mbnavedit
Section:  MB-System 5.0  (1)
Updated:  3 June 2013 
Index


 
NAME

mbnavedit - Interactive navigation editor for swath sonar data.

 
VERSION

Version 5.0

 
SYNOPSIS

mbnavedit [-Byr/mo/da/hr/mn/sc
-D -Eyr/mo/da/hr/mn/sc
-Fformat -G -Iinfile -N -P -T -X -V -H]

 
DESCRIPTION

MBnavedit is an interactive editor used to identify and fix
problems with the navigation of swath sonar data.

In the default mode the edited navigation is output to
a file with the suffix ".nve" appended to the input swath
data filename. The program can also be operated
in a "browse" mode where no navigation is output.
If saved, the edited navigation can be merged
with the swath data using the program mbprocess, which
outputs a processed swath data file.
The mbprocess program is also used to apply
bathymetry edits, recalculate bathymetry, and apply
other corrections to swath bathymetry data. Users
may cause mbprocess to be run automatically by
specifying the -X option when starting MBnavedit.

In previous  versions of MB-System
(version 4.6.10 or earlier), MBnavedit
produced output swath data files directly by reading and
storing all of the swath data information in memory (including
non-survey data records). This approach limited the
amount of data that could be handled
at once, frequently requiring users to process files in
small pieces. The current version only stores
and outputs the navigation data.

Once the navigation
from a swath data file has been
read in, MBnavedit displays autoscaled plots of the longitude,
latitude, speed, heading, and sonar depth time series, along with a plot of
the time interval between navigation values. The user may select
outliers and interpolate over them or, in the case of heading or
speed data, replace the erroneous values with estimates derived
from "course-made-good" or "speed-made-good", respectively.
Data can only be selected and altered in a single
plot at a time (this avoids confusion and prevents mistakes).

The nature of the navigation data being edited depends upon the
data format. Some data formats include the navigation in the
same data records as the ping or survey data. This synchronous
navigation implies that either in the sonar or in later processing,
the raw navigation has been interpolated to yield values at the
same time stamps as the sonar pings. Other data formats do not
hold navigation values in the survey data records, and instead use
separate navigation records with different time stamps. This
asynchronous navigation requires that MBIO interpolate or
extrapolate the navigation as the survey data records are read.
For data formats with synchronous navigation, the navigation
values edited using MBnavedit are those in the survey data
records. For data formats with only asynchronous navigation,
MBnavedit displays and operates on the values from the
navigation records. The MBIO manual page includes a listing
of which type of navigation is used by the supported data formats.

For some data formats, the user can also
inspect plots of roll, pitch, and heaved
data to determine if the ship's vertical reference sensors
were working properly.

The edited data is usually output to a file, but the program
can be operated in a "browse" mode where no data is output.

 
SMOOTHING NAVIGATION


Three algorithms for obtaining and using smooth navigation models are
available. Replacing the original navigation with a smoothed
version can be advantageous in some cases of very noisy
navigation (typically from sonars on towed platforms or
submerged vehicles). The first smoothing scheme is the covolution
of a Gaussian kernal of user-defined time width with the data.
Users may select and flag outlier navigation points; any flagged
points are not used to calculate the Gaussian-weighted mean
navigation values.
The second approach is simple dead reckoning
from the initial position using the current (possibly edited)
heading and speed values. The dead reckoning navigation can also
incorporate user-specified longitude and latitude drift rates.
The third algorithm is an inversion for a smooth
navigation that minimizes
speed and acceleration while fitting the original navigation
in a least squares sense. The inversion weighting against
speed and acceleration are user specified, and only unflagged
navigation values are used in the inversion.

 
HANDLING BAD TIME STAMPS


The time interval plot allows
users to spot problems with time stamps and to change the
time stamps, if necessary. The most obvious time stamp errors
are multiple pings with the same time stamps (producing a zero
time interval value), or
sequential pings with decreasing time stamps (resulting in
negative time interval values). MBnavedit
provides two tools for dealing with zero or negative time intervals:
time stamp interpolation or deletion of the affected pings. Control
dialogs allow users to apply either to the entire buffer at once.
Time stamp interpolation may also be accomplished by selecting
the relevant values in the time interval display, and then
selecting interpolation.

If the navigation is
asynchronous, that generally means the time interval should be
constant since navigation systems are set to output values at
a uniform rate. A problem with the time stamps of asynchronous
navigation should produce spikes in both the time interval plot
and the speed-made-good plot, and can be solved by selecting
the offending point in the time interval plot and interpolating
to reset the time stamp.

