcopy, mbextractsegy, mbfilter, mbminirovnav, mbmosaic, mbpreprocess,
mbrolltimelag, mbroutetime, mbset, mbsvplist, mbsvpselect, mbvoxelclean). This audit
also surfaced the mbsslayout and mbpreprocess source-code bugs described above.

Program mbnavadjustmerge: Added --update-file, --update-survey, and --update-all-files
options that update the beam-validity flags in an mbnavadjust project's section data to
match the current processed version of each swath file, matching pings by timestamp and
copying over only the flag byte - the navigation, attitude, bathymetry, amplitude, and
sidescan values already stored in the project are left untouched. This lets soundings
newly flagged bad by re-editing a file (e.g. with mbclean or mbedit) after it was
originally imported be excluded from the project without a full, riskier re-import of the
file's bathymetry. If a matched ping's beam count no longer matches what is stored in the
project, that ping's flags are left unchanged and a warning is printed rather than risk
misapplying flags to the wrong beams; beams that never held real sounding geometry when
originally imported are likewise left flagged null regardless of what the current
processed file reports for that beam index, since marking such a placeholder beam as
flagged-but-real would otherwise corrupt the scaled short-integer depth encoding used by
the project's section file format. Every updated section's coverage mask and triangulated
surface are automatically regenerated. These options replace an earlier, incomplete
--reimport-file/--reimport-survey/--reimport-all-files implementation that instead
substituted bathymetry, amplitude, and sidescan values wholesale from the reprocessed
file; that implementation was never released and has been removed.

Program mbnavadjustmerge: Added --create-project, --section-length, --section-soundings,
--contour-interval, --color-interval, --tick-interval, --label-interval, --decimation,
--smoothing, and --zoffsetwidth options to create new mbnavadjust projects and change
project settings from the command line, matching functionality previously available only
in the mbnavadjust graphical interface. Added --import and --import-as-survey to import
swath data (a single file or a recursive datalist), and --find-crossings to detect new
crossings between imported sections. Added --autopick and --autopick-horizontal to
automatically pick navigation ties at unanalyzed crossings, together with
--autopick-crossing-type, --autopick-scope, --autopick-survey, --autopick-survey2,
--autopick-file, --autopick-section, and --autopick-overlap-threshold options to restrict
which crossings are considered. Implementing this required extracting the crossing-loading,
bathymetric misfit, and autopick logic out of mbnavadjust_prog.c (previously usable only by
the mbnavadjust graphical interface) into a new shared library, mbnavadjust_core, linked by
mbnavadjust, mbnavadjustmerge, and mbnavadjustfine; the CMake build was restructured so this
library and mbnavadjustmerge no longer require Motif or X11 to build, unblocking headless
and CI builds of the command-line tool.

Program mbnavadjust (and mbnavadjustmerge): Fixed a bug in mbnavadjust_new_project() in
which the section_soundings setting was accepted as a parameter but never actually stored
in the new project, so every newly created project silently used a section_soundings value
of zero regardless of what was requested, whether created via the graphical New Project
dialog or the command line.

Program mbnavadjust: Fixed a crash in the "Invert Navigation" menu item (and the "Auto-Set
Survey-vs-Survey Vertical Offsets" feature, which shares the same code) in which a failed
memory allocation for the sparse least-squares matrix used by the navigation inversion was
never checked before the buffer was zeroed, crashing instead of reporting an error; large
enough projects could also silently compute the wrong, too-small allocation size due to a
32-bit integer overflow in the row-count/column-count multiplication used to size that
matrix, risking heap corruption on a subsequent write rather than a clean allocation
failure. Both are now fixed, with a dialog reported to the user if the allocation still
fails.

Program mbnavadjust: Fixed a bug in which selecting a survey-vs-survey "block" from the
Data Table list and then displaying crossings restricted to that block could show no
crossings at all. The code that extracts the clicked list item's text had a fallback for
when Motif's primary text-retrieval method returns nothing, but the fallback was nested
inside a check that skipped it entirely whenever the primary XmString field itself was
null, rather than being reached whenever it was actually needed.

Program mbnavadjust: Added long-form equivalents (--verbose, --help, --dark-background,
--input=project, --reset-crossings) for all existing single-letter command-line options.

Program mbnavadjustmerge: Added --invert-navigation, --update-grids, and --apply-navigation
options, completing the navigation-adjustment workflow begun with --autopick above.
--invert-navigation solves the network of ties and crossings for a corrected navigation
model, exactly as the "Invert Navigation" menu item does in mbnavadjust. --update-grids
regenerates the project's reference bathymetry grids from the current navigation solution,
equivalent to "Update Grids". --apply-navigation writes the corrected navigation out to the
swath data files' processing parameters, equivalent to "Apply Navigation", and is normally
the last step in the workflow. Implementing this required moving the navigation-inversion
solver, grid-regeneration, and navigation-output logic (previously usable only by the
mbnavadjust graphical interface, over 3000 lines in mbnavadjust_prog.c) into the shared
mbnavadjust_core library alongside the autopick logic moved previously.

Program mbnavadjust (and mbnavadjustmerge): Fixed a bug in mbnavadjust_new_project() in
which newly created projects never had their navigation "use mode" initialized, silently
defaulting to an invalid value of zero. This had no visible effect in the graphical
interface, where a separate program-startup default masked the gap, but meant that
mbnavadjustmerge's --apply-navigation, run against a project created with
--create-project, would silently skip updating each file's processing parameters with no
error reported.

Program mbnavadjust: Fixed a regression from moving the navigation-inversion, grid-update,
and apply-navigation logic into the shared mbnavadjust_core library (see above): the
"please wait" message dialog no longer appeared during Invert Navigation or Update Grids,
since those functions could no longer call GUI dialog functions directly. Restored the
dialog by wrapping the calls at each of their GUI call sites (the Invert Navigation and
Update Grids menu items, the automatic grid update after importing data, and the automatic
grid update when opening a project whose topography grid does not yet exist) with the same
do_message_on()/do_message_off() pattern already used elsewhere in the program, and did the
same for Apply Adjusted Navigation, which had the identical gap. A follow-up fix addressed
a second bug uncovered in the process: do_message_on() itself did not wait for the dialog to
actually become mapped and viewable before returning, so on a dialog's first appearance in a
session, the window manager's mapping could still be pending when the long operation
immediately following it started; since none of these operations return control to the
window system's event loop until they finish, the dialog's initial text could remain
unpainted (an empty box) for the operation's entire duration. Fixed by having do_message_on()
wait for the dialog to become viewable first, mirroring the equivalent wait already used for
the main window at startup.

Program mbnavadjust (and mbnavadjustmerge): During autopicking, a crossing whose section
length is less than 0.25 times the project's desired section length is silently skipped (to
avoid matching short sections at the end of a file); this is now reported to the user with a
message stating the crossing was skipped due to short section length, whether autopick is
run interactively or via mbnavadjustmerge.

Program mbnavadjust: Fixed a segmentation fault when dismissing the Nav Err (crossing
analysis) window while no crossing was currently loaded - for example immediately after
clearing all ties to start over with a project. The dismiss callback freed the window's
graphics contexts unconditionally instead of only when a crossing had actually been loaded
(as the equivalent code in the Quit handler already correctly does), so dismissing the
window a second time without an intervening crossing load double-freed them, crashing in
Xlib's XFreeGC(). Diagnosed directly from the macOS crash report, which resolved exactly to
the offending XFreeGC() call once the crash binary's UUID was confirmed to match the current
build.

Program mbnavadjust: Fixed the Controls dialog showing stale values when opened via the Nav
Err window's Settings->Contours menu item, rather than the current project settings shown
when it is opened via the main window's Option->Controls menu item. The main window's button
has two callbacks - one that refreshes every slider and toggle from the project settings,
followed by one that displays the dialog - while the Nav Err window's button only had the
second, display-only callback, so it showed whatever values happened to be left over from
the last time the dialog was shown or applied. Fixed by adding the missing refresh callback.

Program mbnavadjust: During autopicking, the crossing/section/tie list display and model
plot (if open) did not update again until the entire run finished, since the loop that used
to periodically refresh them lost access to those GUI functions once it was moved into the
shared mbnavadjust_core library. They are now refreshed every tenth crossing processed via a
callback function pointer passed in only by the interactive program; mbnavadjustmerge passes
none, so the shared autopick loop itself has no GUI dependency.

Program mbnavadjust: Fixed the grid region used by Update Grids, which was computed from
each section's original, unadjusted geographic bounds and never updated afterward regardless
of any navigation inversion performed since - a solution that moved sections a significant
distance could leave the grid too small to encompass the shifted data. The region is now
recalculated from each section's original bounds shifted by the range of its current
navigation adjustment. The per-survey grids' region, previously computed but never actually
passed to mbgrid (relying solely on mbgrid's own bounds auto-detection), is now adjusted the
same way and passed explicitly, matching the overall project grid.

Programs mbedit, mbnavedit, and mbvelocitytool: A memory-management and correctness audit
of these three interactive Motif editors (paralleling the earlier audits of src/utilities
and mbview/mbeditviz) found and fixed a critical NULL-pointer-write crash in mbnavedit's
"Invert Navigation" modeling mode, triggered by ordinary use whenever exactly one point is
visible: the inversion matrix's row-count formula went to zero for a single point, and
mb_mallocd() treats a zero-byte allocation as a successful NULL return, so the code
proceeded to write through the NULL buffer. All three programs shared a second bug: their
get_text_string() helper did an unbounded strcpy() from any Motif text field into
fixed-size buffers as small as 10 bytes, with no widget-side length limit set on any of the
fields - fixed by adding an explicit destination-size parameter to the helper in all three
programs. All three also shared an unterminated strncpy() when copying a user-selected file
path from the file-selection dialog, which could read past the destination buffer on
sufficiently long paths. Several additional bugs specific to each program were also fixed:
in mbedit, undersized bottom-detect-type and pulse-type name lookup tables that indexed
past their end on lidar/photogrammetry data, a reversed bit-shift that corrupted the
extracted detection-priority value, and an out-of-bounds neighbor read in the median-spike
filter's along-track window; in mbnavedit, an uninitialized-neighbor read that produced
garbage speed/course-made-good values for single-point buffers, an off-by-one that silently
excluded the first visible point from mouse "pick" mode, and unreliable time-interval
bookkeeping after deleting bad-time records (replaced with a straightforward recompute
pass); in mbvelocitytool, four sites where a chain of unchecked mb_mallocd() calls could let
a later successful allocation mask an earlier failure and use the resulting NULL pointer, a
divide-by-zero (surfacing as a silently propagated NaN) in the per-ping depth-residual
linear fit when only one beam survived flagging, an uninitialized sensor-depth value used
when every beam in a ping was flagged bad, a stray "!= 60" condition that silently skipped
freeing all per-ping data buffers for any ping with exactly 60 beams, and a latent
(then-unreachable) heap overflow in the profile-deletion code that copied array contents
into a differently-sized, already-freed destination buffer rather than moving the whole
profile record.

Man pages: Audited the mbedit, mbnavedit, and mbvelocitytool man pages against their actual
command-line options and current GUI behavior. Fixed a wrong option letter (mbedit's browse
mode is -D, not -B, as the man page stated), two stale/nonexistent options in mbnavedit's
synopsis and options list (-O and -T, neither implemented in the code), and several wrong
default values and figures across all three (data buffer sizes, mbvelocitytool's default
format id, default editable-profile point count, and maximum number of display profiles).
Also fixed a self-contradicting keyboard-macro table in mbedit's man page (Grab and Info
mode keys were listed backwards in one place and correctly in another), a mislabeled
duplicate section heading, and added documentation for several existing but previously
undocumented features: mbedit's "Flag by Beam Angle" filter and median-filter window-size
sliders, its three-way exclusive "Show Flag States / Show Bottom Detect Algorithms / Show
Source Pulse Types" view toggle, and mbnavedit's "Sonar Depth Plot" toggle.

Man pages: Removed the mbps, geod, and proj man pages (and mbps's generated html/pdf docs).
The mbps man page documented a program with no corresponding source file or build target
anywhere in the current source tree - it was already gone from the build, just not from the
documentation. The geod and proj man pages documented command-line tools belonging to the
external PROJ library dependency rather than programs developed as part of MB-System, and
were never actually wired into either build system to begin with. Updated both the CMake
and autotools build files for src/man/man1 and src/html to remove the now-dangling
references to these three pages.

Programs in src/utilities: Added long-option (--long-name) equivalents to every remaining
command-line program in src/utilities that previously supported only traditional single-letter
options, extending the getopt_long() support already in place for about 15 other utilities
(mbinfo, mbdatalist, mbpreprocess, mbsslayout, mbvoxelclean, etc.). This covers 31 programs:
mb7k2jstar, mbabsorption, mbareaclean, mbauvloglist, mbbackangle, mbclean, mbcopy, mbctdlist,
mbdefaults, mbextractsegy, mbfilter, mbformat, mbgetesf, mbgrid, mbhistogram, mblevitus, mblist,
mbmapscale, mbmosaic, mbnavlist, mbprocess, mbrolltimelag, mbroutetime, mbsegygrid, mbsegyinfo,
mbsegylist, mbsegypsd, mbset, mbsvplist, mbsvpselect, and mbtime. Every existing short option
continues to work exactly as before; each program's --help output now lists every long/short
pair. This work surfaced four short options that had been silently accepted by each program's
option parser for the program's entire history (predating even this repository's 2019 move from
Subversion to Git) with no corresponding case handler at all - inert no-ops with no effect and
no documentation anywhere. Investigating each: mbsegylist's -W turned out to be real,
unimplemented functionality - mbsegylist is a segy-format sibling of mblist, which has a working
-W/--use-feet that converts bathymetry and distance output columns from meters to feet, and
mbsegylist's own man page documents its fixed sonar-depth and water-depth output columns in
meters, strongly suggesting the
option string was copied from mblist without ever porting the conversion logic; -W/--use-feet is
now fully implemented in mbsegylist and documented in its man page. The other three (mbauvloglist's
-W, mbsegypsd's -P, mbextractsegy's -D) had no discoverable intended purpose anywhere in the code,
man pages, or usage messages, so rather than guess at functionality they were removed outright.

Programs mbedit, mbnavedit, mbvelocitytool, mbgrdviz, and mbeditviz: Added long-option
(--long-name) equivalents to these five interactive Motif programs' command-line options,
extending the getopt_long() work above from src/utilities to the GUI editors (mbnavadjust was
requested too but already had full getopt_long() support). As with src/utilities, this surfaced
a dead option with no case handler at all: mbedit's -S. Unlike the src/utilities finds, this one
had a full, traceable history back to 1993 - before MB-System's "Version 5.0" rewrite in 2000,
-S set a startup_save_mode flag controlling whether a pre-existing edit save (.esf) file would
be loaded for the input file; the getopt string lost its argument and the case handler was later
dropped entirely as the code was restructured into the modern Motif-callback architecture, but
the underlying feature never actually disappeared - mbedit still has two live callback paths,
one that loads a file fresh and one that loads it using an existing edit save file, offered to
the user via a "use previous edits?" dialog that pops up at startup whenever a save file already
exists. The CLI flag's original job was simply to skip that dialog and answer "yes" automatically,
exactly the kind of thing needed when mbedit is launched non-interactively by another process
(the same rationale as the existing -G/--gui-mode option). Restored as -S/--use-edit-save.
Updated mbedit's man page to document every long-option equivalent in both the synopsis and
options list, matching the format already used by the getopt_long-converted src/utilities
programs, and fixed a duplicate --verbose/-V entry found in the process.

Program mbtrnpp: Added a first man page for this utility, which previously had no
documentation at all. mbtrnpp is an optional real-time preprocessor, normally run
unattended aboard an AUV or other survey platform, that reads multibeam bathymetry
(from a datalist, a single swath file, or a live network socket), applies automated
cleaning and downsampling, and passes the result to an embedded terrain relative
navigation (TRN) process; it is built only when MB-System is configured with TRN
support (--enable-mbtrn with autotools, or -DbuildTRN=ON with CMake, both of which
are the default). The new man page documents the synopsis, description, and every
command-line/configuration-file option (input/output specifiers, TRN map/filter/
convergence settings, reinitialization and decimation options, and the mb-out/trn-out
network output mnemonics), drawn from the option-parsing code in mbtrnpp.c and the
existing README-mbtrnpp.md and mbtrnpp-cfg.example documentation, along with usage
examples. The page is installed by src/man/man1/CMakeLists.txt only when the buildTRN
CMake option is enabled, and by src/man/man1/Makefile.am/Makefile.in only when the
BUILD_MBTRNUTILS automake conditional is set, matching the pattern already used for
the deprecated-program man pages so that the page is never installed alongside a build
that lacks the program itself.

The bugs described above, and the mbtrnpp man page, were identified and written with
the assistance of the AI coding assistant Claude Sonnet 5 (Anthropic, model
claude-sonnet-5), operating as Claude Code under developer supervision and review.

#### 5.8.3beta15 (July 26, 2026)

This release was botched due to a faulty merge of conflicting pull requests. All changes
intended for this release are described above for 5.8.3beta16.

#### 5.8.3beta14 (July 6, 2026)

Programs mbedit, mbnavedit, mbvelocitytool, mbgrdviz, mbeditviz, mbnavadjust: updated
Motif GUI code to eliminate two deprecated functions, replacing XmFileSelectionBoxGetChild()
with XtNameToWidget() and replacing XmStringGetLtoR() with XmStringUnparse(). This appears
to be necessary for the Motif code to work on MacOs Tahoe with prerequisites installed
via MacPorts. 

#### 5.8.3beta13 (June 18, 2026)

Format MBF_KEMKALL (261): Fixed support for platform files used for preprocessing.

Format MBF_EM710RAW (58): Added support for *.all files associate with the HISAS sonar from Kongsberg.

Programs mbpreprocess and mbprocess: Added support for merging navigation from Kongsberg Navlab software 
that is commonly used for Hugin AUV data processing.

Programs mbnavlab2fnv and mbfnv2navlab: Added tools that translate between navlab_smooth.bin and fnv files.

Programs mbnavadjust and mbnavadjustmerge: Fixed problems with new and merged project files resulting 
from treating surveys and blocks of continuous data separately.

Program mbmakedatalist: Compiled C version of macro mbm_makedatalist

Library mbtrnav/gctp: Added modern function definitions to function pointer arrays.

Program mbphotomosaic: Fix bug in which if one photo of a stereo pair is dropped, the other
photo is not used.

Program mbnavadjust: Changed so that surveys can be imported as a single piece even if there
are time breaks between some of the files.

Format MBF_3DWISSL2 (id 234): Add kluge to deal with WiSSL2 lidar bathymetry needing 
additional correction.

#### 5.8.3beta12 (January 7, 2026)

CMake build system: Extended to handle complications of MacOs Tahoe. Building the 
graphical tools in MB-System on MacOs has been complicated for a number of years because 
of the requirement for X11/Motif and also, for programs mbgrdviz, mbeditviz, and mbnavadjust,
OpenGL and GLX. For MacOs versions Sequoia (15) and earlier, the only way to successfully
build and run MB-System has been to install all of the prerequisite packages using the MacPorts
package manager. For reasons that have never been understood, the MB-System graphical 
programs failed to run correctly when built with prerequisites installed through the
alternative package managers Homebrew and Fink. This situation changes with MacOs Tahoe
because now the MB-System graphical programs fail when prerequisites are installed through
MacPorts, but succeed when the prerequisites are installed through Homebrew. This update
to the build system handles the differences between the two MacOs scenarios (before Tahoe
vs Tahoe or later). The installation documentation on the MB-System website will be 
updated to reflect the necessity of using Homebrew for installations on MacOs Tahoe.
A significant issue with all X11 programs running on MacOs Tahoe so far is that when 
windows are resized, the GUI elements are not refreshed properly, and parts of the GUI
wind up overwritten in solid black. Hopefully this will be fixed in a new version of
the X11 server XQuartz. In the meantime, minimizing the program window using the middle
(yellow) button on the upper left of the window (or the command-M shortcut), and then
restoring that window by clicking on it's icon in the dock will properly refresh the GUI
graphics.

Program mbgrd2gltf: Continued updates to this tool for translating gridded topography
to Graphics Library Transmission Format (GLTF) files that can be visualized by GLTF 
viewers.

#### 5.8.3beta11 (December 27, 2025)

Formats 56 (MBF_EM300RAW) and 57 (MBF_EM300MBA): Fixed erroneous calculation of a large
sensordepth value by mbprocess when the draft of a surface vessel has not been defined.

#### 5.8.3beta10 (December 22, 2025)

Program mbbackangle: A skipping existing feature implemented in beta04 had a small error 
in the source code that made it not work as intended. This release contains a bug fix to 
correct that behavior.

#### 5.8.3beta09 (December 4, 2025)

Program mbnavadjustmerge: Fixed options --unset-tie, --unset-ties-file, --unset-ties-survey, 
--unset-ties-by-survey, --unset-ties-block, --unset-ties-all.

Program mbbackangle: A skipping existing feature implemented in beta04 had a small error 
in the source code that made it not work as intended. This release contains a bug fix to 
correct that behavior.

#### 5.8.3beta08 (November 16, 2025)

Programs mbedit and mbeditviz: Now display dual swath Kongsberg multibeam data in the
kmall format (id 261) with two separate acrosstrack profiles. As before the two profiles
are associated with a single ping cycle and set of datagrams.

Format MBF_3DWISSL2 (id 234): Updates to handle the evolving representation for the
3D at Depth 2nd generation Wide Swath Subsea Lidar (WiSSL2)

Programs mbphotomosaic, mbgetphotocorrection, and mbphotogrammetry: Augmented to handle
seafloor photographs that have already been rectified (corrected for distortion). This
capability has not been fully tested at this point.

#### 5.8.3beta07 (October 22, 2025)

Program mbeditviz: Fixed display of swath width when navigation is selected in the survey
view.

Format 234 (MBF_3DWISSL2): Supports data from new 3D at Depth 2nd Generation Wide swath
Subsea Lidar (WiSSL2).

Program mbpreprocess: Added option attitude-zero-heave to zero heave values in attitude
data to be merged with survey data. The immediate use is for integration of Exail Phins C7
navigation and attitude data with multibeam data, all collected on a submerged AUV for
which the platform depth is defined by a pressure sensor rather than the heave output
by the INS.

Programs mbgrdviz, mbeditviz, mbnavadjust: Fixed the mouse button description for Rotate 
View mode so that the right button is properly labeled as zoom rather than exaggeration.

#### 5.8.3beta06 (October 1, 2025)

GMT integration: Fixed compiler directives insuring
that the GMT header file gmt_dev.h does not implicitly include a glib header file not 
needed by MB-System.

#### 5.8.3beta05 (September 30, 2025)

GMT grid i/o functions (src/mbaux/mb_readwritegrd.c): Added compiler directives insuring
that the GMT header file gmt_dev.h does not implicitly include a glib header file not 
needed by MB-System.

GMT module mbcontour: Added compiler directives insuring
that the GMT header file gmt_dev.h does not implicitly include a glib header file not 
needed by MB-System.

GMT module mbgrd2obj: Added compiler directives insuring
that the GMT header file gmt_dev.h does not implicitly include a glib header file not 
needed by MB-System.

GMT module mbgrdtiff: Added compiler directives insuring
that the GMT header file gmt_dev.h does not implicitly include a glib header file not 
needed by MB-System.

GMT module mbswath: Added compiler directives insuring
that the GMT header file gmt_dev.h does not implicitly include a glib header file not 
needed by MB-System.

Programs mbedit, mbeditviz, mbgrdviz, mbnavadjust, mbnavedit, mbvelocitytool: Removed code
ensuring that a message display dialog is displayed when created or updated by processing
all outstanding X11 events, as this causes mbeditviz to get lost in an infinite event
processing loop on Ubuntu 24 installations.

#### 5.8.3beta04 (September 18, 2025)

Many source files: Addressed code style issues raised previously by Kurt Schwehr, 
particularly using bool type for logical variables

Program mbinfo: Recast mbinfo to use long options as well as short options. Added a new
capability to list records comprising a data file and the contents of selected records 
using the --debug-record-types and --debug-record-contents options, which is so far
implemented for formats 58, 59, and 89.

Program mbpreprocess: Added several new "kluge" options:
	--kluge-set-beamwidths
	--kluge-set-beamwidth-acrosstrack
	--kluge-set-beamwidth-alongtrack
	--kluge-ignore-duplicate-pings
	--kluge-xducer-depth-from-heave
	--kluge-xducer-depth-from-sensordepth
	--kluge-xducer-depth-from-heave-and-sensordepth

Macro mbm_route2mission: Fixed end of mission battery behavior to use mode 2 so that the
AUV sonars are only shut off if the batteries are mostly exhausted.

Formats 58 and 59 (MBF_EM710RAW and MBF_EM710MBA): Recast handling of transducer depth
modes so as to work correctly for more data sets, and added mbpreprocess kluge options
to handle the less common combinations of data record types and sonar settings.

Program mbphotomosaic: Augmented handling of camera types to include monocular cameras
and single camera calibration models.

#### 5.8.3beta03 (August 31, 2025)

Program mbotps: Added long option commands, and altered the manual page to document use
of long options. Fixed the --skip-existing {-M} command so that mbotps actually skips
files that already have tide correction defined.

Program mbnavadjust: Now displays the reference grid used for global ties in data section
and global tie listings.

#### 5.8.3beta02 (August 29, 2025)

Program mbeditviz: Fixed bias parameter optimization when soundings are selected by
navigation.

Program mbnavadjust: changed default section sizes to 0.2 km (200 m) and 400,000 soundings.

#### 5.8.3beta01 (August 27, 2025)

Program mbgrd2gltf: Fixed compile problem that occurs when the draco library is installed.

#### 5.8.2 (August 19, 2025)

**Version 5.8.2** is now the current release of MB-System. 

The source code distribution can be downloaded from the MB-System Github repository at:  
[https://github.com/dwcaress/MB-System/archive/refs/tags/5.8.2.tar.gz]()

The changes and bug fixes of 5.8.2 relative to the prior stable release (5.8.1) are
listed in the ChangeLog.md file entries for the preliminary releases 5.8.2beta01 through
5.8.2beta24.

#### 5.8.2beta24 (July 19, 2025)

Program mbgrdviz: Added capability to export an MB-System route file in a file format that
can be loaded into a Kongsberg dynamic positioning (DP) system, enabling using the DP to
run the survey lines described by the route file.

Program mbgrdviz: Added capability to export an MB-System route file in a file format that
can be loaded into the Kongsberg multibeam control software called SIS (Seafloor information
System). The route can be imported in two forms: one where each segment between major
waypoints translates to a separate line in SIS, and another that generates a multisegment
line in SIS.

Program mbpreprocess: Altered the --skip-existing options so that previously preprocessed
files are entirely skipped.

#### 5.8.2beta23 (June 25, 2025)

Program mbgrdviz: Fixed capability to export routes in the form of Kongsberg Dynamic 
Positioning system waypoints, allowing importation of the MB-System derived survey plans
to the bridge control system on MBARI's R/V David Packard.

Format 89 (Teledyne Reson and Norbit (*.s7k)): Removed an errant debug message.

Program mbnavadjust: Greatly improved picking data sections and global ties from the 
model time series plots. Reorganized the List menu so that the choices switching the 
data pick mode on the model plot and the map visualization are together. When the list
shows data sections, global ties, or sorted global ties, then picking on the model plot
or on navigation in the visualization will bring up the analysis window with a data section 
and potentially a reference grid. Otherwise the picking and the analysis window will be
of crossings and crossing ties. 

Program mbpreprocess: Fixed generation of asynchronous navigation, attitude, heading and
sensor depth files for use by mbeditviz.

#### 5.8.2beta22 (June 16, 2025)

Program mbtrnpp: Improved beam decimation and median filtering algorithms and some included
performance analysis plotting tools. Also fixed string construction code that triggered 
buffer overflow signals (falsely) when compiled with strict security rules, as is the 
default for Ubuntu 24.

Program mbgrdviz: Added capability to export routes in the form of Kongsberg Dynamic 
Positioning system waypoints, allowing importation of the MB-System derived survey plans
to the bridge control system on MBARI's R/V David Packard.

Format MBF_3DWISSL2 (234): First work on i/o module for data from the 3D at Depth WiSSL2
(2nd Generation Wide Swath Subsea Lidar) - this is not complete.

Macro mbm_route2mission: Altered the \fB-G\fP option so that instead of causing the AUV 
mission to include surfacing at survey line starting and/or ending waypoints, now \fB-G\fP
causes AUV surfacing to occur at the specified waypoint type.

Program mbimagelist: New utility program that parses \fBMB-System\fP imagelist structures
and can also be used to generate metadata files used by other MB-System programs.

#### 5.8.2beta21 (March 15, 2025)

Program mbeditviz: Improved the algorithm used to solve for optimal roll bias, pitch bias, 
heading bias, time lag, and Snell factor values using sets of soundings selected by area,
region, and navigation. Previously these optimization problems were solved by a brute 
force search for values minimizing the bathymetric variance in the selected soundings.
Now the approach is a more sensible Golden Section Search (e.g. Press et al., Numerical 
Recipies in C, 2nd ed., 1992). Also, the shell output when executing these optimizations
is more useful - in particular, the order of the bias parameters now conforms to the order
used by platform files and mbmakeplatform. In fact, this same order is now used for the 
bias value sliders in the mbeditviz 3D sounding window.

Library mbview: fix bug that prevented building mbview on Ubuntu because of a missing 
include of time.h in src/mbview/mbiew_plot.c tied to X11 event debugging code.

#### 5.8.2beta20 (February 22, 2025)

Program mbpreprocess: Added options --kluge-flipsign-roll and --kluge-flipsign-pitch 
which flip the sign of roll or pitch values, respectively, before they are merged and
applied to the swath bathymetry.

Program mbauvloglist: Added support for new phins.log files for Dorado AUVs with a Phins
INS installed.

Program mbm_route2mission: Fixed the -Ggpsmode option so that the AUV mission script will
actually make the AUV surface at survey line starts and/or ends when gpsmode > 0.

Cmake build system: Augmented the places that Cmake will look for Motif headers and library
with /opt/local/include/ and /opt/local/lib/ in the file build-utils/FindMotif.cmake)

#### 5.8.2beta19 (January 19, 2025)

Program mbgrdviz: Fixed bug in which routes might not be exported correctly when multiple
routes are exported to a single route file.

Program mbgrdviz: Fixed error messages indicating failed projection of some soundings.

Program mbpreprocess: Fixed crash when preprocessing third generation Kongsberg 
multibeam data (*.all files, formats 58 and 59) using a platform model defined in a
platform file created by mbmakeplatform.

Program mbgrid: Reduced the default verbosity so that the shell output only lists files
with data actually used in the gridding.

Format 121 (Generic Sensor Format (GSF)): Fixed crashes that occurred when processing GSF
files derived from Teledyne Reson multibeam data.

Format 89 (Teledyne Reson and Norbit (*.s7k)): Handles the lack of a FileHeader record in
Norbit multibeam data recorded in the s7k format.

#### 5.8.2beta18 (December 8, 2024)

MBlist: Fixed a critical bug in which mblist would never output from processed files 
specified through a datalist using the $PROCESSED tag.

Format MBF_KEMKALL (261): Augmented the i/o module to read and write an undocumented kmall
data record (#MSC) found in EM124 data collected by NERC. Without documentation the record
cannot be parsed, but it is read and rewritten without modification.

Format MBF_KEMKMALL (261): Fixed failure to differentiate between #SKM records from different
navigation + heading + attitude systems. If a platform has two navation/attitude systems, then
the first will map to MB_DATA_NAV1 type data, and the second to MB_DATA_NAV2. The default for
mbpreprocess will be to interpolate from navigation, heading, and attitude data stored in 
MB_DATA_NAV1 records, which for this format means #SKM datagrams with system id 0 (as opposed 
to system id 1).

Miscellaneous: Removed top level files "NEWS", "NOTES", and "INSTALL.md". These files existed
to conform to GNU expectations for a package structure. We are no longer trying to match the
GNU structure, and so have removed these unnecessary files.

Most SeaBeam Classic formats (MBF_SBSIOMRG, MBF_SBSIOCEN, MBF_SBSIOLSI, MBF_SBURICEN, 
MBF_SBURIVAX): Added code to handle rare condition where the ping timestamp has a seconds 
value of 60. Now the code will add one to the minutes value, and set the seconds value to 0.

#### 5.8.2beta17 (November 7, 2024)

Libtrnav (src/mbtrnav/): Additional fixes by Kent Headley to enable building on Ubuntu 24.

#### 5.8.2beta16 (November 6, 2024)

Mbm_route2mission: Change so that no edgetech behaviors are output to the mission script
if no sidescan or subbottom is enabled.

Format MBF_MBPRONAV (165): code changed so that if a file has records in which the date
fields (yyyy mm dd hh mm ss.ssssss) are all zero, then on reading the data will be set
using the value in the time_d (epoch time in seconds) field.

Mbauvloglist: Fixed bug that caused occasional crashes.

Mbphotogrammetry: Now applies CLAHE equalization to images before calculating disparity map.

Libtrnav (src/mbtrnav/): Many fixes by Kent Headley, including casting the code to use
Proj for geodetic transformations when used as part of MB-System while still allowing
use of the old GCTP library when used in other contexts lacking Proj.

### 5.8.2beta15 (October 1, 2024)

Mbmakeplatform: Fixed problems with handling sensor add and sensor modify modes.

Mbgrdviz, mbeditviz, mbnavadjust: Changed the mbview display of swath bounds for selected
navigation to be optional rather than always displayed.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Fixed preprocessing support for the 
Kongsberg M3 multibeam. Added capability to use an MB-System platform file in place of
the sensor offsets embedded in the logged multibeam files.

Mbphotogrammetry: Fixed use of range bounds in filtering the photogrammetric bathymetry.

#### 5.8.2beta14 (September 6, 2024)

Mbphotomosaic: Removed unnecessary --correction-file-color option (redundant with --correction-file)

mbm_grdplot: Fixed -G7 option for plotting images with geodetics defined in world files 
rather than embedded as in GeoTiffs. Specifically allows use of png images with transparency.

Formats 232 (MBF_WISSLR) and 233 (MBF_WISSLP): Fixed initial beam flagging by mbpreprocess
for secondary sounding picks (when the lidar was operated in multipick mode)

#### 5.8.2beta13 (August 23, 2024)

Mbphotomosaic: Fixed use of the  --dark-image-ignore and  --dark-image-multiply options
as parameters embedded in recursive imagelist files.

#### 5.8.2beta12 (August 22, 2024)

Mbnavadjustmerge: Fixed (again, this time hopefully for real) the --reimport-all-files 
option so that large projects can be reimported with a single command. Added a 
--reimport-survey option.

#### 5.8.2beta11 (August 19, 2024)

Mbnavadjustmerge: Fixed the --reimport-all-files option so that large projects can be
reimported with a single command. Added a --reimport-survey option.

#### 5.8.2beta10 (August 16, 2024)

Mbnavadjustmerge: Added --reimport-file and --reimport-all-files options that reimport 
swath files into an mbnavadjust project from the current processed versions of that files. 
Each file is broken into the same sections as previously, regardless of any changes to the 
settings for the maximum section length or the maximum number of soundings in a section.
The original navigation and attitude data are also preserved, but the bathymetry is changed 
to reflect the current processed values. This means that updates to the bathymetry editing 
can now be brought into mbnavadjust projects.

Format 71 (MBF_MBLDEOIH): Fixed a compression bug that occasionally resulted in corrupting
the acrosstrack values of the outermost beams of pings when changed data are inserted into
records using the mb_put_all() or mb_insert() functions. The only know manifestation of this
bug was in importing swath data into mbnavadjust projects.

Mbtrnpp: Fixed #ifdefs and Makefile.am files so that mbtrnpp can still be built with the
old autoconf build system, albeit using GCTP for projections rather libproj.

#### 5.8.2beta09 (August 4, 2024)

mb7k2jstar: This program extracts Edgetech sidescan and subbottom data from Reson s7k 
files and writes current format Edgetech Jstar format files identical to what current
Edgetech sonars record. This functionality is needed only for MBARI Mapping AUV data from
2004-2014, as MBARI was the only user of a payload controller software package named
6046 from Reson that logged Reson 7125 multibeam and Edgetech FSAU sidescan/subbottom
data in the same s7k files. Recognizing that reprocessing old Mapping AUV data requires
this capability (and much of these data are now in public archives at MGDS and NCEI), we
are moving mb7k2jstar back into src/utilities out of src/deprecated, so that it is always
built as part of MB-System. Also, a bug causing seg faults with 2007 data has been fixed.

Mbpreprocess: Added option --kluge-early-mbari-mapping-auv to mbpreprocess. This option 
pertains only to Reson 7125 200 kHz multibeam data collected on the first MBARI Mapping 
AUV from 2006 through 2009. Invoking this kluge triggers \fBmbpreprocess\fP to modify the 
beam quality factors to be consistent with the later (>2009) standard for the original 
bathymetry records in Reson s7k format data.

Mbextractsegy: Fixed bug in extracting and plotting envelope function of subbottom data.

General: Added macros to src/mbio/mb_define.h enabling the printing of byte values as a
binary bitmask using fprintf(). To print a single byte as binary (e.g. "01010101") do 
something like:
	char value;
	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT8"\n", MB_PRINTF_BYTE_TO_BINARY_INT8(value));
Printing of larger int types has a similar form:
	short value;
	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT16"\n", MB_PRINTF_BYTE_TO_BINARY_INT16(value));
	int value;
	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT32"\n", MB_PRINTF_BYTE_TO_BINARY_INT32(value));
	long long value;
	printf("Bitmask: "MB_PRINTF_BINARY_PATTERN_INT64"\n", MB_PRINTF_BYTE_TO_BINARY_INT64(value));
These macros are taken from 
	https://stackoverflow.com/questions/111928/is-there-a-printf-converter-to-print-in-binary-format

#### 5.8.2beta08 (July 27, 2024)

Format 121 (MBF_GSFGENMB): Updated to use new version of libgsf (3.10) released by Leidos.
The following change descriptions are from the libgsf 3.10 change summary:

	Change request GSF_03-10_01
	Support for ME70 sonars
	11/8/2021 
	Sean Donovan, Leidos 
	Description:
		Added GSF_SWATH_BATHY_SUBRECORD_ME70BO_SPECIFIC subrecord identifier. 
		Added support for sonar under EM4 cases. 
	Purpose:
		To add support in GSF for the ME70 multibeam systems

	Change request GSF_03-10_02
	STIG Remediation to address vulnerabilities
	3/12/2024
	Dwight Johnson, NAVO
	Description:
		Various changes to safe memory allocation and usage throughout the encoding and 		
		decoding processes
	Purpose:
		Improved Robustness

	Change request GSF_03-10_03
	Updates to KMALL ping level metadata
	3/12/2024
	Jonathon Beaudoin, Hydro Octave
	Description:
		Added new variables highVoltageLevelDB, sectorTrackingCorr_DB, and 
		effectiveSignalLength_sec within the spare space of the gsfKMALLTxSector Struct. 
		Added encoding and decoding logic for these values.
	Purpose:
		To support backscatter processing

	Change request GSF_03-10_04
	Resolved bug surrounding network transmission of range samples
	3/12/2024
	Jonathon Beaudoin, Hydro Octave
	Description:
		Missing htons call added to range sample processing
	Purpose:
		Bug Fix

	Change request GSF_03-10_05
	Added TVG DB to bathy ping structure
	3/12/2024
	Jonathon Beaudoin, Hydro Octave
	Description:
		Added new array variable TVG_DB to multibeam ping struct. Added encoding and 
		decoding logic for this value.
	Purpose:
		To support backscatter processing

MBnavadjust: Added autosaving the last version of a project file immediately before 
beginning to write a new file. Also fixed some inconsistencies in the UI.

#### 5.8.2beta07 (June 27, 2024)

Mbm_trnplot: Added extraction of TRN localization estimates in longitude and latitude.

Mbtrnpp: Now includes longitude and latitude values of TRN localization estimates into
the log file (in addition to the coordinate reference system used for the reference 
map).

Mbgrdviz: Fixed importation of non-csv raw site files.

Formats 88 and 89 (MBF_RESON7KR and MBF_RESON7K3): Change to allow pings to be valid if
a BeamGeometry record has been read earlier in the file (as opposed to having a 
BeamGeometry record for every ping).

Formats 88 and 89 (MBF_RESON7KR and MBF_RESON7K3): Fixed problem calculating sample times
for attitude data in s7k 1016 Attitude data records.

#### 5.8.2beta06 (June 13, 2024)

MBgrid and mbmosaic: Added an option to generate grids and mosaics in a projected 
coordinate system defined as a Local Transverse Mercator (LTM) projection with the  origin 
at the center of the grid or mosaic. 

MBgrdviz, mbeditviz, mbnavadjust: The mbview visualization library now displays grids
defined in geographic coordinates (longitude and latitude) using a Local Transverse
Mercator projection with the origin at the center of the grid or mosaic. This replaces the
prior use of UTM projections, which introduced rotation and distortion when the grid was
located far from the center of the UTM zone.

MBtrnpp: and TRN: Changed TerrainNav, supporting libraries, and the program mbtrnpp to
calculate projections using the Proj package rather than the GCTP package.

MBtrnpp: Now works with reference topography models defined in a Local Transverse 
Mercator (LTM) projection.

Mbm_trnplot: augmented to allow specifying the CRS of the reference topoography so
that a Local Transverse Mercator (LTM) projection can be used.

#### 5.8.2beta05 (May 19, 2024)

MBextractsegy: changed calculation of section plot bounds to more consistently catch the
seafloor arrival within the plot.

MBpreprocess: fixed initialization of the --kluge-fix-7k-times option.

Docker image: updated documentation in the Docker directory.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA):  Removed an errant debug message that
printed out information when reading height datagrams.

#### 5.8.2beta04 (May 13, 2024)

Mbpreprocess: Added kluge option to fix large shifts in survey record timestamps in 
Teledyne s7k format data (specifically MBARI Mapping AUV multibeam data collected with 
the sonar computer experiencing large shifts in time). This option is accessed as 
--kluge-fix-7k-timestamps=time

Mbroutetime: Now works with the recently changed route file format.

Mblevitus: Fixed problem building mblevitus with the Cmake build system. The problem was
that the Levitus database location was incorrectly embedded in the compiled program.

