MB-System Unix Manual Page: mbnavedit

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    mbnavedit
    Section:  MB-System 5.0  (1)
    Updated:  26 October 2009
    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 menu brings up a popup window which allows the user to
    specify the input swath sonar data file, its MBIO
    format id, the output mode, and the output navigation file name.
    This program uses the MBIO library and
    will read 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 default output navigation filename
    will be infile with ".nve" appended. Under most circumstances,
    users should use the default output filename because mbprocess
    expects this form.
    The popup window also allows the output mode to be set to "browse"
    so that the edited navigation data are not written to a file.
    When a valid file is specified and the OK button
    is clicked, as much data as will fit
    into the data buffer (25000 navigation points)
    is read and the navigition times series
    plots are displayed.
    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.
    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.
    Done

    This button causes the program to write out all of the data from the
    input file and then close the input and output files.
    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.
    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.
    Quit

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

    This button causes a dialog to appear showing some information
    about the program.
    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.
    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(l), mbio(l), mbprocess(l), mbset(l),
    mbedit(l), mbinfo(l)

    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

Last Updated: 26 October 2009

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