If the navigation is synchronous with the sonar
pings, then the time interval will likely vary because the ping
rate for most sonars varies with the sonars altitude above the
seafloor. In this case, time stamp problems will
not produce spikes in the speed-made-good plot
because the navigation has been interpolated
using the existing time stamps. Time interval spikes may also
reflect problems with the sonar (e.g. occasional failure to ping
at the appropriate time) rather than erroneous time stamps.

 
AUTHORSHIP

David W. Caress (caress@mbari.org)




  Monterey Bay Aquarium Research Institute



Dale N. Chayes (dale@ldeo.columbia.edu)




  Lamont-Doherty Earth Observatory

 
OPTIONS

-B

yr/mo/da/hr/mn/sc



Sets the starting time for data allowed in the input data; pings
with times before the starting time will be ignored.
Default: yr/mo/da/hr/mn/sc = 1962/2/21/10/30/0.

-D


Starts up the program in "browse" mode. If a file is opened
in browse mode (either at startup or later), none
of the edited data will be output to a file. The default
is to output the edited data to a file.
-E


yr/mo/da/hr/mn/sc



Sets the ending time for data allowed in the input data; pings
with times after the ending time will be ignored.
Default: yr/mo/da/hr/mn/sc = 2062/2/21/10/30/0.
-F


format



Sets the format at startup for the input and output swath sonar data using
MBIO integer format identifiers. This value can also be set
interactively when specifying the input file.
This program uses the MBIO library and will read or write any swath sonar
format supported by MBIO. A list of the swath sonar data formats
currently supported by MBIO and their identifier values
is given in the MBIO manual page.
Default: format = 11.
-G


This flag causes MBnavedit to treat the Done button as
equivalent to the Quit button. This option is used when
MBnavedit is started automatically by some other process and
only a single file is to edited.
-H


This "help" flag cause the program to print out a description
of its operation and then exit immediately.
-I


infile



Sets the data file from which the input data will be read at startup.
This value can also be set interactively.  If the input file is named
using the MB-System convention of an ".mbXX" suffix (the XX
corresponds to the MBIO format id), then the output file name
will have an "e.mbXX" suffix. Otherwise, the output file will
be infile with ".ed" appended.
-N


Normally, all MB-System processing
programs embed comment records describing the processing actions
and parameters into output swath data files.
This flag, when used in conjunction with the -X flag,
causes MBnavedit to invoke mbprocess with it's
-N option. In turn, this causes mbprocess to
generate an output, processed swath data file without any
comment records.
-O


outfile



Sets the output data file, overriding the file naming conventions
discussed above in the -I option.
-P


Causes MBnavedit to load and work with navigation from
survey data records even if the data format uses asynchronous
navigation records. In this case, the only edits which will
actually be applied to the output data are changes to the
time stamps of the survey records.
-V


Normally, MBnavedit outputs information to the stderr stream
regarding the number of records loaded and dumped.  If the
-V flag is given, then MBnavedit works in a "verbose" mode and
outputs the program version being used, all error status messages,
and a large amount of other information including all of the
beams flagged or zeroed.
-X


This option causes mbprocess to run automatically
on an input swath data file when the MBnavedit editing session
is completed. The -X option effectively means that the
corresponding processed swath data is generated or updated immediately.
The program mbprocess will not be invoked if the
editing session is in the browse mode.


 
INTERACTIVE CONTROLS


File


This button accesses a pulldown menu with two push buttons:
Open and File Selection List,
File->Open


This button brings up a popup window which allows the user to
specify an input swath sonar bathymetry data file, its MBIO
format id, and  the output mode.
This program uses the MBIO library and
will read or write any swath sonar
format supported by MBIO. A list of the swath sonar data
formats currently supported by MBIO and their
identifier values is given in the MBIO manual page.
If the swath sonar data file is named using the MB-System
suffix convention (format 11 files end with ".mb11", format
41 files end with ".mb41", etc.), then the program will
automatically use the appropriate format id; otherwise the
format must be set by the user.
The popup window also allows the output mode to be set to "browse"
so that no edit events are output.
When a valid file is specified and the OK button
is clicked, file will be added to an internal list of swath files
available for editing, and then that file will be loaded into
memory for editing (if another file was already loaded, that file
is closed out gracefully before the new file is loaded).
If the specified input is a datalist (format
id = -1), then all of the files referenced through that datalist
will be added to the internal list, and the first of those files
loaded. When a file is loaded for editing, MBnavedit reads
as much data as will fit into the data buffer (typically 25000 records)
and several pings are displayed as stacked bathymetry profiles.
File->File Selection List