#### 5.8.2beta02 (May 1, 2024)

Format 261 (MBF_KEMKMALL): Fixed bug in handing pings for which there are multiple MRZ 
datagrams that have different timestamps. This bug resulted in MB-System dropping many 
pings in some deepwater Kongsberg data (mostly EM124 data).

#### 5.8.2beta01 (April 29, 2024)

Mbedit: Fixed display of ping profiles to handle condition where a ping contains
two acrosstrack profiles, typically one aft and one forward of the sonar location. Now
the connection between the end of the first acrosstrack profile and the start of the
second is no longer plotted.

MB-System Docker Container: Improved Docker documentation included in the Docker directory.

#### 5.8.1 (March 22, 2024)

CMake build system: Fixed ability to set OTPS location in cmake build system.

CMake build system: Added installation of header files required for external programs to
utilize MB-System libraries.

Format 261 (MBF_KEMKMALL): Updated support for Kongsberg Kmall format to match updated 
specification J.

Format 16 (MBF_SBSIOSWB): Fixed bug that became evident when processing old Scripps
SeaBeam Classic data in format 16 on a MacOs Sonoma machine. This turned out to be
a poorly formed preprocessor macro for rounding floating point values in code dating 
from 1992. 

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA):  Fixed bug in which some bathymetry 
edits were applied to the wrong pings. Third generation Kongsberg multibeams produce
two cross profiles with each ping cycle, but represent these as two separate pings
with the same ping time. MB-System distinguishes between pings using the timestamps
rather than ping numbers (because not all sonars produce ping numbers), so pings
with the same timestamp confuse the beam flag handling code. The solution is to add
a small amount of time to the timestamp of the second ping in each pair. The bug was
that the amount of time added by mbpreprocess was 33 microseconds, but the datagrams
in Kongsberg *.all files specify timestamps only to the millisecond level, and so
the added time was not large enough to be recorded differently in the output files.

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.

Mbpreprocess and format MBF_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_EM710MBA
(59) files.

Mbpreprocess and mbprocess: Now support merging navigation and attitude from Schmidt
Ocean Institute RVDAS format ROV navigation.

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.

Mbgrid: Improved output to shell so that it shows the min max values from each 
contributing input file whether verbose is specified or not.
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.

Mbphotomosaic: Fixed priority-heading option that allows image prioritization on
the basis of camera heading.

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.

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.

SEGY format data: MB-System now recognizes file suffixes *.sgy and *.SGY in addition
to *.segy *.SEGY *.seg and *.SEG

Mbsegyinfo: Fixed calculation and reporting of trace minimum and maximum values.

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.

Mbtrnpp: The optional Terrain Relative Navigation (TRN) software has been augmented 
with code to utilize realtime format 58 (Kongsberg *.all) format multibeam accessed
through a serial stream.

#### 5.8.1beta09 (March 22, 2024)

Format 16 (MBF_SBSIOSWB): Fixed bug that became evident when processing old Scripps
SeaBeam Classic data in format 16 on a MacOs Sonoma machine. This turned out to be
a poorly formed preprocessor macro for rounding floating point values in code dating 
from 1992. 

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA):  Fixed bug in which some bathymetry 
edits were applied to the wrong pings. Third generation Kongsberg multibeams produce
two cross profiles with each ping cycle, but represent these as two separate pings
with the same ping time. MB-System distinguishes between pings using the timestamps
rather than ping numbers (because not all sonars produce ping numbers), so pings
with the same timestamp confuse the beam flag handling code. The solution is to add
a small amount of time to the timestamp of the second ping in each pair. The bug was
that the amount of time added by mbpreprocess was 33 microseconds, but the datagrams
in Kongsberg *.all files specify timestamps only to the millisecond level, and so
the added time was not large enough to be recorded differently in the output files.

Mbgrid: Improved output to shell so that it shows the min max values from each 
contributing input file whether verbose is specified or not.

#### 5.8.1beta08 (March 10, 2024)

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.

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.

SEGY format data: MB-System now recognizes file suffixes *.sgy and *.SGY in addition
to *.segy *.SEGY *.seg and *.SEG

Mbsegyinfo: Fixed calculation and reporting of trace minimum and maximum values.

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.

Mbpreprocess and mbprocess: Now support merging navigation and attitude from Schmidt
Ocean Institute RVDAS format ROV navigation.

Mbpreprocess and format MBF_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_EM710MBA
(59) files.

#### 5.8.1beta07 (February 24, 2024)

CMake build system: Fixed ability to set OTPS location in cmake build system.

CMake build system: Added installation of header files required for external programs to
utilize MB-System libraries.

#### 5.8.1beta04 (February 16, 2024)

Format 261 (MBF_KEMKMALL): Updated support for Kongsberg Kmall format to match updated specification J.

#### 5.8.1beta03 (February 8, 2024)

Mbphotomosaic: Fixed priority-heading option that allows image prioritization on
the basis of camera heading.

#### 5.8.1beta02 (February 7, 2024)

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.

#### 5.8.1beta01 (February 1, 2024)

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.

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.

#### 5.8.0 (January 22, 2024)

**Version 5.8.0** is now the current release of MB-System. 

The source code distribution can be downloaded from the MB-System Github repository at:  
[https://github.com/dwcaress/MB-System/archive/refs/tags/5.8.0.tar.gz]()

In addition to many bug fixes, the changes of 5.8.0 relative to the prior major release (5.7.8) include:

**New build system:**  
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.

**Global ties to reference grids in MBnavadjust:**  
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.

**Realtime Terrain Relative Navigation:**  
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. 

**Photomosaicing tools available:**  
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.

---
### MB-System Version 5.7 Releases and Release Notes:
---

- Version 5.7.9beta72    January 14, 2024
- Version 5.7.9beta71    January 3, 2024
- Version 5.7.9beta70    January 2, 2024
- Version 5.7.9beta69    December 17, 2023
- Version 5.7.9beta68    November 30, 2023
- Version 5.7.9beta66    November 18, 2023
- Version 5.7.9beta65    November 17, 2023
- Version 5.7.9beta64    November 16, 2023
- Version 5.7.9beta63    November 10, 2023
- Version 5.7.9beta62    November 3, 2023
- Version 5.7.9beta61    November 2, 2023
- Version 5.7.9beta60    October 22, 2023
- Version 5.7.9beta59    September 19, 2023
- Version 5.7.9beta58    August 30, 2023
- Version 5.7.9beta57    June 27, 2023
- Version 5.7.9beta53    June 15, 2023
- Version 5.7.9beta52    March 9, 2023
- Version 5.7.9beta51    February 14, 2023
- Version 5.7.9beta50    February 12, 2023
- Version 5.7.9beta49    January 22, 2023
- Version 5.7.9beta48    December 16, 2022
- Version 5.7.9beta47    November 15, 2022
- Version 5.7.9beta46    November 11, 2022
- Version 5.7.9beta45    November 6, 2022
- Version 5.7.9beta44    August 9, 2022
- Version 5.7.9beta43    July 29, 2022
- Version 5.7.9beta42    June 26, 2022
- Version 5.7.9beta41    June 22, 2022
- Version 5.7.9beta40    June 18, 2022
- Version 5.7.9beta38    June 18, 2022
- Version 5.7.9beta37    June 17, 2022
- Version 5.7.9beta36    June 15, 2022
- Version 5.7.9beta35    June 13, 2022
- Version 5.7.9beta34    June 5, 2022
- Version 5.7.9beta33    June 5, 2022
- Version 5.7.9beta32    June 4, 2022
- Version 5.7.9beta30    June 4, 2022
- Version 5.7.9beta29    May 13, 2022
- Version 5.7.9beta28    March 21, 2022
- Version 5.7.9beta27    February 28, 2022
- Version 5.7.9beta26    January 2, 2022
- Version 5.7.9beta25    December 29, 2021
- Version 5.7.9beta24    December 27, 2021
- Version 5.7.9beta23    December 18, 2021
- Version 5.7.9beta22    December 5, 2021
- Version 5.7.9beta21    December 4, 2021
- Version 5.7.9beta20    December 1, 2021
- Version 5.7.9beta19    November 6, 2021
- Version 5.7.9beta18    October 31, 2021
- Version 5.7.9beta17    October 16, 2021
- Version 5.7.9beta16    August 27, 2021
- Version 5.7.9beta15    August 26, 2021
- Version 5.7.9beta14    July 25, 2021
- Version 5.7.9beta13    July 18, 2021
- Version 5.7.9beta12    July 4, 2021
- Version 5.7.9beta11    June 26, 2021
- Version 5.7.9beta10    June 16, 2021
- Version 5.7.9beta09    June 8, 2021
- Version 5.7.9beta07    May 7, 2021
- Version 5.7.9beta06    March 24, 2021
- Version 5.7.9beta05    March 8, 2021
- Version 5.7.9beta04    February 21, 2021
- Version 5.7.9beta03    February 7, 2021
- Version 5.7.9beta02    January 27, 2021
- Version 5.7.9beta01    January 18, 2021
- **Version 5.7.8        January 17, 2021**
- Version 5.7.7          January 17, 2021 (flawed, quickly superceded)
- Version 5.7.7beta09    January 17, 2021
- Version 5.7.7beta08    January 6, 2021
- Version 5.7.7beta06    December 30, 2020
- Version 5.7.7beta05    December 28, 2020
- Version 5.7.7beta04    October 28, 2020
- Version 5.7.7beta03    October 27, 2020
- Version 5.7.7beta02    October 8, 2020
- Version 5.7.7beta01    October 7, 2020
- **Version 5.7.6        October 5, 2020**
- Version 5.7.6beta56    September 28, 2020
- Version 5.7.6beta55    September 16, 2020
- Version 5.7.6beta54    September 14, 2020
- Version 5.7.6beta53    September 13, 2020
- Version 5.7.6beta52    September 9, 2020
- Version 5.7.6beta51    September 4, 2020
- Version 5.7.6beta50    September 2, 2020
- Version 5.7.6beta49    September 2, 2020
- Version 5.7.6beta48    September 1, 2020
- Version 5.7.6beta47    September 1, 2020
- Version 5.7.6beta46    August 31, 2020
- Version 5.7.6beta45    August 26, 2020
- Version 5.7.6beta44    August 24, 2020
- Version 5.7.6beta43    July 23, 2020
- Version 5.7.6beta42    July 21, 2020
- Version 5.7.6beta41    July 12, 2020
- Version 5.7.6beta40    July 7, 2020
- Version 5.7.6beta38    June 8, 2020
- Version 5.7.6beta37    May 26, 2020
- Version 5.7.6beta36    May 17, 2020
- Version 5.7.6beta34    May 14, 2020
- Version 5.7.6beta33    May 5, 2020
- Version 5.7.6beta32    April 22, 2020
- Version 5.7.6beta31    March 2, 2020
- Version 5.7.6beta30    February 20, 2020
- Version 5.7.6beta29    February 17, 2020
- Version 5.7.6beta28    February 13, 2020
- Version 5.7.6beta27    February 3, 2020
- Version 5.7.6beta26    February 2, 2020
- Version 5.7.6beta25    January 20, 2020
- Version 5.7.6beta24    January 16, 2020
- Version 5.7.6beta23    January 11, 2020
- Version 5.7.6beta21    December 12, 2019
- Version 5.7.6beta20    November 26, 2019
- Version 5.7.6beta19    November 22, 2019
- Version 5.7.6beta18    November 21, 2019
- Version 5.7.6beta17    November 15, 2019
- Version 5.7.6beta16    October 29, 2019
- Version 5.7.6beta15    October 21, 2019
- Version 5.7.6beta14    October 8, 2019
- Version 5.7.6beta12    September 20, 2019
- Version 5.7.6beta10    September 18, 2019
- Version 5.7.6beta8     September 9, 2019
- Version 5.7.6beta6     August 26, 2019
- Version 5.7.6beta5     August 6, 2019
- Version 5.7.6beta4     August 2, 2019
- Version 5.7.6beta2     July 25, 2019
- Version 5.7.6beta1     July 6, 2019
- **Version 5.7.5        June 26, 2019**
- Version 5.7.5beta12    June 24, 2019
- Version 5.7.5beta11    June 16, 2019
- Version 5.7.5beta10    June 9, 2019
- Version 5.7.5beta9     June 8, 2019
- Version 5.7.5beta8     April 11, 2019
- Version 5.7.5beta7     March 28, 2019
- Version 5.7.5beta6     March 26, 2019
- Version 5.7.5beta5     March 22, 2019
- Version 5.7.5beta4     March 21, 2019
- Version 5.7.5beta3     March 14, 2019
- Version 5.7.5beta2     March 4, 2019
- Version 5.7.5beta1     February 26, 2019
- Version 5.7.5beta0     February 25, 2019
- **Version 5.7.4          February 12, 2019**
- **Version 5.7.3          February 8, 2019**
- Version 5.7.2          February 4, 2019
- **Version 5.7.1          December 19, 2018**

---

#### 5.7.9beta72 (January 13, 2024)

Build Systems: Made building and installing deprecated programs optional for both
the CMake and Autoconf build systems.

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.

Mbgrdviz: Generated a new version of the MB-System Route files.

Mbm_route2mission: Now works with both old and new format route files.

#### 5.7.9beta71 (January 3, 2024)

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.

#### 5.7.9beta70 (January 2, 2024)

Mblist: Added capability to output beam travel times, angles and other values
needed to recaclulate bathymetry by raytracing.

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.

#### 5.7.9beta69 (December 17, 2023)

Format 192 (MBF_IMAGEMBA): Fixed correction of beam amplitude values (previously
corrected values were not successfully inserted into the data structure).

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.

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.

Mbsslayout: Fixed bug in which a command to swap the starboard and port sidescan
channels was ignored.

#### 5.7.9beta68 (November 30, 2023)

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 ..

Mbnavadjustmerge: Added options to shift global ties singly or all together.

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.

#### 5.7.9beta66 (November 18, 2023)

Mbdatalist: Fixed an unitialized string causing intermittent failure.

#### 5.7.9beta65 (November 17, 2023)

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.

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. 

Mbtrnpp: Fixed bug identified by Kent Headley that caused divide by zeros when calculating swath
width filtering of soundings.

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".

#### 5.7.9beta64 (November 16, 2023)

Reading GMT grids: Fixed a very significant bug that caused GMT grids to be read into 
memory incorrectly by mb_read_gmt_grd() in src/mbaux/mb_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.

#### 5.7.9beta63 (November 10, 2023)

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.

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.

#### 5.7.9beta62 (November 3, 2023)

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.

Updated the copyright notices in the several hundred source files.


#### 5.7.9beta61 (November 2, 2023)

Read functions mb_get_all(), mb_get(), mb_read(): Fixed bug in handling the vertical dimension
while applying alternate navigation. Bathymetry were being corrected wrongly for changes
in the sensordepth.

Datalists: Fixed problem in which processed files would not be read when the raw files do
not conform to MB-System suffix conventions.

Mbbackangle: Changed to not set parameter files when the swath files do not contain the
expected amplitude and/or sidescan data. 

Mbgrd2gltf: Added "#include <cmath>" to src/mbgrd2gltf/bathymetry.cpp to enable compiling on CentOs 7.

Configure.ac and Configure: Modified to find Proj on CentOs 7 systems.

#### 5.7.9beta60 (October 22, 2023)

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.

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.

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_datalist_read3() in place of mb_datalist_read()
or mb_datalist_read2():

    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);

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_read_init_altnav() to initialize reading (instead of mb_read_init()) - here the change is 
to pass in the astatus and apath values obtained from mb_datalist_read3(). 

    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);

If mb_read_init_altnav() is used, astatus is true, and apath is a valid alternative
navigation file, then calls to mb_get_all(), mb_get(), and mb_read() will return survey
records with the alternative navigation merged in place of the embedded navigation.

The only programs utilizing this capability are mbgrid, mbmosaic, and mblist - this allows
generating data products utilizing the alternative navigation.

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.

#### 5.7.9beta59 (September 19, 2023)

Mbnavadjustmerge: Made copying of mbnavadjust projects more efficient.

Mbnavadjustmerge: Add --remove-short-sections option to eliminate undesirably
short sections by merging them with their prior section.

Mbnavadjustmerge: Add --remove-file option to remove a file from an mbnavadjust project.

Mbcontour: Fixed drawing of survey tracklines - restored to generate thin lines.

#### 5.7.9beta58 (August 30, 2023)

Mbm_route2mission: Modifications to accomodate changes to Dorado AUV vehicle software.

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.

Mbnavadjustmerge: Fixed bug in merging projects.

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.

TRN tools: Minor changes to .gitignore (add binaries) and mbtrn/utils/tbinx.cpp (add signal 
handler, reconnect timing, bug fix).

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).

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).

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.

#### 5.7.9beta57 (June 27, 2023)

Mbm_route2mission: Added -T option to embed use of Terrain Relative Navigation in 
MBARI Mapping AUV missions.

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.

Mbnavadjust: Fixed bug in the inversion algorithm.

#### 5.7.9beta53 (June 15, 2023)

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.

Mbtrnpp and related TRN code: Many updates and improvements from Kent Headley

Mbcontour: The navigation line width and color can now be set using the -W argument

Format SOIUSBLN (275): Supports USBL tracking data from R/V Falkor (too) as format 275.

Format SOIROVN (276): Supports ROV SuBastian INS navigation data as format 276.

Mbm_route2mission: Added a depth limit parameter to the -D argument.

Mbgrdviz: Fixed display of vector data.

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

Format RESON7K3 (89): Fixed counting of valid records in the file catalog.

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.

Mbgetphotocorrection, mbphotogrammetry: enabled multi-threading.

Mbauvloglist: Allow merging attitude data from a separate file. Allow decimation of input.

Mbmosaic: Augmented azimuth priority mode so that the azimuth alone can be specified, in which
case the azimuth priority factor is one.

Mbpreprocess: Now outputs integrated navigation for all sensors producing mapping data.

Formats 56 (MBF_EM300RAW) and 57 (MBF_EM300MBA): Fixed catastrophic bug introduced in 
5.7.9beta50 that treated many signed values (like acrosstrack distance) as unsigned.


#### 5.7.9beta52 (March 9, 2023)

Formats 56 (MBF_EM300RAW) and 57 (MBF_EM300MBA): Fixed catastrophic bug introduced in 
5.7.9beta50 that treated many signed values (like acrosstrack distance) as unsigned.

MBgrdviz: Added ability to export routes as TECDIS LST files for display in a variety of
marine chart display software. 

Autotools build system: Altered Makefile.am files in third_party/googlemock and 
third_party/googletest to eliminate benign but alarming error messages during make install 
and make clean commands.

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.

#### 5.7.9beta51 (February 14, 2023)

Format 89 (MBF_RESON7k3): Removed debug message inadvertently left active in 5.7.9beta50.

#### 5.7.9beta50 (February 12, 2023)

General: Changed many sprintf() calls to snprintf() calls. 

General: Fixed many compiler warnings having to do with unused variables, unitialized 
variables, and possible string overflows.

MBnavadjust: Fixed interface issues for importing multiple reference grids and
selecting those while makeing global ties.

Format 261 (MBF_KEMKMALL): Added code to detect and handle gracefully some 
instances of corruption of MRZ datagrams, particularly due to missing bytes.

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.

#### 5.7.9beta49 (January 22, 2023)

Mbm_grdplot, mbm_grd3dplot, mbm_histplot, mbm_plot, mbm_xyplot: Made evince one
of the default Postscript viewers because it is commonly installed on Ubuntu
machines.

General: Addressed compiler warnings due to uninitialized variables, inconsistent
variable typing, and other minor issues.

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.

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.

Format MBF_MBARIROV (165): Added recognition for new filenaming conventions for
MBARI ROV navigation files.

#### 5.7.9beta48 (December 16, 2022)

Mbmosaic: Fixed parsing of the -Ypriority_source option when priority_source is
a filename.

Mbm_grdplot: Fixed handling of image file min max when color_mode == 6.

Mbnavadjust: Added controls allowing the mode of global ties to be changed
interactively.

Mbnavadjust: Changed project file format, adding the the id of the source
reference grid used for each global tie.

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.

Mbnavadjust: Fixed interpolation of global ties to create the starting navigation
model during inversions. Fixed several actions in section and reference grid mode.

#### 5.7.9beta47 (November 15, 2022)

Mbnavadjust: Individual survey grids are now sized to the region of those
surveys rather than the entire project. When the individual surveys are
visualized, only the navigation for that survey are loaded into the mbview
2D/3D map instance. Also fixed picking of section navigation in both crossing
and section (vs reference grid) modes.

Mbnavadjustmerge: Added options set the mode (XYZ vs XY vs Z) of all global ties.

#### 5.7.9beta46 (November 11, 2022)

Mbnavadjust: Added ability to import and use multiple reference grids for picking
global ties of individual swath data sections.

#### 5.7.9beta45 (November 6, 2022)

FNV files: The fast navigation or *.fnv files are created as ancillary files
allowing navigation to be read without reading the full swath files. The *.fnv
files are in the MBF_MBPRONAV (166) format. Format 166 has always supported
comment records as lines beginning with the '#' character, but fnv files have
always been created without any comment records. Many MB-System programs read
fnv files directly without using the MBF_MBPRONAV i/o module. Now all format
166 files will be written with a first record documenting the contents of the
file:

    fprintf(mb_io_ptr->mbfp,  "## <yyyy mm dd hh mm ss.ssssss> <epoch seconds> "
                  "<longitude (deg)> <latitude (deg)> <heading (deg)> <speed (km/hr)> "
                  "<draft (m)> <roll (deg)> <pitch (deg)> <heave (m)> <portlon (deg)> "
                  "<portlat (deg)> <stbdlon (deg)> <stbdlat (deg)>\n");
                  
whether they are written by the MBF_MBPRONAV i/o module or by functions in
applications like mbprocess or mbpreprocess. All instances reading these files
will ignore these file header records.

Mbgrdviz: augmented and corrected the headers of route and site files output by
mbgrdviz, better self documenting the formats of these files.

Mbnavadjust: Added ability to import a reference bathymetry grid that can be
used to define global ties. Also modified so that when the main display list mode
limits what is shown to "with selected survey" or other modifiers, these constraints
also limit what navigation is shown in the project visualization. So, if one selects
a survey and then sets the list mode to show only the selected survey, then the
visualization will also only display the navigation from that survey, the crossing
ties or global ties from that survey, and only allow picking on that survey's
navigation.

Mbareaclean: Fixed issue in which mbareaclean does not apply filters for files
without pre-existing *.esf files.

Mbbackangle: Plots of the backscatter vs grazing angle distribution are no longer
histogram equalized.

Mbprocess: Modified the threaded processing function process_file() so that each
instance carries a thread id that can be checked during debugging.

#### 5.7.9beta44 (August 9, 2022)

Mbphotomosaic: Fixed problem in which an image correction model from mbgetphotocorrection
was read but not applied.

Mbeditviz: Fixed display of beam info when picking in info mode in the 3D
soundings display.

#### 5.7.9beta43 (July 29, 2022)

Mblist and mbnavlist: Fixed failure to deallocate proj object.

Mbtrnpp: Added UTM projection to top level using Proj, but this is not used yet.
The UTM projection used within the TRN codebase remains defined in the very old
GCTP package, which is embedded with TRN.

TRN execution and plotting scripts (e.g. src/mbtrn/tools/mbtrnpp-plot/trnucli-plot.sh):
Changed the shebang call from #!/usr/local/bin/bash to #!/usr/bin/env bash for
portability.

Mbnavadjust: Recast global ties to utilize a full 3D covariance model just like
the crossing ties, in preparation for allowing graphical picking of global ties
relative to a reference bathymetry model.

Mbnavadjustmerge: Added ability to remove disconitinuities in mbnavadjust projects.
Recast global ties to utilize a full 3D covariance model just like
the crossing ties, in preparation for allowing graphical picking of global ties
relative to a reference bathymetry model.

Mbm_trnplot: Added mission names to mbtrnpp result plots.

Cmake Build System: Incorporates an initial attempt at a cmake based build system
that will provide an alternative to the existing AutoTools based build system.
Updated documentation for both build systems is not included yet.

#### 5.7.9beta42 (June 26, 2022)

Format 261 (MBF_KEMKMALL): Fixed bug in handling beam amplitude data from null
beams.

Mbtrnpp: Fixed trnu logging.

Mbnavadjust: Altered the navigation adjustment inversion algorithm to apply
linear interpolation of global ties to create a starting model for the
inversion. Fixed picking on tie offsets in the modelplot window.

#### 5.7.9beta41 (June 22, 2022)

Mbm_makedatalist: Fixed to work with *.kmall files, and added -Bsize option
to impose a size threshold for files included in the output datalist.

TRN: Several fixes to the TRN (terrain relative navigation) capability.

#### 5.7.9beta40 (June 18, 2022)

Mbtrnpp: Fixed decimation algorithm more so it doesn't crash in Linux.

#### 5.7.9beta38 (June 18, 2022)

Mbtrnpp: Added option --auv-sentry-em2040 to configuration file and command line
options in order to enable use of the special pressure depth encoding in EM2040
data collected on AUV Sentry. Previously this option was hard coded in mbtrnpp.c.
By default this option is disabled, so in order for mbtrnpp to work with Sentry
EM2040 multibeam either in realtime or playback modes this option must now be
specified.

#### 5.7.9beta37 (June 17, 2022)

Mbtrnpp: Fixed decimation algorithm.

Mbgrdtilemaker: Fixed building of this new tool.

#### 5.7.9beta36 (June 15, 2022)

Mbgrdviz: Fixed export of Risi survey scripts from routes.

Mbm_trnplot: Fixed plotting macro to work when the users path does not include
the current directory.

Mbgrdtilemaker: Now copies the source background grid into the directory
containing the octree tiles with the name source_grid.grd.

#### 5.7.9beta35 (June 13, 2022)

Mbtrnpp: Added options to set the TRN search area on the command line and in
cfg files. Fixed wrapper script mbtrnpp.sh so that the number of cycles
to be used is set correction.

Mbm_trnplot: Fixed plotting macro to work with the current mbtrnpp output.

Mbgrd2octree: Recast program that translates a topography grid in a projected
coordinate system (like UTM) into a TRN octree model. This program now used
MB-System-like arguments, e.g. mbgrd2octree --input=grid --output=octree

Mbgrdtilemaker: Added new program to generate a tileset of octrees for TRN from a
reference grid in a projected coordinate system (like UTM). This tileset can be
used by mbtrnpp.

#### 5.7.9beta34 (June 5, 2022)

Mbtrnpp and other elements of the Terrain Relative Navigation infrastructure:
Augment mbtrnpp command set to include new commands for forced TRN resets
with specified starting navigation offsets and particle filter spread size.

#### 5.7.9beta33 (June 5, 2022)

Mbtrnpp and other elements of the Terrain Relative Navigation infrastructure:
Test tools and mbtrnpp command set augmented to enable using TRN in an ROV
context with realtime bathymetry available via LCM - this development is not
complete.

#### 5.7.9beta32 (June 4, 2022)

Fixes to src/mbtrnav/Makefile.am to allow successful build of TRN tools on
Mac Homebrew.

#### 5.7.9beta30 (June 4, 2022)

Fixes to the Autotools build system allowing MB-System to be built in full on
Arm architecture Mac computers running the Monterey OS and fixing the build of
the TRN tools on Linux.

MBnavadjust: Incremental changes towards handling global ties relative to a
reference grid - defined a single section naverr mode but don't have it
working yet.

#### 5.7.9beta29 (May 13, 2022)

Fixes to the Autotools build system allowing MB-System to be built in full on
Arm architecture Mac computers running the Monterey OS and fixing the build of
the TRN tools on Linux.

#### 5.7.9beta28 (March 21, 2022)

Mbm_trnplot: Added --display option that immediately displays the plots.

General: Reduced the internal maximum file path name length from 4096 to 1024
characters.

Format MBF_RESON7K3 (89): Fixed reading/writing of the PingMotion (7012),
Beamformed (7018), and FileCatalog (7300) records.

Mbnavadjust: Changed default range for z-offsets in calculating the 3D misfit
from +/- 5 m to +/- 1 m. Made progress towards allowing interactive picking of
global ties relative to a reference topography grid.

#### 5.7.9beta27 (February 28, 2022)

Mbtrnpp: Improved TRN result logging, including having all log files from a
session placed in the same directory named according to the start time. Also
added automated plotting of the TRN results using a new plot macro
mbm_trnplot.

Mbm_trnplot: New plotting macro that generates two map views of the results from
an mbtrnpp session.

Mbeditviz: Supports selective editing or ignoring of multipick soundings.

Mbm_route2mission: Added new battery behavior that turns off the mapping sonars
after data logging has been turned off at the end of the survey, before ascent
to the surface.

Mbvoxelclean: fixed memory management fault.

General: Increased the size of MB_PATH_MAX to 4096 bytes to allow for longer
file paths - this now conforms to the common file path maximum for Linux
distributions.

Terrain Relative Navigation: Many changes to mbrnpp and TRN related code by
Kent Headley

Mbphotomosaic: Fixed further issues with specifying options within the imagelist.

Mbnavadjust: Changed inversion - the relaxation stage now terminates if it starts
to diverge, a mod that reduces the tendency of the inversion to blow up.

Mbmakeplatform: Fixed header file array definition issue that caused compile
failures when testing cmake based builds.

#### 5.7.9beta26 (January 2, 2022)

Mbphotomosaic: Augmented available commands that can be specified in imagelist
files with --priority-weight and section-length-max. The --priority-weight allows
one to up-weight or down-weight sets of images in a photomosaic. The --section-length-max
command allows one to exclude groups of pixels that are projected into too large
of an extent when projected onto the seafloor topography model.

Mbm_makeimagelist: Augmented to comment out the first five image pairs in each
image survey directory, as the first three or four images are usually quite
dark.

#### 5.7.9beta25 (December 29, 2021)

Mbphotomosaic: Fixed problem specifying the image correction table file in
an imagelist structure.

Mbphotomosaic and mbgetphotocorrection: Altered the image correction table file
generated by mbgetphotocorrection and read by mbphotomosaic to include
correction tables for color as well as intensity. Since we are using the YCbCr
color space this means generating tables of average chroma (color) difference
in red and blue as well as a 3D table of average luma (intensity).
If RGB and YCbCr values have ranges 0-255, then:

  Y  = 0.299R + 0.587G + 0.114B (Luminance, intensity, B/W signal)
  
  Cb = 0.564(B - Y) + 128 (blue color difference)
  
  Cr = 0.713(R - Y) + 128 (red color difference)
  
and

  B = (Y + 1.773 * (Cb - 128));
  
  G = (Y - 0.714 * (Cr - 128) - 0.344 * (Cb - 128));
  
  R = (Y + 1.403 * (Cr - 128));
  
If the specified color correction file includes the Cr and Cb tables, then the
--correct-color command will cause mbphotomosaic to use those tables to correct
for color. Each source image pixel being corrected has a lateral location within
the source image and a standoff (altitude) relative to the seafloor; these 3D
positions correspond to locations in the 3D correction tables. As with the
intensity, the Cr and Cb corrections are a multiplicative factor calculated to
map the the value in the relevant location in the table to a reference value.
The reference value may be the average central values in the correction tables
or a value specified by the user with the --reference-intensity=intensity and
--reference-crcb=cr/cb commands.

#### 5.7.9beta24 (December 27, 2021)

Mbphotomosaic and mbgetphotocorrection: Altered the image correction table file
generated by mbgetphotocorrection and read by mbphotomosaic to include the
reference gain and exposure settings used by mbgetphotocorrection. This means
that these settings no longer have to be explicitly set in the mbphotomosaic
command.

Mbphotomosaic: Added an option --reference-intensity=intensity that sets the
reference intensity used by mbphotomosaic when mbgetphotocorrection image
correction tables are being used. The algorithm now works as follows:
  Before correction the pixel values are transformed from BGR colorspace into
  the YCbCr color space, that is from blue, green, red triples into
  Y (intensity), Cb (blue difference chroma), Cr (red difference chroma) triples.
  The correction involved changing the intensity, and then the YCbCr triples are
  transformed back into BGR triples for use in the photomosaic.
  The correction applied to each source pixel (or section) is a value
  that is multiplied by the source pixel intensity - a value of 1.0 will leave
  the source pixel unchanged, a value > 1.0 will make the pixel lighter, and a
  value < 1.0 will make the pixel darker.
  Each source pixel or section has an x-y location in the source image and
  a vertical standoff relative to the seafloor topographic model - these
  coordinates specify a location in the image correction table for the
  relevant camera. The value in the lookup table at that spot is the average
  intensity of all pixels with that location.
  The correction value is calculated as the multiplier that would transform
  the lookup table value to a desired reference intensity:
      C = reference_intensity / table_intensity

#### 5.7.9beta23 (December 18, 2021)

Mbphotomosaic and mbgetphotocorrection: Another iteration trying to get image
gain and exposure correction to work correctly. Altered the imagelist file format
to include camera gain and exposure settings. These can be extracted from the
metadata embedded into images written by the MBARI Prosilica driver code
(adapted from URI/WHOI/UM).

Mbm_makeimagelist: Altered the imagelist file format
to include camera gain and exposure settings. These can be extracted from the
metadata embedded into images written by the MBARI Prosilica driver code
(adapted from URI/WHOI/UM). Added --check-bayer option to allow checking the bayer images
for the original camera gain and exposure settings when those are not carried over
to the derived color images.

#### 5.7.9beta22 (December 5, 2021)

Mbphotomosaic and mbgetphotocorrection: Another iteration trying to bet image
gain and exposure correction to work correctly.

#### 5.7.9beta21 (December 4, 2021)

Mbphotomosaic, mbgetphotocorrection, mbphotogrammetry, mbm_makeimagelist: Altered
imagelist file format and functions reading recursive imagelist structures. Now
each stereo rig dataset has a single imagelist that can include both stereo pairs
and  single images (when one photo from a stereo pair is missing). Also, the
imagelists created by mbm_makeimagelist now include the camera gain and exposure
settings.

Mbphotomosaic, mbgetphotocorrection: Now can correct for image gain and exposure settings.

#### 5.7.9beta20 (December 1, 2021)

Mblist: Added K and k options to the output, where K prints the fraction of non-null
beams that are good (unflagged) and k prints the fraction of all possible beams
that are good. These fractions are by definition bounded by 0 and 1.

Mbphotomosaic, mbgetphotocorrection, mbphotogrammetry: Added capability to load
a time series of image quality values through new options:

-   --image-quality-file=file
-   --image-quality-threshold=value
-   --image-quality-filter-length=value

#### 5.7.9beta19 (November 7, 2021)

Format 89 (MBF_RESON7K3): Increased the maximum possible number of beams from 512
to 1024.

#### 5.7.9beta18 (October 31, 2021)

Mbgrid: Enabled shifting of output grid bounds using a new -Yshiftx/shifty option.

Mbtrnpp: Fixed build issue TRN libraries.

#### 5.7.9beta17 (October 16, 2021)

Mbgrid and mbmosaic: Fixed setting output grid format with the -G option. The
definition and parsing of the options is now consistent with GMT 6.

Mbnavadjust: Added option to unset skipped crossings.

Mbnavadjust: Changed vertical scaling of the time series model plot and the
tie plots so that these are centered on the midpoint values rather than zero.

Mbgrdviz: Changed how routes are output as Risi survey scripts - now the lateral
positions of waypoints are relative east and north meters in UTM rather than
local x,y calculated using mtodeglon and mtodeglat from a simple spheroid.

Mbm_grdplot: Fixed so that it does not crash if the input grid has either no
valid values (all are NaN) or all valid values are the same.

#### 5.7.9beta16 (August 27, 2021)

Mbnavadjust: Made listing of survey vs survey blocks much faster.

#### 5.7.9beta15 (August 26, 2021)

Mbnavadjust: Speeded up model tie plots and insured that changes to projects will
be saved when users quit.

Mbview (mbgrdviz, mbeditviz, mbnavadjust): Addressed a number of code style issues
particularly using bool rather than int for true/false values.

Mbm_route2mission: added acoustic modem status signal to MBARI AUV missions
immediately at the end of the "start survey" behavior.

#### 5.7.9beta14 (July 25, 2021)

Most programs: Fixed possible overflow associated with code that sets user, host,
and date information to be included in output files. This functionality has been
concentrated into a function mb_user_host_date() found in src/mbio/mb_defaults.c

Many programs and i/o modules: Increased use of assert() to prevent overflow
conditions when using sprintf to construct strings.

#### 5.7.9beta13 (July 18, 2021)

Mbextractsegy - fixed plotting so that the last plot is correct.

TRN: updated TRN documentation.

#### 5.7.9beta12 (July 4, 2021)

Build system: Fixed location of RPC and XDR headers for Ubuntu 21.

TRN: updated TRN documentation.

#### 5.7.9beta11 (June 26, 2021)

Build system: The configure script and the resulting Makefiles are
generated using GNU Autotools 2.71 instead of 2.69.

Mbnavadjustmerge: Enabled new options --set-global-tie-relative
which allows setting a global navigation tie with offsets calculated
relative to the current navigation adjustment model.

Mbphotomosaic: Improved algorithm for mapping the imagery from the
source images to the destination image. Now the code loops over all
destination pixels in each quadrilateral of interest and obtains the
corresponding source image pixels. Therefore no gaps are left in the
destination image due to a resolution and sampling mismatch between
the source and destination images.

Mbm_grdplot, mbm_grd3dplot, mbm_grdcut, mbm_grdinfo, mbm_grdtiff:
Fixed thesemacros to work with the new gmt grdinfo output that
changed for GMT 6.2.0.

#### 5.7.9beta10 (June 16, 2021)

Mbnavadjust: Fixed importation of swath files, which was failing. Fixed crash
that happened when a navigation inversion was performed in the same session as
swath data importation.

Mbauvloglist: Fixed parsing of short values in MBARI Dorado AUV MVC log files.

Mbm_grdplot: Fixed histogram equalization in cases where grdhisteq returns an
incomplete or short equalized color table.

#### 5.7.9beta09 (June 8, 2021)

Mb_rt raytracing functions: Added tracking of travel times in arrays returned by
mb_rt() for plotting raypaths. This adds a parameter to the mb_rt() function call,
which is used by utilities/mb_process.cc and mbvelocitytool/mbvelocity_prog.c.

Mbm_grdplot: If \fB\-MGL\fP\fIF\fP is given in conjunction with \fB\-MGL\fP\fIscalebar\fP
then the map scale will be surrounded by a white filled, black bounded box on
top of the map.

Mbm_grdplot: Chooses more reasonable easting/northing annotation intervals when
plotting maps in projected coordinate systems like UTM.

Mbm_grd2arc: Fixed so that the call to gmt convert is actually made.

Mbm_grdtiff: Fixed so that the temporary GMT defaults are actually applied to the
output image. By default this enforces a white background on the output GeoTiff
image, which enables the new tool mbtiff2png to set the white areas to transparent
when it converts a GeoTiff image to a PNG image for import into GIS.

Mbeditviz: Fixed sparse filtering functions, which were inadvertently broken a
few months ago.

Mbgetphotocorrection: Made multithreaded.

Mbphotomosaic: (1) Made multithreaded. (2) Added ability to map blocks of pixels from
source images to the destination image instead of mapping individual pixels. The
size of the square blocks is specified using --section=sizeInPixels. (3) Added PNG
format image output, which allows no data regions to be transparent. PNG images
cannot have geodetics embedded, and so depend on a *.pgw world file to be importable
into GIS. (4) Added image correction modes based on source pixel range or standoff.

Mbtiff2png: New tool that converts GeoTiff images to PNG images while setting no data
regions transparent on the basis of being white, lighter than a specified threshold,
black, or darker than a specified threshold.

Mbvoxelclean: Fixed application of acrosstrack and range filters.

#### 5.7.9beta07 (May 7, 2021)

mbm_histplot: Fixed the use of the -C option to specify cellwidth for the
histogram to be plotted.

Formats 232 (MBF_3DWISSLR) and 233 (MBF_3DWISSLP): Changed so that MB_FLAG_SECONDARY
is no longer used for multiple picks per laser pulse.

MBnavadjust and MBnavadjustmerge: Restructured the code so that more capability
of mbnavadjust can be duplicated in the command line tool mbnavadjust merge.
Working to add ability to reimport surveys into a project.

MBvoxelclean: Added --neighborhood option and fixed amplitude range options.

Mblist: Fixed function of the -O%fnv and -O%FNV commands to produce *.fnv files.

#### 5.7.9beta06 (March 24, 2021)

Mbpreprocess: Fixed to work with the old s7k format (88) MBF_RESON7KR.

Format 88 (MBF_RESON7KR): Fixed to not recognize collections of ping records
that are mission bathymetry and/or travel time records as complete.

Mbnavadjust: When importing files, only export navigation records to the *.mb166
files in the project directory for ping records (previously data were output
for input navigation records as well).

#### 5.7.9beta05 (March 8, 2021)

Mbauvloglist: Added available output field of speed calculated from the velocity
vector in the kearfott.log log file, with tag calcKSpeed. Also added new -C option:
in the case that navigation is being merged from an external file specified with
the -N option, the -C option suppresses output of records with timestamps from
before or after the time bounds of the navigation data. The default remains to
output those records with zero values for the merged navigation outside the time
bounds.

General: Changed code that deletes temporary files from using a system()
call to using the stdio function remove(). Affects src/mbio/mb_process.c,
src/utilities/mbdatalist.cc, and src/mbvelocitytool/mbvelocity_prog.c.

TRN: Updates to src/mbtrn, src/mbtrnav, src/mbtrnutils from Kent Headley.

Mbm_grdplot, mbm_3dgrdplot, mbm_grdtiff, mbm_grdinfo: Changed " -r " tests for
file readability to " -e " tests for file existence. This is to accommodate
filesystems that use ACL rather than old style unix file modes - the old stat
based readability test in Perl fails on ACL filesystems.

#### 5.7.9beta04 (February 21, 2021)

Mbpreprocess: Fixed handling of data formats that do not have specially defined
preprocessing functions. This fix was prompted by problems with SeaBeam 2112 data
in format 41 (MBF_SB2100RW).

General changes: More work to achieve thread safety for mbprocess: removed use
of static variables in several components of MBIO.

Mbgrid: Fixed error handling so that if the program is shut down by an error,
the exit code is nonzero.

MBIO: Added extraction function mb_extract_lonlat(), which returns swath data
similar to mb_extract() but with beam and pixel positions defined in longitude
and latitude rather than acrosstrack and alongtrack distances relative to the
reference point.