This button brings up a popup window displaying the internal list of
swath files available for editing. The list has four columns.
The first (left-most) column is either blank or shows "<locked>" or "<loaded>".
If a file is loaded for editing by this program, it shows as "<loaded>".
If a file is being edited or processed by another program, it shows as
"<locked>". Locked files cannot be opened for editing, and any file
loaded for editing by MBnavedit will show as "locked" to other
programs. The second column is either blank or shows "<nve>". This indicates if
a file has been previously edited so that an edited navigation file already
exists. The third and fourth columns show the filename path and the MBIO
format id, respectively.
Users can select one of the files in the available list. If the "Edit Selected File"
button is clicked, the selected file will be opened for editing (and any
file already loaded will be closed first). If the "Remove Selected File"
button is selected, then the selected file will be removed from the available
list.
Controls


This button activates a pulldown menu with five buttons:
Time Stepping, Nav Modeling, Time Interpolation,
Delete Bad Times, and Position Offset. Each
of these buttons brings up a dialog window containing widgets
that set parameters or perform actions.
Controls->Time Stepping->Time Span Shown


This slider sets the number of seconds of data shown at a time.
This value is also set by the Show Entire Buffer button (sets
time shown to all available data) and the Pick Time Interval
function (sets time shown to an interactively specified interval).
Controls->Time Stepping->Time Step


This slider sets the number of seconds to step when the Forward
or Reverse buttons are pushed.
Controls->Navigation Modeling->Off


This toggle button turns navigation modeling off.
Controls->Navigation Modeling->Gaussian Mean


This toggle button enables navigation smoothing by convolution
with a Gaussian kernel of user defined time width.
When this toggle button is highlighted, a smooth
navigation model is calculated and displayed
as a blue line in both the longitude and latitude plots.
The Show Smooth Inversion toggle buttons
also appear (already enabled)
for both the longitude and latitude plots
among the plot display toggles on the left side of the main
MBnavedit window.
Controls->Navigation Modeling->Dead Reckoning


This toggle button enables dead reckoning navigation calculation.
When this toggle button is highlighted, a dead reckoning
navigation model is calculated from the initial position
using the current heading and speed data and displayed
as a blue line in both the longitude and latitude plots.
The Show Dead Reckoning toggle buttons also appear (already enabled)
for both the longitude and latitude plots
among the plot display toggles on the left side of the main
MBnavedit window.
Controls->Navigation Modeling->Smooth Inversion


This toggle button enables inversion for a smooth navigation
model which fits the original positions in a least squares
sense while minimizing speed and acceleration.
When this toggle button is highlighted, a smooth
navigation model is calculated and displayed
as a blue line in both the longitude and latitude plots.
The Show Smooth Inversion toggle buttons
also appear (already enabled)
for both the longitude and latitude plots
among the plot display toggles on the left side of the main
MBnavedit window.
Controls->Navigation Modeling->Gaussian Mean Time Window


This slider sets the width in seconds of the Gaussian smoothing
kernel. If Gaussian mean smoothing is enabled, changing this slider
causes the smoothing to be recalculated and the results shown on
the longitude and latitude plots.
Controls->Navigation Modeling->Dead Reckoning Longitude Drift


This slider sets the longitude drift rate in degrees/hour
applied to the dead reckoning navigation calculation. If
dead reckoning is enabled, changes
to this slider cause the dead reckoning calculation to be
redone and the results shown on the longitude and latitude plots.
Controls->Navigation Modeling->Dead Reckoning Latitude Drift


This slider sets the latitude drift rate in degrees/hour
applied to the dead reckoning navigation calculation. If
dead reckoning is enabled, changes
to this slider cause the dead reckoning calculation to be
redone and the results shown on the longitude and latitude plots.
Controls->Navigation Modeling->Speed Deviation


This text entry sets the penalty weighting against speed
applied in the inversion for a smooth navigation. Higher values
result in a smoother model; lower values result in a model
that more closely follows the original navigation. The
default value is 100. This value is not actually set until
the Apply button to the left is clicked.
Controls->Navigation Modeling->Acceleration


This text entry sets the penalty weighting against accleration
applied in the inversion for a smooth navigation. Higher values
result in a smoother model; lower values result in a model
that more closely follows the original navigation. The
default value is 100. This value is not actually set until
the Apply button to the left is clicked.
Controls->Navigation Modeling->Apply