Mbareaclean: Fixed memory management bug causing crashes.

#### 5.7.9beta03 (February 7, 2021)

General changes: Replacing use of strtok() function with strtok_r(). Strtok() is
intrinsically not thread safe or reentrant and is considered poor use under all
circumstances. Source files with this change include:
  src/mbio/mbr_edgjstar.c src/mbio/mbr_hypc8101.c src/mbio/mbr_hysweep1.c
  src/mbio/mb_format.c src/mbio/mb_get_value.c src/bsio/mbbs_tm.c
  src/utilities/mblevitus.cc src/mbvelocitytool/mbvelocity_callbacks.c
  src/mbnavedit/mbnavedit_callbacks.c src/mbnavadjust/mbnavadjust_callbacks.c

General changes: Replace atof() with strtod() for thread safety. Source files
with this change include:
  src/gmt/mbgrdtifforg.c src/bsio/mbbs_tm.c src/mbio/mb_navint.c
  src/mbio/mbr_edgjstar.c src/mbnavadjust/mbnavadjust_fine.c

General changes: Replace atoi() with strtol() for thread safety. Source files
with this change include:
  src/gmt/mbcontour.c src/gmt/mbgrdtifforg.c src/gmt/mbswath.c
  src/gsf/gsf.c src/utilities/mbgrid.cc src/utilities/mbprocess.cc

General changes: Protect against overflows copying comments in all of the
mbsys_XXX_extract() and mbsys_XXX_insert() functions the in the source files
mbsys_XXX.c

MBnavadjust: Fixed bug that failed to save new navigation ties if the program was
closed without solving for a new model. Now closing the program will always save
any unsaved ties.

MBeditviz and MBview: Removed unneeded functions from mbview/mb3dsoundings_callbacks.c
that were breaking test Cmake builds.

#### 5.7.9beta02 (January 27, 2021)

Fixed bug in format 58 and 59 support for bathymetry recalculation. The per beam heave 
values were being calculated incorrectly when bathymetry was recalculated by raytracing.

Fixed bug in format 57 in which reprocessing did not trigger recalculation of multibeam 
pseudosidescan.

These bugs were introduced during the 2020 code modernization.

#### 5.7.9beta01 (January 18, 2021)

Mbedit and mbnavedit: Use extern for Widget definitions in mbedit_creation.h
and mbnavedit_creation.h to avoid duplicate symbol link errors when building
code according to current C / C++ standards. The other graphical utilities
already use this construct.

#### 5.7.8 (January 17, 2021)

Version 5.7.8 is now the current release of MB-System. Changes since the 5.7.6
release include:

Configure: Fixed handling of X11 libraries and header files in the autotools
build system in order to circumvent more changes to dependencies installed on
Macs using the Homebrew package manager. The first attempt at this turned out
to cause X11 runtime failures on Linux systems, and so release 5.7.7 was rapidly
superceded by this 5.7.8 release.

mbdatalist: Fixed memory leak in src/mbio/mb_check_info.c that could occur when
parsing *.inf files.

Formats 88 (MBF_RESON7KR) and 89 (MBF_RESON7K3): Fixed bug in handling of
PingMotion data records (7012) that caused memory overruns and seg faults.

Mbclean: Fixed two bugs. The first involved setting the left/right bounds of
flagging by acrosstrack distance using the -Y option, and the other resulted in
slope flagging being applied when not requested when the -Y option was used alone.

Mbpreprocess: Added option to set directory where output files are written instead
of writing the output files parallel to the input swath files.

Format 121 (MBF_GSFGENMB): Modified handling of multibeam snippet backscatter so
that samples associated with beams flagged as bad are nulled, and so that modified
backscatter is written to the output file by mbprocess.

Mbeditviz: Modified 3D sounding view so that the depth buffering is actually used.

Mbm_makedatalist: Now ignores the most recent file when the -L option is used.

Mbprocess: Fixed raytracking library used by mbprocess so that it is thread
safe. The relevant code is in mbsystem/src/mbaux/mb_rt.c

Format 261 (MBF_KEMKMALL): Fixed bug in handling version 0 MWC datagrams.

Mbphotomosaic: Fixed bug in pixel processing that occasionally produced overflows
leading to seg faults.

Mbphotomosaic: Fixed bug in imagelist processing that prevented use of images
taken with the right camera of a stereo pair.

Mbimagecorrect: New program that performs some simple brightness and contrast
corrections using standard OpenCV algorithms.

Mbprocess: Recast the program to process files in parallel using separate threads.
This was implemented in the C++ main code using the C++11 standard thread API.
The default is to use a single processing thread and therefore to process the
files serially; the new -Cthreads option enables the use of multiple threads.
For now, the built-in record keeping of memory allocation/deallocation is disabled
for mbprocess because this functionality is not thread-safe.

Mbnavadjust: The navigation adjustment inversion has been improved by tuning the
parameters used for the overdetermined least squares solution.

Mbswath2las: Shell for not-yet-working program to export soundings from swath data
to some variant of the LAS format used for point cloud data.

Mbvoxelclean: Added option to filter based on beam amplitude minimum and maximum
values.

Mbeditviz: Fixed coloring of soundings using beam amplitude values (colormap
was applied incorrectly).

Mbeditviz: Added option to display the selected sounding point cloud with
soundings colored according to associated amplitude value. Also added the
sounding amplitude value to the information listed when soundings are selected
in the "info" mode.

Mbedit: Added the sounding amplitude value to the information listed when
soundings are selected in the "info" mode.

Mbnavadjust: Previously autopicking of crossings skipped crossings including
short sections where short was defined as less than 0.25 times the length of
the first section of the associated file. This is problematic when the survey
platform is stationary at the beginning of a file, resulting in a first section
with a short track length (sections are terminated either on track length or total
number of soundings). Now short is defined as less than 0.25 times the current
desired section length for the project.

Format 58 (MBF_EM710RAW): This format supports third generation Kongsberg multibeam
data as recorded in *.all files; the augmented format 59 (MBF_EM710MBA) is used
for processing. Data are translated from format 58 to 59 using mbpreprocess. Data
have been collected using a partially nonfunctional EM122 such that most of the
backscatter snippet records are missing. The existing code treats pings for which
the snippet records are missing as incomplete and drops them. The format 58 i/o
module has been modified so that if a special flag is set, any snippet records
will be ignored and all pings will be treated as having an empty but existing
snippet record. Users can set this flag with a special --kluge-ignore-snippets
argument to mbpreprocess.

Mbpreprocess and i/o modules with defined preprocessing functions: All existing
preprocess functions have been augmented so that a call with a null pointer to
the data structure will trigger an option to set i/o flags after reading from a
file is initialized but before any data are read. The only case at present where
this is used is format 58 (MBF_EM710RAW), where the mbpreprocess option
--kluge-ignore-snippets causes the reading code to treat pings with bathymetry
as complete whether snippet records exist or not, and to zero the snippet information
for those pings.

Mbm_makedatalist: Added -L option which will omit the last file found from the
output datalist. The  intent  of this  option  is  to exclude the most recent
file in an actively data logging context, since the most recent file is still
being logged. This presumes that filenames sort in time order as listed  by  the
ls  command,  an assumption that does not hold for all file naming conditions or
if the -T option has been used to disable time ordering. Also added a behavior
particular to Kongsberg multibeam data as originally logged - files named "9999.all"
are now ignored.

Mbotps: Modified mbotps to place temporary files in the user's home directory
instead of the current working directory when the latter case results in file
paths greater than 80 characters long. This is because OTPS has it's filename
variables defined as 80 character strings.

Format 88 (MBF_RESON7KR): Fixed handling of the various attitude data record
types by function mb_extract_nnav(), which in turn allows mbnavlist to work
correction with format 88 data when keyed to those data record types.

Mblist: Added output option 'n' for survey line number. This value is only defined
for SEGY format data files (format 160).

#### 5.7.8beta01 (January 17, 2021)

The autoconf build system had been changed so that libXt and libX11 come
before libXm in the link commands. This fixes runtime errors in all of
the graphical utilities on Linux systems. This problem probably relates
more directly to the use of the gcc compiler system.

#### 5.7.7 (January 17, 2021)

The version 5.7.7 was fatally flawed in that the graphical tools would not run
on Linux (or more probably, when built using gcc rather than llvm). The problem
was that the autoconf build system had been changed in order to fix
build failures in the Homebrew package manager, and these changes inadvertently
including changing the library link order so that libXt and libX11 came before
libXm. This problem was fixed rapidly and a new major release 5.7.8 put the
same day.

#### 5.7.7beta09 (January 17, 2021)

mbdatalist: Fixed memory leak in src/mbio/mb_check_info.c that could occur when
parsing *.inf files.

Configure: Fixed handling of X11 libraries and header files in the autotools
build system in order to circumvent more changes to dependencies installed on
Macs using the Homebrew package manager.

#### 5.7.7beta08 (January 6, 2021)

Formats 88 (MBF_RESON7KR) and 89 (MBF_RESON7K3): Fixed bug in handling of
PingMotion data records (7012) that caused memory overruns and seg faults.

Mbclean: Fixed two bugs. The first involved setting the left/right bounds of
flagging by acrosstrack distance using the -Y option, and the other resulted in
slope flagging being applied when not requested when the -Y option was used alone.

Mbpreprocess: Added option to set directory where output files are written instead
of writing the output files parallel to the input swath files.

Format 121 (MBF_GSFGENMB): Modified handling of multibeam snippet backscatter so
that samples associated with beams flagged as bad are nulled, and so that modified
backscatter is written to the output file by mbprocess.

Mbeditviz: Modified 3D sounding view so that the depth buffering is actually used.

Mbm_makedatalist: Now ignores the most recent file when the -L option is used.

#### 5.7.7beta06 (December 30, 2020)

Mbprocess: Fixed raytracking library used by mbprocess so that it is thread
safe. The relevant code is in mbsystem/src/mbaux/mb_rt.c

#### 5.7.7beta05 (December 28, 2020)

Format 261 (MBF_KEMKMALL): Fixed bug in handling version 0 MWC datagrams.

Mbphotomosaic: Fixed bug in pixel processing that occasionally produced overflows
leading to seg faults.

Mbphotomosaic: Fixed bug in imagelist processing that prevented use of images
taken with the right camera of a stereo pair.

Mbimagecorrect: New program that performs some simple brightness and contrast
corrections using standard OpenCV algorithms.

Mbprocess: Recast the program to process files in parallel using separate threads.
This was implemented in the C++ main code using the C++11 standard thread API.
The default is to use a single processing thread and therefore to process the
files serially; the new -Cthreads option enables the use of multiple threads.
For now, the built-in record keeping of memory allocation/deallocation is disabled
for mbprocess because this functionality is not thread-safe.

Mbnavadjust: The navigation adjustment inversion has been improved by tuning the
parameters used for the overdetermined least squares solution.

Mbswath2las: Shell for not-yet-working program to export soundings from swath data
to some variant of the LAS format used for point cloud data.

#### 5.7.7beta04 (October 28, 2020)

Mbvoxelclean: Added option to filter based on beam amplitude minimum and maximum
values.

Mbeditviz: Fixed coloring of soundings using beam amplitude values (colormap
was applied incorrectly).

#### 5.7.7beta03 (October 27, 2020)

Mbeditviz: Added option to display the selected sounding point cloud with
soundings colored according to associated amplitude value. Also added the
sounding amplitude value to the information listed when soundings are selected
in the "info" mode.

Mbedit: Added the sounding amplitude value to the information listed when
soundings are selected in the "info" mode.

Mbnavadjust: Previously autopicking of crossings skipped crossings including
short sections where short was defined as less than 0.25 times the length of
the first section of the associated file. This is problematic when the survey
platform is stationary at the beginning of a file, resulting in a first section
with a short track length (sections are terminated either on track length or total
number of soundings). Now short is defined as less than 0.25 times the current
desired section length for the project.

Format 58 (MBF_EM710RAW): This format supports third generation Kongsberg multibeam
data as recorded in *.all files; the augmented format 59 (MBF_EM710MBA) is used
for processing. Data are translated from format 58 to 59 using mbpreprocess. Data
have been collected using a partially nonfunctional EM122 such that most of the
backscatter snippet records are missing. The existing code treats pings for which
the snippet records are missing as incomplete and drops them. The format 58 i/o
module has been modified so that if a special flag is set, any snippet records
will be ignored and all pings will be treated as having an empty but existing
snippet record. Users can set this flag with a special --kluge-ignore-snippets
argument to mbpreprocess.

Mbpreprocess and i/o modules with defined preprocessing functions: All existing
preprocess functions have been augmented so that a call with a null pointer to
the data structure will trigger an option to set i/o flags after reading from a
file is initialized but before any data are read. The only case at present where
this is used is format 58 (MBF_EM710RAW), where the mbpreprocess option
--kluge-ignore-snippets causes the reading code to treat pings with bathymetry
as complete whether snippet records exist or not, and to zero the snippet information
for those pings.

Mbm_makedatalist: Added -L option which will omit the last file found from the
output datalist. The  intent  of this  option  is  to exclude the most recent
file in an actively data logging context, since the most recent file is still
being logged. This presumes that filenames sort in time order as listed  by  the
ls  command,  an assumption that does not hold for all file naming conditions or
if the -T option has been used to disable time ordering. Also added a behavior
particular to Kongsberg multibeam data as originally logged - files named "9999.all"
are now ignored.

#### 5.7.7beta02 (October 8, 2020)

Mbotps: Modified mbotps to place temporary files in the user's home directory
instead of the current working directory when the latter case results in file
paths greater than 80 characters long. This is because OTPS has it's filename
variables defined as 80 character strings.

#### 5.7.7beta01 (October 7, 2020)

Format 88 (MBF_RESON7KR): Fixed handling of the various attitude data record
types by function mb_extract_nnav(), which in turn allows mbnavlist to work
correction with format 88 data when keyed to those data record types.

Mblist: Added output option 'n' for survey line number. This value is only defined
for SEGY format data files (format 160).

#### 5.7.6 (October 5, 2020)

Version 5.7.6 is now the current release of MB-System. 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. These programs are:

- mb7k2jstar
- mb7k2ss
- mb7kpreprocess
- mbauvnavusbl
- mbhsdump
- mbhysweeppreprocess
- mbinsreprocess
- mbkongsbergpreprocess
- mbneptune2esf
- mbrollbias
- mbrphsbias
- mbstripnan
- mbswplspreprocess
    
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.

#### 5.7.6preparation (October 4, 2020)

Mbnavlist: Fixed bug in parsing -O option that sometimes resulting in the output
of undesired values.

Mbm_makeimagelist: New macro that constructs imagelist files of stereo photograph
pairs as collected by MBARI's low altitude survey system. This is the first
Python3 macro in MB-System.

Format 88 (MBF_RESON7KR): Fixed calculation of speed when using the mb_extract_nav()
function for navigation records.

Mbpreprocess: Fixed problems with the --kluge-time-jumps option for fixing
jumps in timestamps.

Mbsslayout: Add blanking interval to option --altitude-bottompick-threshold=threshold[/blank]
so that when picking the bottom return in the sidescan time series, nearfield backscatter
can be ignored out to the time interval in seconds given by the value blank.

#### 5.7.6beta56 (September 28, 2020)

Mbsegylist: Add print option of 'l' for the line number contained in the segy file header.

Format 132 (MBF_EDGJSTAR): Edgetech Jstar format. The i/o module has been modified
to handle broken records gracefully by searching byte by byte for the next valid
start of record.

Mbnavadjust: Reinstated use of both first and second derivitive penalty function
in the final stage of inversion for a navigation adjustment model.

Mbnavadjustmerge: Now copies triangle files along with section swath files when
copying a project. This means these triangle files will not need to be remade
in the new project.

#### 5.7.6beta55 (September 16, 2020)

Mbtrnpp: Fix potential variable overflow and incorrect metrics value assignment
in netif code.

#### 5.7.6beta54 (September 14, 2020)

Mbnavadjust: Changed "Zero All Z Offsets" action to apply to only the crossings
or ties currently displayed in the list, not literally all set ties.

Mbtrnpp: Fixed TRN content of TRN updates when TRN processing fails due to
insufficient or inconsistent data.

Mbtrnpp: Add support for trnu client reset callback (does reset using best
offset) and supporting metrics, add file swap event to reinit plot

#### 5.7.6beta53 (September 13, 2020)

Format 261 (MBF_KEMKMALL): Fix to AUV Sentry mode for kmall format - zero heave
in processed ping records (XMT) when platform is an AUV.

Mbnavedit: fixed handling of interpolation/extrapolation when timestamps are repeated.

TRN plotting scripts - changed hard coded bash location to /usr/local/bash

#### 5.7.6beta52 (September 9, 2020)

mbtrnpp: Added tide model correction. Added metrics covering non-survey data
publishing.

Mbnavadjust: Now ignores pings with zero navigation values on import.

Format 261 (MBF_KEMKMALL): Fixed embedding of changed navigation and sensordepth
values by mbprocess - these values needed to be changed in both MRZ and XMT records.

#### 5.7.6beta51 (September 4, 2020)

mbtrnpp: Added time stamp and position to TRN status messages generated for pings
with no valid soundings. Bug fix: stats and cycle exec time metrics get incorrect
values on some platforms, because of mixed reference to real time and precision
clocks; now use consistent references

#### 5.7.6beta50 (September 2, 2020)

mbtrnpp: Now outputs TRN status messages even when the input data do not include
valid soundings and so do not get processed by TRN. Also reduced the debug level
of the network interface code.

#### 5.7.6beta49 (September 2, 2020)

mbtrnpp: Fixed bugs in parsing commands and also in management shellscript mbtrnpp.sh

#### 5.7.6beta48 (September 1, 2020)

mbtrnpp: Fixed bug that opened a new log file at each reinitialization without
closing the old log file, eventually using up all of the available file descriptors
and crashing. Added some diagnostic output. Updated related test clients and servers
used to demonstrate socket based i/o to and from mbtrnpp.

#### 5.7.6beta47 (September 1, 2020)

mbtrnpp: Modified the socket based TRN output packet and the related internal
representation.

#### 5.7.6beta46 (August 31, 2020)

mbtrnpp: Now reinitializes the Terrain Relative Navigation (TRN) filter using
the best available position rather than the last estimated navigation offset.
If no good convergence has been reached, then the center of the particle filter
cloud will be offset from the current navigation by zero. If a good convergence
has been found at some point, the most recent good convergence offset value
will be used to center the new particle filter cloud. Good convergence is not
defined by the convergence criteria within the TRN filter code, but is instead
defined by mbtrnpp according to a maximum standard deviation magnitude (by
default 5.0 meters) and a minimum number of successive iterations that achieve
better than that threshold (by default 200)

Format 261 (MBF_KEMKMALL): Added hook to allow a program (currently on mbtrnpp)
to set a flag that enables a correction specific to EM2040 data collected on
AUV Sentry. The sensor depth value is recorded in a nonstandard location within
the *.kmall data on AUV Sentry. In post processing this is handled with a special
kluge option to mbpreprocess. The program mbtrnpp can now force the i/o module to
make this same correction when reading raw *.kmall data.

Format 72 (MBF_MBARIMB1): Fixed bug in handling sensordepth values.

#### 5.7.6beta45 (August 26, 2020)

Mbtrnpp: Changed most shell output from stdout to stderr. Altered logic for
triggering TRN reinits.

Formats 12 (MBF_SBSIOCEN), 13 (MBF_SBSIOLSI), 14 (MBF_SBURICEN), 15 (MBF_SBURIVAX):
Fixed string overrun while writing long comment records.

#### 5.7.6beta44 (August 24, 2020)

Format 89 (MBF_RESON7K3): Fixed handling and processing of backscatter data,
which had a variety of problems. Now, the pseudo-sidescan reported by MB-System
as sidescan can be recalculated by mbprocess from the desired backscatter
source. The default is to use the best source of backscatter available, with
the order of "bestness" being:

1. Calibrated snippets
1. Snippets
1. Calibrated sidescan
1. Sidescan

You can force mbpreprocess to use a desired backscatter source with the 
--multibeam-sidescan-source option, where:

-  --multibeam-sidescan-source=C ==> Calibrated snippet records
-  --multibeam-sidescan-source=S ==> Snippet records
-  --multibeam-sidescan-source=W ==> Calibrated sidescan records
-  --multibeam-sidescan-source=B ==> Sidescan records

Format 89 (MBF_RESON7K3): Added support for additional informational data
records.

Mbsegylist: Fixed formatting time strings.

Mbnavlist: Fixed formatting time strings.

Mbextractsegy: Fixed embedding the seafloor depth value correctly into output
segy trace headers when the data are being extracted from Edgetech Jstar format
data (MBIO format 132).

Mbnavadjust: Changed the inversion control parameters such that the second
phase of the navigation adjustment solution, a coarse progressive relaxation
intended to achieve large scale shifts between surveys, now has a maximum
iteration count of 10000 (previously 1000) and a convergence criterea of
0.00001 (previously 0.0001).

Mbgrd2octree: New program to translate a GMT bathymetry grid to an octree
representation in the form used by the Stanford/MBARI Terrain Relative
Navigation software. The octree files have a suffix convention of *.ob for
octree binary. The input bathymetry grids are assumed to be in UTM coordinates
with square cells.

Mbtrnpp: Made the --platform-target-sensor option functional. Added options
        --reinit-qain --reinit-xyoffset=max --reinint-zoffset=min/max

Mbeditviz: Now outputs error message to shell when a file can't be imported
because it lacks an *.inf file.

#### 5.7.6beta43 (July 23, 2020)

Mbsvplist: Added capability to extract sound velocity profile (SVP) models from
MB_DATA_CTD type records as well as MB_DATA_SOUND_VELOCITY_PROFILE type records
(which is the default). This is controlled with the -A option: -AS specifies
use of SVP records, and -AC specifies use of CTD records. At present, the only
relevant data formats are the old Reson (88) and current Teledyne (89) *.s7k
formats.

Mbvelocitytool: Fixed the -B and -E options to specify the allowed begin and
end times of swath data used for modeling; previously these options were
ignored. Also fixed a memory leak involving the display SVP profiles.

Mbgetphotocorrection: The --show-images option now uses the OpenCV imshow()
function to briefly display the images being read and processed.

Mbphotomosaic: The --show-images option now uses the OpenCV imshow() function
to briefly display the images being read and processed.

Mbphotogrammetry: The --show-images option now uses the OpenCV imshow()
function to briefly display stereo pairs being read and processed, along with
the disparity function calculated for the image pair.

#### 5.7.6beta42 (July 21, 2020)

Mbtrn and mbtrnav: Updates and bug fixes to replay-trn_server.

Mbphotomosaic, mbgetphotocorrection, mbphotogrammetry: Added image quality value
to the parameters returned by function mb_imagelist_read(), and augmented the
definition of an imagelist entry to optionally include a quality column that
has values in the range 0.0 to 1.0. Augmented mbphotogrammetry to output an
imagelist of all image pairs it processes, and to populate the new quality
field with the fraction of all possible bathymetry values that are successfully
calculated, a number 0.0 >= quality >= 1.0. Also augmented mbphotomosaic and
mbgetphotocorrection with new options "--image-quality-threshold=value" that
set a threshold quality value (by default 0.0) below which images or image pairs
are ignored.

Format 89 (MBF_RESON7K3): Fixed calculation and use of azimuthal beam angles
in RawDetection and SegmentedRawDetection records. This bug resulted in
bathymetry recalculated by raytracing in mbprocess having the acrosstrack
and alongtrack distances transposed. To fix the problems caused by this bug
mbpreprocess and then mbprocess should be rerun.

#### 5.7.6beta41 (July 12, 2020)

Mblist: Fixed bug in which output in the CDL format was broken, which in turn
broke output in netCDF.

Mbphotomosaic: Fixed generation of photomosaics in projected coordinate systems
(e.g. UTM).

Mbphotomosaic, mbgetphotocorrection, mbphotogrammetry: Changed source file names
from the \*.cpp suffix to the \*.cc suffix to be consistent with other C++ source
files in MB-System.

#### 5.7.6beta40 (July 7, 2020)

Mbphotomosaic, mbgetphotocorrection, mbphotogrammetry: Added three programs used
for processing seafloor photography collected during seafloor mapping surveys
(i.e. from a survey platform with navigation and attitude data). These programs
depend on the OpenCV version 4 package, and so add a large and complex dependency
to MB-System. The source files are in the new directory src/photo. These programs
are not currently built by default - the configure script must be run with a
--enable-opencv option in order to enable building the photo tools. No documentation
exists at this point for these tools. A key aspect is that the photography data
are referenced through recursive imagelist structures (introduced in 5.7.6beta32)
analagous to the datalists used for sonar and lidar data. The photomosaicing and
photo correction tools will work with both single and stereo camera datasets. The
photogrammetry tools works only with stereo pair data. These tools also depend
on camera calibrations - the tool(s) for that are not yet included in MB-System.

Qt based tool prototypes: Improved the build system handling of Qt5 and OpenGL
programs. The test libraries and programs enabled by running configure with the
--enable-qt option are now located in four directories: src/qt-mbgui,
src/qt-mbgrdviz-1, src/qt-mbgrdviz-2, and src/qt-mbgrdviz-3.

GMT integration: The GMT 6.1.0 release contains a change to the API that broke
the build of the GMT module mbswath. It also contained changes to the module
initialization code that caused mbswath, mbcontour, and mbgrdtiff to crash.
The code has been modified with (more) proprocessor directives determined by
the installed GMT version to build with GMT versions 5.2, 5.4, 6.0, 6.1, and
the current master that will become 6.2. For GMT versions >= 6.0 the MB-System
code no longer depends on either the gmt/src/gmt_mb.h header file or the obsolete
gmt_begin_module() function.

#### 5.7.6beta38 (June 8, 2020)

Mblist: Fixed problem in which the centermost (nadir) beam was generally set to 0.

Format MBF_KEMKMALL (261): Brought reading and writing of *.kmall files up to
revision G of the Kongsberg data format specification. Also fixed problems in the
logic relating calculated depths as stored in the format to the depth values
reported by the MB-System API functions, and with the beam angles calculated for
use in recalculating bathymetry through raytracing. However, problems remain
with extracting the installation bias parameters and time latencies that must
be applied to the asynchronous ancillary data in order to properly calculate
these values. At present, recalculation of bathymetry by raytracing still does
not work correctly with this format - in some cases additional attitude biases
and time latencies must be applied, and in others the result is simply not right.

Formats MBF_EM710RAW (58) and MBF_EM710MBA (59): Added allowed sonar models
- unexpectedly we are seeing *.all files from some current generation sonar
installations, so we have to allow EM304 and EM712 sonar models with the
obsolete format.

#### 5.7.6beta37 (May 26, 2020)

Mbnavadjust: Fixed problems in the inversion algorithm.
The complexity of this algorithm results from the tendency
of overdetermined least squares solutions to work best at providing uniform scale,
zero mean solutions. Consequently we construct the solution in three steps.
First we solve for the average offsets
between continuous surveys, and make this the starting model for the second step.
Then we solve for a coarse ("chunk") perturbation model in which each chunk is a
dataset consisting of about five sections worth of continuous survey data. This is
done through an iterative damped relaxation procedure, and the resulting perturbation
model is added to the starting model for the third and final step. The final step
is to solve for a perturbation satisfying all of the navigation ties at full
resolution. The problem is set up as an overdetermined least squares matrix
problem and is solved using LSQR. The regularization is just penalizing the
first derivative of the perturbation at present - we are not currently penalizing
the second derivative.

Mbnavadjust: Fixed crash on Linux when executing the Auto Set Vertical Offset
function (didn't dimension arrays large enough).

Writing GMT grids: Fixed crash reported by Joaquim Luis on Windows when writing
GMT grids - the problem was a function call that caused GDAL to allocate a string
but then it allowing that pointer to be freed in GMT functions. The solution is
to ensure that memory allocated with GMT or GDAL libraries is freed from those
same libraries. I also had to alter the configure.ac to add a conditional
HAVE_GDAL that mimics one used in the GMT build system so that GDAL related
headers are included by gmt_dev.h. The relevant code is only used if GDAL is
available. If GMT version is >= 6.1.1 then the function gmt_strdup_noquote()
is called to allocate a PROJ4 string stored in the grid header; otherwise strdup()
is called. Building on Windows will now require GMT 6.1.1 or later.

Mblevitus: Fixed errors that had been inadvertently created as part of commit #448.
Thanks to Joaquim Luis for finding and fixing this.

#### 5.7.6beta36 (May 17, 2020)

Mbgrd2obj: Had to add #ifdef's on GMT version because the number of parameters
passed to gmt_init_module() changes between GMT 5.3 through 6.0 and 6.1.

Mbnavadjust: Changed calculation of overlap for a crossing so that the value is
not small in the case that a small section (by area) is entirely inside the bounds of a
much larger section. This case happens when adjusting navigation from surveys at
at two very different scales (e.g. AUV survey with ship hull mounted survey,
or ROV survey with AUV survey).

Mbnavadjustmerge: Added function to merge two adjacent surveys into one with an
internal discontinuity.

#### 5.7.6beta34 (May 14, 2020)

Mbgrd2obj: New GMT module that converts GMT topographic grids to OBJ format 3D
model files that can be imported to visualization software or printed on 3D
printers.

Mbset and mbmakeplatform: Joaquim Luis reports that these programs will not
compile on Windows Visual Studio "because of the too many nested if-else  problem."
I have attempted to fix this problem two ways. In mbset.cc I now use a switch  
statement instead of many if {} else if {} statements to find the meanings of
all the input options. In mbmakeplatform I now have many separate if {} statements
testing the input arguments, but each first also tests a bool that indicates
if a prior if {} statement matched the argument. We will find out from Joaquim
if either, neither, or both methods work.

Tests: The Travis-CI tests of new checkins to the repository are failing for one
of the many builds - the Ubuntu Xenial (16.04) build. The failures are occuring
on all programs that call GMT grid io, but the existing logs do not tell me why.
I have added print statements to the tests in
  mbsystem/test/utilities/mbbackangle_test.py
and
  mbsystem/test/utilities/mbgrid_test.py.
I don't know how to get that output into the log that Travis-CI makes available.

TRN tools: Kent Headley have added a config file mechanism to mbtrnpp, and fixed
a number of other issues in a series of commits. These changes are in src/mbtrn,
src/mbtrnav, and src/mbtrnutils.

#### 5.7.6beta33 (May 5, 2020)

Mbnavadjust: Changed handling of fixed surveys when updating the project grid
or applying the solution. Previously the files of fixed surveys were ignored,
even if they previously had been adjusted before being set to fixed. Now, the
unchanged *.na0 file will be output and the navadjust state will be updated
so that mbprocess will apply the unchanged navigation.

Mbcopy: A compile failure occurs for src/utilities/mbcopy.cc on Windows as
reported by Joaquim Luis. The issue is that under Visual Studio C++ some
external symbols referenced in the mbsys_simrad.h header file are not
available to the C++ code in mbcopy.cc. This is not true for clang or gcc.
The symbols in question are double arrays holding the beam angles for different
operation modes of the Simrad multibeams supported by this i/o module.
The solution attempted here is to move the array definitions to mbsys_simrad.c
and to provide a non-standard function to access pointers to those arrays. By
non-standard I mean this does not fit with the normal set of MBIO API functions,
and does not exist for i/o modules generally. The function mbsys_simrad_beamangles()
has been added to mbsys_simrad.c and the prototype in mbsys_simrad.h is wrapped
with extern "C" so it can be called from mbcopy.cc.

Mbcopy: The current processing model for old Simrad multibeam data in format 51
is to first use mbcopy to translate it the extended second generation Kongsberg
format 57, and then process it as one would more modern data. It was discovered
that this translation was failing to properly copy navigation records. This
was fixed.

Format MBF_EMOLDRAW (51): Because the compile error referenced above involved
1990's era Simrad multibeam data in format 51, it was necessary to test processing
of such data. This revealed that recent changes to program logic from using
MB_YES/MB_NO/MB_MAYBE values to bool variables (true/false) had broken the basic
data record reading logic for the MBF_EMOLDRAW i/o module. This has been fixed.

Build system for Qt5 based tools: Improved the build system handling of Qt5
programs. The test program enabled by running configure with the --enable-qt
option has been renamed mbgrdvizqt, but still resides in src/qttest. The
approach now is to do the following:
(1) The configure script creates the Qt project file src/qttest/mbgrdvizqt.pro
    and then modifies the values of variables specifying the required MB-System
    and GMT libraries and headers.
(2) The configure script runs qmake in src/qttest to generate a Makefile named
    src/qttest/Makefile.qmake
(3) The configure script generates a Makefile in src/qttest that in turn will
    run make itself using Makefile.qmake for targets all, install, uninstall,
    and clean.
This approach now works on a Mac. It's time to test on Linux.

#### 5.7.6beta32 (April 22, 2020)

Mbgrid: Fixed failure of the two gridding algorithm using beam footprints in
which the footprint size blows up at low grazing angles. The fix is to not
use soundings for which the grazing angle is less than five degrees.

Mbgrid and mbmosaic: Replaced int values with bool values where appropriate.

Build system: Added option to enable building tools based on Qt5 to the autotools
build system. If the configure script is given the --enable-qt option, it
checks if Qt5 has been installed, and if so, determines the compiler and linker
flags required to build tools using Qt5. At present, the only Qt5 based code
is in the directory src/qttest, and this code does not successfully compile
and run. Therefore it is not recommended to run configure with the --enable-qt
option. However, the build system is now ready to support Qt5 based tools as
they are developed.

Mbgrdtiff: Paul Wessel contributed a new version of mbgrdtiff that constructs
the image by a direct call to the grdimage module. This version will only build
and work with GMT 6.1 and later. The original code included code building the
image, duplicating functionality in grdimage. The new version is now
    mbsystem/src/gmt/mbgrdtiff.c
and the original version
    mbsystem/src/gmt/mbgrdtifforg.c.
The build system has been augmented to check the GMT version and build mbgrdtiff
from the original when that is <6.1 and the new file when that is >= 6.1.

General (mb_define.h, mb_format.c, mb_format.h): Added definition of format=-2
as recursive imagelists. Analagous to datalists, this construct supports timestamped
lists of single or stereo photographs. Like datalists, the imagelists can be
recursive. This is a precursor to bringing into MB-System tools for processing
seafloor photography collected during surveys, particularly for photomosaicing.

Mbsslayout and future photomosaicing: The parameters use to define convergence
when intersecting a vector with a topography model in mb_intersectgrid.c have
been improved, yielding more accurate intersection locations for backscatter samples
or source image pixels when laying out sidescan or photography data.

Mbnavedit: Changed minimum range of draft (sensordepth) plot to be +/- 0.05 meters.

Mbeditviz: Fixed problem with preserving changes to edits that are recorded in
*.esf files.

Mbtrnpp: merged recent changes by Kent Headley to the source files in
src/mbtrn, src/mbtrnav, and src/mbtrnutils.

Mbset: changed output to clearly indicate when parameter files are created
(or not) or modified (or not). This involved adding a function
mb_pr_compare() to mb_process.c that can be used in mbset.c to check
whether the modified process parameter structure actually differs from
the original structure.

Formats MBF_OICGEODA (141) and MBF_OICMBARI (142): Fixed support for old OIC
format DSL120 interferometric sonar data. Processing of these data now works
with mbpreprocess and mbprocess again. The sidescan data were compromised
by treating unsigned amplitude values as signed, and treating null samples as
valid.

Testing: Reinstated OSX test build as part of the Travis CI runs triggered by
commits to the Github repository.

Code style: Kurt Schwehr is systematically altering the code to conform to best
practices and adding build tests. The improvements included in this beta release
include work on mbview and programs using mbview, the auxilliary library in src/mbaux, 
particularly including mb_cheb.c, mb_intersectgrid.c, and mb_zgrid.c,
and on mbedit.

Code style: Tom O'Reilly and David Caress added README.md files in each of the 
subdirectories under src/.

#### 5.7.6beta31 (March 2, 2020)

Mbvoxelclean: Fixed memory leak. Added --acrosstrack-minimum and --acrosstrack-maximum
filters. Cleaned up shell informational output.

Mbeditviz: The program now keeps only a limited number of esf (edit save file)
files open for writing rather than opening esf files for all loaded swath files.
The program was failing when the total number of open files exceeded the operating
system maximum (1024 on MacOs and CentOs). The default maximum number of open
esf files is now 25.

Mbeditviz: Colorized flagged soundings the same as for mbedit (filtered == blue,
manually edited == red).

Format 233 (MBF_WISSLR): Corrected use of ev_offset and az_offset (across and
alongtrack distance offsets at the optical head) in preprocessing. Also added
a capability to apply Snell's law type tweak to the lidar pulse angles throuhg
mbpreprocess (--kluge-beam-tweak=value).

Code style: Kurt Schwehr is systematically altering the code to conform to best
practices and adding build tests. The improvements included in this beta release
include work on mbview and programs using mbview.

Code style: Github user abnj contributed some code cleanup by removing $Id tags
used when the code was in a Subversion repository.

#### 5.7.6beta30 (February 20, 2020)

Mbprocess, mbfilter, mbvoxelclean, mbclean, mbinfo, mbdatalist: Fixed bugs in
handling of status values returned by functions that caused early program
termination.

Code style: Kurt Schwehr is systematically altering the code to conform to best
practices and adding build tests. The improvements included in this beta release
include work on mbview and programs using mbview.

#### 5.7.6beta29 (February 17, 2020)

Mbnavadjust: Fixed bugs in mbnavadjust creating by modifying the handling of
function status returns.

Mbcopy: Fixed bug in parsing the end time values specified with the -E option.

Code style: Kurt Schwehr is systematically altering the code to conform to best
practices and adding build tests. The improvements included in this beta release
include work on mbview and programs using mbview: mbgrdviz, mbeditviz, mbnavadjust.

#### 5.7.6beta28 (February 13, 2020)

Format 89 (MBF_RESON7K3): Added support for data record type 7058. Also added
ability to handle s7k data files missing the file header record.

Format 233 (MBF_WISSLR): Embedded fix for timing glitch in early WiSSL data.

Mbotps: Discovered that the path length for the temporary files written by
mbotps must be less than 100 characters or the OTPS program predict_tide will
fail. Altered the filenames used for these temporary files to be as short as
possible.

mbvoxelclean: Fixed datalist reading logic.

mbprocess: Fixed bug introduced in 5.7.6beta27 that caused mbprocess to exit
in the middle of processing files referenced by a datalist.

Code style: Kurt Schwehr is systematically altering the code to conform to best
practices and adding build tests. The improvements included in this beta release
include work on mbedit, mbnavedit, and mbnavadjust.

#### 5.7.6beta27 (February 3, 2020)

mbpreprocess: Corrected prior fix to error in calculating lever arms, which
didn't include all of the sign changes needed in mb_platform.c.

mbgrid: Fixed flaw in min or max weighted mean algorithm that produced array overflows in 
mbgrid.

#### 5.7.6beta26 (February 2, 2020)

Format 181 (MBF_SAMESURF): Fixed compiler warnings, including warnings from a
mismatch of 32 bit and 64 bit integer pointers due to the early 1990's vintage
of this contributed library.

mbpreprocess: Fixed error in calculating lever arms that resulted in incorrect
static offsets to bathymetry calculated at the preprocess stage using platform models.
Fixes are in src/mbio/mb_platform.c.

mbotps: The tidal correction program has been recast to use the current global
atlas tidal model from the Oregon State University Tide Group. This model is
called tpxo9_atlas - the model files must be obtained from OSU now as they are
no longer available for anonymous download. When the MB-System documentation is
updated to include the steps required to obtain and install the tidal model,
we will output a formal 5.7.6.

Code style: Kurt Schwehr is systematically altering the code to conform to best
practices and adding build tests. The improvements included in this beta release
include cleaning up the SURF format library, work on mbedit, mbnavadjust, and
the GMT modules mbswath, mbcontour, and mbgrdtiff.

#### 5.7.6beta25 (January 20, 2020)

Info files: The top level information files README, ChangeLog, and GPL have been removed. 
The Markdown format versions (README.md, ChangeLog.md, GPL.md) remain and have been updated.

Mbeditviz: Fixed a bug recently introduced (inadvertently) that caused a crash when 
bringing up the sounding 3D cloud.

Mbm_grd2arc: Fixed failure with GMT 6. Basically, there is a GMT module grdconvert that 
accomplishes exactly the same task, so this macro is unnecessary. It has been recast to 
simply call gmt grdconvert. It will be listed as deprecated, but left in the distribution 
to maintain the viability of old processing scripts.

Code style: Kurt Schwehr is systematically altering the code to conform to best practices 
and adding build tests. The tests are performed by running
    make check
and are executed automatically by the Travis CI service integrated with Github
whenever commits are made to the Github repository. The current changes mostly consist of 
cleaning up the code of the graphical utilities such as mbedit, mbnavedit, mbnavadjust.

#### 5.7.6beta24 (January 16, 2020)

Build system: The configure.ac file now uses the AX_CXX_COMPILE_STDCXX(11) macro
to require that the code conform to the C++11 standard. Some preprocessor
directives have been added to src/utilities/mbprocess.cc to handle the case of
building with gcc 4.8.1 through 4.8.5, which has errors in implementing structure
constructors consistent with this standard. Also, instances of isnan() calls
throughout the codebase have been changed to std::isnan(), and in these cases
the "#include <math.h>" has been replaced by "#include <cmath". The order of
libraries in src/mbtrn/Makefile.am has been changed so that libmframe.la is
installed before libr7kr.la (which depends on libmframe.la). With respect to
libproj, configure.ac now checks for Proj 4 vs Proj 6 using
proj_normalize_for_visualization() for the Proj 6 API and pj_init_plus() for
the Proj 4 api. Since proj_normalize_for_visualization() did not get added to the
Proj 6 API until release 6.1.0, this means that the deprecated Proj 4 api
will continue to be used when building with Proj releases 5.0 through 6.0.
In practice, the build system sets preprocessor values that determine at compile
time which Proj API is used by the functions in src/mbio/mb_proj.c.

Code style: Kurt Schwehr is systematically altering the code to conform to best practices 
and adding build tests. The tests are performed by running
    make check
and are executed automatically by the Travis CI service integrated with Github
whenever commits are made to the Github repository.

#### 5.7.6beta23 (January 11, 2020)

MBprocess, mbpreprocess, mb_make_info(): Altered mbprocess and mbpreprocess so
that both run about half as slow (twice as fast) as before. This optimization is
accomplished by having mbprocess and mbpreprocess generate fbt and fnv files
directly rather than by system() calls to mbcopy and mblist, and by having the
system() call to mbinfo include the overall area bounds so that mbinfo only
reads the output file once while generating inf files (instead of reading the
data twice).

MBnavadjust: Added GUI elements related to defining a reference bathymetry model.
In the future, it will be possible to tie swath files to a reference bathymetry
imported from a grid file.

MBbackangle: Fixed error in datalist read logic that was preventing it reading
more than the first file (problem created by changing the handling of status and
error values from MBIO calls).

MBextractsegy: Fixed error in the milliseconds of traceheader timestamps.

MBlist: Improved calculation and handling of swath bounds values.

MBinfo: Augmented the -M data mask option to allow pre-definition of the file's
area bounds. Previously, the data mask has been requested using -Mmask_nx/mask_ny
where mask_nx/mask_ny are the dimensions of the mask. In this case, the file is
read twice - first to get the area bounds of all data while getting the other
data statistics output by mbinfo, and second to populate the data mask defined
by the area bounds and the dimensions mask_nx and mask_ny. Now, if the the option
is given by -Mmask_nx/mask_ny/lonmin/lonmax/latmin/latmax, then the last four values
define the area bounds and the data need only be read once. Mbprocess now calls
mbinfo in this way, allowing a speedup of the mbprocess execution.

MBgrid: Added data min max values to the per file shell output when verbose > 0

MBsvpselect: This program depends on geodesic calculations that are now part of
the Proj software package (from version 6 onwards). Previously the src/utilities
directory had included the files geodetic.h and geodetic.c to provide this capability;
those are now not included. Consequently, if MB-System is built with Proj versions 4 or 5,
then mbsvpselect will not be built.

Code style: Kurt Schwehr is systematically altering the code to conform to best practices 
and adding build tests. The tests are performed by running
    make check
and are executed automatically by the Travis CI service integrated with Github
whenever commits are made to the Github repository.

src/utilities: All programs in src/utilities have been migrated to C++.

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. These programs are:

- mb7k2jstar
- mb7k2ss
- mb7kpreprocess
- mbauvnavusbl
- mbhsdump
- mbhysweeppreprocess
- mbinsreprocess
- mbkongsbergpreprocess
- mbneptune2esf
- mbrollbias
- mbrphsbias
- mbstripnan
- mbswplspreprocess

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.

#### 5.7.6beta21 (December 12, 2019)

GMT modules (mbcontour, mbswath, mbgrdtiff): modified the #ifdefs to allow building with 
GMT 6.1 and later.

MBnavadjustmerge: augmented --set-tie option to allow changing the z-offset value of an 
existing tie.

MBprocess: Change behavior when reading grid files for backscatter correction fails - the 
functions in mb_readwritegrd.c used to wait 1 millisecond before trying to read again; now 
the code waits for 25 milliseconds.

Code stye: Kurt Schwehr is systematically altering the code to conform to best practices

#### 5.7.6beta20 (November 26, 2019)

Mbprocess: Fix to handle temporary failures to read GMT grd files. The GMT grid
reading code will now return with an error rather than causing the program to
exit. This allows the code to keep trying to read the grid file until it succeeds.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices. Current changes include replacing MB_YES/MB_NO with boolean
true and false, and changing the type of the associated variables from int to
bool.

mbtrnpp: Changes by Kent Headley to mbtrnpp in src/mbtrnutils and supporting
source directories src/mbtrn and src/mbtrnav.

#### 5.7.6beta19 (November 22, 2019)

Mbprocess: Attempting to fix processing of format 71 files within an mbnavadjust
project.

#### 5.7.6beta18 (November 21, 2019)

Everything: Now fully compatible with PROJ 6.X. The configure script will detect
the presence or absence of PROJ 6 or later - if the PROJ installation predates
PROJ 6 then the old header files and API are used. PROJ 6 and later include a
comprehensive database of coordinate reference systems (e.g. projected coordinate
systems and/or datums), making the projected coordinate system list kept in the
file src/share/Projections.dat unnecessary. For now this file will continue to
be part of the MB-System distribution to support installation with obsolete
versions of PROJ.

mbtrnpp: Removed some unnecessary test data and code from the src/mbtrnav/gctp/
directory.

mbtrnpp: Fixed a number for formatting and type issues hampering building the
TRN code on MacOs.

#### 5.7.6beta17 (November 15, 2019)

MBeditviz: Added option to display 3D soundings colored according to the map's
coloring (including selected colortabel and any histogram equalization).

MBeditviz: Added GUI elements to support multiple modes of gridding.

Mbm_route2mission: Modified to output waypoint_bottom behaviors with the
current suite of options specified.

Format 72 (MBF_MBARIMB1): Fixed handling of heading (degrees not radians).

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices. Current changes include replacing MB_YES/MB_NO with boolean
true and false, and changing the type of the associated variables from int to
bool.

mbtrnpp: Many changes by Kent Headley to this in src/mbtrnutils and supporting
source directories src/mbtrn and src/mbtrnav.

#### 5.7.6beta16 (October 29, 2019)

MBnavadjust: Fixed bug in calculating the range of contour values and the size
of the memory allocation for contours.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices. Current changes include replacing MB_YES/MB_NO with boolean
true and false, and changing the type of the associated variables from int to
bool.

#### 5.7.6beta15 (October 21, 2019)

Format 261 (MBF_KEMKMALL): Fixed preprocessing of Kongsberg multibeam data in the
kmall format, particularly with regard to merging WHOI-NDSF processed navigation
for surveys by AUV Sentry and ROV Jason.

Format 72 (MBF_MBARIMB1): Added support for a format used to store filtered and
decimated multibeam bathymetry as generated by mbtrnpp for use by the terrain
relative navigation module.

Mbpreprocess: Added an option named --kluge-auv-sentry-sensordepth that causes
mbpreprocess to replace the sensor depth value with the antenna height recorded
in the position record. This allows processing of AUV Sentry Kongsberg EM2020
using the embedded navigation, attitude, and sensor depth. At this time the
Kongsberg EM2040 is not accepting the input depth datagrams, and so the sensor
depth field is populated with incorrect values. Once a post-processed navigation,
attitude, and sensor depth model is available for merging, this kluge option is
no longer needed.

Terrain Aided Navigation (TRN) tools: Working towards supporting realtime UDP
based reading of Kongsberg kmall format data into program mbtrnpp. Removed
test data from the gctp projection package embedded within the TRN server
source tree.

mbtrnpp: Augmented this tool to acquire realtime Kongsberg multibeam data over
a UDP port. Note that configure must be invoked with the --enable-mbtrn  and
--enable-mbtnav options for the terrain relative navigation tools to be built.
We do encourage general users to avoid building with these options - the TRN
tools are experimental, changing rapidly, and for now specific to MBARI AUVs.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices. Current changes include replacing MB_YES/MB_NO with boolean
true and false, and changing the type of the associated variables from int to
bool.

#### 5.7.6beta14 (October 8, 2019)

MBnavadjustmerge: Added options --unset-short-section-ties=min_length and
--skip-short-section-crossings=min_length that allow the deletion or prevention
of ties made using short sections of data. This increases the reliability of the
autopicking of ties. The track length threshold is specified with the
command.

MBnavadjust: Restrict autopicking of ties incorporating short sections of data.
The track length threshold is 1/4 of the target segment track length specified
in the options dialog.

Format 88 (MBF_RESON7KR) and Format 89 (MBF_RESON7K3): Corrected handling of
reverse-mounted receive and/or transmit arrays.

MBpreprocess: Fixed handling of --filter-apply-nav option.

MBclean: Added flagging/unflagging by beam angle as part of the -Y option
  -Yangle_left/angle_right/3 to flag outside angle_left to angle_right
  -Yangle_left/angle_right/4 to unflag outside angle_left to angle_right

Terrain Aided Navigation (TRN) tools: The TRN related code has been refactored
and reorganized by Kent Headley. There are now three related directories under
src: src/mbtrn src/mbtrnav src/mbtrnutils. The former program mbtrnpreprocess
is now mbtrnpp. The source for mbtrnpp is now in src/mbtrnutils rather than
src/utilities.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta12 (September 20, 2019)

Mbset: Fix to mbset so that the mbp_navadj_mode is set to MBP_NAVADJ_OFF
instead of MBP_NAV_OFF and MBP_NAVADJ_LLZ instead of MBP_NAV_ON.

Mbminirovnav: Fix so that variations in the NAV* and CTD* files are handled
properly.

Mbnavadjustmerge: Fixed handling of
--unset-skipped-crossings-by-block=survey1/survey2
commands.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta10 (September 18, 2019)

Mbnavadjust: Changed the contouring displayed during analysis of crossings to
be based on a triangular mesh representation of the bathymetry data for each
section. The Delauney set of triangles used for each section is saved to a
file in the project directory. These can be made the first time each section
is displayed by mbnavadjust, or they can be made offline using the program
mbnavadjustmerge.

Mbnavadjustmerge: Added options to pre-generate the triangular mesh files for
each section in an mbnavadjust project (--triangulate, --triangulate-all,
--triangulate-section=file:section, and --triangulate-scale=scale).

Mbtrn library: Updated to current code written by Kent Headley.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta8 (September 9, 2019)

MBIO library beam flagging and detect types: The handling of multi-pick
soundings has been modified. This refers to sensors that can report more than
one sounding per beam, including both multibeam sonars and lidars. At present
the relevant data format are MBF_RESON7K3 (89), MBF_3DWISSLR (232), and
MBF_3DWISSLP (233). There are two major changes.
First, the detects array returned by mb_detects() now packs two
parameters into the 32-bit values: the detect type uses bits 0-7 and the
detect priority uses bits 8-11. The priority value will be 0 except when a
sensor is reporting multiple sounding per beam (sonar) or pulse (lidar); in
that case the primary (best) sounding will have a priority of 0, and other
secondary soundings (less than best) will have priorities > 0. If the sensor
ranks the soundings then the priorities will reflect the ranking order with
lower = better.
Second, all secondary soundings will initially be assigned beamflags with a
new value indicating that status (MB_FLAG_FLAG + MB_FLAG_SECONDARY). At this
time, the bathymetry editing programs mbedit, mbeditviz, and mbclean will
treat secondary soundings as not-to-be-used, which means those soundings will
not be displayed or available for unflagging. Eventually these editors will be
enabled to optionally display and unflag secondary soundings.

Mblist: The output of beam flag values now includes secondary soundings.
The possible output characters representing the beam flags are now:
'-'=null, 'G'=good, 'M'=manual, 'F'=filter, 'S'=sonar, 'N'=secondary (multi-pick),
and 'I'=interpolated.

Mbminirovnav: Rewritten to handle the actual variability of MBARI MiniROV raw
navigation, attitude, depth, and DVL data logs.

Formats MBF_3DWISSLR (232) and MBF_3DWISSLP (233): Augmented to handle a new
version of the 3D at Depth RAA swath file format generated by the WiSSL
(wide swath subsea lidar).

Mbnavadjust: The navigation adjustment optimization algorithm has been modified.
The problem is to find a perturbation (adjustment) to the original navigation
that matches features in overlapping and crossing swath bathymetry data.
The first stage of the inversion is to solve for the average position offsets between
different surveys, and then remove that signal out of the navigation offset
observations. The second stage of the inversion involves an iterative
relaxation towards a coarse navigation adjustment model. The third stage is to
obtain a full resolution perturbation model by solving a large, sparse,
overdetermined least squares problem that satisfies the remaining navigation
offset signal. The algorithm change is that the coarse
stage 2 solution is linearly interpolated over the gaps between directly
constrained navigation points before proceeding to the third stage. This
reduces the tendency of the overall solution to trend towards zero adjustment
along unconstrained sections of survey lines.

Mbtrn library: Updated to current code written by Kent Headley.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta6 (August 26, 2019)

Mbm_route2mission: AUV spiral descent option now includes a behavior to disable
DVL aiding of the INS during the descent.

Formats MBF_3DWISSLR (232) and MBF_3DWISSLP (233): these i/o modules have been
updated to handle both a new version (1.3) of the 3D at Depth Wide
Swath Lidar (WiSSL) *.raa format data.

Mbtrn library: Updated to current code written by Kent Headley.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta5 (August 6, 2019)

Integration with PROJ: Reverted to use of deprecated PROJ4 API due to problems
with use of projections by the mbview library. This will get fixed, but it's more
complicated than first thought.

Mbtrn library: Updated to current code written by Kent Headley.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta4 (August 2, 2019)

Format MBF_GSFGENMB (format 121, Generic Sensor Format, GSF): The version of
libgsf used to read and write Generic Sensor Format (GSF) files has been
updated to version 3.0.9. The libgsf library code is released by Leidos under
a LGPL2.1 license, and is included directly into the MB-System source code with
minor changes. For 3.0.9 the only changes required are to avoid redefinition
of several key system functions (e.g. fseek); these redefinitions are avoided
using a preprocessor command that is only activated in the MB-System build
system. The command
  mbformat -F121
now outputs the version of the GSF library embedded in MB-System as a part of
the format description.

Integration with PROJ: The API for the PROJ coordinate transformation library
libproj has changed with the release of version 6. The build system now tests
which version of PROJ is installed and builds MB-System using the available
API.g

Mbgrid: Mbgrid had an undocumented ability to set the interpolation tension using
a third argument to the -C option. This has been removed. The tension value is set
with the -T option, consistent with the documentation.

Mbgrid and mbmosaic: The functions used by mbgrid and mbmosaic to integrate with
GMT's i/o capabilities to write the output grids have been augmented to embed
the geographic coordinates in the fashion supported by GDAL and many software
packages that utilize it.

Mbcontour, mbswath, mbgrdtiff: The preprocessor commands in the source files
for the GMT modules in MB-System have been updated to handle the existence
of versions 5.0 through 6.0+.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta2 (July 25, 2019)

Formats MBF_3DWISSLR (232) and MBF_3DWISSLP (233): these i/o modules have been
updated to handle both the original (v1.1) and updated (v1.2) 3D at Depth Wide
Swath Lidar (WiSSL) *.raa format data.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.6beta1 (July 6, 2019)

MBnavadjust: Fixed bug that resulted in Naverr window contours not being
displayed when the diference between the minimum and maximum depth of a section
is less than one meter.

Formats MBF_3DWISSLR (232) and MBF_3DWISSLP (233): working towards the code
successfully reading and writing the 3D at Depth WiSSL *.raa format version 1.2.

#### 5.7.5 (June 26, 2019)

Version: Set for release 5.7.5

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

mb_platform.c: Fixed problem introduced in code style changes

mbpreprocess: Fixed problem introduced in code style changes

mbfilter: update man page

#### 5.7.5beta12 (June 24, 2019)

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.5beta11 (June 16, 2019)

Format 89 (MBF_RESON7K3): Fixed bug in support of the Teledyne 7k version 3 format
that caused mbpreprocess to crash.

Mbnavadjustmerge: Fixed bug due to failure to initialize new project structures.

Code stye: Kurt Schwehr is systematically altering the code to conform to best
practices regarding header inclusion and reduced variable scope, particularly
for loop indices.

#### 5.7.5beta10 (June 9, 2019)

Build system: Set Autotools build system to force use of standard C (i.e. C99).

#### 5.7.5beta9 (June 8, 2019)

Format 89 (MBF_RESON7K3): The Teledyne 7k version 3 format is now supported as
format 89. This format is used for all multibeam sonars built by Teledyne,
including Reson, Blueview, and Hydrosweep. By default, MB-System now treats
files with the *.s7k suffix as format 89 rather than 88. However, old Reson data,
specifically Reson data that does not store the bathymetry soundings in 7028
RawDetection records, should still be processed using format 88.

Format 261 (MBF_KEMKMALL): Support for Kongsberg multibeam data in the kmall
format is functional excepting for the recalculation of bathymetry by raytracing.

Mbprocess: Fixed problem with backscatter correction of sidescan and amplitude
data

General: Incorporates a large number of changes by Kurt Schwehr that nudge this codebase
towards some level of compliance with software development best practices.

Unit testing: Incorporates code contributed by Kurt Schwehr in the directories
mbsystem/test, mbsystem/third-party, and mbsystem/travis that will achieve
automated build testing and unit testing.

Build system: Added enable-test option to configure.ac so that the default
configure command does not try to compile the unit test code contributed by Kurt.

Mbvelocitytool: Fixed memory leak.

#### 5.7.5beta8 (April 11, 2019)

Format 89 (MBF_RESON7K3): Progress towards support of Teledyne 7k version 3 format.
The i/o module builds but is not fully functional yet. Most records parse
correctly but the bathymetry calculation is incomplete.

Format 261 (MBF_KEMKMALL): We are close to complete with support for the new
Kongsberg kmall format. Testing and debugging continues.

#### 5.7.5beta7 (March 28, 2019)

Windows compatibility: A number of changes from Joaquim Luis that allow building
under Windows.

Reson 7k version 3 support: Mods to mbsys_reson7k3.c and mbsys_reson7k3.h
from Christian Ferreira working towards new i/o module supporting version of the
7k format from Teledyne now used for Teledyne Reson abnd Teledyne Atlas
multibeams.

#### 5.7.5beta6 (March 26, 2019)

Build system: Modified configure.ac to fix a problem building with the new
Proj 6.0.0. MB-System uses a longstanding Proj API that is deprecated in Proj 6.
The relevant header file is proj_api.h, which can only be used if compiled
with the preprocessor macro ACCEPT_USE_OF_DEPRECATED_PROJ_API_H set. This compiler
flag has been added to the autoconf test for usability of this header file.

#### 5.7.5beta5 (March 22, 2019)

Mbm_grdplot, mbm_grd3dplot, mbm_grdtiff, mbm_histplot, mbm_plot, mbm_xyplot:
Set these plot macros to use "open" on Macs and on Linux to use "gio open" if
available, "xdg-open" if "gio" is not available. Also got rid of another
instance of orphan file creation by the plotting shellscripts (e.g. gmt.conf$$).

#### 5.7.5beta4 (March 21, 2019)

Mbm_grid: Fixed problem in which execution of mbm_grid left behind an orphaned
datalist file. Also changed this macro to output a bash shellscript rather than
a csh shellscript.

Mbm_bpr: Added support for various variants of Sonardyne AMT pressure data.

Mbm_grdtiff: Changed this macro to output a bash shellscript rather than
a csh shellscript.

Mbm_route2mission: Fixed handling of the user specified time to first waypoint
in the output MBARI AUV mission script.

Mbextractsegy: Recast output section plot generation script to call mbm_grdplot
using the arguments -MIE300 -MITg that cause that macro to render the output
postscript files into 300 dpi png image files.

Mbm_grdplot, mbm_grd3dplot, mbm_grdtiff, mbm_histplot, mbm_plot, mbm_xyplot:
These plot macros now embed the user, computer, and time of creation associated
with the output plot generation shellscript.

#### 5.7.5beta3 (March 14, 2019)

Mbcopy: Fixed problem with fbt file generation by mbcopy that was introduced with
5.7.5beta2

#### 5.7.5beta2 (March 4, 2019)

Format 261 (MBF_KEMKMALL): There is progress towards support for the new
Kongsberg kmall format. Only EM2040 data supplied by Kongsberg is being
used for testing with mbinfo, mbcopy, and mbprocess, so far. The memory
management faults are fixed, but it isn't all working yet.

Mbcopy: Changed logic so that in a full copy all data records are passed on to the
output even if they generate nonfatal errors (e.g. out of time or location bounds).

#### 5.7.5beta1 (February 27, 2019)

Mbm_bpr: Augmented to work with Sonardyne AMT pressure data using PRS data records
in addition to PR2 records.

Mbotps: Fixed some issues with applying a tide station correction to time
models.

#### 5.7.5beta0 (February 25, 2019)

Format 261 (MBF_KEMKMALL): Added support for new Kongsberg kmall format with
MBIO id 261 and name MBF_KEMKMALL. At this point the support has memory management
problems resulting in sporadic and inconsistent crashing.

#### 5.7.4 (February 12, 2019)

Plotting macros (mbm_grdplot, mbm_grd3dplot, mbm_plot, mbm_xyplot, mbm_histplot):
Fixed problem with plotting macro mbm_plot that caused failure of the plotting
shellscript.

#### 5.7.3 (February 8, 2019)

Plotting macros (mbm_grdplot, mbm_grd3dplot, mbm_plot, mbm_xyplot, mbm_histplot):
This version changes how automatically displaying the Postscript plot is handled. Previously
these plotting macros written in perl hard coded the user defined Postscript viewer program into
the plot generation csh shellscripts they generate, where the Postscript viewer was
defined by mbdefaults or by an environment variable. Now the plot macros write
plot generation shellscripts using bash rather than csh, and code is embedded that
executes a Postscript viewer defined at run time. This Postscript viewer can still
be defined by the user's mbdefaults or environment variables, but otherwise will be
the default application for viewing Postscript files on that computer, determined
by the programs xdg-open (Linux, OpenBSD), open (Mac), or cygstart (Cygwin). Thus,
the Postscript viewer program is determined at runtime by the plot generation
shellscript rather than at the time the shellscript is generated.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Fixed bug reported by Steve Roberts
in which some beams that have NaN values for depth in the original *.all files are
treated as null during the first read, but are reset to valid but NaN during
preprocessing. This fix works with data already processed through prior versions of
MB-System as well as data newly processed from *.all files.

#### 5.7.2 (February 4, 2019)

All files: Updated copyright to 2019.

Mbdumpesf: Fixed the application of the ignore options, applying fixes provided by
Povl Abrahamsen of the British Antarctic Survey in October 2017 (!)

Mbclean: Fixed problem with heading-change-rate based flagging.

Mbm_grdplot: supported generating plots of images (ie. Geotiffs) in addition to
grids. Added two plot modes: -G6 will plot the image using the embedded georeferencing,
and -G7 will plot the image using the bounds specified with the -R option as the
bounds of the image.

Format 56/57 (MBF_EM300RAW MBF_EM300MBA): Fixed crashing with some EM122 data by
disabling attempted parsing of "extraparameters" datagrams, which appear to not
conform to the format specification.

Mbdefaults, Mbm_* plotting macros: Changed the definition of the programs used to
view Postscript plots generated through the mbm_* plotting macros and for images
(e.g. geotiffs generated using mbgrdtiff). Previously, the programs used by
MB-System to view postscript files and images were explicitly defined using
mbdefaults. Defining the viewing programs is still possible with mbdefaults, but
the default is now to use the operating system's command line program
that automatically opens a specified file using the user's default application
for that kind of file. On Linux systems, this program is "xdg-open". On MacOs, this
program is "open". On Cygwin systems, this program is "cygstart".

#### 5.7.1 (December 19, 2018)

Initiated use of version tagging in Git.

---
### MB-System Version 5.6 Releases and Release Notes:
---

- Version 5.6.20181218   December 18, 2018
- **Version 5.6.20181217   December 17, 2018**
- Version 5.6.20181214   December 14, 2018
- Version 5.6.20181129   November 29, 2018
- Version 5.6.20181016   October 16, 2018
- Version 5.6.002        September 14, 2018
- Version 5.6.002        September 11, 2018

---

#### 5.6.20181218 (December 18, 2018)

Generated release package using github

mbm_vrefcheck: Removed, never completed, never worked.

mbm_dslnavfix: Removed, obsolete.

#### 5.6.20181217 (December 17, 2018)

Memory management: Fixed memory leak associated with allocation and deallocation
of edit save file (*.esf) data.

#### 5.6.20181214 (December 14, 2018)

Format 121 (MBF_GSFGENMB): Changed GSFlib version to 3.08. MB-System also now
builds and installs the program dump_gsf. Fixed several array overruns in the GSFlib
source code distributed by Leidos.

MBgrid: Added two new gridding algorithms, minimum weighted mean and maximum
weighted mean. These are both implementations of Gaussian weighted mean in which
only valid soundings that are close to the minimum (or maximum) value in each
grid cell are used. A threshold value in meters defines what close means; only
soundings no further from the minimum (or maximum) than the threshold are used.
These algorithms are useful when bathymetry data include areas that are not truly
representable with a 2D grid because of vertical walls or multiple values (e.g.
overhangs). These algorithms allow one to choose to follow the shallowest or
deepest surfaces in the gridded model. These algorithms were specifically added
to handle subsea lidar data that maps animals as well as the seafloor.

#### 5.6.20181129 (November 29, 2018)

MBgrdtiff, mbm_grdtiff: Added -Nnudge_x/nudge_y option to apply a positional offset
in meters relative to the input grid or mosaic.

MBgrdviz, mbeditviz: Changed mechanism by which files selected from navigation in
mbgrdviz are opened into mbeditviz. Previously the selection of too many files
in mbgrdviz would cause a crash when the pulldown menu item to open those into
mbeditviz was selected (too many == something like >10). Now an arbitrarily large
number of files can be selected because a temporary datalist is written by mbgrdviz
and then opened into mbeditbiz.

MBpreprocess: Added options --head1-offsets=x/y/z/heading/roll/pitch and
heading2-offsets=x/y/z/heading/roll/pitch which allow one to set the positional
and angular offsets between the separate heads on a dual head sonar or lidar. These
offset values are used in calculating bathymetry from raw travel times and angles.
The values specified with the new options generally override values embedded in
either the i/o module source code or the input data files. The initial usage is
for lidar bathymetry in the MBF_3DWISSLR and MBF_3DWISSLP formats.

MBclean: Added -Nthreshold option to detect and remove pings affected by
significant interference. This option works by calculating the rms deviation between
the soundings of each ping and the pings immediately before and after. When the
rms deviation exceeds the specified threshold, all unflagged soundings in that
ping are flagged as bad.

#### 5.6.20181016 (October 16, 2018)

Many files: Changed type of pingnumber variable from int to unsigned int.

MBprocess: Fixed problem with the creation of *.resf files in which the edit
events did not properly include the multiplicity factor required for data
from multi-head sensors.

MBvoxelclean: New program mbvoxelclean identifies and flags artifacts in swath
bathymetry data using a 3D density filter. The notion applied is that true targets
(e.g. the seafloor) result in dense regions of soundings while sparse soundings
in the water column or the subsurface are erroneous and can be flagged as bad.
This technique is more appropriate for lidar data than multibeam sonar data.
The resulting sounding edit events are output to edit save files which can be
applied to the data by the program mbprocess. These are the same edit save
files created and/or modified by mbedit, mbeditviz, mbedit,
and \fBmbclean\fP.

#### 5.6.002 (September 14, 2018)

Format 88 (MBF_RESON7KR): Corrected application of attitude offsets to bathymetry
calculation in mbsys_reson7k_preprocess().

#### 5.6.001 (September 11, 2018)

Format 88 (MBF_RESON7KR): Fixed problem in the mbsys_reson7k_preprocess() function
in which the interpolated and time latency corrected attitude values calculated
for each beam bottom return time were not fully corrected for the receive head
angular offsets.

---
### MB-System Version 5.5 Releases and Release Notes:
---

- Version 5.5.2350       September 6, 2018
- Version 5.5.2348       August 20, 2018
- Version 5.5.2347       August 17, 2018
- Version 5.5.2346       August 13, 2018
- Version 5.5.2345       August 10, 2018
- Version 5.5.2344       August 3, 2018
- Version 5.5.2343       July 10, 2018
- **Version 5.5.2342       June 29, 2018**
- Version 5.5.2340       June 26, 2018
- Version 5.5.2339       June 25, 2018
- **Version 5.5.2336       June 6, 2018**
- Version 5.5.2335       May 6, 2018
- Version 5.5.2334       April 18, 2018
- Version 5.5.2333       April 18, 2018
- Version 5.5.2332       April 17, 2018
- Version 5.5.2331       April 10, 2018
- Version 5.5.2330       March 7, 2018
- Version 5.5.2329       February 12, 2018
- Version 5.5.2328       January 31, 2018
- **Version 5.5.2327       January 23, 2018**
- Version 5.5.2324       January 18, 2018
- Version 5.5.2323       December 7, 2017
- Version 5.5.2322       November 25, 2017
- **Version 5.5.2321       October 26, 2017**
- Version 5.5.2320       October 18, 2017
- **Version 5.5.2319       October 16, 2017**
- **Version 5.5.2318       September 29, 2017**
- **Version 5.5.2314       August 24, 2017**
- **Version 5.5.2313       August 9, 2017**
- Version 5.5.2312       July 14, 2017
- Version 5.5.2311       June 20, 2017
- **Version 5.5.2309       June 4, 2017**
- Version 5.5.2306       May 27, 2017
- Version 5.5.2305       May 13, 2017
- Version 5.5.2304       May 6, 2017
- Version 5.5.2303       April 28, 2017
- Version 5.5.2302       April 20, 2017
- Version 5.5.2301       April 17, 2017
- Version 5.5.2300       April 15, 2017
- Version 5.5.2299       April 10, 2017
- Version 5.5.2297       April 5, 2017
- Version 5.5.2296       March 31, 2017
- Version 5.5.2295       March 26, 2017
- Version 5.5.2294       March 21, 2017
- Version 5.5.2293       March 6, 2017
- Version 5.5.2290       January 2, 2017
- Version 5.5.2289       December 2, 2016
- Version 5.5.2287       November 29, 2016
- Version 5.5.2286       November 8, 2016
- Version 5.5.2285       November 3, 2016
- **Version 5.5.2284       October 23, 2016**
- Version 5.5.2282       August 25, 2016
- Version 5.5.2281       August 7, 2016
- **Version 5.5.2279       July 8, 2016**
- **Version 5.5.2278       July 1, 2016**
- Version 5.5.2277       June 25, 2016
- Version 5.5.2275       May 17, 2016
- **Version 5.5.2274       May 5, 2016**
- Version 5.5.2271       April 1, 2016
- **Version 5.5.2270       March 24, 2016**
- Version 5.5.2268       March 14, 2016
- **Version 5.5.2267       February 11, 2016**
- Version 5.5.2265       February 11, 2016
- Version 5.5.2264       February 2, 2016
- **Version 5.5.2263       January 7, 2016**
- Version 5.5.2260       December 22, 2015
- Version 5.5.2259       October 27, 2015
- Version 5.5.2258       October 5, 2015
- Version 5.5.2257       September 1, 2015
- Version 5.5.2256       August 24, 2015
- Version 5.5.2255       August 11, 2015
- Version 5.5.2254       July 23, 2015
- **Version 5.5.2252       July 1, 2015**
- **Version 5.5.2251       June 30, 2015**
- Version 5.5.2250       June 29, 2015
- Version 5.5.2249       June 26, 2015
- **Version 5.5.2248       May 31, 2015**
- Version 5.5.2247       May 29, 2015
- **Version 5.5.2246       May 27, 2015**
- **Version 5.5.2243       May 22, 2015**
- **Version 5.5.2242       May 16, 2015**
- Version 5.5.2241       May 12, 2015
- Version 5.5.2240       May 8, 2015
- Version 5.5.2239       May 6, 2015
- Version 5.5.2238       April 14, 2015
- Version 5.5.2237       March 23, 2015
- Version 5.5.2234       March 5, 2015
- **Version 5.5.2233       February 23, 2015**
- Version 5.5.2232       February 21, 2015
- Version 5.5.2231       February 20, 2015
- Version 5.5.2230       February 18, 2015
- Version 5.5.2229       February 14, 2015
- Version 5.5.2228       February 6, 2015

---

#### 5.5.2350 (September 6, 2018)

Mbnavadjust: Added a sorted ties list view for which the list of ties is ordered
from largest misfit magnitude to smallest where the misfit is measured between
the tie offset and the offset of the most recent inversion. This allows one to
easily inspect the most poorly fit ties. Also augmented stored information about
global ties. Also made some changes to the inversion algorithm.

#### 5.5.2348 (August 20, 2018)

Reson 7k V3 support: Added files mbr_reson7k3.c mbsys_reson7k3.c mbsys_reson7k3.h
while working towards support of version 3 7k data (by Christian Ferreira).

#### 5.5.2347 (August 17, 2018)

Mbtrnpreprocess: precruise update of mbtrnpreprocess and related tools used for
optional install of AUV terrain relative navigation. Excepting for a few debug
print statement changes, this matches the 20180814 mbtrnpreprocess installation
of Kent Headly on MBARI Mapping AUV 2.

#### 5.5.2346 (August 13, 2018)

Mbauvloglist: augmented dimensioning of fields array to allow up to 500 data fields.

Mbnavadjust: Changed output of project so a single navigation offset model file is
output that can be parsed to get x, y, and z offset components for plotting etc.

Format MBF_SBURIVAX (format id 15): Augmented the i/o module to handle negative
longitude values (the format should use unsigned shorts but clearly data exist
using signed values).

#### 5.5.2345 (August 10, 2018)

Mbmakeplatform: Fixed segmentation fault when modifications to the platform model
are specified before a command that initializes the platform.

Mbcopy and Format 88 (MBF_RESON7KR): Added hook to mbcopy  so that it can output
bathymetry only records when copying format 88 (*.s7k) data. This option is
enabled by using the -N argument twice, and is used to generate data files that
mimic the minimal data record stream requested by mbtrnpreprocess.

Mbnavadjust: Undid the modification of 5.5.2340 that stores only valid, unflagged
soundings in the section files, which are format 71. This turned out to be a very
bad idea because it sometimes breaks the contouring used for display of the
navigation crossings.

Mbnavadjust: Changed so that sensordepth values are included in the navigation points
stored in the project file (*.nvh file).

#### 5.5.2344 (August 3, 2018)

Mbcontour, mbswath, mbgrdtiff, mbbackangle, mbprocess, mbgrid, mbmosaic, libmbaux,
mbgrdviz, mbeditviz, mbnavadjust, libmbview: Implemented a number of low level
changes suggested by Paul Wessel and Joaquim Luis in order to maintain compatibility
with GMT versions >= 5.5.4 and achieve compatibility with the coming GMT6.

Format 88 (MBF_RESON7KR): Fixed handling data from a Reson 7125 installation with
the receive head mounted backwards (this is something one might do in an AUV
context in order to achieve a desired cable run).

Mbtrnpreprocess: Changes from Kent Headley (this program is being actively developed).

src/mbtrn: Changes from Kent Headley (these tools and library are being actively developed).

#### 5.5.2342 (June 29, 2018)

Mbgpstide: New program contributed by Gordon Keith. This program generates tide
files from the height above ellipsoid data in the 'h' datagrams of Simrad files.
There is an option to include fixed offsets and geoid differences. This development
was funded by Geoscience Australia with the understanding that the
code would be made available to the general MB-System distribution.

#### 5.5.2340 (June 26, 2018)

Autoconf build system: Restructured to build successfully with the mbtrn capability
enabled using the --enable-mbtrn option of the configure script.

Mb_input_init() in src/mbio/mb_read_init.c: Allows calling program to initialize
arbitrary input method by supplying functions to open, read bytes, and close the
input. This capability is used by mbtrnpreprocess to read multibeam data over a
socket directly from a sonar.

Binary file i/o functions in src/mbio/mb_fileio.c: Can now read from an arbitrary
input method defined by the mb_input_init() function.

Mbtrnpreprocess: moved from src/mbtrn to src/utilities.

Mbnavadjust: now stores only valid, unflagged soundings in the section files, which
are format 71. Previously all soundings, including null and flagged, were stored.

#### 5.5.2339 (June 25, 2018)

Mbgrid: Modified to use correct gridding algorithm when reading fbt files
lacking the sonar type value.

Mbcopy: Modified to ensure that the sonar type value is embedded in fbt files
written by mbcopy.

Format MBF_LDEOIH (MBIO format id 71): I/O module modified to ensure the sonar
type value is embedded in fbt files.

Mbm_bpr: added generic data input format

src/mbtrn: added directory under src named mbtrn that contains code to enable
terrain relative navigation (TRN) on autonomous underwater vehicle (AUV) platforms.
These programs and library, particularly including mbtrnpreprocess, are built
optionally providing the configure script is run with the --enable-mbtrn option.

Mbtrnpreprocess: Program to read multibeam data from a Reson 7K sonar in realtime,
decimate and filter the bathymetry data, and provide the data to a terrain relative
navigation (TRN) client that localizes the AUV position relative to a pre-existing
map using the current bathymetry data.

#### 5.5.2336 (June 6, 2018)

Mbpreprocess and format MBF_3DWISSLR (232): Add option --kluge-fix-wissl-timestamps
to fix a timestamp problem with the initial version of the 3D at Depth WiSSL (wide
swath lidar).

Mbbackangle and mbprocess: Lidar intensity correction calculations now appropriate
for linear data instead of log-scaled data.

src/mbaux/mb_intersectgrid.c: Added function mb_topogrid_bounds() that returns the
lon-lat bounds of a topography grid previously loaded using the mb_topogrid_init()
function.

#### 5.5.2335 (May 6, 2018)

Mbm_bpr: Added ability to parse pressure data from Sonardyne AMT beacons. Also
added optional smoothing of the BPR depth data used to calculate tides.

Mbotps: Made the options -Ctidestationformat, -Ntidestationfile, and
-Utidestationlon/tidestationlat introduced last month actually work. One can now
use nearby tide station data to correct tide models calculated for the location
and time of survey data.

Mbm_route2mission: Altered to reflect the increased mission duration possible
for MBARI Mapping AUVs.

Format 88 (MBF_RESON7KR): Fixed handling of beams when using the version 2
raw detection data records.

#### 5.5.2334 (April 18, 2018)

Mbprocess, mbareaclean, mbclean, mbedit, mbeditviz, mbrphsbias, mbneptune2esf:
Reset MB_ESF_MAXTIMEDIFF_X10 value in mb_process.h to 0.0011 to handle old
beamflags with millisecond truncated timetags.

Mbareaclean, mbclean, mbrphsbias: Fixed the previous fixes .

#### 5.5.2333 (April 18, 2018)

Mbprocess, mbareaclean, mbclean, mbedit, mbeditviz, mbrphsbias, mbneptune2esf:
Decreased time range where multiplicity of pings will consider close records
as the same from 100 to 1 microsecond.

#### 5.5.2332 (April 17, 2018)

Mbprocess, mbareaclean, mbclean, mbedit, mbeditviz, mbrphsbias, mbneptune2esf:
Fixed problem recocognizing multiplicity of pings when ping times are close to
but not exactly the same. This problem was recognized in XSE data from a
SeaBeam 3020 multibeam, but could potentially have impacted data from other
sensors.

#### 5.5.2331 (April 10, 2018)

Mbm_makedatalist: Fixed problem with use of perl sort function when handling
Kongsberg multibeam data. Also fixed problem with specifying a directory using
the -I option.

Mbotps: Added new options -Ctidestationformat, -Ntidestationfile, and
-Utidestationlon/tidestationlat. Together these commands allow users to input
observations from a tide station; these observations can be used to calculate
corrections to tidal model values in the vicinity of the tide station. If tide
station data are specified, then MBotps calculates the difference between the
observed and modeled tide at that station for each data point in the input tide
station data. This difference time series is then used as a correction to the
output tide models, whether at a location specified with the -Rlon/lat option or
for swath data specified with the -Idatalist option.

Mbmakeplatform: Fixed initialization of the organization and documentation_url
fields.

Mbtrnpreprocess: Continued development of this new tool, particularly adding
interprocess communication via TCP-IP sockets.

#### 5.5.2330 (March 7, 2018)

Proj: Removed the embedded Proj source package from the MB-System archive and
distribution. From now on Proj is strictly a prerequisite for building MB-System.

Mbtrnpreprocess: Added initial version of new tool for real-time multibeam data
filtering as part of the implementation of terrain aided navigation on MBARI
AUVs. Specifically, mbtrnpreprocess accesses realtime s7k data from a Reson 7125
multibeam sonar, decimates and filters the bathymetry, and than passes the
decimated and filtered soundings on to an application that attempts to locate
the AUV in real time relative to a pre-existing multibeam bathymetry survey. This
allows repeat AUV surveys to execute exactly the desired survey tracks.

Format MBF_3DWISSLP (233): Many fixes to the code supporting WiSSL lidar data.

#### 5.5.2329 (February 12, 2018)

Format MBF_3DWISSLP (233): Rewrote the processing format for the 3D at Depth
wide swath lidar (WiSSL) system delivered to MBARI in December 2017. The new
version of the format is more compact and is read and written much faster.

Edit Save Files (*.esf) and mbedit, mbclean, mbareaclean, mbeditviz: Fixed
problem in which flags were sometimes not applied
to all soundings in pings that are less than 0.1 milliseconds earlier or later than
another ping or scan.

MBeditviz: Replaced use of the global edit files (*.gef) by mbeditviz with use of
new edit files called reverse edit save files (*.resf). The *.gef files were generated
by mbpreprocess using mbgetesf. The *.resf files are generated by mbprocess.

Mbm_route2mission: Fixed generation of Dorado AUV missions with waypoint_bottom
behaviours.

#### 5.5.2328 (January 31, 2018)

Edit Save Files (*.esf): The edit save file format has been augmented to include
a mode value that can include implicitly setting all soundings not set by a beamflag
in the file to a null value (mode == 1) or a valid value (mode = 2). The default
remains to change sounding beamflag values only for beams explicitly set by an
edit event. The only means to create ESF files with implicit beamflag modes is
using mbgetesf with -M4 or -M5, and the only use of implicit beamflag modes is in
the MBedtiviz *.gef files. The new ESF files have a version 3 tag; old ESF files
will continue to work fine.

MBgetesf: Augmented to output edit save files in two new modes. If -M4 is specified,
the beamflags of null beams will not be output, but the ESF mode is set so that
the beamflags of any soundings not specified will be set null. If -M5 is specified,
the beamflags of valid beams will not be output, but the ESF mode is set so that
the beamflags of any soundings not specified will be set valid.

MBpreprocess: Generates *.gef files using mbgetesf with the -M4 rather than -M2
option.

MBinfo: Fixed memory allocation problem that led to crashes reading data in formats
MBF_3DWISSLR (232) and MBF_3DWISSLP (233).

#### 5.5.2327 (January 23, 2018)

Build system: Restructure the use of the mb_config.h file so that compiling on
Ubuntu 17 succeeds (issue related to stdint.h includes)

#### 5.5.2325 (January 23, 2018)

MBinfo: Fixed bug in JSON output (Christian Ferreira)

#### 5.5.2324 (January 18, 2018)

MBpreprocess: Added support for the 3D at Depth
wide swath lidar (WiSSL) system delivered to MBARI in December 2017.