This button causes the values in the Speed Deviation and
Acceleration text entries to its right to be applied. If
smooth inversion is enabled, then clicking this button
will cause the inversion to be recalculated and the results
displayed in the longitude and latitude plots.
Controls->Navigation Modeling->Dismiss


This button causes the Navigation Modeling dialog
to disappear.
Controls->Time Interpolation->Apply


This button causes the time stamps of all data in
the current buffer associated
with negative or zero time intervals to be interpolated so
that the time intervals are positive. The Time Interpolation
dialog disappears after this action is taken.
Controls->Time Interpolation->Dismiss


This button causes the Time Interpolation dialog
to disappear.
Controls->Delete Bad Times->Apply


This button causes all data in
the current buffer associated
with negative or zero time intervals to be deleted.
The Delete Bad Times
dialog disappears after this action is taken.
Controls->Delete Bad Times->Dismiss


This button causes the Delete Bad Times dialog
to disappear.
Controls->Position Offset->Longitude Offset


This text widget allows the user to set the desired
longitude offset in degrees.
Controls->Position Offset->Latitude Offset


This text widget allows the user to set the desired
latitude offset in degrees.
Controls->Position Offset->Apply


This button applies the current longitude and latitude
offsets to all of the navigation data.
The Position Offset
dialog disappears after this action is taken.
Controls->Position Offset->Dismiss


This button causes the Delete Bad Times dialog
to disappear.
Start


This button causes the set of displayed pings to step backward to the
beginning of the current buffer.
Reverse


This button causes the set of displayed pings to step nstep
pings backward in the current buffer.  The middle mouse button causes
the same action.
Forward


This button causes the set of displayed pings to step nstep
pings forward in the current buffer.  The right mouse button causes
the same action.
End


This button causes the set of displayed pings to step forward to the
end of the current buffer.
Next Buffer


This button causes the program to write out the data from the
current buffer and then read in and display the next buffer.
If there is no more data to be read in after the current buffer
has been written out, then the input and output files are closed.
Show All


This button causes the plots to expand to show all of the data
in the current buffer.
Pick Zoom


This button allows users to focus the plots on a particular
time interval. Once the button is pushed, the left mouse button
is used to select the left edge of the time selection. Similarly,
the middle mouse button selects the right edge of the time selection.
Both ends of the time selection can be adjusted multiple times.
Once the time interval of interest is selected to the users
satisfaction, pressing the right mouse button will cause the
plots to be redrawn with the selected beginning and ending
times.
Done | Next File


When the last file in the list of files available for editing has been loaded,
this button shows as "Done". Otherwise, it shows as "Next File". In either
case, this button causes the program to write out all of the edited navigation
data and then close the current file. If the current file is not the last
one in the available list, then the next unlocked file will be loaded for editing.
Quit


This button causes the program to exit gracefully.  If a data file
has been loaded, all of the edits will be output before exiting.
About


This button causes a dialog to appear showing some information
about the program.
Interpolate


This button causes the selected data to be
replaced by linear interpolation
of the surrounding unselected data. If the selection extends to the
edge of the data, the selected data will be replaced by the first
unselected datum on the other side.
Interpolate Repeats


This button causes any repeated values in the selected data to be
replaced by linear interpolation between the first of the repeated
values and the next different value.
Revert Selection


This button causes the selected data to revert to their
original values.
Use Solution


This button only appears when one of the two navigation
modeling algorithms is activated from the Navigation Modeling
dialog.
This button causes any selected longitude or latitude values
to be replaced by values from navigation modeling. Either
dead reckoning or smooth inversion navigation modeling
must be enabled. The longitude and latitude values are
replaced in pairs (if a longitude value is selected, the
corresponding latitude value will also be replaced, and
vice versa). The typical sequence is to:

    1) adjust the modeling until an acceptable solution

       is achieved.

    2) click on the Select All toggle button

    3) click in either the longitude or latitude plot

       so that all values in that window are selected

    4) click on the Use Solution button so that the

       navigation model is adopted for all longitude

       and latitude values
Flag


This button only appears when either of the Gaussian mean or the smooth inversion navigation
modeling algorithm is activated from the Navigation Modeling
dialog.
This button causes any selected longitude or latitude values
to be flagged to be ignored by the navigation smoothing
algorithm. Flagged positions are shown in orange.
Unflag


This button only appears when the Gaussian mean or smooth inversion navigation
modeling algorithm is activated from the Navigation Modeling
dialog.
This button causes any selected longitude or latitude values
to be unflagged. Flagged positions are ignored by the navigation smoothing
algorithm. Any positions which are unflagged will once again be
used by the modeling method. Flagged positions are shown in orange.
Unflagged positions are shown in either black (if they are unchanged)
or purple (if they have been altered by interpolation or application
of a modeling solution).
Pick