Formats MBF_3DWISSLR (232) and MBF_3DWISSLP (233): Added support for the 3D at Depth
wide swath lidar (WiSSL) system delivered to MBARI in December 2017.

MBm_route2mission: Fixed implementation of inserting surfacing events into missions
at line start and end waypoints.

Many source files: Changes to variable names in GMT grid header and CPT structures for GMT 6.

#### 5.5.2323 (December 7, 2017)

MBnavadjust: fixed crashes that happened when files or surveys are held fixed.

#### 5.5.2322 (November 25, 2017)

Mbpreprocess: Now set so that input Imagenex DeltaT data in the vendor format
MBF_IMAGE83P (191) will be output in the processing format MBF_IMAGEMBA (192)
after pre-processing.

Mb7k2jstar: Now outputs in the current jstar format rather than a >10 year old
variant.

Formats MBF_EDGJSTAR (132) and MBF_EDGJSTR2 (133) supporting Edgetech Jstar (*.jsf)
files: Changed code to support recent and current versions of Jstar format files.
The code should recognize and convert older variants, particularly those written
by past versions of MB-System.

Various source files (mk_cheby.c, geod_for.c, mbsys_xse.c, mbsys_sb2100.c,
mbsys_elacmk2.c, mbsys_elac.c, mbr_xtfr8101.c, mbbs_defines.h):
Added curly brackets, changed beamflag setting calculations, and reformatted
some lines in order to silence compiler warnings.

#### 5.5.2321 (October 26, 2017)

Mbgrdviz: fixed bug in displaying overlays.

Mbpreprocess: Added some kluge fixes to time jumps in ancillary data. New commands
are --kluge-ancilliary-time-jumps and --kluge-mbaripressure-time-jumps.

Mbextractsegy: fixed bug in the output plotting script.

Format 88 (MBF_RESON7KR): Fixed confusion between Depth and Height s7k data records.

#### 5.5.2320 (October 18, 2017)

Mbgrdviz: Now, when overlays are displayed in mbgrdviz, the only areas rendered
are those where both the primary and overlay grids are defined.

#### 5.5.2319 (October 16, 2017)

Mbprocess: Fixed bug that caused mbprocess to (sometimes) never finish while
continuing to write to the output file.

#### 5.5.2318 (September 29, 2017)

Mbnavadjust: Fixed bug that often, but not always, caused the inversion to blow
up and crash the program.

General: Fixed problem with data record type informational messages

General: Fixed problem with time gap nonfatal error detection

MBpreprocess: Added --skip-existing option that causes MBpreprocess to skip
preprocessing of files referenced in the input datalist that have already been
preprocessed. This allows efficiently adding new files to a survey, particularly
in a shipboard context where one is trying to process new data as they are
collected.

MBotps: Added -S option that causes MBotps to skip calculating a tidal correction
model for files referenced in the input datalist that already have models calculated
by mbotps. The skipped files will not be viewed as out-of-date by mbprocess, and
thus will not be reprocessed if mbprocess or mbm_multiprocess are run.
This allows efficiently adding new files to a survey, particularly
in a shipboard context where one is trying to process new data as they are
collected.

MBgrdviz: Added capability to output site data as Winfrog waypoint (*.WPT) files.

MBeditviz: Added capability to optimize an additional bias parameter (sort of...)
in the 3D sounding view. The new parameter is a "snell correction", referring to
adjusting the receive beam angles of multibeam data by applying a Snell's law
correction equivalent to changing the speed of sound used for beam forming. This
parameter is expressed as a ratio of the new to original sound speed, so that
a snell correction value of 1.00 corresponds to no change, a value of 0.995
corresponds to a slight reduction in the sound speed, and a value 1.005
corresponds to a slight increase in the sound speed. This correction is intended
for near-bottom surveys from submerged platforms (ROVs or AUVs) where sound speed
is calculated from CTD data (and values may plausibly be slightly erroneous) and
where errors due to raytracing through an incorrect model of the water column
sound speed are unlikely to be significant. This correction is generally not useful
for multibeam data collected from a surface vessel.

MBminirovnav: Added new program that processes raw MBARI MiniROV data logs to
produce standard MBARI ROV navigation files (format MBF_MBARIROV)
MBpreprocess: Add option to skip preprocessing files in the input datalist that
have already been fully preprocessed.

MBsegygrid: Added a trace mode=2 to the -Smode[/start/end[/schan/echan]] command
for which start and end refer to shot numbers and all traces within that range of
shot numbers are plotted. Effectively  the channel numbers are ignored by setting
all trace channels to 0 and plotting channel 0.

MBsslayout: Changed arguments to have '-' rather than '_' characters between
words in multiword commands (e.g. --topo_grid_file is now --topo-grid-file).
Also now have code identifying the fileroot of the input file and using that in
the construction of output file names so that the input format suffix is not
embedded in the middle of the output filename. Also improved the swathplotting
script generated by mbsslayout.

Formats 132 (MBF_EDGJSTAR) and 133 (MBF_EDGJSR2): Fixed preprocessing function in
the i/o module so that altitude values read in by mbpreprocess are actually applied
in the output file.

Format 160 (MBF_SEGYSEGY): Added recognition of this format by file suffixes
*.SEG and *.seg (in addition to *.SEGY and *.segy).

MBm_makedatalist and Formats 56, 57, 58 59 (MBF_EM300RAW, MBF_EM300MBA, MBF_EM710RAW,
MBF_EM710MBA): The mbm_makedatalist macro will now attempt to sort Kongsberg data
into time order based on filenames when the file suffixes follow the MB-System
convention (*.mb56, *.mb57, *.mb58, *.mb59). Previously this functionality was
only applied to files with the *.all suffix. This capability is applied by default
but can be disabled with the -T option.

#### 5.5.2314 (August 24, 2017)

Mbprocess: Fixed bug in which mbprocess sometimes crashed for files that have not
had bathymetry edited or filtered.

Mbprocess: Code used to read GMT grid files modified so that if the GMT API call
to read a grid fails, that call will be repeated every 0.1 seconds for 10 seconds
until it succeeds. This should allow multiple instances of mbprocess to read the
same grid files used for processing without interfering (the current GMT libraries
have problems with multiple simultaneous reading of a grid file over some network
mounted filesystems).

Format 88 (MBF_RESON7KR): Augmented the preprocess function to properly implement
a correction to the sound speed value used for beamforming, with consequential
changes to the recalculated bathymetry.

Mbpreprocess: Changed so that it ancillary data is specified to be read from
external file(s) but one of those files does not exist, the program terminates
with an error message.

#### 5.5.2313 (August 9, 2017)

Format 88 (MBF_RESON7KR): Fixed problem handling Reson data preprocessed or
processed using a version older than 5.3.2004 which in some cases causes the
alongtrack and acrosstrack values to be swapped.

#### 5.5.2312 (July 14, 2017)

MBedit: Added togglebutton to the View menu that allows to control whether
flagged soundings are displayed (previously flagged but valid soundings were
always displayed).

MBauvloglist: Added ability to recalculate MBARI Mapping AUV CTD data using
corrected calibration coefficients. This allows one to output a corrected time
series of sound speed.

Proj: Removed the embedded Proj library from MB-System. One must now have Proj
installed separately in order to build MB-System (which is always the case
anyway).

MBpreprocess: Added several new options.

MBgrdtiff, mbcontour, mbswath, mbps: Changed defines in *.c files to reflect the
versioning of GMT 6

#### 5.5.2311 (June 20, 2017)

MBnavadjust: Fixed bug that preventing importing data into a new project.

#### 5.5.2309 (June 4, 2017)

Applied reformatting to all *.c and *.h files using the tool clang-format as
suggested by Joaquim Luis.

Updated copyright statements to 2017.

Updated mbotps to use the current best OSU tidal model (atlas_tpxo8_1).

#### 5.5.2306 (May 27, 2017)

Format 88 (MBF_RESON7KR): Fixed a couple of bugs in the i/o module identified
by Kurt Schwehr.

Format 121 (MBF_GSFGENMB): Fixed handling of attitude records.

#### 5.5.2305 (May 13, 2017)

MBdatalist: Fixed bug involving operating on datalist files other than the default
datalist.mb-1.

MBpreprocess: Added option --kluge-soundspeed-tweak=factor that applies a
multiplicative correction to the water sound speed at the sonar arrays. This
both changes the beam angles by a Snell's law correction and affects the
calculation of bathymetry using the travel times.

MBconfig: Added options to print out the installation location, the compile
flags needed to compile code using MB-System libraries, and the linker flags
needed to link programs that call functions in MB-System libraries.

MBextractsegy: Force jpeg renderings of the section plots to be portrait style.

MBinfo: Fix bug in XML output disabling output of minimum good beam counts in
some cases.

#### 5.5.2304 (May 6, 2017)

MBpreprocess: Fixed generation of *.baa, *.bsa, and *.bah files so they include
only data relevant to the associated swath file, which means samples from
10 seconds before the first survey data through 10 seconds after the last survey
data. The program now removes any pre-existing *.ata, *.sta, *.ath, *.baa,
*.bsa, and *.bah files.

MBconfig: New program to provide command line access to the ### MB-System Version
and the locations of the Levitus database and the OTPS tide prediction software.

MBlevitus: The variable storing the location of the Levitus database file has
been changed from "ifile" to "levitusfile".

Datalist parsing: The mb_datalist_read() function changed with the 5.5.2299
revision, including adding a new argument. The old version of that function is
now available within the API as mb_datalist_readorg().

#### 5.5.2303 (April 28, 2017)

MBpreprocess and MBeditviz: Changed the ancillary files used to store the
asynchronous attitude and heading data used by MBeditviz for time latency modeling
from text to binary. The text *.ata, *.sta, and *.ath files generated by
mbpreprocess (and formerly by mb7kpreprocess and mbkongsbergpreprocess) are
replaced by *.baa, *.bsa, and *.bah files respectively. The size of the the binary
files is about half of the previous text files; the i/o speed for loading data
is improved as well.

Configure script: Fixed problems with specifying the location of the netCDF,
GDAL, and GMT config programs.

MBswath: Fixed bug that caused occasional crashes.

#### 5.5.2302 (April 20, 2017)

Formats 56 and 57 (MBF_EM300RAW and MBF_EM300MBA): Fixed handling of sensordepth
and heave data by mbpreprocess and mbprocess. Tide correction and recalculation
by raytracing work correctly again. Added preprocessing function to the i/o
module. Users should now use mbpreprocess for preprocessing old Kongsberg
multibeam data so that navigation is properly interpolated and beam flagging
works correctly.

Mbm_plot, mbm_grdplot, mbm_xyplot: The plotting macros now handle negative scaled
(reverse) axes properly (e.g. sound speed plots with depth increasing downwards).

Mbdatalist: Now supports long command line options (old short options are
deprecated but still work).

#### 5.5.2301 (April 17, 2017)

Mbpreprocess and Format 88 (MBF_RESON7KR): Fixed application of kluge-beam-tweak
option for Reson 7k (format 88) data.

#### 5.5.2300 (April 15, 2017)

Formats 58 and 59 (MBF_EM710RAW and MBF_EM710MBA): Fixed memory leak.

Formats 59 (MBF_EM710MBA): Fixed calculation of interpolated heave when
recalculating bathymetry by raytracing.

Format 88 (MBF_RESON7KR): Fixed memory leaks.

Mbm_arc2grd: Rewritten to use GMT modules grdconvert and grdedit.

#### 5.5.2299 (April 10, 2017)

Formats 58 and 59 (MBF_EM710RAW and MBF_EM710MBA): Fixed handling of sensordepth
and heave data during preprocessing. Program mbkongsbergpreprocess is now
deprecated and will be removed from the distribution soon. Users should now
use mbpreprocess for preprocessing Kongsberg multibeam data.

Format 88 (MBF_RESON7KR): Fixed bug in handling of TVG data records.

Mbdatalist: Added a new option -D that causes mbdatalist to list the unique
datalist files referenced as a recursive datalist structure is parsed. The
recursion level of each datalist file is indicated in the listing.

Mblist and mbnavlist: Augmented the -Zsegmenttag option for printing out segment
start lines in the output. Normally the string segmenttag is a single character
that is recognized by GMT as a segment beginning when parsing tabular data. Now,
if segmenttag == "swathfile" the segment start lines will consist of the character
'#' followed by the path to the source swath file, and if segmenttag == "datalist"
the segment start lines will consist of the character '#' followed by the path
to the source datalist file

#### 5.5.2297 (April 5, 2017)

All i/o modules: Added sensordepth_source to the arguments of the
mbr_info_XXXXXXXX() functions in the i/o modules.

Mbpreprocess: Added ability to define default sources (in terms of data record
types) for the various asynchronous ancillary data types in Kongsberg and Reson
data.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Kongsberg reports some bathymetry
bottom picks that are interpolated or extrapolated from valid soundings. Until
now MB-System has treated these interpolated soundings as valid but flagged.
MB-System now recognizes interpolated soundings as a different type, neither
valid nor null. These soundings can no longer be seen or edited with MBedit or
MBeditviz.

Mbm_makedatalist: Added option to suppress processed files (e.g. *p.mb88) from
inclusion in the output datalist.

#### 5.5.2296 (March 31, 2017)

Mbm_makedatalist: Major capability augmentation for this tool, preparing for
automated setup of the processing environment. This macro will now construct
datalists from files matching a user specified  filename suffix, and will
attempt to sort raw Kongsberg multibeam data files into time order.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Fixed to handle EM712 data and
other Kongsberg multibeams now generating more than 512 beams.

Mbm_grd2arc: Fix provided by Monica Schwehr for compatibility to *.grd files
generated with the current GMT.

#### 5.5.2295 (March 26, 2017)

Mbm_plot, mbm_grdplot, mbm_xyplot, mbm_3dgrdplot: Changes to the manual pages
to reflect the new syntax for map scales (the -MGL option in the MB-System plot
macros) in GMT 5.3.X

Mbnavadjust: Fixed bug in calling scripts within the project directory for users
that do not include "." in their path environment variable. Problem identified
by Monica Schwehr.

Mbpreprocess: Added functionality to handle specialized, format-specific
preprocessing tasks and to handle changes to data timestamps. Currently set to
work with generic data, Reson 7k data (format 88), and 3DatDepth Lidar data
(format 231). Code written for mbpreprocess to work with Kongsberg data, but
not yet tested.

Format 88 (MBF_RESON7KR) and Mb7kpreprocess: Mb7kpreprocess is deprecated, with
preprocessing of Reson 7k data to be done by mbpreprocess.

Format 121 (MBF_GSFGENMB): Integrated latest release of GSF from Leidos (3.07)

#### 5.5.2294 (March 21, 2017)

Mbsvpselect: Fixes by Ammar Aljuhne and Christian Ferreira of MARUM.

#### 5.5.2293 (March 6, 2017)

Mb7kpreprocess: Fixed bug in handling old MBARI Mapping AUV with navigation
and attitude data in deprecated "Bluefin" records.

Mbnavlist: Added ability to output positions in a projected coordinate system.

Mblist: Use ping count as ping number when the data format does not include
ping or shot number.

Format 21 (MBF_HSATLRAW): Fixed bug in handling zero length comments.

Format 231 (MBF_3DDEPTHP): Fixed bug in handling angular offset values in
preprocessing.

#### 5.5.2292 (January 30, 2017)

Mblist: Added ability to output positions in a projected coordinate system,
to output positions of the sensor instead of soundings or pixels, or to output
positions relative to the sensor in the world frame.

Mbm_route2mission: Fixed handling of waypoint spacing for constant depth segments
of missions.

Mbnavadjust: Now outputs the altered project less frequently (every tenth new tie
instead of every tie).

#### 5.5.2291 (January 12, 2017)

Mbnavedit: interpolation of selected navigation values now also flags the original
values so they are not used in calculating a navigation model.

General: fixed a number of memory leaks by switching all remaining mb_malloc(),
mb_realloc(), and mb_free() calls to mb_mallocd(), mb_reallocd(), and mb_freed().

Mbnavadjust: prevent occasional corruption of the mbnavadjust project by not
allowing excessively large offset values to result from unstable inversions.

#### 5.5.2290 (January 2, 2017)

Mbinfo: applied fixes from Suzanne O'Hara to JSON output from mbinfo.

Mbnavadjust: Fixed problem in which tie snav times became incorrect - these values
are now reset when the project is read.

Mbgrid and mbmosaic: added code to mbaux/mb_readwritegrd.c that will enable use
of new GMT5 grid mode flags, solving the problem of creating geographic grids
that can be directly read into ESRI ArcGIS. These modes will appear in GMT 5.3.2
sometime early in 2017. Thanks to Paul Wessel for diagnosing and fixing this
longstanding issue.

Mbgrid and mbmosaic: implemented suggestion by Paul Wessel that the calculation
of grid dimensions be done with a lrint() rounding call rather than implicit
truncation. This will change the behavior of the -Edx/dy/units option, but the
resulting grid dimensions will be more consistent with users expectations.

#### 5.5.2289 (December 2, 2016)

Mbnavadjust: Fixed auto set vertical level function to use the same block inversion
now used for the first stage of the main inversion. Also set this function so that
for z offset changes less than a threshold (currently 0.10 m) the x and y offsets
are not repicked.

Mbnavadjustmerge: Fixed import and export of tie lists to allow moving ties between
projects.

#### 5.5.2287 (November 29, 2016)

Mbm_makesvp: added capability to extract sound speed values from survey data
records as well as ctd data records, and to optionall produce sound speed models extending
to the surface and the deep ocean even if the data are available only for a limited
depth range.

Mbnavadjust: Modified the inversion algorithm to once again have a first stage
solution for "block" (survey) average offsets followed by the main inversion to
satisfy all of the navigation tie offsets in detail.

Mbnavadjust: updated the documentation of the inversion algorithm.

Mbprocess: fixed rare singularity in the raytracing code.

#### 5.5.2286 (November 8, 2016)

Mbsvplist: Added -R command to set longitude-latitude bounds within which the
-S option will cause ssv values to be output.

Mbgrdviz: Added start5 and end5 waypoint types to routes.

#### 5.5.2285 (November 3, 2016)

Mbnavadjust: Added a first step in the inversion in which mbnavadjust solves for
average offsets for each survey ("block"). The offsets associated with this
average model are removed from the tie offsets before the full inversion. The
smoothing penalty is thus applied to deviations from the average model rather
than the full navigation adjustment model.

#### 5.5.2284 (October 23, 2016)

Fixed some typos preparing for full release.

#### 5.5.2283 (October 23, 2016)

mbmakeplatform: fixed bug that caused core dumps when built with gcc.

mbaux/mb_cheb.c: Added open source least squares solver LSQR by Michael A. Saunders
(in C version translated from Fortran by Michael P. Friedlander),

Mbnavadjust: Switch navigation matrix solution algorithm to LSQR.

Mbnavadjust: Fixed bug that reset the z-offset-width value to 5-m every time
a project was read.

Mb7kpreprocess: Now will use complete platform description when reading older
Reson 7k data.

Mb7kpreprocess: Now allows users to specify the the sources of asynchronous ancillary data
(position, sensor depth, heading, attitude) to be merged with the survey data.

Mbgrdviz, mbeditviz, mbnavadjust: pick actions will now print out positions to
the shell in both decimal degrees and degrees + minutes.

Mbextractsegy: Now uses psconvert from GMT instead of convert from imagemagick.

mbm_grdplot: Once again handles section plots from mbextractsegy properly.

mbm_arc2grd, mbm_dslnavfix, mbm_grd2arc, mbm_grd2geovrml, mbm_grd3dplot,
mbm_grdcut, mbm_grdinfo, mbm_grdplo, mbm_grdtiff, mbm_grid, mbm_histplot,
mbm_plot, mbm_utm, mbm_xyplot: Modified to work properly with GMT 5.3

mbprocess: fixed correction of sidescan and amplitude data using topographic
grid so that the correction is actually calculated and applied.

#### 5.5.2282 (August 25, 2016)

Mbnavadjustmerge: Added --set-ties-xyonly-by-time=timethreshold option.

Mbnavadjust: Improved program behavior with respect to generating the grid used
for the project visualization view.

Mbedit: Changed behavior so that using the slider to change the number of pings
viewed also changes the number of pings to step proportionately.

#### 5.5.2281 (August 7, 2016)

Mbnavadjustmerge: Added --unset-skipped-crossings-by-block=survey1/survey2
and --unset-skipped-crossings-between-surveys options, and made the
--import-tie-list=filename and --export-tie-list=filename options work
correctly.

Mbclean: Added option to flag outer beams and/or unflag inner beams
by acrosstrack distance (-Y option).

#### 5.5.2279 (July 8, 2016)

Bathymetry editing (mbedit, mbeditviz, mbclean, mbareaclean): fixed problem in
which mbprocess failed to successfully apply new edits generated using mbeditviz
on files with existing, old esf (edit save files) files. Yet another consequence
of adapting to very short ping intervals...
Existing edit save files can now be fixed using mbclean -T0.0011.

Mbm_grdtiff: Added support for image display program feh.

#### 5.5.2278 (July 1, 2016)

Mbkongsbergpreprocess (Formats 58 & 59): Fixed modification of png_xducer_depth
value to not include lever arms or heave, as SIS records sensor depth value
in height datagrams that are already compensated for lever arms and heave.

#### 5.5.2277 (June 25, 2016)

Mbm_xyplot, mbm_grdplot: fixed problem generating plots using linear axes. Recent
changes to GMT cause gmt mapproject to generate an error when passed non-map
(e.g. non lon lat) values with a linear projection (after three decades of
working just fine....). Created a workaround by treating linear plots as a
special case.

Mbeditviz, mbedit, mbclean: Fixed problem with edit save files in which old format
*.esf files where generated by mbeditviz. This does not work well with data where
separate ping timestamps differ by less than 10 milliseconds (e.g. current
generation Kongsberg multibeams reporting fore and aft pings from each ping cycle
and 3DatDepth lidar data).

Mbkongsbergpreprocess (Formats 58 & 59): Fixed handling of sonar depth and heave
values in Kongsberg multibeam data logged using SIS on a submerged platform.

Format 201 (MBF_HYSWEEP1): Changed handling of file header data to enable the
extraction of platform definition data by the program mbmakeplatform.

MBmakeplatform: Now capable of extracting the list of sensors and the associated
offsets from Hypack HSX files, and outputting an MB-System platform file.

MBhysweeppreprocess: Now allows for sensor offsets to be defined by an
MB-System platform file, which can be extracted from HSX data files with
mbmakeplatform, and can be modified and augmented using the same program.

MBeditviz: Added a new sounding filter mode that calculates the sounding density
for a 3D "voxel" representation of the selected volume, and then flags soundings
in voxels containing less than a threshold of soundings. This algorithm flags
isolated soundings, an approach that is particularly useful for submarine
lidar data. This filter is accessible from the "action" menu of the 3D sounding
window.

#### 5.5.2276 (May 31, 2016)

MBeditviz: Added algorithm to flag isolated soundings by analyzing the 3D
distribution of currently selected soundings. Soundings are flagged in voxels
containing less than a desired threshold of soundings. This option is accessed
from the <Action> menu of the 3D sounding view.

Format 201 (MBF_HYSWEEP1) and mbhysweeppreprocess: Fixed handling of data that
have beam takeoff angles calculated without attitude correction. Changed the
default heave sign convention.

Format 231 (MBF_3DDEPTHP): Now handles files with broken data records a bit more
gracefully.

#### 5.5.2275 (May 17, 2016)

MBnavadjust: Fixed display of navigation in visualization view. Fixed overwriting
of zoffsetwidth value when projects are read in. Fixed autopicking when view mode
is survey-vs-survey blocks.

MBkongsbergpreprocess: Added capability to merge sonardepth from a separate ascii
file consisting of Unix time and sonardepth pairs.

Makefiles and mbr_gsfgenmb.c: Fixed typos noted by Joaquim Luis.

General: Fixed several warnings generated by the new gcc version in Ubuntu 16.

#### 5.5.2274 (May 5, 2016)

Configure.cmd and "How to Get" web page: Updated with instructions for
installing in Ubuntu, including Ubuntu 16.04.

MBgrdviz, MBeditviz: New radiobox in the Controls->Projections dialog allows
user to change interactive pick annotations so that longitude and latitude
values are shown as degrees + decimal minutes or decimal degrees, as desired

MBeditviz: Fixed bug involving some isnan calls according to suggestion by
Gordon Keith - MB-System now builds on Ubuntu 16.04.

Mbswath: Fixed bug in handling format for single input files, as suggested by
Joaquim Luis.

Mbnavadjustmerge: Added commands to set the mode of all ties as XYZ, XY only, or
Z only.

Many source files: Added a number of #ifdef preprocessor statements to handle
building on Windows, generally following suggestions by Joaquim Luis.

Many source files: Fixed a number of warnings related to typing and prototyping
issues.

#### 5.5.2271 (April 1, 2016)

MBnavadjust: Added numbers of crossings and ties to the table listing of
survey-vs-survey blocks.

Formats 58 and 59 (MBF_EM710RAW & MBF_EM710MBA): added EM850 to supported
third generation Kongsberg multibeams.

#### 5.5.2270 (March 24, 2016)

MBnavadjust: Now plots ties within missions (surveys) in dark blue and ties
between mission in light blue in the bathymetry visualization.

Mbm_route2mission: Calculates AUV ascent time with a 1.5 safety factor instead
of a 1.2 safety factor to ensure the new Mapping AUV always makes it to the
surface before timing out.

#### 5.5.2269 (March 23, 2016)

MBkongsbergpreprocess, and formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA) for
current generation Kongsberg multibeam data: Changed so that the default source
for attitude data used in recalculating bathymetry from travel times and angles
is the "active" source originally used by the sonar rather than always being
motion sensor 1.

MBnavadjust: Fixed creation of bathymetry grid (gridding scripts were not being
set executable). Removed data from fixed files from the bathymetry grid.

MBkongsbergpreprocess: Now by default uses the same attitude data stream used
by the sonar in realtime, as opposed to using data from "motion sensor 1"
regardless of whether that was the active realtime sensor.

Bathymetry editing programs (MBedit, MBeditviz, MBareaclean, MBclean): fixed
beam edit code so that no attempt is made to sort zero length arrays of beam
flags.

#### 5.5.2268 (March 14, 2016)

Mbnavadjust: Added integrated mbgrdviz-style visualization of the bathymetry in
an Mbnavadjust project. Users can select crossings or ties by clicking on the
navigation in the map view. If two selected sections do not already have a
defined crossing, a crossing can be created and analyzed. The new version of
mbnavadjust will upgrade old projects to include the bathymetry grid. The
new GUI commands include <Update Grids> under the <Action> menu, and
<Visualize Survey> under the <View> menu. The documentation, such as it is,
does not yet cover these new features.

Mbm_multicopy and mbm_multidatalist: Fixed bugs identified (along with fixes) by
Martin Ernst of HafenCity University in Hamburg, Germany.

Mbswath, mbcontour, mbgrdtiff: added #ifdefs for compatibility with the upcoming
GMT 5.3 release. A number of GMT functions called by the MB-System GMT modules
are being renamed.

Format 21 (MBF_HSATLRAW): Added some logic to handle problems in a very old HSDS
dataset collected on the R/V Ewing and available at the archive formally known
as NGDC.

#### 5.5.2267 (February 11, 2016)

Mbeditviz: Added capability to do automated optimization for bias parameters
from the 3D soundings view. Optimization options are accessed from the "Action"
menu.

Mb7kpreprocess: Added capability to tweak beam angles through a Snell's law
type correction (kluge mode 9).

Mbgetesf, mbdumpesf, mbedit, mbeditviz, mbareaclean, mbclean, mbprocess:
Fixed problem handling certain old ESF files (edit save files) that had timestamps
truncated to milliseconds instead of microseconds. New ESF files now have a
header indicating the version and time of creation. Version 2 ESF files are
presumed to have timestamps consistent with datafiles to a +/-1 microsecond
precision.

Documentation: Corrected instructions for building MB-System on Ubuntu machines.

#### 5.5.2264 (February 4, 2016)

Mbgrid, mbm_dslnavfix, mbm_grd2arc, mbm_grd3dplot, mbm_grdplot, mbm_grdtiff,
mbm_histplot, mgm_plot, mbm_utm, mbm_xyplot: Replaced call to "grdinfo" with
call to "gmt grdinfo" for compatibility with GMT5 installations that do not
include soft links to the old GMT4 programs.

Mbauvloglist: Added ability to calculate and output potential temperature when
parsing an MBARI Dorado AUV CTD log. Includes adding a potential temperature
calculation function to src/mbio/mb_absorption.c

Mbpreprocess: Fixed problem with application of changes to roll and pitch values.

MBnavadjustmerge: Enabled exporting and importing lists of ties.

#### 5.5.2263 (January 7, 2016)

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA) for current generation Kongsberg
multibeam data: Fixed problems handling tide correction and applying heave when
recalculating bathymetry through raytracing.

Format 59 (MBF_EM710MBA): Worked on preprocessing function called by mbpreprocess.
Not done yet...

Format 88 (MBF_RESON7KR): Worked on preprocessing function called by mbpreprocess.
Not done yet...

mbio/mb_access.c: Added explicitly setting the target sensor id to the
mb_preprocess() function call.

Mbm_grdtiff: Fixed bug in grdinfo call.

GMT integration: Removed GMT header files from mbsystem/gmt because GMT 5.2.1
now installs full development headers. MB-System is now not compatible with any
version of GMT prior to 5.2.1.

Configure build system: Now uses built in configuration tools in GMT and netCDF
so that command line arguments to the configure script specifying GMT and netCDF
library locations are no longer necessary.

mbio/mb_io.h and mbio/mb_platform.c: Added fields to platform structure:
                  mb_longname     documentation_url;
                  double          start_time_d;
                  double          end_time_d;
                  int             start_time_i[7];
                  int             end_time_i[7];

Mbmakeplatform: Added commands:
                  --platform-documentation-url=string
                  --platform-start-time=yyyy/mm/dd/hh/mm/ss.ssssss
                  --platform-end-time=yyyy/mm/dd/hh/mm/ss.ssssss

#### 5.5.2259 (October 27, 2015)

Mbpreprocess: Now called format-specific preprocess function if available and
applied generic preprocessing otherwise. The first format specific preprocessing
to be defined is for Reson 7k data (MBIO format 88).

Mb7kpreprocess: Modified optional fixing of multibeam ping times assuming a
specified constant ping interval.

Mbmakembplatform: Added manual page.

mbio/mb_navint.c: Added MBIO API functions mb_apply_time_latency() and
mb_apply_time_filter().

Mbeditviz: Fixed application of time latency to sonardepth.

#### 5.5.2258 (October 5, 2015)

Mbnavadjust: Added output of route files including all unfixed ties for each
survey and all crossings for each survey.

Mbmakeplatform: Added new program to create or modify platform files.

Format 58 (MBF_EM710RAW): Added functions needed for mbmakeplatform to
automatically extract a platform model with sensor offsets.

Format 59 (MBF_EM710MBA): Added functions needed for mbmakeplatform to
automatically extract a platform model with sensor offsets.

Format 88 (MBF_RESON7KR): Added functions needed for mbmakeplatform to
automatically extract a platform model with sensor offsets.

Mb7kpreprocess: Added kluge mode (-K6) to fix a time stamp problem with recent
MBARI Mapping AUV data. Specifically, due to the application of time disciplining
to the Reson computer clock using two occasionally inconsistent time sources,
sometimes there are abrupt shifts in the ping time stamps for one to three pings.
This mode detects and corrects these time tears.

#### 5.5.2257 (September 1, 2015)

Mbpreprocess: Using platform functions to handle sensor offsets. Read platform
file or command line offsets and calculate sensor offsets. Updated bathymetry
calculations.

General: Added functions mb_platform_orientation and
mb_platform_orientation_target on mbio/mb_platform. Cleaned
mb_platform_orientation_offset. Change all MB_PLATFORM_MATH* functions to
DEEGREES inputs/outputs on mbio/mb_platform_math. Fixed bug on
mb_platform_lever.

#### 5.5.2256 (August 24, 2015)

Mbeditviz: Improved the way to handle sensor offsets. Improved
mbeditviz_apply_timelag the way to handle angles corrections. Cleaned
mbeditviz_beam_position to make it more clear.

mbio/mb_platform_math.c: Added new math functions
mb_platform_math_attitude_offset_corrected_by_nav and
mb_platform_math_attitude_rotate_beam to handle sensor offset corrections.

#### 5.5.2255 (August 11, 2015)

Mbnavadjust: Set limits on application of smoothing via penalizing the first
and second derivatives of the navigation pertuturbation (particularly the
second derivative) in the inversion algorithm. This change has been implemented
to prevent the inversion from becoming unstable as the smoothing parameter is
made larger.

Mbprocess: Fixed problem with handling of sensor depth changes due to tide
correction or lever arm correction.

#### 5.5.2254 (July 23, 2015)

Autotools build system: Disabled dist and distclean targets in the makefiles
produced by the configure script. We do not use the autotools system to
generate production distributions, so the existence of these targets defined
by default caused some confusion.

Mbset and mbprocess: Added NAVSHIFTX and NAVSHIFTY options to the mbprocess
parameter file definition.

Mbgrid: Fixed the -Kbackground option for the case of producing grids in
projected coordinate systems.

General: Improved the way to handle sensor offsets on mbio/mb_platform.c
and changed the way is currently used in mb7kpreprocess. Added
mbio/mb_platform_math.c to the archive. This source file includes math
functions to calculate angular offsets.

#### 5.5.2252 (July 1, 2015)

Mbedit, mbnavedit, mbnavadjust, mbvelocitytool: Fix X11 font initialization
problem created in the 2251 commit.

#### 5.5.2251 (June 30, 2015)

Mblist, mbnavlist, mbctdlist: Changed time outputs so that decimal second
values will be formatted according to the locale (e.g. decimal delineation by
commas in Europe).

Mbedit, mbnavedit, mbnavadjust, mbvelocitytool, mbgrdviz, mbeditviz: Set up
preprocessor defines to allow fonts to be defined using the CFLAGS
environment variable.

#### 5.5.2250 (June 29, 2015)

Mbedit, mbnavedit, mbvelocitytool, mbgrdviz, mbeditviz: Removed call to X11
function XtSetLanguageProc() in all graphical tools. This call apparently
causes the program locale to be reset according system defaults, even if the
program implicitly begins in the standard C locale. If the system locale uses
"," rather than "." as the decimal point marker (e.g. a normal European locale),
then a GMT 5 initialization will probably fail on reading fonts, at least on
many if not all Linux distributions. Thanks to Giancarlo Troni for figuring this
one out.

General: Added mbio/mb_platform.c to the archive. This source file includes the
functions to read, write, and use platform, sensor, and sensor offset definitions.
At this time the mb_platform_*() functions are only used in mb7kpreprocess, but
they will soon be used in mbprocess and all the preprocess programs.

Mbprocess: changed application of tide corrections so that these corrections are
applied to the platform depth values rather than the bathymetry values. The result
is the same, but now the navigation (or trajectory) of the processed files is
corrected in addition to the bathymetry.

#### 5.5.2249 (June 26, 2015)

Format 121 (MBF_GSFGENMB): Kluge added to the GSF format i/o module to handle
beam angles incorrectly constructed so that angles from vertical are negative
for port side beams when all aziumuthal angles are uniformaly zero (=starboard).

General: Added platform, sensor, and sensor offset definitions to mb_io.h for
use in flexibly defining a platform consisting of many sensors with relative
positional and angular offsets. Also added functions to read and write
platform files using these definitions. Have not completed the function to perform
lever arm calculations using this platform definition. Initially these functions
will be used in mb7kpreprocess, but ultimately these will be used generally
in MB-System.

Mb7kpreprocess: initial implementation using the new platform file and structure
definitions.

#### 5.5.2248 (May 31, 2015)

Mbgrdviz and mbview: Fixed casts between int and pointer that seem to be
responsible for mbgrdviz crashes.

#### 5.5.2247 (May 29, 2015)

General: Cleaned up missing function prototypes through much of the codebase
(excepting externally written libraries gsf, sapi, bsio) in an effort to fix
crashes of mbgrdviz and other programs.

#### 5.5.2246 (May 27, 2015)

Mbswath, mbcontour, mbgrdtiff: Updated GMT5 header files in src/gmt to enable
building on Ubuntu Linux, CentOs Linux, and CygWin while maintaining
compatibility with GMT 5.1.2.

Mbedit, mbnavedit, mbvelocitytool, mbgrdviz, mbeditviz: Incomplete tweaks to
font handling to enable use of fonts other than Helvetica, Times, and Courier.

#### 5.5.2243 (May 22, 2015)

Rewrote the configure.ac file to fix logic flaws in the configure script.

#### 5.5.2242 (May 16, 2015)

Mbswath, mbcontour, mbgrdtiff: Updated files in src/gmt for compatibility with
GMT 5.1.2.

#### 5.5.2241 (May 12, 2015)

Format 59 (MBF_EM710MBA): Fixed flag causing erroneous warning that beam flags
are not supported for this format (beam flags are supported).

Many source files: further changes to precompiler directives suggested by Joaquim Luis
in order to enable building under Windows.

#### 5.5.2240 (May 8, 2015)

Format 241 (MBF_WASSPENL): Fixed recognition of *.nwsf suffix.

Mbclean: fixed bug in beam position calculation identified by Joaquim Luis.

#### 5.5.2239 (May 6, 2015)

Format 241 (MBF_WASSPENL): Now supports WASSP multibeam data conforming to
the WASSP ICD 2.4. MB-System is storing beam flags in unused bytes in the
existing CORBATHY data records (specifically the "empty" field in the
CORBATHY beam data specified in ICD 2.4).

Many source files: changes to precompiler directives suggested by Joaquim Luis
in order to enable building under Windows.

Mbnavadjust: Modified the inversion to separate the vertical and lateral
covariance so that lateral offsets do not bleed into the vertical offset
model.

Mb7kpreprocess: Fixed bug that treated null soundings as good for datasets
without detection records.

Mbdumpesf: Added capability to output in the edit save file format in addition
to ASCII text, and to ignore specified types of edit events (e.g. copy an esf
file while removing all beam null events).

Build system: Fixed bug that caused configure to fail if netCDF has a pkg-config
installation while GMT5 is in a specified but nonstandard location.

#### 5.5.2238 (April 15, 2015)

Mbnavadjust: Recast and improved the inversion. Added a "perturbation" model
display which does not include the average offsets between the individual surveys
in projects involving multiple surveys.

Mbcontour, mbswath, mbgrdtiff: Included fixes suggested by Joaquim Luis for
compatibility with the next GMT5 release.

Mbclean: Removed -M3 and -M4 options that previously caused the program to null
(or zero) rather than flag bad soundings. This is an obsolete feature that only
made sense prior to existence of mbprocess.

Mbbackangle: Fixed mbm_grdplot call to no longer use an obsolete option.

#### 5.5.2237 (March 23, 2015)

Mbnavadjust, mbnavedit: Removed references to GMT and netCDF in the Makefile.am
file in both source directories.

#### 5.5.2236 (March 23, 2015)

Mbnavadjust, mbnavadjustmerge: Added a new type of constraint referred to as a
global tie. Each data section can have one of its navigation points tied to
the fixed global frame of reference with a specified x, y, z offset (or just x
and y, or just z) and x, y, and z uncertainties in the offset values. These
global ties are set using mbnavadjustmerge. The relevant mbnavadjustmerge
commands are:
    --set-global-tie=file:section[:snav]/xoffset/yoffset/zoffset[/xsigma/ysigma/zsigma]
    --set-global-tie-xyz=file:section[:snav]
    --set-global-tie-xyonly=file:section[:snav]
    --set-global-tie-zonly=file:section[:snav]

Mbnavadjustmerge: Added ability to unset (delete) global ties and crossing ties.
The relevant mbnavadjustmerge commands are:
    --unset-global-tie=file:section
    --unset-tie=file1:section1/file2:section2

Mbnavadjust, mbnavadjustmerge: Explicitly added references to libgmt and libpsl in
the src/mbnavadjust/Makefile.am file so that the mbnavadjust and mbnavadjustmerge
executables are linked to those libraries. This is to solve a mysterious dependency
of mbnavadjust on libgmt on CentOs6 - the program was failing due inability to find
libgmt.so.5 even though the code does not reference any GMT or GMT5 function or header
file. Presumably this change will go away when the mystery is solved.

Mbsslayout: fixed automatically generated plottin script.

Mbm_route2mission: Added multibeam maximum range value.

#### 5.5.2234 (March 5, 2015)

Plot macros (mbm_grdplot, mbm_grd3dplot, mbm_grdtiff, mbm_histplot, mbm_plot,
mbm_xyplot): Now generate plotting scripts that will not attempt to display the
plot on the screen if invoked with a "-N" command line argument.

Format 64 (MBF_MR1PRVR2): Added include of <sys/time.h> in mbbs_defines.h to
facilitate building under cygwin.

Multi-macros (mbm_multiprocess, mbm_multicopy, mbm_multidatalist): Changed to
use datalist.mb-1 as default input and to use 4 as the default number of CPUs.

Mbedit: Added fast scroll through a file if the forward or back mouse buttons
are held down more than 2 seconds.

Mbextractsegy, mbsslayout: Changed output section/line plotting script so that
it will not attempt to display the plot on the screen if invoked with a "-N"
command line argument.

Mbprocess: Reduced informational output when not in verbose mode to make the
output from use of mbm_multiprocess cleaner.

#### 5.5.2233 (February 23, 2015)

Release 5.5.2233

Mbm_grdplot, mbm_grdtiff: Generated plot scripts now set foregound and background
colors based on the -D option.

Mbmroute2mission: Now allows the maximum planned climb rate of the AUV to be
specified with the -U option

#### 5.5.2232 (February 21, 2015)

Mbm_plot, mbm_grdplot, mbm_grd3dplot, mbhistplot: Changed handling of gmt defaults
so that any local gmt.conf file is deleted before any gmtset calls are made, and
the resulting gmt.conf file is deleted before the plot script ends.

Mbswath: fixed calculation of beam or pixel footprints in mode requesting real
footprint plotting.

#### 5.5.2231 (February 20, 2015)

Mb7kpreprocess: Switched beam angle calculation to the mb_beaudoin() function
already used by mbkongsbergpreprocess (contributed by Jonathan Beaudoin).

Mbm_bpr: Made compatible with GMT5.

#### 5.5.2230 (February 18, 2015)

Mbgrdtiff: Fixed ordering of rows and columns in the output image.

Mbm_route2mission: Added output of a mission alititude profile plot.

Mbauvloglist: Added capability of binary output.

Mb7kpreprocess: Fixed so that bathymetry calculation uses roll merged at
the bottom detect time for all of the possible combinations of Reson 7k
data record types.

Mbpreprocess: Fixed to exclude zero longitude or latitude values from the
tables used for interpolation onto ping times.

Mbrolltimelag: Fixed automatically generated roll-slope correlation plot.

#### 5.5.2229 (February 14, 2015)

Format 121 (MBF_GSFGENMB): The i/o module will now allocate and initialize arrays
of beamflags and alongtrack distance when those are not included in the input file.

Mbfilter: removed failing check for existence of sidescan data.

Mbsegygrid: flipped grid convention for compatibility with GMT5.

Mbm_plot, mbm_grdplot, mbm_grd3dplot, mbm_histplot: further changes for compatibility
with GMT5.

Mbm_route2mission: Compatibility with GMT5.

Mbcontour, mbswath: More changes for compatibility with GMT5.

#### 5.5.2228 (February 6, 2015)

Install_makefiles: the old install_makefiles build system no longer
functions and has been removed.

Mbgrid: When using the two-step weighted footprint slope algorithm, mbgrid
only reads files on the second pass through the input datalist that contained
useful data in the first pass.

Major changes made to integrate MB-System with GMT5:
  The code will no longer compile or work with GMT4.5.
  Changes include:
    -updating functions in libmbaux  that read and write GMT grids
    -deletion of src/mbaux/mb_pslibface.c
    -changes to all programs that read or write GMT grids,
    -the former programs mbcontour, mbswath, and mbgrdtiff are now GMT5
      modules built as part of a shared library.
    -changes to all of the plot macros (e.g. mbm_grdplot) that make use of GMT

Format 88 (MBF_RESON7KR): Update Reson 7k i/o module to handle TVG records.

---
### MB-System Version 5.4 Releases and Release Notes:
---

- **Version 5.4.2220       January 22, 2015 (Last GMT4-compatible archive revision)**
- Version 5.4.2219       December 11, 2014
- Version 5.4.2218       December 4, 2014
- Version 5.4.2217       December 1, 2014
- **Version 5.4.2213       November 13, 2014**
- Version 5.4.2210       November 10, 2014
- **Version 5.4.2209       November 4, 2014**
- **Version 5.4.2208       October 29, 2014**
- Version 5.4.2204       September 5, 2014
- **Version 5.4.2202       August 25, 2014**
- Version 5.4.2201       August 20, 2014
- **Version 5.4.2200       July 24, 2014**
- **Version 5.4.2199       July 19, 2014**
- Version 5.4.2196       July 14, 2014
- Version 5.4.2195       July 9, 2014
- Version 5.4.2194       July 8, 2014
- **Version 5.4.2191       June 4, 2014**
- **Version 5.4.2188       May 31, 2014**
- Version 5.4.2187       May 28, 2014
- Version 5.4.2186       May 26, 2014
- Version 5.4.2185       May 11, 2014
- **Version 5.4.2183       April 16, 2014**
- Version 5.4.2182       April 8, 2014
- Version 5.4.2181       April 4, 2014
- **Version 5.4.2176       March 18, 2014**
- **Version 5.4.2168       February 19, 2014**
- **Version 5.4.2163       January 31, 2014**
- Version 5.4.2162       January 24, 2014
- **Version 5.4.2159       January 18, 2014**
- Version 5.4.2158       January 18, 2014
- **Version 5.4.2157       October 14, 2013**
- Version 5.4.2155       October 13, 2013
- Version 5.4.2154       September 26, 2013
- Version 5.4.2153       September 22, 2013
- **Version 5.4.2152       September 16, 2013**
- Version 5.4.2151       September 12, 2013
- Version 5.4.2149       September 2, 2013
- Version 5.4.2148       August 28, 2013
- Version 5.4.2147       August 27, 2013
- Version 5.4.2144       August 26, 2013
- Version 5.4.2143       August 24, 2013
- Version 5.4.2141       August 24, 2013
- Version 5.4.2139       August 19, 2013
- Version 5.4.2138       August 18, 2013
- Version 5.4.2137       August 9, 2013
- Version 5.4.2136       August 8, 2013
- **Version 5.4.2135       August 7, 2013**
- Version 5.4.2133       July 29, 2013
- Version 5.4.2132       July 26, 2013
- Version 5.4.2130       July 20, 2013
- Version 5.4.2129       July 8, 2013
- Version 5.4.2128       June 18, 2013
- Version 5.4.2123       June 10, 2013
- Version 5.4.2082       May 24, 2013

---

#### 5.4.2219 (December 11, 2014)

Mbnavadjust: Fixed fixed memory management issue related to fbt files.

Mb7kpreprocess: Moved toward correct handling of sensor offsets.

Mbpreprocess: Moved toward correct handling of sensor offsets.

#### 5.4.2218 (December 4, 2014)

Mbinfo: Fixed JSON format output to file (previously missed final closing bracket).


#### 5.4.2217 (December 1, 2014)

Mbclean: Implemented additional flagging tests contributed by Suzanne O'Hara,
including speed range (-Pspeed_min/speed_max), ping navigation bounds
(-Rwest/east/south/north), and zero longitude and latitude values (-Z).
Also, a minimum depth at nadir test embedded by Dana Yoerger for all data
(circa 2010) has been recast into a minimum range test option (-Krange_min).

Format 71 (MBF_MBLDEOIH) and fbt files: fixed a problem with the i/o module
as updated in 5.4.2216.

#### 5.4.2216 (November 30, 2014)

Format 251 (MBF_PHOTGRAM): We have added a new data format and associated data
system supporting photogrammetric topography calculated from stereo pair
photographs. This format includes navigation and attitude data. Each 2D group
of bathymetry values is derived with a single stereo pair. A file consists of a
sequence of stereo pair bathymetry, each set of which has a timestamp, navigation
and attitude as well as bathymetry values. The format 251 files are generated
from stereo pairs (and navigation and attitude data) by a set of tools that
are not currently in MB-System, but which will be added to MB-System in the
future.

Mbeditviz and Mbgrdviz: Now allow selection of a single navigation point.

Mbeditviz and mbgrid: Now handle point topography data (e.g. xyz soundings, lidar
soundings, photogrammetry topography) differently than multibeam soundings even
when the footprint algorithm is specified. Point data are now treated as such,
and no longer are associated with nonsensical beam footprints.

Format 71 (MBF_MBLDEOIH) and fbt files: We have defined a new data record header (version 5)
that represents the number of bathymetry beams, amplitude beams, and sidescan
pixels as four-byte int values rather than two-byte short values. This supports
data constructs that have more than 32768 bathymetry values, as can be the case
for dense photogrammetry data derived from stereo-pair photography. The i/o module
only uses the version 5 header when there are more than 32768 bathymetry values
in the associated sonar ping, lidar scan, or photographic stereo pair. Otherwise,
the previously existing version 4 header is used. Consequently, for all previously
supported data types there will be no change to the MBF_MBLDEOIH format or to
fbt files.

General: MB-System now defines several types of bathymetry data:
      MB_TOPOGRAPHY_TYPE_UNKNOWN        0
      MB_TOPOGRAPHY_TYPE_ECHOSOUNDER            1
      MB_TOPOGRAPHY_TYPE_MULTIBEAM        2
      MB_TOPOGRAPHY_TYPE_SIDESCAN        3
      MB_TOPOGRAPHY_TYPE_INTERFEROMETRIC    4
      MB_TOPOGRAPHY_TYPE_LIDAR                  5
      MB_TOPOGRAPHY_TYPE_CAMERA                 6
      MB_TOPOGRAPHY_TYPE_GRID                 7
      MB_TOPOGRAPHY_TYPE_POINT                   8
The immediate utility of differentiating between data types is to
allow gridding algorithms to handle data appropriately. As discussed
above, the footprint gridding algorithms are now only applied by
mbgrid or mbeditviz to multibeam bathymetry. Other differences in
data processing will be added in the future.

General: The sort function and related comparison function declarations
in MB-System have been corrected to be consistent with qsort() from stdlib.

#### 5.4.2213 (November 13, 2014)

Mbkongsbergpreprocess: Added -E option to allow specification of offsets between
the depth sensor and the sonar. This is relevant only to submerged platforms
such as AUVs or ROVs. Also added -P option to enable filtering of pressure
depth data.

Format 59 (MBF_EM710MBA): Set the navigation and attitude source records to be
survey data so that mbnavedit and mbnavlist work by default with values from the
survey records rather than asynchronous raw sensor data. The navigation and attitude
sources for format 58 (MBF_EM710RAW) remain the asynchronous records.

Mbnavedit: Strictly define the font definitions for pushbutton widgets
(some X11 environments are making bad choices when given latitude).

#### 5.4.2210 (November 10, 2014)

Mbkongsbergpreprocess: Changed handling of water column records. The default
behavior is now to not write water column records to the output format 59 files.
Users can specify -W1 to have the water column records written in the output files.

Format 41 (MBF_SB2100RW): Bug fix for Seabeam format 41 so the code handles
records without the maximum number of beams. Contributed by Bob Covill.

Mbprocess: Added ability to apply static bathymetry corrections defined according
to beam angle in addition to corrections according to beam number. Contributed
by Bob Covill.

Mbvelocitytool: When loading a swath file, mbvelocitytool will now also read in
and apply an associated *.esf (edit save file) if it exists. This prevents
soundings that have been identified as bad from biasing the calculations.
Contributed by Bob Covill.

Mbm_grdcut: Fix to the manual page. Contributed by Jenny Paduan.

#### 5.4.2209 (November 4, 2014)

MBnavadjustmerge:  Completed the manual page for this new program that allows
one to merge and manipulate MBnavadjust projects.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Recast the i/o architecture to
handle the full variablity of multibeam data in these formats.

#### 5.4.2208 (October 29, 2014)

Mbkongsbergpreprocess:  Fixed calculation of beam
takeoff angles for raytracing from the raw range and angle data records by
including code made available by Jonathan Beaudoin. Recalculation of
bathymetry in current generation Kongsberg multibeam data appears to work
now.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Support Mesotech M3
multibeam data recorded in *.all files.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA): Fixed calculation of beam
takeoff angles for raytracing from the raw range and angle data records by
including code made available by Jonathan Beaudoin. Recalculation of
bathymetry in current generation Kongsberg multibeam data appears to work
now.

#### 5.4.2204 (September 5, 2014)

Mb7kpreprocess:  Changed handling of roll, pitch, and heave compensation
to deal with deep water Reson 7150 data.

Format 88 (MBF_RESON7KR): Changed handling of roll, pitch, and heave compensation
to deal with deep water Reson 7150 data.

Mbdefaults: Added control of default color and shading settings for mbgrdviz and
mbeditviz.

Format 231 (MBF_3DDEPTHP): Fixed the mbsys_3datdepthlidar_insert_nav() function
to apply changes to all pulses.

Mbgrdviz and Mbeditviz: Default color and shading settings now can be set using
mbdefaults.

#### 5.4.2202 (August 25, 2014)

Format 88 (MBF_RESON7KR): Enlarged the maximum number of beams to 1024 in order
to handle 7150 data with >800 beams.

Format 21 (MBF_HSATLRAW): Augmented to trim trailing blank space at the end of
lines before parsing - this allows reading Hydrosweep DS data in the form
held by NIO.

#### 5.4.2201 (August 20, 2014)

Mbm_grdplot: Added two "sealevel" color palletes that use Haxby colors for
negative values (e.g. topography below sea level) and either greens or browns
for positive values (e.g. topography above sea level). The Sealevel 2 palette
was contributed by Jenny Paduan.

Mbeditviz: Changed default illumination parameters to magnitude=1.0 and
elevation=5.0.

Mbgrdviz: Changed default illumination parameters to magnitude=1.0 and
elevation=5.0.

Mbnavadjust: Added views for 10% coverage crossings.

Mb7kpreprocess: Added kluge function to "tweak" the beam angles as if the speed of
sound used for beamforming had been wrong.

#### 5.4.2200 (July 24, 2014)

Format 121 (MBF_GSFGENMB): Fixed bug in which null sensor depth and altitude
values are handled incorrectly.

#### 5.4.2199 (July 20, 2014)

Format 121 (MBF_GSFGENMB): Modified GSF 3.06 source files gsf.c gsf_indx.c to
disable recasting of fundamental file io functions (fopen(), fseek(), ftell(),
stat()) when the compile flag -DUSE_DEFAULT_FILE_FUNCTIONS is defined. This
allows MB-System builds to just use the normal file functions without changing
the build behavior of the code in other contexts. The issue is that Leidos is
supporting 64-bit file i/o in binaries for 32-bit architectures. The consequence
of this change in MB-System is that MB-System will not support GSF files that
are 2 GB or larger when built on or for 32-bit systems.

mbpreprocess: Fixed bug in merging of asynchronous attitude data. This program
is not ready for general use.

#### 5.4.2196 (July 14, 2014)

mbotps: Added -P option to specify the location of the OTPS package.

mbsslayout: Made to work (again) with Reson 7k data with embedded Edgetech
sidescan and subbottom data.

mb7kpreprocess: Made to work (again) with Reson 7k data with embedded Edgetech
sidescan and subbottom data.

mbextractsegy: Made to work (again) with Reson 7k data with embedded Edgetech
sidescan and subbottom data.

#### 5.4.2195 (July 9, 2014)

Format 88 (MBF_RESON7KR): Fixed bug in mbsys_reson7k_extract_altitude().

Format 132 (MBF_EDGJSTAR): Added mbsys_jstar_insert_altitude() to support
mbpreprocess and mbsslayout. Fixed handling of heading on extract and insert.

mbm_route2mission: Removed confusing juxtaposition of estimated AUV mission time
with actual AUV mission termination time in the output AUV mission script.

mbpreprocess: Added ability to merge altitude data. Tested successfully with
raw Edgetech sidescan data collected without embedded navigation, attitude,
or anything really.

mbsslayout: A new program to lay out raw sidescan onto the seafloor, most
often on a 3D seafloor topographic model. Achieved functionality, at least
for use with Edgetech sidescan data in Jstar format.

#### 5.4.2194 (July 8, 2014)

Format 121 (MBF_GSFGENMB): Updated source files in src/gsf/ to GSF release 3.06.

Format 121 (MBF_GSFGENMB): Fixed scaling of array values in GSF files to allow
depth and distance resolutions better than 1 cm.

Formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA) to support EM2040D data, in which
dual sonars ping simulatneously.

#### 5.4.2191 (June 4, 2014)

Install_makefiles: Fixed old build system so that it successfully compiles and
links the new, unfinished program mbsslayout.

#### 5.4.2189 (June 4, 2014)

Format 121 (MBF_GSFGENMB): Fixed bug that caused programs reading GSF data to hang
when the GSF file ends with a partial or corrupted data record.

MBeditviz: Added capability to set the color of selected soundings (e.g. soundings
associated with a particular file or particular section of trackline).

Format 88 (MBF_RESON7KR): Added support for pitch stabilization.

MB7kpreprocess: Added support for pitch stabilization in Reson 7k data.

#### 5.4.2188 (May 31, 2014)

Format 121 (MBF_GSFGENMB): Fixed bug that caused crashes when the GSF file
contains a zero length comment.

Format 64 (MBF_MR1PRVR2): Fixed bug that caused crashes when copying data from
MR1 file to an fbt file when comments are longer than supported in fbt files.

MBnavadjust: Fixed bug that reset the selected survey while doing autopicks.

#### 5.4.2187 (May 28, 2014)

Format 201 (MBF_HYSWEEP1): Added code to ignore bad RMB records found in some
NOAA HSX data.

Format 88 (MBF_RESON7KR): Support for calibrated snippet records (contributed
by David Finlayson).

MB7kpreprocess: Support for calibrated snippet records (contributed
by David Finlayson).

MBnavadjustmerge: Fixed to handle projects not in the current working directory.

#### 5.4.2186 (May 26, 2014)

MBeditviz: Fixed interactive application of pitch bias and heading bias changes.

MBnavadjustmerge: New program to merge two existing MBnavadjust projects.

#### 5.4.2185 (May 17, 2014)

MBrolltimelag: Now checks for case when all beams are flagged.

MBlist: Added beamflag values to those that can be printed ('F' or 'f').

Bathymetry editing: Fixed bug that prevented successful flagging of some beams
when files include simultaneous pings with different numbers of beams.

GSF library: Updated to new release 03.05. This release is licensed using LGPL 2.1.

#### 5.4.2185 (May 11, 2014)

Several programs: Fixed formatting error in printing system time_tm.tv_sec values.

MBsvpselect: Fixed sscanf format warning.

MBcopy: Fixed array dimensioning bug that occasionally caused buffer overflows.

MBnavadjust: Moved some declarations from mbnavadjust_prog.c to mbnavadjust.h in
preparation for breaking project i/o out into a separate source file to be shared
with the new program mbnavadjustmerge.

MBsslayout: Added shell of program under development to read sidescan in raw time
series form, lay the sidescan out regularly sampled on a specified topography
model, and output the sidescan to format 71 (MBF_MBLDEOIH) files.

HSDS formats (MBF_HSATLRAW, MBF_HSLDEDMB, MBF_HSURIVAX, MBF_HSURICEN): Fixed bug
in handling of system gain arrays (16 rather than 59 values).

MBsegygrid: Attempted to incorporate actual nonvertical geometry into the
subbottom sections - not satisfactory yet.

MBrolltimelag: Fixed bug regarding the default roll source. The program will
now work with roll values derived from survey records by default.

Format 88 (MBF_RESON7KR): Cleaned up some debug print statements.

MBinsreprocess: Incomplete new MB6 program to reprocess INS data of various sorts
to improve on realtime Kalman filtered navigation and attitude data.

MBsslayout: Incomplete new MB6 program to perform layout of time series sidescan
onto a 3D topography model. This will replace mb7k2ss and extend the functionality
to conventional sidescan data in several data formats.

Mbm_route2mission: Fixed output AUV mission script to have "\r\n" line ends on
all lines.

Format 222 (MBF_SWPLSSXP): Revised implementation of SEA SwathPlus SXP data format
(format id 222) contributed by David Finlayson.

Format 121 (MBF_GSFGENMB): Changed the source for the internally supplied GSF
library to be the new 3.05 release. This includes for the first time a proper
open source license (LGPL 2.1).

#### 5.4.2184 (April 22, 2014)


src/bsio/Makefile.in: Added to archive (previously mistakenly left out).

#### 5.4.2183 (April 16, 2014)

Many programs: Fixed handling of system time character string provided by
function ctime() to prevent occasional overflows.

Format 222 (MBF_SWPLSSXP): Revised implementation of SEA SwathPlus SXP data format
(format id 222) contributed by David Finlayson.

MBswplspreprocess: Preprocess program for SEA SwathPlus SXP data format
(format id 222) contributed by David Finlayson. This was formerly known as
mbsxppreprocess.

#### 5.4.2182 (April 8, 2014)

Format 231 (MBF_3DDEPTHP): Added new raw Lidar record to be used by 3DatDepth.

Format 201 (): Corrected bug in handling of navigation in projected coordinate
systems.

mbio/mb_navint.c and mbio/mb_define.h: Added a new function mb_navint_prjinterp()
that interpolates navigation and speed from internal runnings lists assuming the
navigation is in eastings and northings rather than longitude and latitude.

#### 5.4.2181 (April 4, 2014)

Release 5.4.2181

htmlsrc/mbsystem_home.html & htmlsrc/mbsystem_faq.html: Actually committed
pictures of Christian Ferreira and Krystle Anderson to the archive

#### 5.4.2180 (April 2, 2014)

htmlsrc/mbsystem_home.html & htmlsrc/mbsystem_faq.html: Updated references
to the MB-System team in the html documentation to include Christian Ferreira
and Krystle Anderson.

htmlsrc/mbsystem_how_to_get.html: Updated installation instructions
in the html documentation.

MB7kpreprocess: recoded the application of time domain filtering of pressure
depth data to be much more efficient.

Format 132 (MBF_EDGJSTAR): Supported obsolete sidescan records with 80 byte
traceheaders.

MBextractsegy: Now works with Edgetech Jstar files.

MBauvloglist: reset default printing of timestamp values.

Mbset: modified so that when mbset is used to turn off a mode that implies
use of an external file, the associated filename is also erased. For example
    mbset -PSVPMODE:0
will now also erase (null) the filename set by -PSVPFILE.

Mbm_grd3dplot, mbm_grdplot, mbm_histplot, mbm_plot, mbm_xyplot: added support
for the evince postscript viewer.

Format 172 (MBF_HIR2RNAV) and format 173 (MBF_MGD77TXT): fixed segmentation
faults while handling comment records.

MBlist: The 'N' output option will now use actual ping numbers if those are
available (instead of ping count in the file).

MBroutetime: Now exits with error message if no start line or end line waypoints
are read from the input route file.

#### 5.4.2176 (March 18, 2014)

Release 5.4.2176

#### 5.4.2175 (March 18, 2014)

Configure.ac: Removed reference to src/mbsvptool (src/mbsvptool/mbsvptool.c
was moved to src/utilities/mbsvpselect.c for 5.4.2173).

MBnavadjust: The program generates route files of crossings and ties that
can be viewed in mbgrdviz. The coloring of the crossings and ties when
displayed in mbgrdviz has changed. The route files generated are:
    True Crossings (unfixed)
    >50% Crossings (unfixed)
    >25% && <50% Crossings (unfixed)
    <25% Crossings (unfixed)
    Ties (unfixed)
    Ties (fixed)
For the crossing files, individual crossings are colored as:
    Unset - Red
    Skipped - Yellow
    Set - Green
For the tie files, individual ties are colored as:
    Ties (unfixed) - Blue-Green
    Ties (fixed) - Purple

All source files: Updated copyright notices to 2014.

#### 5.4.2173 (March 17, 2014)

MBsvpselect: Added program contributed by Ammar Aljuhne and Christian Ferreira
of MARUM (University of Bremen). This program chooses and implements the best
available sound speed model for each swath file in a survey. The user  provides
a  list of the available sound speed models and specifies the criteria used for
model selection. The program uses mbset to turn on bathymetry recalculation by
raytracing through the sound speed model selected for each swath file.

MBsvplist: The SVP files output by mbsvplist now include a header line that
is recognized by mbsvpselect. This header line includes the time stamp and
position associated with the SVP record's location in the swath file.

MBpreprocess: Added an incomplete manual page for this incomplete MB-System 6
program.

#### 5.4.2172 (March 14, 2014)

MBmosaic: Added option to apply priorities based on the platform heading.

Format 64 (MBF_MR1PRVR2): Hawaii Mapping Research Group (HMRG) data format
updated to use the current library and thereby support post-2005 data.
Removed old HMRG mr1pr library from mbsystem/src and added current bsio
library.

MBgrdviz: Modified handling of routes so that if a route header contains a line
like:
      ## ROUTEEDITMODE:0
then the route cannot be changed in MBgrdviz.

MBnavadjust: Changed so that when a project is output, mbnavadjust writes out
five different route files in which each tie point or crossing is a two point route
consisting of the connected snav points
- route files of ties (fixed and unfixed separate) represent each tie as a
two point route consisting of the connected snav points
- route files of crossings (<25%, >= 25% && < 50%, >= 50%, true crossings)
represent each crossing as a two point route consisting of the central
snav points for each of the two sections.

Mbvelocitytool: made all filename and command strings type mb_path, which is
a 1024 byte char array.

Format 173 (MBF_MGD77TXT): Added format to read and write MGD77 format
underway geophysical data files with "\r\n" characters at the ends of the
data records.

Format 174 (MBF_MGD77TAB): Added format to read and write MGD77T format
underway geophysical data files with tab delimiters and "\r\n" characters
at the ends of the data records.

#### 5.4.2168 (February 19, 2014)

Mbinfo: Fixed bug in variance calculation (memory overwrites of the relevant arrays).

#### 5.4.2165 (February 18, 2014)

Format 241 (MBF_WASSPENL): Made format suffix ".000" recognizable as format 241.


#### 5.4.2164 (February 15, 2014)

Format 241 (MBF_WASSPENL): added new format for WASSP multibeam sonar.

Format 151 (MBF_OMGHDCSJ): applied patch supplied by Bob Covill.

Mbrolltimelag: fixed so that the program works with data formats for which the
roll source is the survey records.

Mbauvloglist: added capability to merge navigation from external files.

#### 5.4.2163 (January 31, 2014)

Format 71 (MBF_MBLDEOIH): fixed a recently introduced error in scaling of
bathymetry values. This error impacts the fbt files, and consequently will
mess up bathymetry gridding and plotting. It's important to update installations
to 5.4.2163.

MBextractsegy: Fixed so correct navigation is inserted in both the source and
group position fields in the segy traceheader.

#### 5.4.2162 (January 24, 2014)

Format 88 (MBF_RESON7KR): fixed crash when generating sidescan from pings with no valid beams.

Format 201 (MBF_HYSWEEP1): fixed crash when generating sidescan from pings with no valid beams.

Build system: Altered so the configure script works with standard options.

#### 5.4.2161 (January 21, 2014)

MBedit: fixed use of beamflag setting macros that were messed up yesterday.

#### 5.4.2160 (January 20, 2014)

General: fixed many compiler warnings.

General: implemented changes suggested by Joaquim Luis in order to enable
building MB-System on Windows systems.

#### 5.4.2159 (January 18, 2014)

Release 5.4.2159.

#### 5.4.2158 (January 18, 2014)

Many changes, including:
  - Support for new format of lidar data
  - Fixes to support swath data with sub-cm lateral resolution
  - Fix so that mbnavadjust works when built with shared libraries.
    - this involved changes to the contouring code in the mbaux library.
  - Augmentation of the AUV mission planning capability
  - Improvement to mbm_grdplot output for maps of small areas
  - Fixes to the configure build system
    - now allows MB-System to be built using an externally installed
      libproj or the proj library bundled with MB-System
    - using --disable-gsf now works properly to build without any use of
      or entanglement with libgsf.

#### 5.4.2157 (October 14, 2013)

Mbm_makesvp: New macro to extract sound speed and depth data from a datalist of
swath files, and generate a sound velocity profile model from averages of the
sound speed values in regular depth ranges. This macro uses mbctdlist to extract
the sound speed values embedded in swath data files is intended for use with
mapping data from submerged platforms (e.g. ROVs and AUVs) carrying CTD or
sound speed sensors.

#### 5.4.2155 (October 13, 2013)

MBvelocitytool: Fixed problems with bad calculations after loading more than
one swath data.

MBgrdtiff, mbm_grdtiff: Added capability to output a *.tfw "world" file parallel
to the GeoTiff image. Some software does not recognize the coordinate system
information embedded in the GeoTiff file.

MBsegygrid: Added capability for simple time domain low-pass filtering.

MBrphsbias: Added incomplete new program that will, when complete, use a brute
force multidimensional search obtain optimized estimates for bias parameters
from a specified dataset. There is no documentation yet as the program currently
does nothing but compile and read data.

#### 5.4.2154 (September 26, 2013)

MBkongsbergpreprocess, MB7kpreprocess, MBhysweeppreprocess, mbprocess:
Fixed errors in navigation interpolation introduced in 5.4.2152.

Format 84 (MBF_XTFR8101): Fixed initialization of the storage data structure.

Committed from CCGS Sir Wilfrid Laurier at 116d 04.4876' W, 68d 57.30' N.

#### 5.4.2153 (September 22, 2013)

Format 201 (Hysweep HSX): fixed sign error in handling of pitch values.

#### 5.4.2152 (September 16, 2013)

Formats 58 (Kongsberg raw), 59 (Kongsberg extended), 88 (Reson 7k):
Fixed problem with interpolation of heading for Kongsberg and Reson data.
Eliminated possibility of negative headings being inserted into the storage
data structure.

Format 222: Inserted initial implementation of SEA SwathPlus sxp data format
(format id 222) contributed by David Finlayson with minor changes. This format
support is still developmental.

Build system: Applied patch contributed by Frank Delahoyde with additional fixes
to configure.ac and the src/*/Makefile.am files.

#### 5.4.2151 (September 12, 2013)

Many *.c files: hundreds of small changes to eliminate compiler warning messages
on various types of systems.

Build system: Changes to configure.ac, autogen.sh, and src/*/Makefile.am files
based on suggestions from Frank Delahoyde of SIO and Kurt Schwehr of Google.

#### 5.4.2149 (September 2, 2013)

Src directories src/mbio and src/utilities: Fixed a number of debug print
statements that treated pointer values as %ul rather than %p.

#### 5.4.2148 (August 28, 2013)

Buildsystem: More tweaking of configure.ac file, including making the comments
output more sensible.

#### 5.4.2147 (August 27, 2013)

Buildsystem: More tweaking of configure.in file trying to get MB-System to build
on Ubuntu 12.04.02LTS. Moved configure.in to configure.ac to conform to current
autoconf file naming conventions.

#### 5.4.2144 (August 26, 2013)

Buildsystem: Added src/mbgrdviz/Makefile.in and src/mbeditviz/Makefile.in to the
subversion source archive.

Format 201 (Hysweep HSX): Changed mbr_rt_hysweep1() in mbr_hysweep1.c so that
survey records without navigation and/or attitude data do not have an error
set. This means that data missing nav and/or attitude will still be
processable.

Format 121 (GSF): Now recognizes and appropriately treats null values for
position, attitude, speed, and sonar depth.

#### 5.4.2143 (August 24, 2013)

MBsxppreprocess: Added nonfunctional stub for program mbsxppreprocess to be
developed by David Finlayson.

#### 5.4.2141 (August 24, 2013)

Build system, MBgrdviz, MBeditviz, MBview: Moved source files for MBgrdviz
and MBeditviz from src/mbview to src/mbgrdviz and src/mbeditviz, respectively.
This move separates the application source files for MBgrdviz and MBeditviz
from the source files of the mbview library.

#### 5.4.2139 (August 19, 2013)

Build system: Further modification to the src/mbview/Makefile.am file.

#### 5.4.2138 (August 18, 2013)

Build system: Further modifications to the Makefile.am files.

MBopts: Now allows users to specify the tide model used by OTPS. Also now works
with all three variants of the OTPS package.

MBareaclean: Fixed memory allocations problems.

MBgrdviz: Added capability to launch mbnavedit and mbvelocitytool on selected
swath data (contributed by Christian Ferreira).

#### 5.4.2137 (August 9, 2013)

Build system: Still attempting to fix problems with the autoconf build system on
Ubuntu machines. Change mbsystem/src/opts/Makefile.am so that building this
utility does not depend on GMT libraries (since it doesn't).

#### 5.4.2136 (August 8, 2013)

Build system: Attempted to fix problems with the autoconf build system on
Ubuntu machines. Reset the automake version to 2.65 from 2.69 as specified
in the mbsystem/configure.in file. Also added a conditional reference to
libmbgsf to the requirements for mbcopy in mbsystem/src/utilities/Makefile.am.

#### 5.4.2135 (August 7, 2013)

Mbdatalist: Fixed generation of old-format fbt files.

Web page documentation: Updated basic web pages included in the distribution.

#### 5.4.2134 (July 31, 2013)

Heading and nav interpolation (src/mbaux/mb_spline.c): Fixed function
mb_linear_interp_degrees() so that negative latitude values are allowed.

Mbkongsbergpreprocess: Added checking so that interpolated heading and
navigation are in the correct domains.

#### 5.4.2133 (July 29, 2013)

Heading and nav interpolation (src/mbaux/mb_spline.c): Modified function
mb_linear_interp_degrees() so that return values must be in the range
  0.0 <= value < 360.0
to fix bad heading values near due north.

Mbclean: added -Ttolerance option which will recast the timestamps of edit
events read from edit save files to match the pingtimes, where the tolerance
value in seconds defines how close the timestamps must be to be considered the
same. This is used to override timestamp differences greater than 0.0011 seconds
that can arise when edits are extracted from one set of files (perhaps processed
using software other than MB-System) using mbgetesf and then applied to a
different set of files (presumably as part of MB-System processing).

#### 5.4.2132 (July 26, 2013)

Format 88 (Reson s7k): Fixed layout of snippet backscatter into sidescan in the
near-nadir region.

Format 88 (Reson s7k): Mbprocess now routinely recreates multibeam sidescan
during processing. This allows backscatter from beams flagged as bad to be
excluded from the multibeam sidescan.

Mbinfo: Fixes to XML output from mbinfo (Christian Ferreira)

Format 201 (Hysweep): Substantially changed i/o logic to handle the many
different variants of data logged through Hysweep.

Format 201 (Hysweep): Augmented to handle sidescan data in conjunction with
multibeam bathymetry. The i/o module will lay the raw sidescan out on the
bathymetry to generate "processed" sidescan. That will be included in any output
file as MSS records (an MB-System extension to the HSX format), which can be
corrected and filtered in the usual way.

Format 88 (Reson s7k): Fixed bug in which sidescan generated from backscatter
records was flipped port to starboard. Also fixed layout of backscatter in the
near-nadir region.

#### 5.4.2129 (July 8, 2013)

Build system: Attempted to implement changes to the build system suggested by
Kurt Schwehr and Hamish Bowman.

Mbrolltimelag: Augmented to allow specification of the time lag interval used
in correllation calculations with arbitrary start and end times.

Mbnavlist: Fixed problems with outputting attitude data from some variants of
Kongsberg data.

Mbgrid: Changed the convergence criteria for the zgrid interpolation algorithm
to simply be that the largest change in the grid value is no more than 1 mm.

Formats 56 and 57: Augmented handling of Kongsberg EM1002 data to recognize and
fix erroneous transmit and receive beamwidth values.

Mbprocess and mbvelocitytool: Augmented raytracing code to handle high angle
rays without rounding errors producing a square root of a negative number.
This fixed problems with sample EM1002 data.

#### 5.4.2128 (June 18, 2013)

Mblist: Fixed bug that flagged as bad all sidescan pixels with negative values.

src/mbio/projections.h and src/utilities/levitus.h: Removed from svn version
control as these are created during the build process.

Build system: Implemented changes to the build system contributed by
Kurt Schwehr that enable building MB-System without support for GSF or inclusion
of the GSF source code from SAIC. This optional removal of GSF support addresses
the lack of a proper open source or free software license for the GSF source
code distribution from SAIC. MB-System distributions that include GSF code or
require the GSF library cannot be included in official open source package
collections such as Debian.

Mbgrid: Changed the usage of the zgrid interpolation by mbgrid. Release 5.3.1989
included changes to speed up interpolation by calculating a smooth model for a
low resolution grid and then resampling this onto the full resolution grid. This
approach has the problem that the low resolution interpolation can work poorly
near data. Mbgrid still does low resolution interpolation as part of the
slope estimation stage of algorithms 5 and 6 and as part of background
interpolation, but once again does the primary interpolation stage at full
resolution.

#### 5.4.2123 (June 10, 2013)

Many changes implementing fixes to the new build system from Bob Covill,
Hamish Bowman, and Christian Ferreira. Moved key auto-generated header file
from mbsystem/src/mbsystem_config.h to mbsystem/src/mbio/mb_config.h.

Mbm_route2mission: added support for more than one type of survey behavior
in an AUV mission as controlled by waypoint type in the route files
exported from mbgrdviz.

Moved program hsdump to mbhsdump.

Fixed some potential buffer overflows and other errors identified by
Hamish Bowman.

Changed the header of the mbm_* perl macros to #!/usr/bin/env perl as
suggested by Hamish Bowman and Kurt Schwehr.

#### 5.4.2082 (May 24, 2013)

Configure.cmd: Added -DBYTESWAPPED to the recommended pre-options for the
configure script on Macs.

MBF_EM710RAW (format 58) and MBF_EM710MBA (format 59): Added EM2045 to the
list of supported Kongsberg multibeam sonars (also known as the EM2040D).

#### 5.4.2081 (May 23, 2013)

Build System: Have implemented an autotools-based build system with a
configure script, following on the initial work by Bob Covill and others.
The man page and web page documentation have been moved into the source
tree. The old install_makefiles build system has been updated to still work.

---
### MB-System Version 5.3 Releases and Release Notes:
---

- Version 5.3.2053       April 4, 2013
- Version 5.3.2051       March 20, 2013
- Version 5.3.2042       March 12, 2013
- **Version 5.3.2017       March 3, 2013**
- **Version 5.3.2013       January 29, 2013**
- **Version 5.3.2012       January 25, 2013**
- **Version 5.3.2011       January 17, 2013**
- Version 5.3.2010       January 14, 2013
- **Version 5.3.2009       January 10, 2013**
- **Version 5.3.2008       January 6, 2013**
- Version 5.3.2007       January 5, 2013
- Version 5.3.2006       January 4, 2013
- Version 5.3.2005       December 31, 2012
- Version 5.3.2004       December 12, 2012
- Version 5.3.2000       November 14, 2012
- Version 5.3.1999       November 13, 2012
- Version 5.3.1998       November 6, 2012
- Version 5.3.1994       October 27, 2012
- Version 5.3.1988       September 29, 2012
- Version 5.3.1986       September 12, 2012
- **Version 5.3.1982       August 15, 2012**
- Version 5.3.1981       August 2, 2012
- **Version 5.3.1980       July 13, 2012**
- **Version 5.3.1955       May 16, 2012**
- Version 5.3.1941       March 6, 2012
- **Version 5.3.1917       January 10, 2012**
- **Version 5.3.1912       November 19, 2011**
- **Version 5.3.1909       November 16, 2011**
- **Version 5.3.1907       November 9, 2011**
- **Version 5.3.1906       September 28, 2011**

---

#### 5.3.2062 (May 17, 2013)

Mbprocess: Fixed a couple more mistakes on lines 5659 and 5662 in mbprocess.c.

#### 5.3.2061 (May 16, 2013)

Perl macros: Renamed all perl source files in mbsystem/src/macros by removing
the *.pl suffix. This is another change to allow use of the GNU autotools for
building MB-System. The easy way for automake to handle executable scripts is
to just copy them to the bin directory; renaming the scripts is harder to set
up.

#### 5.3.2060 (May 14, 2013)

Mbsvplist: Added -N option to limit the number of SVP profiles that can be
output. (contributed by Suzanne O'Hara)

#### 5.3.2059 (May 14, 2013)

Mbprocess: Fixed bug in mbprocess in which angle rotation calculations mixed
degrees and radians when attitude is merged as part of an external navigation
stream. (Contributed by Bob Covill)

Mbsvplist: Added -T option to output CSV delimited table
(contributed by Suzanne O'Hara)

#### 5.3.2056 (May 7, 2013)

Formats 221 and 222: Added empty i/o module files to ultimately support two
new formats, both handling data from SEA SWATHplus interferometric sonars:
    MBF_SWPLSSXI - 221
    MBF_SWPLSSXP - 222
The new files include:
    mbio/mbsys_swathplus.c
    mbio/mbsys_swathplus.h
    mbio/mbr_swplssxi.c
    mbio/mbr_swplssxp.c

#### 5.3.2055 (May 7, 2013)

Many files: fixed issues that result in compiler warnings.

Mb7k2ss: Fixed problem that overwrote the first extracted sidescan line.

Mbgrid: Added gridding algorithm 6, called footprint weighted mean. This
differs from algorithm 5, called footprint slope weighted mean, in that it
omits the use of the local slope, and thus requires only a single pass
through the data.

Format 121 (GSF): Added fix from Christian Ferreira to reset the
depth_corrector value to zero if necessary

#### 5.3.2053 (April 4, 2013)

Mb7k2ss: Fixed line breakouts so that the first line is output separate from
the second.

Formats 162, 163, 168, 169 (text xyz variants): Fixed i/o modules to handle files
with leading white space before the first column.

Mbset: Added -N option to turn off merging of navigation from MBnavadjust and
also remove the *.na0 files.

Mbgrid, mbmosaic, mbm_grid: Fixed documentation descriptions of the options
controlling the spline interpolation, particularly the tension.

Mbm_grdtiff: Fixed the image display program called in the tiff-creating
script created by mbm_grdtiff.

Mbdatalist: Recast the output format for the -S option. One now gets a single
line of output for each file unless the -V option is also specified.

#### 5.3.2051 (March 20, 2013)

Formats 58 and 59 (mbf): The calculation of "sidescan" from raw backscatter
samples has been improved. The sidescan can now be successfully
recalculated by mbprocess following application of bathymetry edits.

Mbprocess: Recalculation of Konsberg multibeam sidescan now enabled for
formats 58 (mbf_em710raw) and 59 (mbf_em710mba) with command
mbset -PSSRECALCMODE:1.

Mbedit: soundings originally flagged by the sonar now return to that
state if they are unflagged and then reflagged interactively.

Mbgrdviz: Disabled "goaway" buttons in dialogs to minimize crashes.

Mbeditviz: Disabled "goaway" buttons in dialogs to minimize crashes.

Mbm_grdplot: Updated macros to derive system defaults from mbdefaults.

Mbm_grdtiff: Updated macros to derive system defaults from mbdefaults.

Mbm_histplot: Updated macros to derive system defaults from mbdefaults.

Mbm_grd3dplot: Updated macros to derive system defaults from mbdefaults.

Mbm_vrefcheck: Updated macros to derive system defaults from mbdefaults.

Mbm_plot: Updated macros to derive system defaults from mbdefaults.

#### 5.3.2042 (March 12, 2013)

MBkongsbergpreprocess: Fixed calculation of transmit time for sector subpings.

Format 58 (mbf_em710raw): Improved translation of bottom pick parameters to
beam flags.

MBgrdviz: Added export of routes to Hypack lnw format and to degrees + decimal
minutes format.

#### 5.3.2017 (March 3, 2013)

Mb7k2ss: Program exits if topography grid specified but reading the file fails.

#### 5.3.2016 (March 2, 2013)

Mb7k2ss: Fixed plotting correlation functions.

Mbm_xyplot: Fixed handling of NaN values in input data - no longer includes NaN
inputs in sorting to determine min max.

#### 5.3.2015 (March 1, 2013)

Format 88 (mbf_reson7kr): Fixed some debugging print statements of hexadecimal
values.

Mbm_route2mission: Added command line control of multibeam sonar settings.

Mbprocess: Fixed handling of tide data with just one value.

Mbeditviz: Fixed calculation of corrected attitude and position for pings at
start and end of files.Previously badly mislocated pings happened unpredictably.