Clicking on this toggle button sets the edit mode to "pick". In
this case, clicking the left mouse button will cause the
nearest data value to toggle between selected (red) and
unselected.
Select


Clicking on this toggle button sets the edit mode to "select". In
this case, clicking and dragging the left mouse button will
cause any data value touched by the cursor to become selected.
Deselect


Clicking on this toggle button sets the edit mode to "deselect". In
this case, clicking and dragging the left mouse button will
cause any data value touched by the cursor to become unselected.
Select All


Clicking on this toggle button sets the edit mode to "select all". In
this case, clicking in any of the editable plots will cause all
of the data in that plot to be selected.
Deselect All


Clicking on this toggle button sets the edit mode to "select all". In
this case, clicking in any of the editable plots will cause all
of the data in that plot to be unselected.
Time Interval Plot


This toggle button turns the time interval plot on and off.
Show Original Data (Time Interval Plot)


When this toggle button is on, the time interval plot includes a
green line representing the original time interval values.
Longitude Plot


This toggle button turns the longitude plot on and off.
Show Original Data (Longitude Plot)


When this toggle button is on, the longitude plot includes a
green line representing the original longitude values.
Show Dead Reckoning (Longitude Plot)


When this toggle button is on, the longitude plot includes a
blue line representing the dead reckoning longitude values.
Show Smooth Inversion (Longitude Plot)


When this toggle button is on, the longitude plot includes a
blue line representing the smooth inversion longitude values.
Latitude Plot


This toggle button turns the latitude plot on and off.
Show Original Data (Latitude Plot)


When this toggle button is on, the latitude plot includes a
green line representing the original latitude values.
Show Dead Reckoning (Latitude Plot)


When this toggle button is on, the latitude plot includes a
blue line representing the dead reckoning latitude values.
Show Smooth Inversion (Latitude Plot)


When this toggle button is on, the latitude plot includes a
blue line representing the smooth inversion latitude values.
Speed Plot


This toggle button turns the speed plot on and off.
Show Original Data (Speed Plot)


When this toggle button is on, the speed plot includes a
green line representing the original speed values.
Show Speed-Made-Good (Speed Plot)


When this toggle button is on, the speed plot includes a
blue line representing the speed-made-good values derived
from the longitude and latitude time series.
Use Speed-Made-Good (Speed Plot)


When this button is pushed, any selected data in the speed
plot will be replaced by the current estimates of speed-made-good.
Heading Plot


This toggle button turns the heading plot on and off.
Show Original Data (Heading Plot)


When this toggle button is on, the speed plot includes a
green line representing the original speed values.
Show Course-Made-Good (Heading Plot)


When this toggle button is on, the heading plot includes a
blue line representing the course-made-good values derived
from the longitude and latitude time series.
Use Course-Made-Good (Heading Plot)


When this button is pushed, any selected data in the heading
plot will be replaced by the current estimates of course-made-good.
Roll, Pitch, and Heave Plots


This toggle button turns the roll, pitch, and heave plots on and off.
Unlike the other plots, the data in these plots is not editable.
These data are shown purely to allow users to determine if the
vertical reference sensors were working properly at the time the
data was collected (note: many swath data formats do not contain roll,
pitch, and heave data).


 
MOUSE ACTIONS


Left Mouse Button


The left mouse button is used to pick data values.  Unselected data
values are shown as filled black squares and selected values
as empty red squares.  The manner in which data are selected or
unselected is controlled by the edit mode, as set by the
Pick, Select, Deselect, Select All, and
Deselect All buttons.
Middle Mouse Button


The middle mouse button causes the set of displayed data to
step backward in the current buffer by the amount of time
set on the Time Step slider.
The control button Reverse causes
the same action.
Right Mouse Button


The right mouse button causes the set of displayed data to
step forward in the current buffer by the amount of time
set on the Time Step slider.
The control button Forward causes
the same action.


 
SEE ALSO

mbsystem(1), mbio(1), mbprocess(1), mbset(1),
mbedit(1), mbeditviz(1), mbinfo(1)

 
BUGS

This program doesn't handle the roll, pitch, and heave data in a general way.



 
Index

NAME

VERSION

SYNOPSIS

DESCRIPTION

SMOOTHING NAVIGATION

HANDLING BAD TIME STAMPS

AUTHORSHIP

OPTIONS

INTERACTIVE CONTROLS

MOUSE ACTIONS

SEE ALSO

BUGS

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