Mbfilter: Fixed handling of nonfatal read errors.

Format 94 (mbf_l3xseraw): Made storage available for sound speed profiles much
larger to handle some ridiculous data samples.

Mbauvloglist: Added code to output readable date and time values if desired.

mbm_xbt: Fixed code to more generally handle actual headers in Sippican MK12 data.

mbaux/mb_spline.c: Fixed extrapolation error in linear interpolation code.

Formats 162, 163, 168, 169 (xyz, yxz, xyt, yxt): Augmented code to handle text
triples with NaN values.

Mbotps: made /usr/local/otps the default location for the OSU Tidal Prediction Software (OTPS)

Format 21 (mbf_hsatlraw): Fixed failure to initialize the internal storage structure.

#### 5.3.2013 (January 29, 2013)

Format 94 (mbf_l3xseraw): Fixed bug causing memory faults in Linux when data
with large svp records are encountered. SVP records can now have as many as
8192 entries.

#### 5.3.2012 (January 25, 2013)

Mbkongsbergpreprocess: Fixed bug causing seg faults on Linux

#### 5.3.2011 (January 17, 2013)

Format 88 (mbf_reson7kr): Removed debug messages left in by mistake

#### 5.3.2010 (January 14, 2013)

Format 88 (mbf_reson7kr): Fixed reporting of angular beam widths, particularly
for pre-2009 data in which the alongtrack value was reported incorrectly.

Mbgrid: Changed the weighted footprint algorithm to correctly use the beamwidth
scaling parameter set with the -W option.

#### 5.3.2009 (January 10, 2013)

Format 88 (mbf_reson7kr): Fixed a bug introduced at 5.3.2004 in first-time
parsing of current Reson 7k data that caused erroneous flagging of some beams.

#### 5.3.2008 (January 6, 2013)

#### 5.3.2007 (January 5, 2013)

Mbkongsbergpreprocess: Fixed -O option to direct all output to a single file.
Mb7kpreprocess: Fixed -O option to direct all output to a single file.

#### 5.3.2006 (January 4, 2013)

Mbkongsbergpreprocess: Fixed -D option to put output files in the specified
directory.

#### 5.3.2005 (December 31, 2012)

Mbsvplist: Added -M option to control SVP printing. If mode=0 (the default), then
the first SVP of each file will be output, plus any SVP that is different from
the previous SVP. If mode=1, then only the first instance of each unique SVP will
be output, even through multiple files referenced through a datalist structure.
If mode=2, then all SVPs will be output even if they are duplicates (equivalent
to the -D option). The -D option is retained for compatibility.

Format 88 (mbf_reson7kr): MB-System now recognizes files with a *.7k suffix as
Reson multibeam data in format 88. Usually Reson data are logged to files with
a *.s7k suffix.

Mbm_route2mission: Updated the calculation of the number of photos to be taken
during a Dorado-class AUV bottom photography mission.

Formats 58 (mbf_em710raw) and 59 (mbf_em710mba): Added support for for the
"Extraparameters" datagram.

Formats 58 (mbf_em710raw) and 59 (mbf_em710mba): Changed the encoding of binary
values in the format 58 and 59 files written by MB-System to be little-endian
(Intel byte order). The Kongsberg format specification allows byte encoding to
be little or big-endian, and previously MB-System has consistently used big-endian.

Mblist: Fixed bug regarding the output of transmit pulse length values.

Mbprocess: Altered mbprocess so that input SVP files are checked for zero
thickness layers.

#### 5.3.2004 (December 12, 2012)

Mbsvplist: Added -S option to output surface sound speed from survey data rather

Mb7kpreprocess: Changed lever arm correction specified with the -D option to
involve three dimensions rather than just two.

Format 88 (mbf_reson7kr): Fixed so that mbctdlist and mbsvplist can output
surface sound speed values from Reson 7k data.

Format 88 (mbf_reson7kr): Fixed so that the storage of bathymetry acrosstrack and
alongtrack distance values in bathymetry (7006) records is correct. MB-System has
output incorrect 7006 records since the Reson 7k format (88) was first supported.
The error was that the acrosstrack and alongtrack distance values were transposed
relative to the format specification and the data output by the PDS2000 datalogger
(a reality that only became apparent when I finally had access to a sample of
PDS2000-logged data). The format 88 i/o module has been augmented to detect if
data being read derives from pre-fix versions of MB-System, and to fix the data
if necessary. The existence of this error and its fix should be invisible to
users, except that data written by pre-fix MB-System will probably import to
other software packages with the acrosstrack and alongtrack distances switched.

Mbmosaic: Fixed azimuthal priority weighting so that directional mosaicing is
more reliable.

#### 5.3.2000 (November 14, 2012)

Mbinfo: Changed mbinfo to gracefully handle the situation of reading a file that
has no data records while the -P option is specified (gracefully means not
seg faulting).

Mbmosaic: fixed bug in the use of the azimuth weighting factor.

#### 5.3.1999 (November 13, 2012)

Mbm_route2mission: Added multibeam pulse length as a command line argument.

Mbnavadjust: Added capability to solve for a z-offset model in which each
survey has a uniform or constant z-offset, and then reset all ties automatically using
those z-offsets.

Format 88 (mbf_reson7kr): Fixed bug that caused seg faults with pings that have no valid soundings.

#### 5.3.1998 (November 6, 2012)

Mb7kpreprocess: Added -C option to apply roll bias and pitch bias during preprocessing. Fixed
rotation calculations so that side-looking and up looking mapping data can be handled
properly.

Mbmosaic: added checks for valid topography grid file.

Mbprocess: Fixed rotation calculations so that side-looking and up looking mapping data
can be handled properly.

Mbm_route2mission: added handling of third specified altitude value in AUV missions.

Mbeditviz: Fixed rotation calculations so that side-looking and up looking mapping data
can be handled properly.

Formats 56 (mbf_em300raw) and 57 (mbf_em300mba): added support for asynchronous attitude
output, in particular by mbnavlist -K18.

#### 5.3.1995 (October 27, 2012)
#### 5.3.1994 (October 27, 2012)

Mbfilter: when filtering sidescan the output file now includes any bathymetry available in the
original file. The bathymetry can be used by mbmosaic for calculating apparent grazing
angles and data priorities.

Mbmosaic: substantially rewrote the calculation of apparent grazing angle for sidescan
data to be more reliable and to optionally use a topographic model supplied by a
topography grid (specified with the -T option).

Mb7k2ss: removed functions associated with laying out sidescan on a 3D topographic
model. These functions are now found in src/mbaux/mb_intersectgrid.c.

Format 88 (mbf_reson7kr) and mb7kpreprocess: added support for multibeam sidescan
derived from either the backscatter records or the snippet records. The snippets are
generally better, and are the default source when . The program mb7kpreprocess can be
set to generate the multibeam sidescan from either record type. The multibeam sidescan is stored using
MB-System-only "processed sidescan" records as an MB-System-specific extension
to the 7k format.

libmbaux: added functions to the mbaux library that locate the intersection of
arbitrary vectors from a sonar platform with a topographic grid. This code is
located in src/mbaux/mb_intersectgrid.c, and includes functions formerly found
in src/utilities/mb7k2ss.c. These functions are now used to lay sidescan out
on a seafloor topographic model and to calculate the apparent grazing angles
needed for angle-based priority calculation in mbmosaic.

Mbgrid: fixed -Cclip[/mode] option so that -C0/3 will in fact fully interpolate
the resulting grid.

Format 88 (mbf_reson7kr): fixed travel time and angle calculation for current
generation data using v2detectionsetup data records.

Mbgrid and mbmosaic: Added -Rfactor option that will allow users to specify that
the output grid extent will be the data extent expanded by a multiplicitive
factor. For instance, specifying factor = 1.1 means the grid is expanded 5% to
the west, east, south and north for a total expansion of 0.1 or 10%.

#### 5.3.1989 (October 4, 2012)

Mbm_grdplot & mbm_grdtiff: Fixed application of strict color table bounds in
mbm_grdplot and mbm_grdtiff.

mb7k2ss: Added -Q option so that sidescan lines can be constructed based on the
times starting and ending waypoints were reached.

Format 71 (mbf_mbldeoih): Fixed scaling of sidescan values to handle data with
small values.

Mbgrid and mbmosaic: Fixed the zgrid interpolation code, and also changed the
usage so that the interpolation stages will proceed much more rapidly. This is
now accomplished for large grids by iteratively calculating a smooth Laplacian model
for a low resolution grid and then resampling this onto the desired full resolution
grid using bilinear interpolation.

#### 5.3.1988 (September 29, 2012)

Format 71 (mbf_mbldeoih): Implemented automatic scaling of sidescan values to improve
fidelity of stored values to the original values.

MBeditviz: Fixed region selection to include topography min and max within that
region.

Reson 7k data (format 88, mbf_reson7kr): fixed calculation of beam angles from
7026 7k Detection records.

MBnavadjust: the tie (or block) view now honors the "With Selected Survey" and
"With Selected File" display modes.

MB7kpreprocess: Added control for the use or nonuse of attitude sensor time delay
data embedded in MBARI "Bluefin Navigation" records.

MB7k2ss: Added option to define sidescan line start and end points using a list
of times generated using mbroutetime (duplicating an option of mbextractsegy).

MB7k2ss: When extracting sidescan data from 7k data files to separate format 71 files,
use navigation, heading, sonar depth, and attitude data from multibeam data records
in the 7k data file (previously these values derived from asynchronous navigation,
heading, attitude, etc, records).

#### 5.3.1986 (September 12, 2012)

MBnavadjust now treats data from interferometric sonars different than data
from other sonars. When interferometric bathymetry is imported, the many soundings
are binned and averaged into 1-degree wide "pseudo-beams" to allow reasonable
(both visually and computationally) contouring.

Added MBIO function mb_sonartype() that returns the type of sonar associated
with some data, using the definitions:

- #define    MB_SONARTYPE_UNKNOWN        0
- #define    MB_SONARTYPE_ECHOSOUNDER    1
- #define    MB_SONARTYPE_MULTIBEAM        2
- #define    MB_SONARTYPE_SIDESCAN        3
- #define    MB_SONARTYPE_INTERFEROMETRIC    4

Added function to mbnavadjust that will estimate vertical offset between surveys
and then set relevant ties accordingly.

Fixed some plotting defaults for mbm_histplot.

Added -MXexcludepercent option to mblist to exclude a user defined
percentage of outer beams from mblist output. (contributed by Suzanne O'Hara)

#### 5.3.1982 (August 15, 2012)

Fixed significant issue in mb7kpreprocess and in Reson 7k format support in general.
The code was not handling the current raw detection data records correctly.

Fixed mbotps so that it handles requests for sound speed models on locations that
are dry land in the Topex mdoels more gracefully.

Fixed minor info printing issue with mbnavadjust (now doesn't report failure to
invert unless there is a failure to invert).

Improved performance of navigation and attitude merging for both mb7kpreprocess
and mbkongsbergpreprocess

Added new functionality to mbkongsbergpreprocess (contributed by Suzanne O'Hara):

- Added -D<outputDirectory> argument to allow users to set new directory for
    output files; original code always created output in input directory.
    This is a problem where users should not be modifying original directories.
    Using this flag allows the user to use the datalist option and is easier
    than copying the original mb58 data to a different directory or to using a
    script that loops through all the data using the -D option
    
- Added -C flag to output counts. Current code always outputs many rows of
    information that can be confusing. The default now is to work silently
    unless there is a problem.

#### 5.3.1981 (August 2, 2012)

Fixed problem with mbprocess in which the heading was unexpectedly replaced by course-made-good.
Now this can only happen with HEADINGMODE:1 or HEADINGMODE:2 in the parameter file.

Fixed error in the definition of the OMG HDCS format in mbf_omghdcsj.h
This fix provided by Bob Covill.

#### 5.3.1980 (July 13, 2012)

Augmented support for L3 XSE format (94) so that data from recent SeaBeam 3000 and SeaBeam 3050
multibeams can be processed.

Added option to mbinfo to generate output in XML (contributed by Christian Ferreira)

Augmented the i/o module for Reson 7k data to work with data files that do not
include the 7006 bathymetry records but instead include the raw detection 7027
records.

Altered mbnavlist so that longitude and latitude values are output with a
precision about equivalent to 0.1 mm, the same as mblist and mbinfo.

Altered mbprocess so that navigation shifts and offsets are applied to merged
navigation. Navigation derived from mbnavadjust is not affected.

Added new program mbkongsbergpreprocess, which reads data from a third generation
Kongsberg multibeam sonar (e.g. EM122, EM302, EM710),  interpolates  the asynchronous
navigation, heading, and attitude onto the multibeam data, and writes a new file
with that information correctly embedded in the multibeam  survey  data.  The  input
files  may  be  in  the  vendor  format  MBF_EM710RAW  (format id 58) or the MB-System
extended format MBF_EM710MBA (format id 59); the output  files  will  always  be  in
the  MB-System  extended  format MBF_EM710MBA (format id 59).

Updated GSF library to new release 3.04 from SAIC.

Removed local($[) = 0 initializations from all perl macros for compatibility with the
current version of perl (some macros were missed when this was done before 5.3.1955).

Fixed problem with mbprocess in which merged roll and pitch data were not applied
to the bathymetry unless the bathymetry was being recalculated by raytracing.

Added ability to change the read and write buffers for file i/o, initially just
for Reson 7k and Kongsberg current generation data. This allows one to tune for
the highest throughput file i/o for a given situation (e.g. 10 MB buffers achieve
5-10% faster throughput on the MBARI network).

Altered i/o module mbr_image83p.c for Imagenex DeltaT data so that if no roll or
pitch data are stored, the sonar is treated as if it is pointed down rather than
horizontal. Also fixed the module so that the profile tile angle parameter is
used correctly.

#### 5.3.1955 (May 16, 2012)

Removed ($[) = 0 initializations from all perl macros for compatibility with the
current version of perl.

Updated PROJ4 to the 4.8.0 release.

Added code for a new i/o module reading (but not yet writing) Benthos 1624 sidescan
data in the XTF format. This read-only i/o module has a format id of 211. This code
has been contributed by Jens Renken (MARUM/University of Bremen). The intent is to
complete the i/o module to allow full processing of the Benthos 1624 data.

Added a new macro, mbm_bpr,  to translate pressure data from a Seabird SBE53 pressure sensor
used as a Bottom Pressure Recorder (BPR) into tidal data that can be used to correct swath
bathymetry data.

Changed default Postscript viewer for Linux or Mac to be gv rather than Ghostview.

Added option to mbinfo (-X1) to generate output in the json format. If the -O option
is used to make metadata files, then the addition of -X1 will cause the output files
to be named "*_inf.json" rather than "*.inf". Suzanne O'Hara (LDEO) contributed this
improvement.

Augmented mbsvplist with option -C which causes the program to output the number of
unique SVPs in each file to stdout. Suzanne O'Hara (LDEO) contributed this
improvement.

Fixed multiple problems with mbcontour and the underlying contouring library that
were producing crashes in many circumstances.

Updated the MBARI AUV mission generator mbm_route2mission to reflect current operational
parameters for the MBARI Mapping AUV.

Applied fixes to the Marine Sonics sidescan i/o module (mbr_mstiffss.c) contributed
by Val Schmidt of UNH/CCOM.

Changed the color table in mbnavadjust to eliminate yellow contours, which are difficult to see.

Added output of potential temperature to mbctdlist.

Altered subbottom section plots generated by mbextractsegy. The first cut plots
generated when mbextractsegy is used to extract subbottom data into segy files are broken
into multiple section plots for long files (representing survey lines if extracted
according to a route file). Previously, all section plots for a given line had a time sweep
encompassing the data for the entire line. Now, if the total sweep exceeds 1 second, then
the sections plots will be generated using only the sweep required for each section alone.

Improved the robustness of calculating longitude latitude bounds for segy data using
mbsegyinfo.

Added capability to mbsegygrid to grid and plot subbottom sections based on distance between
the end points of a survey line. This approach to plotting subbottom sections removes the
impact of speed variations and deemphasizes data where the sonar platform moved slowly
or stopped.

#### 5.3.1941 (March 6, 2012)

Fixed sidescan filtering with mbfilter. The filtered sidescan output in
format 71 files had incorrect acrosstrack locations.

Fixed problems with sidescan generation for current generation
Kongsberg data (formats 58 and 59). The code previously tended to choose too
small of a pixel size, resulting in a sidescan swath narrower than the real
swath width.

Fixed swath contouring and track plotting by mbcontour and mbm_plot. Subtle changes
in the GMT pslib resulted in contours and tracks only partly plotting in some
Postscript devices. The MB-System code now explicitly chooses when to call
stroke operations in the Postscript, rather than leaving that up to pslib.

Fixed format 24 (mbf_hsldeoih) so that certain old files with extra bytes in some
comment records can be read correctly.

Added output of raw values from current generation Kongsberg data (formats 58 and 59)
to mblist.

#### 5.3.1937

Changed the resolution of navigation in fbt (format 71) files and
fnv files to be 1e-9 degrees, equivalent to about 0.1 mm. Similarly change
the navigation resolution in the output of mbinfo, and thus in inf files.
This affects mbr_mbldeoih.c, mbsys_ldeoih.c mbsys_ldeoih.h in src/mbio,
and mbinfo.c and mblist.c in src/utilities.

Add importing and display of "vector" data in mbview and mbgrdviz. The
vector files are GMT-style segmented files of lon, lat, topography value triples.
These are displayed as lines colored according to the value. Controls for
setting the color tables still have to be added.

Changed mbgrid so that any background (option -K) is calculated first,
before significant memory is allocated. This avoids crashes due to
attempted forks that overrun available memory.

Fixed beamwidth calculation for Reson 7k data. Fix in mbr_reson7kr.c
and mbsys_reson7k.c.

Fixed overflow during iterative search for beam angle values in
mbr_em710raw.c

Added capability to mbauvloglist to output angle values in degrees rather
than radians.

Added code to mbnavadjust to detect when the uncertainty ellipsoid of one
or more ties contains a zero value that will cause the inversion to fail.
In this case, the program prints out which ties are problematic, and declines
to calculate the inversion.

Fixed beamwidth values stored in fbt files.

Added JSON output option to mbinfo. This addition provided by Suzanne O'Hara of
LDEO/IEDA.

Added graceful exit to mbm_grdplot when a call to grdinfo fails. Fix provided by
Hamish Bowman of the University of Otago.

Bug fixes to mbr_mstiffss.c related to reading Marine Sonics sidescan data. This fix
provided by Val Schmidt of CCOM/JHC at University of New Hampshire.

#### 5.3.1917 (January 10, 2012)

Added preliminary support for HYSWEEP HSX format as MBIO format 201. Added program 
mbhysweeppreprocess to preprocess the HSX data.

Fixed bug in mb_lever() function in mb_angle.c.

GSF 3.03 update.

#### 5.3.1912 (November 19, 2011)

Formats 58 and 59 (third generation Kongsberg multibeam data):
Augmented code to handle bathymetry data in which beams are reported
as having valid soundings but actually have zero ranges and NaN
bathymetry, acrosstrack distance, and alongtrack distance values.

Formats 58 and 59 (third generation Kongsberg multibeam data):
Fixes to the handling of attitude ecords, particularly with regard
to writing the records.

#### 5.3.1909 (November 16, 2011)

Program mbnavlist:
Fixed attitude record output so that use of -K18, -K55, -K56, or -K57
results in output lines for all attitude records, even when position
or heading data are not available for interpolation.

Formats 58 and 59 (third generation Kongsberg multibeam data):
Fixed the i/o modules to successfully output attitude and netattitude
records identified as MB_DATA_ATTITUDE1,  MB_DATA_ATTITUDE2, or
MB_DATA_ATTITUDE3.

#### 5.3.1907 (November 9, 2011)

Program mblist:
Added output of beam bottom detection algorithm (amplitude or phase)
to mblist. One can now use Q and q as valid output values that can
be included in the arguments to the -O option.

Program mbnavlist:
Added ability to output navigation data keyed to primary or
ancillary attitude data. For instance, use of the -K18 option will
cause the mbnavlist output to occur for all attitude samples in the
primary attitude data stream. The timestamps will be those of the
attitude records, and any position, speed, or sonar depth values
requested will be interpolated onto the attitude timestamps.

Program mbm_route2mission:
Enabled the generation of AUV missions in which multibeam beamformed
data ("water column") are recorded in addition to bathymetry and
backscatter.

Program mb7kpreprocess:
Fixed integration of MBARI AUV INS log data into the processing of
Reson 7k data.

Program mbrolltimelag:
Fixed a bug that rarely produced a failure of time lag correlation
calculation.

Third generation Kongsberg data (formats 58 & 59:
Fixed handling of different attitude records, in that the code
now recognizes multiple sources of roll, pitch, and heave when
they appear in a datastream. The data records identified as the
primary attitude source are identified as type MB_DATA_ATTITUDE (18)
while ancillary records will be identified as MB_DATA_ATTITUDE1 (55),
MB_DATA_ATTITUDE2 (56), or MB_DATA_ATTITUDE3(57).

#### 5.3.1906 (September 28, 2011)

Program mbnavadjust:
Added -D option to invert foreground (normally black) and background
(normally white) colors in the interactive plots

Format 88 MBF_RESON7KR (Reson 7k multibeam data):
Fixed deallocation of MBF_RESON7KR data structures.

Program mb7kpreprocess:
Fixed some filtering code in mb7kpreprocess.

Program mbrolltimelag:
Added -K option to mbrolltimelag - this duplicates the new -K option
in mbnavlist and is used when mbrolltimelag calls mbnavlist to extract
the roll time series.

Program mbnavlist:
Augmented mbnavlist to allow extraction of data keyed to data records
other than navigation or survey data. A new -Kkind option allows
users to specify output at the times of attitude, heading, or other
record types.

Programs mbedit, mbeditviz, mbnavedit, mbclean, mbprocess:
Added ability to disable file locking using the program mbdefaults
and the .mbio_defaults file in the user's home directory.
If a user disables file locking by running
     mbdefaults -U0
then the programs mbedit, mbeditviz, mbnavedit, mbclean, and
mbprocess will not set new file locks and will ignore any existing
file locks. In short, a user can disable the entire file locking
mechanism in MB-System.

New macros mbm_multicopy, mbm_multidatalist, mbm_multiprocess:
Added three new macros authored by Christian Ferreira. These are
mbm_multicopy, mbm_multidatalist, and mbm_multiprocess. All three
are used to execute tasks on large numbers of swath files by starting
multiple processes in parallel. The mbm_multicopy macro accomplishes
copying of files from one format to another. The mbm_multidatalist
macro accomplishes the creation of ancillary files. The mbm_multiprocess
macro accomplishes processing with mbprocess. These all require the
Parallel-Forkmanager Perl module available from www.cpan.org.

Program mbclean:
Added flagging by acrosstrack distance to mbclean. Also added esf
file locking for compatibility with mbedit and mbeditviz, and
fixed handling of old edits.

Program mbgrid:
Fixed a problem with the footprint algorithm of mbgrid
that sometimes left holes that could not be filled by interpolation.

Macro mbm_route2mission:
Added ability to mix constant altitude and constant depth behaviors
within a single AUV mission to mbm_route2mission.

Format 88 MBF_RESON7KR (Reson 7k multibeam data):
Fixes to handling of asynchronous attitude data in format 88 (Reson s7k)
and calculation of time lag estimates.

Program mbextractsegy:
Adjustments to the default plots of segy data by mbextractsegy.

Macro mbm_route2mission:
Fixes to generation of MBARI AUV missions by mbm_route2mission.

Format 88 MBF_RESON7KR (Reson 7k multibeam data):
Fixed extraction of raw, asynchronous attitude data from Reson 7k
data using rollpitchheave records (e.g. from the MARUM AUV), which in
turn fixes the calculation of attitude time lag estimates using
mbrolltimelag.

Program mb7kpreprocess:
Fixed application of time lag model by mb7kpreprocess for the case
of Reson 7k data using rollpitchheave records (e.g. from the MARUM AUV).

Program mblist:
Added -UN option to mblist that ignores output of lines
associated with zero longitude or latitude values. This option
will be used by mbdatalist to create *.fnv files.

Format 71 MBF_LDEOIH (generic swath):
Provided a means to continue using the old definition of
swath format MBF_LDEOIH (format 71) for fbt files.
Users can now use mbdefaults to set the format 71 version that
will be generated when fbt files are created by mbdatalist and
mbprocess. If
     mbdefaults -Fold
is executed, the .mbio_defaults file in the user's home directory
will be altered so that all new fbt files are in the old format.
The purpose of this backwards compatibility is to allow users to
take advantage of the Fledermaus capability for editing bathymetry
in MB-System processing environments. This involved changes to mbcopy
as well as to the MBF_LDEOIH i/o module.

Program mbnavadjust:
Changed the swath data import code so that sections will be created even
when all beams have been flagged as bad. This is to allow surveys
to remain intact, with no breaks, because the concept of a continuous
survey is increasingly important in MBnavadjust. Also altered the
status displays and listings to show survey id along with file and
section id's.

Format 71 MBF_LDEOIH (generic swath):
Updated the definition of swath format MBF_LDEOIH (format 71),
which is used for the "fast bathymetry" or *.fbt files in MB-System
processing environments. The previous form of *.fbt files had a
serious limitation in that bathymetry from multibeams operated
near the seafloor in deep water did not represent the full
numerical resolution of those data. The updated format allows for
depth and distance resolution to 0.001 m even in the deep ocean.
Old *.fbt files are read transparently, but newly written files
will be in the new form.
IMPORTANT: In order to avoid compatibility issues, all users
operating on the same projects should upgrade to this version or
higher once one user upgrades.

Format 88 MBF_RESON7KR (Reson 7k multibeam data):
Updated support for Reson 7k data to include the "1022" record.
We still don't know what this is, but the code now reads and
writes it without complaint.

Program mbinfo:
Fixed mbinfo handling of swath files with no good data
(Thanks Suzanne O'Hara)

MBIO function mb_get_format():
Changed mb_get_format() function in mb_format.c so that formats
are inferred from parameter files if they exist.

Program mbnavadjust:
Supplemented informational output to stdout from MBnavadjust.

Format 71 MBF_LDEOIH (generic swath):
Started development of new version of format 71 (mbf_ldeoih).

Program mb7kpreprocess:
Fixed translation of beam quality values into MB-System beam flags
by mb7kpreprocess.

Program mbextractsegy:
Fixed calculation of line breaks by mbextractsegy.

MBIO function mb_get_format():
Augmented mb_get_format() in mb_format.c to look for the format id
value in mbprocess parameter files before trying to make sense of
file suffixes.

Program mbedit:
Fixed MBedit's handling of files not conforming to the MB-System
filename suffix convention.

Macro mbm_xyplot:
Allow users of mbm_xyplot to specify both axis annotation with the
-B option and axis labeling with the -L option.

Program mbeditviz:
Implemented workaround for MBeditviz crash problem on Poseidon Linux.
MBeditviz would shut down whenever a second map view was requested with
an Xserver error named GLXBadContextTag. Previously, the OpenGL rendering
within X11/Motif widgets has been implemented with the graphics calls
always sent through the X11 window server. I have now set the code to
allow direct rendering through hardware when that is possible. For reasons
I do not understand, this change results in MBeditviz no longer crashing
on my Poseidon Linux test machine.

Programs mbedit, mbnavedit, mbeditviz:
Fixed font issue for MBedit, MBnavedit, and MBeditviz by using courier
rather than monaco as a fixed-width font for the available file list
widgets.

Program mbprocess:
Added support for the "Rolling Deck to Repository" (R2R) navigation format
as both an MB-System format (format id 172) and an mbprocess navigation
merging format (NAVFORMAT=10)

Macros mbm_grdplot and mbm_grdtiff:
Modified mbm_grdplot and mbm_grdtiff so that the -Y option strictly enforces
the colormap min max bounds set with the -Z option.

Formats 132 MBF_EDGJSTAR and 133 MBF_EDGJSTR2 (Edgetech Jstar):
Fixed support for Edgetech Jstar files (formats 132 and 133) so that the
output of mb7k2jstar and mbprocess are compatible with Edgetech programs.

Programs mbedit, mbeditviz, and mbnavedit:
Added file locking to mbedit, mbeditviz, and mbnavedit. All three programs
can now load datalists and display lists of files available for editing.
These lists show whether the file has been previously edited and if the
file is locked. Locked files cannot be loaded or edited. As before, mbprocess
also locks files during processing and skips files that are locked by
other programs. The program mbdatalist can be used to detect (-S) and remove
(-Y) orphan file locks in files referenced by datalist structures.

Program mbprocess:
Fixed bug in mbprocess.c involving parsing of NMEA GGA strings when
reading in navigation for merging with survey data.

Program mbnavadjust:
Changed MBnavadjust to allow more file modes, in turn allowing
more control over which data has the most influence over the navigation
solutions. In addition to the previously existing modes (Fixed, Good, Poor),
surveys can now be set to FixedXY and FixedZ modes where the navigation
of the files so identified will have the specified coordinates fixed
(unadjusted) and the other coordinate(s) treated as Good. In particular,
this allowed us to simultaneously adjust navigation from overlapping
MBARI Mapping AUV and ABE surveys in which the Mapping AUV pressure depth
was clearly more accurate than the ABE vehicle depths. By setting the
MBARI data to mode FixedZ, we were able to force the solution to adjust
the ABE navigation to match the Mapping AUV vertical reference, while still
allowing lateral (XY) adjustments of all the AUV navigation.

Program mbnavadjust:
Changed MBnavadjust to output user, cpu, and time of changes to
project files and as comments to the adjusted navigation files. Also changed
mbprocess to handle comments in adjusted navigation files.

Program mbm_copy:
Fixed -C option of mbm_copy.

Format 192 MBF_IMAGEMBA (Imagenex DeltaT):
Fixed i/o module for extended format Imagenex DeltaT data (format 192) by removing code
that recalculated bathymetry unnecessarily.

Program mbdatalist:
Added -Y option to mbdatalist to remove any leftover lock files.

Parsing *.inf files:
Fixed bug in parsing file start and end times in *.inf files.

MBIO functions mb_defaults(), mb_env(), and mb_lonflip():
Changed mb_defaults(), mb_env(), and mb_lonflip() functions to always return
MB_SUCCESS status even when ~/.mbio_defaults file does not exist. Working with
system defaults should not be an error.

Program mbeditviz:
Changed mbeditviz_import_file() function in mbeditviz_prog.c to reset global
status to MB_SUCCESS on entry.

Program mbclean:
Incomplete implementation of Dana Yoerger's changes to mbclean. Not yet tested.

Program mbnavedit:
Increased verbosity of mbnavedit for -X option.

---
### MB-System Version 5.2 Releases and Release Notes:
---

- **Version 5.2.1880       December 30, 2010**

--

#### 5.2.1880 (December 30, 2010)

Augmented mbotps to output tide in both
     time_d tide
and
     year month day hour minute seconds tide
using a -Atideformat command line option.

Added new kluge processing option to mb7kpreprocess (-K2)
that zeros alongtrack angles. This fixes some recent sample
Reson 7k data.

Recast lever arm calculation due to roll and pitch rotations
in mb_angle.c.

More changes to the handling of current generation Kongsberg
data in mbr_em710raw.c.

Fixed handling of beam alongtrack distance values during bathymetry
recalculation by raytracing.

Improved beam info display in mbeditviz.

Fixed mbnavadjust recalculation of the 3D cross-correlation function
after changing the vertical offset.

Changed mbr_image83p.c, mbr_imagemba.c, and mbsys_imae83p.c so that
calculation of beam angles happens during the first read of the data.

Replaced strsep() with strtok() in mbr_edgjstar.c. This is to allow
MB-System to be more easily built on Solaris systems.

Fixed mbset so that it recognizes sidescan cutting commands (SSCUTNUMBER,
SSCUTDISTANCE, SSCUTSPEED).

---
### MB-System Version 5.1 Releases and Release Notes:
---

- Version 5.1.3beta1875  November 23, 2010
- Version 5.1.3beta1874  November 7, 2010
- Version 5.1.3beta1862  June 7, 2010
- Version 5.1.3beta1858  May 18, 2010
- Version 5.1.3beta1855  May 4, 2010
- Version 5.1.3beta1851  April 14, 2010
- Version 5.1.3beta1844  March 30, 2010
- Version 5.1.3beta1843  March 29, 2010
- Version 5.1.3beta1829  February 5, 2010
- **Version 5.1.2          December 31, 2009**
- Version 5.1.2beta15    December 30, 2009
- Version 5.1.2beta14    December 28, 2009
- Version 5.1.2beta13    December 28, 2009
- Version 5.1.2beta12    December 26, 2009
- Version 5.1.2beta11    Ausust 26, 2009
- Version 5.1.2beta10    Ausust 12, 2009
- Version 5.1.2beta09    Ausust 7, 2009
- Version 5.1.2beta08    Ausust 5, 2009
- Version 5.1.2beta06    July 2, 2009
- Version 5.1.2beta05    June 14, 2009
- Version 5.1.2beta02    March 13, 2009
- Version 5.1.2beta01    March 9, 2009
- **Version 5.1.1          December 31, 2008**
- Version 5.1.1beta26    November 18, 2008
- Version 5.1.1beta25    September 28, 2008
- Version 5.1.1beta23    September 19, 2008
- Version 5.1.1beta21    July 20, 2008
- Version 5.1.1beta20    July 10, 2008
- Version 5.1.1beta19    June 6, 2008
- Version 5.1.1beta18    May 16, 2008
- Version 5.1.1beta17    March 21, 2008
- Version 5.1.1beta16    March 14, 2008
- Version 5.1.1beta15    February 8, 2008
- Version 5.1.1beta14    January 15, 2008
- Version 5.1.1beta13    November 16, 2007
- Version 5.1.1beta12    November 2, 2007
- Version 5.1.1beta11    October 17, 2007
- Version 5.1.1beta10    October 8, 2007
- Version 5.1.1beta5     July 5, 2007
- **Version 5.1.0          November 26, 2006**
- Version 5.1.0beta4     October 5, 2006
- Version 5.1.0beta3     September 11, 2006
- Version 5.1.0beta2     August 9, 2006
- Version 5.1.0beta      July 5, 2006

---

#### 5.1.3beta1875

Altered -P option in mbsvplist. Previously this option (which turns on
bathymetry recalculation by raytracing in mbprocess using the water sound
speed models extracted from the data files) set the raytracing to
correct the takeoff angles for the difference between the sound speed
used for beamforming (surface sound velocity or SSV) and the sound speed
at the sonar depth in the water sound speed model. Now, mbsvplist sets
mbprocess to leave the takeoff angles unchanged. This is more more
consistent with the expectation that raytracing through the original
sound speed model should yield values matching the original bathymetry.

Altered mbprocess bathymetry recalculation by raytracing to better handle
cases where large heave values bring the sonar array above the nominal
water line. In this case, a static heave offset is calculated, raytracing
is done from the top of the water sound speed model, and the heave offset
is added to the raytracing result.

Improved the autopicking function of mbnavadjust.

Fixed a bug in handling the per-beam heave values in current generation
Kongsberg data (formats 58 & 59).

Changed mbm_route2mission to allow command line argument control of AUV
speed during ascent/descent, survey lines, and transit lines. Also added
control of the "deltaDepthRestart" value controlling how far up the AUV
should float after an altitude abort before resuming the mission.

More changes to support of Kongsberg current generation multibeam
data in formats 58 and 59. As previously noted, the angles used to recalculate
bathymetry from raw travel times by raytracing are estimated by iteratively
seeking to match the original bathymetry reported by the sonar. These angles
are estimated when data are first read as format 58 and then embedded in
format 59 data (presumably when mbcopy is used to translate format 58 files to
format 59)for later use by mbprocess. The default algorithm matches the original
bathymetry to within about 0.1% altitude by calculating an effective heave for
each ping and takeoff angles for each beam. A second algorithm (which can only
be activated by uncommenting an #ifdef statement in mbr_em710raw.c) matches the
original bathymetry by modifying both the takeoff angles and the travel time
measurement - this achieves matching of the original bathymetry to about 0.02%
of altitude. Use of the second algorithm is not recommended because modifying
the fundamental observations (travel times) to match the sonar's calculation
is, well, unsatisfying and wrong. The bad option is there because I took the
time to code it to see how well it would work.

#### 5.1.3beta1874

The function mb_get_info() now properly applies the lonflip value. This
in turn allows mbgrid to infer correct bounds in situations where the
lonflip is important (e.g. data across the +/-180 degree boundary when
lonflip is -1 or 1).

Changed MBnavadjust so that an "Inversion Smoothing" value replaces a
no-longer-used "Inversion Precision" value. This value, accessible under
the Options dialog, sets the importance of smoothing in the adjusted
navigation model. The default is 4.00, and possible ranges are 0.10 to
10.0, where the smoothing penalty weight applied to the first and
second derivatives of the adjusted navigation perturbation is ten
raised to this power.

Added support for Kongsberg EM2040 multibeam in formats 58 and 59.

Changed MBnavadjust so that default settings for section length and
contour interval are appropriate for high resolution surveys such
as those produced by AUV's equipped with >100 kHz multibeams.

Fixed plotting macros mbm_plot, mbm_grdplot, mbm_xyplot, mbm_grd3dplot
so that the calls to display postscript graphics using gv in the output
plotting scripts scale plots to fit on the screen.

Fixed mbm_route2mission to use proper camera control when generating
mission scripts for the MBARI Benthic Imaging AUV.

Added -W option to set the desired swath width of sidescan output from
mb7k2ss.

Updated the i/o module supporting OMG HDCS (the John Hughes Clarke format)
to handle HDCS version 4. These mods contributed by Bob Covill.

Fixed mb7kpreprocess to check for and ignore repeated ancillary and
survey data records.

Update GSF code to version 3.02, released 28 September 2010.

Set MBeditviz to resolve format id's in output parameter files when
filenames do not follow known suffix conventions.

Added support for a number of new data records in the Reson 7k data format,
following the 19 June 2009 addendum to the 7k format version 1.00 specification.

Changed mb_malloc() calls in mb_format.c and mb_buffer.c to mb_mallocd() calls
for greater debugging capability.

Added some debugging statements to mbprocess.c.

Changed mbm_grdplot macro to use the variable names embedded in seismic section
GMT grid files generated by mbsegygrid.

Improved autopicking in MBnavadjust to the point where it is actually useful.
Also fixed bug that caused eventual seg faults when analyzing many crossings
in a single session.

Fixes to  Reson s7k (format 88) support allowing mbnavlist to use position
records as navigation channel 3. This in turn allows mbrolltimelag to work
with Reson 7k data collected by MARUM (University of Bremen).

Added file name and line output to debug messages in mbr_l3xseraw.c to aid
in later work to fully support the current XSE data format.

Set mbrolltimelag to only attempt to generate a variable time lag model
plot if more than one robust time lag values have been generated.

Updating in preparation for beta release version 5.1.3beta1874.

#### 5.1.3beta1862

Moved src/mbaux/mb_rt.c to src/mbio/mb_rt.c and made this
raytracing code part of libmbio rather than libmbaux.

Fixed deallocation of raytracing data in mbprocess.

Added source type flag (CW or chirp) definition to src/mbio/mb_status.h

Add mb_io_pulses() function definition to src/mbio/mb_io.h as a
pointer for functions in i/o modules that extract source type (CW or chirp)
for individual beams. Added mb_pulses() function calls to src/mbio/mb_define.h
and src/mbio/mb_access.c.

Added mbsys_simrad3_pulses() function to i/o module for current
generation Kongsberg (Simrad) data in src/mbio/mbsys_simrad3_pulses().

Altered i/o module for current generation Kongsberg (Simrad) data
so that bathymetry calculation using raytracing works correctly.
This involves src/mbio/mbr_em710raw.c and src/mbio/mbsys_simrad3.c.
The problem is that the current raw beam and angle datagram stores
travel times and angles uncorrected for motion and attitude. My
attempts to properly calculate the attitude and motion
compensation have not succeeded (as measured by succeeding in replicating
the original bathymetry when used with the original sound speed model).
This version achieves accurate estimation of the compensated angles
for each sounding by finding a ray (through iteration) that replicates
the original sounding position by raytracing through the original
sound speed model. The depth difference is stored as a per-beam heave
correction, and the angles are stored normally. This calculation is
done only on the raw data format 58. When mbcopy is used to translate
the data to the processing format 59, the compensated angles are stored
in extended bathymetry datagrams. This scheme suffices to allow full
processing of the data, but is not satisfying in that I clearly still do not
fully understand the raw data format

Fixed issues with a number of manual pages.

#### 5.1.3beta1860

Further changes to mbnavadjust:
- The inversion stops if it is diverging rather than converging on a navigation adjustment 
	model solution.
- The program will insure that all crossings have the later section second by flipping the 
	order of crossings if necessary while reading an old project.
- The program also resorts the crossings when it reads a project.

#### 5.1.3beta1858

Slight modification to mbm_grdplot map annotation scheme (degrees + minutes
for maps up to 4 degrees across where only degrees shown before for maps
wider than 1 degree).

Changes to mbm_route2mission to accommodate new capability of MBARI
Mapping AUV to record full water column data from the Reson 7125 multibeam.

Move mb_mergesort() function prototype from mb_esf.c to mb_define.h.

MBnavadjust augmented with capability to check for new crossings and
to recalculate overlap coverage of existing crossings after inversions.
Users can also toggle previously analyzed crossing to "unset" status.

MB7kpreprocess augmented to handle Reson 7111 data sample from NGDC.

Fixed incorrect listing MB_DATA defines in mb_status.h.

Added per-beam heave data to mbsys_simrad3 ping structure to support
bathymetry recalculation for EM710, EM302, EM122 data. Defined new
processed bathymetry record for use in format 59, and set code to
transparently read the old record and write only the new record.
Mostly fixed handling of attitude data in bathymetry recalculation.
There still seems to be a problem with handling heading data.

#### 5.1.3beta1855

Fixed error in beam angle calculation for third generation Simrad multibeam
data (formats 58 and 59, EM710, EM302, EM122) that made bathymetry recalculation
by raytracing badly wrong.

#### 5.1.3beta1851

Fixed problem where mb7kpreprocess made beams that should have been null
valid but flagged.

Fixed bug that caused mbclean to fail to actually flag some beams
identified for flagging.

Added button to zero all z offsets on crossings for cases where tidal
corrections have been made before data were imported into a mbnavadjust
project.

Fixed mbgetesf manual page.

Fixed mode control in mbgetesf so one can extract the complete beam flag
state from a swath file. MBgetesf is now used by MBeditviz to get the
original beam flag state of raw swath bathymetry when processed files
are read.

Fixed sorting of beamflag edit events in edit save file data as used by
MBedit, MBeditviz, MBclean, MBareaclean, and MBprocess. This fixes a
problem wherein some edits performed by MBeditviz were dropped by
MBprocess. Also, MBgetesf is now used by MBeditviz to get the original
beam flag state of raw swath bathymetry when processed files are read.

#### 5.1.3beta1844

Fixed yet another bug in MBnavadjust - this time getting the
importation of old project files correct and, more importantly,
getting the z-offset sign correct in the Naverr display.

#### 5.1.3beta1843

Updated mb7k2ss man page.

Fixed bug in mbrolltimelag regarding popen/pclose use.

Fixed bug in mb_process.c file locking.

Fixed mbotps man page.Fixed bug in MBeditviz and added hot keys for
editing (only partially successful because it's hard to reliably get
the keyboard focus onto the rendering OpenGL widget.

Fixed mbotps man page.

Augmented MBnavadjust to allow referencing high resolution bathymetry
(e.g. AUV surveys) to lower resolution bathymetry (e.g. hull mounted
multibeam surveys). The navigation of specified files (typically the
data collected from the surface where GPS is available) can be fixed
so that everything else floats and is adjusted relative to those data.

mbprocess - improved error reporting to show why files are not being processed.

mbmosaic - fixed aspects of the footprint calculation, particularly
fixing a bug that prevented footprints from being fully covered.

Added -S option to mbprocess for debugging file status values used to
determine whether processed data files are "out of date".

Greatly improved mbnavadjust by adding a interim solution for a smooth
navigation adjustment model fitting ties to fixed (immovable) data and
by making all of the internal crossing and tie conventions consistent.
MBnavadjust now outputs version 3.0 nvh project files, but will transparently
read and translate earlier version nvh project files.

#### 5.1.3beta1829

From now on beta releases will be named according to the corresponding
source archive revision in the MB-System Subversion source code archive.
This will allow us (and users) to more precisely track code changes relative
to the beta releases.

Fixed support of Reson 7k data (format 88) to work with MARUM
AUV data. Includes changes to mb7kpreprocess.

Fixed 64 bit issues with Simrad, Reson 7k, and L3 XSE data
(formats 58, 59, 88, 94).

Fixed 64 bit issues with mbnavedit, mbclean, and mbneptune2esf.

Added buttons to MBedit to immediately go to the start or end of the data.

Fixed sidescan beamwidths used by the Edgetech Jstar format i/o
modules (formats 132 & 133).

Fixed memory management errors in MBgrdviz and mbfilter.

Fixed more 64 bit  and memory management issues in MBeditviz and MBgrdviz.

Added a plot reset button and an ability to autoscale on unflagged soundings
only in the MBeditviz 3D sounding cloud display.

Fixed handling of site and route points far from the display view in MBgrdviz.

Put actual (but still incomplete) text into the MBeditviz man page.

Changed print format for unsigned long values from %ld to %lu to avoid copious
warning messages in Ubuntu.

--
### MB-System Version 5.1.2 Release Notes:
--

Fixed pixel calculation algorithm in mbmosaic. Previously, sidescan
data from each pixel were being treated as extending over a
larger area than is correct.

Resurrected program mbfilter with an new implementation. Allows
low pass, high pass, and contrast enhancement filtering of amplitude
and sidescan data. Implemented so that filtered data are stored
in ancillary files ending in *.ffa (amplitude) and *.ffs (sidescan).
The data type selection options of mbswath, mbm_plot, and mbmosaic
all now allow users to select filtered data.

Improved handling current generation Simrad multibeam data (e.g.
EM710, EM122) through formats 58 (MBF_EM710RAW) and 59 (MBF_EM710MBA).
There still seems to be a problem with calculating the takeoff angles
for recalculating bathymetry by raytracing, probably due to a problem
interpolating the correct roll and pitch values.

Changed processing kluge 004. Previously kluge 004 caused mbprocess
to not output survey data with time stamps prior to the last good ping.
Now the dropped data will have time stamps prior to or equal to that
of the last good ping.

Fixed problem reading and writing format 16 (MBF_SBSIOSWB) data on
little-endian systems.

Added support for new ROV Doc Ricketts navigation data as format 165.

Added a Gaussian mean smoothing algorithm to MBnavedit. This is primarily
intended for smoothing USBL or LBL based navigation of submerged platforms
(e.g. ROVs or submersibles).

Altered the install_makefiles perl script used to generate the makefiles
during installation of MB-System. The install_makefiles script now
automatically determines whether the local architecture is big or
little "endian". Consequently, the "BYTESWAPPED" parameter no longer
needs to be set in install_makefiles, and has been removed. The "GRAPHICAL"
parameter has also been removed. Now, install_makefiles builds the
graphical utilities only if the Motif libraries and header file
location are specified with the MOTIFLIBs and MOTIFINCDIR parameters.
Also, install_makefiles now allows users to specify the use of independent
installations of the GSF and PROJ4 libraries. By default, the versions of
these libraries distributed with MB-System will be built and used.

Fixed bug in mbedit in which the view mode switched spontaneously after
loading a new file and advancing the view buffer.

Improved efficiency of attitude interpolation when reading Simrad multibeam
data. This greatly improves the speed at which Simrad multibeam data files
are read and processed.

Fixed bug in mbm_grdplot which sometimes produces broken color tables.

Updated GSF library code to GSF release 3.01.

Fixed bug in EM710 support (format 59) involving netattitude datagrams.

Changed licensing from GPL version 2 to GPL version 3.

#### 5.1.2beta07

Fixed MB-System compatibility with GMT 4.5.0

Fixed mbps memory handling.

MBgrdviz now displays ping/shot numbers when navigation is picked.
MBextractsegy now embeds line numbers into the output segy files.

#### 5.1.2beta08

Fixed mbauvloglist to work with all MBARI AUV logs.

Fixed mbm_route2mission so that the AUV mission segment duration always
corresponds to the actual mission segment length.

Added file locking to the mbprocess system. Now, when mbprocess starts
working on a swath file, it creates a *.lck file parallel to the swath file
and deletes the *.lck file when processing is complete. Other instances of
mbprocess will skip a locked file. This allows users to run multiple instances
of mbprocess on multiple machines on the same datalist structure. This
crude sort of parallel processing can greatly speed up reprocessing of
large datasets. This locking functionality will be extended to the processing
tools mbedit, mbeditviz, and mbnavedit in the future.

#### 5.1.2beta09

Fixed bug in SeaBeam 2112 support that misplaced some sidescan data
on little-endian machines.

Fixed the mbview library so that MBgrdviz will enable display of routes,
sites, and navigation on all open windows when such data is loaded into
one of the windows.

Fixed cause of frequent MBgrdviz crashes when displaying multiple windows.

Implemented timed background plotting in MBgrdviz so that full resolution
displays automatically appear within a few seconds of the end of mouse
interactions. Previously one had to click the "Full" button to get a full
resolution view. At this point, the redisplay fails to happen occasionally.

Greatly increased speed of reading third generation Simrad data (formats 58 & 59,
EM710, EM302, EM122).

#### 5.1.2beta11

Fixed mb7k2ss to avoid creating shadow zones in the extracted sidescan.

Fixed support for dual-head Simrad EM3002 data (formats 56 and 57).

Changed mbdatalist so that the -Z option (create datalistp.mb-1 datalist
file referencing an input datalist with the $PROCESSED tag set) can be
executed in conjunction with creating ancillary files with the -O or
-N options.

#### 5.1.2beta12

Updated proj library to 4.7.0 release. If the installing user chooses to
use the proj distributed with MB-System, then the programs proj and geod
will now be built and installed in the bin directory.

Rooted through the entire codebase fixing obvious failure points for
64-bit compilation. Most of the issues identified so far relate to
storing address values in variables declared as "int".

Completed moving the code base into subversion hosted at Lamont by
first updating the subversion archive to 5.1.2beta11 and then committing
the copious mods related to the 64-bit cleanup.

Changed the suffix of the Perl source files in src/macros from
".perl" to ".pl".

Changed the section name for the MB-System man pages from "l" to "1"
for programs and "3" for libraries and functions. This is in line with
common practice and follows a similar change by GMT.

Modified support for Edgetech JSTAR sidescan/subbottom files (formats 132 & 133)
to work with a new data sample from GEOMAR. MB-System can now automatically
distinguish between low frequency (132) and high frequency (133) sidescan
data.

Modified support for Reson 7k multibeams (format 88) to work with a
new data sample from GEOMAR. Altered interpretation of initial beam quality
flags, improving initial beamflags.

Fixed problems with survey generation in mbgrdviz.

Improved read-only support for XTF format Reson 8XXX data
(format 84 MBF_XTFR8101), but still don't have time stamping of
attitude data correct.

Augmented edit save file format and beam flag handling in order to deal
successfully with multiple head multibeams that produce multiple pings
with identical time stamps. This affects mbprocess, mbedit, mbeditviz,
mbclean, and mbareaclean.

Added program mbotps to generate open ocean tidal models at specified
times and locations using the Oregon State Tidal Prediction Software
(OTPS) package. This program will build whether OTPS is installed or
not, but will only work if the OTPS programs are installed and in the
user's path. The OTPS predictions are based on global barotropic inverse
tidal solutions obtained with OTIS and available for download at:
     http://www.coas.oregonstate.edu/research/po/research/tide/

Added program mbsegypsd to calculate sonograms from segy time series data.
Sonograms are 2D displays of power spectral density (PSD) functions (y-axis)
versus time (x-axis). One PSD is calculated for each trace in the segy file.
This program requires linking with the FFTW (Fastest FFT in The West) package.

#### 5.1.2beta13

Fixed many more issues relating to clean compiles on 64 bit machines.
In particular, store GSF and netCDF data stream id's in their own
int-size variables rather than a pointer-size FILE variable, and
declare mbview instance parameters as size_t rather than int so that
passing these values through Xt event notify function calls as pointer
values is clean. Also changed casting of pointer values to long for
debug printing so that the pointer values are now casted to size_t
values. This should allow for compatibility with Windows 64 bit builds,
as Windows 64 bit C has a different type model than the rest of the
universe (e.g. long = 32 bit on Windows but long = 64 bit for gcc).

#### 5.1.2beta14

Fixed a few more issues relating to clean compiles on 64 bit machines.
We're iterating towards a working version by getting problem reports
from people like Hamish Bowman, Bob Arko, and Bob Covill.

#### 5.1.2beta15

Fixed EM3002 support to reliably detect whether data comes from a single
or double head sonar (formats 56 & 57).

Fixed problem with EM710 support (formats 58 & 59).

#### 5.1.2

Incorporates all changes listed above.

Fixed memory management bug for formats 56 and 57 (Simrad EM3002 etc).

---
### MB-System Version 5.1.1 Release Notes:
---

Fixed longstanding error in src/mbio/mb_angle.c in the application
of roll and pitch angles. Previously, the pitch rotation was applied
first, which is incorrect, but only produced obvious errors with
large pitch values. Now roll is applied first, and the translation
between sonar coordinates and raytracing coordinates is correct.

Ping number, and more importantly for seismic data, shot number
annotation of navigation tracks is now supported by mbm_grdplot.

Improved handling of navigation plotting and annotation by
mbcontour, mbm_plot, and mbm_grdplot. It is now easier to specify
time, ping number, and filename annotation of navigation tracks.

Major modifications have been made to MBnavadjust. MBnavadjust
now picks offsets in z (depth) as well as x (longitude) and
y (latitude). An autopicking algorithm has been implemented,
and a display of the optimal navigation adjustment model added
as well.

The acrosstrack view of MBedit now shows the real alongtrack
positions of the soundings.

Fixed bug in mbsys_gsf.c that incorrectly calculated the alongtrack
distance of sidescan samples in "snippet" sidescan data contained in
GSF format (121) multibeam data. On occasion this bug produced
egregiously wrong alongtrack values.

Fixed bug in mbgrid that caused failure to write Arc Ascii grids
with option -G4.

Augmented i/o module for XSE format (94) to support current version
of SeaBeam 2112 sonars on WHOI ships. This data format now has
an MB-System extension to its multibeam records that includes
interpolated navigation values. Previously only asynchronous
navigation was handled.

Fixed bug in old Simrad i/o module regarding EM121A data.

Added prototype of MBeditviz, a tool that combines 3D bathymetry
editing and patch test capability.

MBeditviz can be started from MBgrdviz. Any selected files (using
navigation selection) will be loaded.

Fixed further issues with the XSE format i/o module.

Added swath file copy function to mbdatalist.

Fixed calculation of grazing angles in mblist by adding sonar
depth to the calculation.

Added some additional large format page sizes to the plot macros
mbm_plot, mbm_grdplot, mbm_grd3dplot, mbm_xyplot, and mbm_histplot.

Added mblist capability to output tables using column delimiters
other than tabs (e.g. commas to make csv files).

Modified mbnavedit so that any nav points that repeat previous lon
and lat values will be automatically flagged as bad.

Fixed footprint calculation in mbmosaic, correcting problems in
sidescan mosaic creation.

Altered mbm_utm to work with comma delimited input data as well as
white space delimited data.

Updated proj library to current version 4.5.0.

Updated gsf to the current version 2.07.

Sidescan extracted from MBARI Mapping AUV data can now be laid out
on a topography grid rather than laid out with a flat bottom
assumption (mb7k2ss).

The sidescan and amplitude correction scheme (mbbackangle & mbprocess)
can now use a topography grid to calculate grazing angles.

Altered several programs so that sidescan data can have valid zero or
negative values. Stopped applying a shift to Simrad sidescan and amplitude
values to force them to be positive.

Added decimation feature to mblist, mbnavlist, and mbsegylist. Also added
and/or fixed the delimiter, segment, and binary output features for all
three listing programs.

Added mbcopy capability to merge bathymetry and beam flags from a third
"merge" swath file. This is a Gordon Keith contribution.

MB-System programs will now recognize filename suffixes of the form
".MB***" as well as ".mb***". Capitalized versions of many vendor
format suffixes are also supported.

Fixed error in mblist manual page.

Fixed mbswath handling  of time gap errors that made plotting of
single beam data problematic.

Fixed problem with processing mgd77 data. Can now use mbedit to process
single beam echosounder bathymetry.

Made checking for data min maxes and bounds more robust to improve
parsing through large databases.

Added some generic gain values to mblist as part of the "raw" list.
To do this, added mb_gains() function to MBIO. This is currently
defined for SeaBeam 2112, Simrad, and Reson 7k multibeams.

Added new program mbabsorption to calculate the sound absorption of
seawater as a function of salinity, pH, temperature, depth, and
frequency.

Changed macro mbm_grdplot so that the -T option causes the coastline
to be drawn without grayscale filling of dry areas. To obtain the
previously default behavior, add -MTG128.

Added support for newer Simrad multibeam data (e.g. EM710) in
vendor format MBF_EM710RAW (format id 58) and processing
format MBF_EM710MBA (format id 59)

Updated format MBF_OMGHDCSJ (151), which supports the John Hughes
Clark HDCS (SwathEd) format, to handle all of John's "version 3"
data. John's "version 4" format is not yet supported.

Added calculation and use of three dimensional covariance in
the xyz nav offsets used by mbnavadjust.

Added processing kluge006 to mbprocess. This "kluge" allows users to
change the sonar draft value without changing the calculated bathymetry.
This fixes a problem in which Atalante Simard data were exported by
Caris into GSF with an incorrect sonar draft.

Added program mbtime to allow command line conversion between calendar
times and unix time values.

Fixed mbprocess so that changes to the sonar depth/draft derived from
mbnavadjust are output to the processed data. Previously the bathymetry
was corrected, but not the sonar depth/draft.

Fixed formats 58/59 to support EM302, EM122 in addition to EM710. Also
supported "network attitude" datagram as source of attitude.

Changed mbnavadjust inversion to use simplistic iterative relaxation
rather than a full matrix solver. This targeted solver is faster and
avoids some bad behavior around survey starts and ends.

Fixed mbedit scaling for swath widths less than 6 m.

Added formats 191 and 192 to support Imagenex Delta T multibeams.
Format 191 supports the 83P vendor format and format 192 is an
extended processing format. This format also supports data from
the Odom ES3 multibeam sonar.

Lengthened filename char arrays in mbedit, mbnavedit, and mbvelocitytool
to prevent possible overflows with large paths.

Updated the GSF code to new GSF version 2.09

Fixed support of UNB OMG HDCS format 151 to handle situation where
ancillary sidescan files are missing.

Added new program mbctdlist to allow mblist style text output of
CTD data from swath files. Initially relevant only to Reson 7k format data.

Applied patches to mbgrid and mbmosaic to handle lonflipping of bounds in
projected coordinates.

Added format 26 to support Hydrosweep DS data format used by SOPAC.

Fixed support for EM302 sonars.

Augmented mbgrid footprint gridding algorithm. When used with the -F5
option, mbgrid now does a first pass, low resolution grid to provide
a local slope estimate. During the second pass, final gridding,
individual beam footprints are tilted to reflect the local slope,
increasing the high-resolution fidelity of the resulting topographic
model.

Enhanced the patch test capability of mbeditviz. MBeditviz can now be
used to model time lag as well as roll, pitch, and heading bias. In order
to use the time lag function, users must place files parallel to each
swath file containing time series of attitude, heading, and sonardepth.
These files contain the full asynchronous times series for heading,
sonardepth, roll, and pitch and the synchronous time series for roll
and pitch (asynchronous means the raw sensor data sampled more frequently
than the sonar ping rate, and synchronous means the sensor data sampled
at ping times).
Each time series file uses epoch times in seconds as the first column.
These files are:
    *.ath - asynchronous heading - time heading
    *.ats - asynchronous sonardepth - time sonardepth
    *.ata - asynchronous attitude - time roll pitch
    *.sta - synchronous attitude - time roll pitch
Asynchronous data are not available in all formats. When available, the
asynchronous data can be extracted using mbnavlist. The synchronous
attitude can be extracted using mblist.

Added support for EM12D data in the Caraibes netcdf form as format 76.
Contributed by Gordon Keith.

Removed a number of obsolete programs and macros from the distribution.
The following are no longer distributed with MB-System:
     mbanglecorrect
     mbbackangleold
     mbbath
     mbcleanold
     mbeditold
     mbfilter
     mbgetmask
     mbmask
     mbmerge
     mbm_dslnavfix.perl
     mbm_fmtvel.perl
     mbm_vrefcheck.perl
     mbm_rollerror.perl
     mbnaveditold
     mbsmooth
     mbtide
     mbunclean

---
### MB-System Version 5.1.0 Release Notes:
---

The version 5.1.0 release of MB-System contains both bug fixes
and new capabilities relative to the 5.0.9 release.

A typo in the mbgrid man page was fixed.

A catastrophic error in the i/o module for the MBF_ASCIIYXZ
format was fixed.

The proj library was updated to use code from the Proj 4.4.9 release.

The proj and GSF libraries internal to MB-System have been
renamed libmbproj and libmbgsf to avoid name conflicts with
proj and gsf in package managers like fink for MacOsX.

Fixed mbprocess problem with per-beam heave values when applying
rotational bathymetry correction - previously did not initialize
heave values for non-null but flagged beams.

A minor change to mbbackangle to output the slope correction
status (-Q) in the comments in the output file.

Altered mbbackangle so that it outputs at least one table,
even if there are no survey pings in a file. This prevents
mbprocess from failing on data files with no survey pings.

Also altered mbbackangle so that it outputs a single global
correction table based on all of the input data. This can
be used for uniform correction of sidescan and amplitude
data.s

A new program mbrolltimelag calculates the cross-correlation
between roll data and the difference between the seafloor
slope and the roll. If there is a time lag in the roll data,
then the two series should have a cross correlation maximum
at a nonzero time lag.

New macro mbm_histplot for simple histogram plots.

MBgrdviz now has a profile display capability. Profiles can
be displayed and exported from two point picks, selected routes,
and selected navigation. The profile view is enabled from the
view menu.

Fixed problems with output of ESRI ARC ascii grids from
mbgrid and mbmosiac.

Added interactive control over the target of precision of the
navigation inversion in MBnavadjust.

Added output of Winfrog pts file to mbm_route2mission.

Added output of Winfrog pts file to mbgrdviz.

MBedit now automatically chooses appropriate acrosstrack and
vertical annotation intervals when files are opened.

MBextractsegy now will extract subbottom data to segy files
in sequential line files based on waypoints in a route file.
The program generates a plotting shellscript that will in
turn generate profile plots of the segy data. Long lines will
be broken up into multiple plots.

Updated manual page for mbm_route2mission.

A bug in mbgrdtiff has been fixed that mislocated the geoTIFF
images by 1/2 pixel, thanks to Gordon Keith.

The plotting macros mbm_plot, mbm_grdplot, mbm_xyplot,
mbm_3dgrdplot, and mbm_histplot all now use the current
GMT default parameter PLOT_DEGREE_FORMAT rather than
the old DEGREE_FORMAT.

Upgraded the mbsystem/gsf code to GSF version 2.0.4. Since the
libgsf code now has #ifdef statements allowing compilation
under MacOSX, the code contained in MB-System no longer has
modifications relative to the generic GSF releases.

Added support for Simrad EM710 data in formats 56 and 57.

Fixed byte count problem with comment records in format 94 (XSE data).

Added GMT_end() calls to all programs calling gmtlib and pslib functions
so that GMT "advisory file locking" does not system() calls to GMT programs.

Put (void *) casts into qsort() calls to avoid compiler warnings.

The macro mbm_grdplot now handles calls for a linear plot with
decreasing x values (e.g. using -Jx-0.01/20 to specify the projection).

A new edit mode called "grab" has been added to MBedit. In this
mode, the user drags a rectangle on the ping display. When the mouse
is released, all unflagged beams within that rectangle are flagged.

All MB-System programs that read or write grids have been altered
so that they will work with GMT 4.1.3 built in the default fashion
(i.e. GMT built with "advisory file locking" enabled).

Fixed mbgrdtiff so that it creates geographic GeoTIFF images with
the longitude bounds consistent with the user's default or
specified lonflip value.

MBlist can now print out values associated with the port-most and
starboard-most non-null beams and pixels. Use the special '=' or '+'
characters in the -O option.

Support was added for a new MBARI ROV navigation format (format id 170)

Support was added for SEGY seismic data as single beam format (id = 160).
Heading values are stored in an unused space in the trace header - this
is an MB-System specific modification that will only be found in segy
files generated by mbextractsegy.

Ping number, and more importantly for seismic data, shot number
annotation of navigation tracks is now supported by mbcontour and
mbm_plot.

Fixed problem reading some Simrad multibeam data with slightly broken
bathymetry records.

----
### MB-System Version 5.0 Releases and Release Notes:
---

- **Version 5.0.9          February 20, 2006**
- **Version 5.0.8          February 8, 2006**
- Version 5.0.8beta5     February 3, 2006
- Version 5.0.8beta4     February 1, 2006
- Version 5.0.8beta3     February 1, 2006
- Version 5.0.8beta2     January 27, 2006
- Version 5.0.8beta      January 24, 2006
- **Version 5.0.7          April 7, 2005**
- **Version 5.0.6          February 19, 2005**
- **Version 5.0.5          October 6, 2004**
- **Version 5.0.4          May 22, 2004**
- **Version 5.0.3          February 27, 2004**
- **Version 5.0.2          December 24, 2003**
- **Version 5.0.1          December 12, 2003**
- **Version 5.0.0          December 5, 2003**
- Version 5.0.beta31     April 29, 2003
- Version 5.0.beta30     April 25, 2003
- Version 5.0.beta29     March 10, 2003
- Version 5.0.beta28     January 14, 2003
- Version 5.0.beta27     November 13, 2002
- Version 5.0.beta26     November 3, 2002
- Version 5.0.beta25     October 15, 2002
- Version 5.0.beta24     October 4, 2002
- Version 5.0.beta23     September 20, 2002
- Version 5.0.beta22     August 30, 2002
- Version 5.0.beta21     July 25, 2002
- Version 5.0.beta20     July 20, 2002
- Version 5.0.beta18     May 31, 2002
- Version 5.0.beta17     May 1, 2002
- Version 5.0.beta16     April 5, 2002
- Version 5.0.beta15     March 26, 2002
- Version 5.0.beta14     February 25, 2002
- Version 5.0.beta13     February 22, 2002
- Version 5.0.beta12     January 2, 2002
- Version 5.0.beta11     December 20, 2001
- Version 5.0.beta10     November 20, 2001
- Version 5.0.beta09     November 6, 2001
- Version 5.0.beta08     October 19, 2001
- Version 5.0.beta07     August 10, 2001
- Version 5.0.beta06     July 30, 2001
- Version 5.0.beta05     July 23, 2001
- Version 5.0.beta04     July 20, 2001
- Version 5.0.beta03     July 19, 2001
- Version 5.0.beta02     June 30, 2001
- Version 5.0.beta01     June 8, 2001
- Version 5.0.beta00     April 6, 2001

---
### MB-System Version 5.0.9 Release Notes:
---

The version 5.0.9 release of MB-System is purely a bug fix
release, and includes only a few changes relative to the 5.0.8
release.

The macros mbm_grdtiff, mbm_grd2arc, mbm_grd3dplot, mbm_grdinfo,
mbm_grdtiff, mbm_grd2geovrml, and mbm_grdcut have been fixed to
work properly with the output of the GMT 4.1 version of grdinfo.

The code in src/mbio/mb_swap.c has been fixed so it will compile
using the Solaris cc compiler.

MBprocess had been fixed so that it will read navigation
formats using julian days properly.

MBnavedit has been altered so that speed and acceleration weighting
values in the smooth inversion function can be less than 1.0.


---
### MB-System Version 5.0.8 Release Notes:
---

The version 5.0.8 release of MB-System includes several changes
relative to the 5.0.7 release.

MB-System 5.0.8 requires GMT 4.1 in order to build successfully.

The format 75 (MBF_MBNETCDF) i/o module has been altered to
handle multiple pings with the same time stamp without breaking
the beam edit (edit save file) scheme, which depends upon
unique time stamps. When multiple pings with the same time
stamp are encountered, the subsequent pings have multiples
of 2 msec added so that each has a detectably unique time
stamp. This issue relates to Thompson Seafalcon II multibeam
data; this sonar collects five simultaneous acrosstrack swathes.
Since this is a deep water sonar, the maximum 10 msec time
addition should not introduce excessive error in navigation
or other aspects of the data.

The Edgetech Jstar format is now supported through the new
MB-System formats 132 and 133. The Jstar format is relevant
to Edgetech FSDW systems (and related sonar products). The
FSDW systems include chirp subbottom profiler and dual
frequency chirp sidescan sonar. Format 132 treats the low
frequency sidescan as survey data, and format 133 treats
the high frequency sidescan as survey data.

Incorrect trace scaling of subbottom and sidescan data
in the Reson 7k format (format 88) has been fixed.

A new program called mb7k2jstar has been added that extracts
Edgetech subbottom and sidescan data from Reson 7k format (88)
files and writes that data in Edgetech Jstar (132/133) format
files.

The comments in the install_makefiles script has been updated
to show the correct parameters needed to build MB-System on
a current Solaris system.

A feature to apply longitude and latitude offsets to navigation
data has been added to MBnavedit.

The program mbextractsegy can now extract subbottom profiler
data in segy format from both Reson 7k files (format 88) and
Edgetech Jstar files (formats 132 and 133).

MBprocess kluge005 has been defined to cause survey data
timestamps to be replaced by the timestamps of the corresponding
merged navigation records. This allows timestamps fixed using
MBnavedit to be inserted into processed data.

The program mbsegygrid can now apply a simple time-varying
gain to traces before gridding. This gain may begin at either
the start of each trace or at the seafloor arrival time. The
user may also set the length of time the gain is applied;
samples after the end of the gain window are zeroed.

The method for determining the best altitude value to be used
in correcting amplitude and sidescan data has been improved
in programs mbbackangle and mbbprocess.

The program mbgrid once again uses the Zgrid algorithm for
thin plate spline interpolation. The code allows for the GMT
Surface algorithm to be used instead by compiling with a
-DUSESURFACE compile flag.

The macros mbm_grdplot and mbm_grd3dplot have been altered so
that histogram equalization will work even if grdhisteq returns
a smaller number of valid intervals than requested.

The capability of plotting amplitude vs. grazing angle histograms
from mbbackangle results has been fixed for sidescan data.

A further significant architectural change was implemented for  release
5.0.8  in  order  to support data formats that have no explicit maximum
number of beams or pixels. The memory management of arrays used to hold
bathymetry,  amplitude,  and  sidescan data has been made dynamic. Now,
when data records are encountered that include larger numbers of  beams
or  pixels  than  will  fit  in  the arrays previously allocated, those
arrays are reallocated to the required size. This is handled  automati-
cally for all of the internal arrays used by MBIO functions. Of course,
applications using MBIO must  allocate  arrays  that  are  passed  into
functions  like  mb_read, mb_get_all, and mb_get to be populated by the
desired data. In order for these arrays to be managed dynamically,  the
application  must  first register each array by passing the location of
the array pointer to a new function called mb_register_array.

The program MBgrdtiff has been altered so that the geoTiff images
produced are more generally portable.

A program called mbrolltimelag has been written to analyze attitude
time lag. This macro extracts raw attitude and apparent slope values
from multibeam data, and then calculates the cross correlation between
roll and apparent slope over a specified range of time lags. If there
is a an attitude time lag, then the bathymetry collected over a planar
bottom should be dominated by a jitter that is correlated, with a time
lag, with the roll signal.

The format 56 (vendor Simrad multibeam format) i/o module has been
altered to support data logged on byteswapped platforms (e.g. Windows
Intel PC's.). The Simrad multibeam formats 56 and 57 now support
recently introduced raw angle/range and water column imagery datagrams.
These i/o modules also now handle cases where the beams listed in a
sidescan datagram do not exactly match the beams listed in the corresponding
bathymetry datagram differently than before. Previously the entire
ping would have been dropped. Now, the ping is preserved but the raw
sidescan samples are not used to generate binned sidescan.

The program mbdatalist has been augmented to allow users to easily identify
some problems with swath data files and the processing parameters
specified in parameter files. The -n and -o options are used to generate
ancillary files for all swath files referenced through a recursive datalist
structure. These options now invoke mbinfo with the -n option, causing
the "inf" files to include listings of easily identified data problems.
The -q option of mbdatalist now extracts and lists these data problems
as well as problems with the processing parameters.The possible data problems
include:

- No survey data found
- Zero longitude or latitude in survey data
- Instantaneous speed exceeds 25 km/hr
- Average speed exceeds 25 km/hr
- Sounding depth exceeds 11000 m
- Unsupported Simrad datagram

To populate the "inf" files of existing datalist structures with data problem
notices, use mbdatalist with the -n option.

The program mbvelocitytool now allows users to interactively set the
center as well as the range of the water sound speed model plot window.

Fixed mbm_plot so that it calculates reasonable plot bounds at high
latitudes.

The program mbset now accepts '=' as well as ':' as separators between
parameter names and values in -P option arguments (as suggested by
Bob Covill).

The install_makefiles script has been altered so that the editable
parameters are located towards the top of the file rather than below
the documentation of example settings for different operating systems.

The program mbareaclean now incorporates a mean filter as well as a
median filter (contributed by Gordon Keith).

The program mbmosaic will now mosaic grazing angle or acrosstrack slope as
well as amplitude or sidescan data (contributed by Gordon Keith).

The program mblist will now output some format specific values from
Simrad multibeams (formats 56 and 57). In particular, some
system parameters, raw amplitude values, and raw sidescan samples
may now be output (Contributed by Gordon Keith).

A new macro called mbm_makedatalist can easily generate a datalist
referencing all identifiable swath files in a specified directory.

There is a known but not understood bug in MBnavedit. When built on
SUSE 10 systems, use of the smooth inversion function causes the first
line of the output edited navigation to have NaN values for the
longitude and latitude.

---
### MB-System Version 5.0.7 Release Notes:
---

The version 5.0.7 release of MB-System includes several changes
relative to the 5.0.6 release.

MBprocess and MBset now support merging sonar depth
(or draft) from separate time series files. This is
controlled by the SONARDEPTHMODE, SONARDEPTHFILE,
and SONARDEPTHFORMAT mbprocess parameters.

A bug in mbgrid has been fixed that affected the footprint
gridding algorithm used with bathymetry from sonars on
submerged platforms.

MBedit has new view options. The default is the the
traditional waterfall view. Users may now also view the
soundings from an alongtrack view perspective and an
acrosstrack view perspective without static vertical
offsets between pings. The view mode is controlled from
the View menu and from keyboard macros (characters '2',
'3', and '4').

The 5.0.6 release mistakenly left the code in mbr_em300raw.c
in debug mode, causing copious stderr output when reading
raw Simrad data (format 56). This has been corrected.

Problems with the output in debug mode of mbr_em300raw.c and
mbr_em300mba.c have been fixed.

The handling of the tickinfo string in the plot macros
mbm_plot, mbm_grdplot, mbm_grd3dplot, and mbm_xyplot have
been fixed.

The orientation of the filename annotation by mbcontour
has been fixed, and control over that orientation has been
added to mbcontour and mbm_plot.

Fixed problem of uninitialized data in mbr_mbpronav.c.

Fixed problem with occasional incorrect scaling of sonar
depth in mbldeoih format (71) data.

Fixed problem in which sonar depth could be calculated
from implausible pressure values in some single beam
or navigation formats.

Improved handling of interpolated asynchronous data,
especially sonar depth, in Reson 7k data (format 88).

A capability to interpolate over repeated values was added
to mbnavedit.

Fixed a problem with the beam footprint gridding algorithm
in mbgrid that caused beam footprints to be miscalculated
for submerged sonars.

Fixed MBgrdviz crashes related to route data by fixing
problem with allocation and deallocation of route
arrays in the mbview library.

Moved tide correction to end of processing tasks so that
it doesn't mess up grazing angle calculations for amplitude
and sidescan correction.

Added option to mbm_grdplot allowing the user to specify
a separate grid file to be contoured. This code was
contributed by Gordon Keith.

---
### MB-System Version 5.0.6 Release Notes:
---

The version 5.0.6 release of MB-System includes several changes
relative to the 5.0.5 release.

The man page for mbprocess has been updated with full
documentation of the navigation formats supported for
merging by mbprocess.

The merging of heading and attitude data from navigation files
has been fixed.

The ability to merge attitude data from a separate file
has been added to mbprocess, and the mbprocess and mbset
man pages have been updated.

A problem producing ascii grids from mbgrid and mbmosaic
has been identified, and a fix suggested by Gordon Keith
adopted.

A problem with the -D option of mblist has been identified,
and a fix suggested by Gordon Keith adopted.

A new program called mbneptune2esf has been contributed by
Gordon Keith. MBneptune2esf  imports manual data flagging
performed using Simrad's NEPTUNE software and flags those
beams  in  the corresponding MB-System files.

A new program called mbauvnavusbl has been added to the
distribution. MBauvnavusbl reads a primary navigation file
(usually from a submerged platform swath survey) and also
reads secondary navigation (e.g. USBL fixes).  The program
calculates position offsets between the raw survey navigation
and the secondary navigation every 3600 seconds (10 minutes),
and then linearly interpolates and applies this adjustment
vector for each primary navigation position. The adjusted
navigation is output.

The ability to annotate tracklines on swath plots with
the swath filenames has been added to mbm_plot and
mbcontour. The annotation occurs at the beginning of the
data associated with each file. This option can be used
most simply by specifying -NF in mbm_plot. The suggestion
and initial implementation were contributed by Gordon Keith.

A problem with setting file paths in parameter files in
the different directories associated with recursive
datalists has been fixed. The nature of and fix to this
bug were determined by Gordon Keith.

Fixed makefiles to link libpsl.a with all programs making
libgmt.a calls. This was necessitated by changes to the
GMT4.0 release relative to the GMT4.0beta release.

Implemented latest GSF release (2.0.3).

Fixed, but not satisfactorily, a problem reading some older
EM3000 data with the current format 56 i/o module.

Added release version of simple grid visualization demo
mbgrdviz.

Improved the ability of mbgrid to embed background
datasets.

---
### MB-System Version 5.0.5 Release Notes:
---

The version 5.0.5 release of MB-System includes several changes
relative to the 5.0.4 release.

The program mbgrid can now obtain background data from GMT grid
files using grd2xyz as well as through raster databases using
grdraster. See the -Kbackground option documentation in the
mbgrid manual page.

The macro mbm_xbt has been substantially updated.

The -G option of mbinfo now avoids reporting zero starting
positions (it always ignored zero positions for the reported
data bounds).

Provides read-only support for Edgetech sidescan and subbottom
profiler data in the new Reson 6046 format (format id 88).

A new program mbextractsegy allows for the extraction of
subbottom profiler data into separate files in the SEGY
format (this can apply only to data formats that incorporate
subbottom data in with swath sonar data, and at present only
supports format 88).

A new program mbsegyinfo is a utility for reading a segy
format seismic data file and outputting some basic statistics.
The table generated shows the filename, data counts, navigation
totals, time and navigation of the first and last data records,
minimum and maximum data values, and the geographic bounding box
of the data.

A new program mbsegylist is a utility to output specified
header values from segy seismic data files to stdout.
The option -Ooutput_format is used to control the type and
order of values output. By default, mbsegylist produces
ASCII files in spreadsheet style, with data columns separated by
tabs. Alternatively, the output can be binary, with each field
represented as a double precision float (-A option).

A new program mbsegygrid generates grids from subbottom
profiler data (and seismic reflection data, and potentially
other seismic data) in the SEGY format. These grids can then
be displayed using GMT (through mbm_grdplot if desired).

The program mbm_plot now works properly when start and end times
are specified using the -MMB and -MME options.

A bug involving the handling of edit save filenames by mbset and
mbprocess has been fixed.

Errors in handling Simrad datagrams and edit save files on
byteswapped  machines (e.g. Intel or AMD processors) have been
fixed.

The program mbdatalist has a new option -Z which causes a
standard "datalistp.mb-1" file to be created. This is a
convenience file that applies the $PROCESSED flag to be
applied to the swath files referenced in a datalist named
"datalist.mb-1".

Problems with the creation of amplitude vs. grazing angle
correction tables using mbbackangle, and the use of those
tables by mbprocess, have been fixed. The default settings
for mbbackangle and amplitude vs. grazing angle correction
by mbprocess have been changed.

The default angle mode for raytracing has been changed so
that starting angles are adjusted using Snell's Law for the
difference between the SSV and the initial depth in the SVP.
This change affects mbvelocitytool, mbsvplist, mbset, and
mbprocess.

The program mbsvplist now has an option -P that not only
outputs SVPs in a swath file to individual ancillary SVP
files (as with the -O option), but also sets the first SVP
output file to be used by mbprocess to recalculate the
bathymetry.

Problems with the MGD77 format i/o module have been fixed
according to suggestions from Bob Covill.

--
### MB-System Version 5.0.4 Release Notes:
---

The version 5.0.4 release of MB-System includes several changes
relative to the 5.0.3 release.

All of the interactive tools (MBedit, MBnavedit, MBvelocitytool,
MBnavadjust) have been changed to require linking with the Motif 2.0
or later library (or compatible open source versions such as OpenMotif
or LessTif).

The MB-System distribution is now compatible with GMT 4.0b. There have
been minor changes to the pslib and gmtlib APIs, so it is necessary
to specify the linked version of GMT in the mbsystem/install_makefiles
script. Set:
    $GMTVERSION = "4.0";
if you are using GMT 4.0b, or set:
    $GMTVERSION = "3.4";
if you are still using GMT 3.4

MBnavadjust has a significant new feature in which the contours
displayed by the Nav Err window can be pre-generated. This greatly
increases the speed with which the bathymetry crossings can be
analyzed.

A "Flag View" feature has been added to MBedit, allowing users to
flag all of the beams in the current display. Key macros have also
been defined for both the "Flag View" and "Unflag View" buttons.

The raw Hydrosweep DS format (format 21) i/o module now estimates
travel times from the bathymetry when data files lacking travel time
records are read. This allows users to recalculate bathymetry by
raytracing even if the travel times are not recorded.

---
### MB-System Version 5.0.3 Release Notes:
---

The version 5.0.3 release of MB-System includes two bug fixes
relative to the 5.0.2 release.

We have fixed a bug in the i/o modules for Simrad multibeam
data (formats 56 and 57) that caused a failure to gracefully
handle unsupported datagrams on byteswapped systems (e.g.
Intel processors running Linux).

We have fixed a bug that caused edit save files to be incorrectly
read on byteswapped systems (e.g. Intel processors running Linux).

We have fixed a bug in the i/o modules for binary SeaBeam 2100
data (formats 42 and 43) that caused data to be written incorrectly
on byteswapped systems (e.g. Intel processors running Linux).

---
### MB-System Version 5.0.2 Release Notes:
---

The version 5.0.2 release of MB-System includes two bug fixes
relative to the 5.0.1 release.

We have fixed a bug in the i/o module for Elac Bottomchart data
in the XSE format (94) in which the sonar depth was added to
bathymetry values when new data files were written.

We have also fixed problems related to reading and writing
SeaBeam 2100 data in the binary formats 42 and 43.

---
### MB-System Version 5.0.1 Release Notes:
---

The version 5.0.1 release of MB-System includes two bug fixes
relative to the 5.0.0 release. The program mbgrid has been
fixed so that it compiles correctly under Red Hat Linux. The
program mbcopy has been fixed so that time and space bounds
are successfully applied to pings with a time gap error.

Also, the distribution now has a top directory name of mbsystem-5.0.1
rather than just mbsystem. This will allow users to unpack the
distribution in the target location without overwriting an existing
older MB-System installation. Users can then rename the directory to
mbsystem or create a soft link to mbsystem-5.0.1 named mbsystem
(e.g. ln -s mbsystem-5.0.1 mbsystem).

---
### MB-System Version 5.0.0 Release Notes:
---

The version 5.0 release 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 tools.

- 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.
- 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.

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.

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.
- 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 it is recommended that
    the data be copied to an extended format (57) that stores
    both bathymetry beam flags and processed sidescan. Format 57
    is also used for processing data from the current Simrad
    multibeam sonars.

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 new 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.