MGD77SNIFFER(1) Generic Mapping Tools MGD77SNIFFER(1)NAMEmgd77sniffer - Scan for errors in MGD77 data
SYNOPSISmgd77sniffer NGDC-ids [ -Afieldabbrev,scale,offset ] [ -Cmaxspd ] [
-Dd|e|E|f|l|m|s|v[r] ] [ -gfieldabbrev,imggrid,scale,mode ] [ -Gfield‐
abbrev,grid ] [ -H[i][nrec] ] [ -Ifieldabbrev,rec1,recN ] [ -K ] [
-Lcustom limits file ] [ -N ] [ -Q[b|c|l|n][[/]threshold] ] [
-Rwest/east/south/north[r] ] [ -Sd|s|t ] [ -Tgap ] [ -V ] [
-Wc|g|o|s|t|v|x ] [ -bo[s|S|d|D[ncol]|c[var1/...]] ]
DESCRIPTIONmgd77sniffer scans old (pre-Y2K) and new format ASCII MGD77 files for
errors using point-by-point sanity checking, along-track detection of
excessive slopes, and optional comparison of cruise data with global
gravity and predicted bathymetry grids. Detected data problems are out‐
put by default as verbose descriptions of each detected error, often
resulting in multiple messages per scanned record. Data problems are
optionally output (-De option) using a computer-parseable format (see
E77 ERROR FORMAT description below). Default error thresholds are
derived from histograms of all MGD77 geophysical data collected between
1952 and January, 2006. Thresholds are adjustable with the -L option.
NGDC-ids
Can be one or more of five kinds of specifiers:
1) 8-character NGDC IDs, e.g., 01010083, JA010010etc., etc.
2) 2-character <agency> codes which will return all cruises from
each agency.
3) 4-character <agency><vessel> codes, which will return all
cruises from those vessels.
4) =<list>, where <list> is a table with NGDC IDs, one per line.
5) If nothing is specified we return all cruises in the data
base.
(See mgd77info -L for agency and vessel codes). The ".mgd77" or
".nc" extensions will automatically be appended, if needed (use
-I to ignore certain file types). Cruise files will be looked
for first in the current directory and second in all directories
listed in $MGD77_HOME/mgd77_paths.txt [If $MGD77_HOME is not set
it will default to $GMT_SHAREDIR/mgd77].
REQUIREMENTS
The mgd77sniffer links with Generic Mapping Tools 4.0 or later along
with the supplemental GMT packages x2sys and mgd77. See
http://gmt.soest.hawaii.edu for GMT details. Grids for comparison with
cruise data may be downloaded via the web.
OPTIONS-A Apply scale factor and DC adjustment to specified data field.
Allows adjustment of cruise data prior to along-track analysis.
CAUTION: data must be thoroughly examined before applying these
global data adjustments. May not be used for multiple cruises.
-C Set maximum ship speed in m/s, or knots with -N option. Ship
speeds exceeding 10 m/s (~20 knots) are flagged as excessive by
default.
-D Suppress default warning output and only dump cruise data row-
by-row such as values, gradients, grid-cruise differences, E77
error summaries for each record, re-created MGD77 records or
sniffer limits. Append r to include all records (default omits
records where navigation errors were detected).
-Dd output differences between cruise and grid data. Requires -G
option. Output columns include:
lat lon dist cruiseZ gridZ diff [cruiseZ2 gridZ2 diff2 ...]
Note: grid values are subtracted from cruise data so a positive
difference implies cruise > grid. For multiple grid comparison,
cruiseZ gridZ diff are repeated for each grid comparison in com‐
mand line order.
-De output E77 error classification format. Error output is
divided into (1) a header containing information globally appli‐
cable to the cruise and (2) individual error records summarizing
all errors encountered in each cruise record. mgd77sniffer
writes E77 directly to <ngdc_id.e77> file handle. See E77 ERROR
FORMAT below for additional details.
-DE Same as -De but no regression tests will be carried out.
-Df output delta Z (change in geophysical field) column and
delta S (change in distance) for each geophysical field. Dis‐
tance between observations often differ for different fields
depending on instrument sampling rate, so ds is included for
each geophysical observation. Output columns include:
d[twt] ds d[depth] ds d[mtf1] ds d[mtf2] ds d[mag] ds d[diur] ds
d[msd] ds d[gobs] ds d[eot] ds d[faa] ds
-Dl display mgd77sniffer limits. Customize this output to create
a custom limits file for the -L option. No additional arguments
are required. Output columns include:
fieldabbrev min max maxSlope maxArea
-Dm output MGD77 format records in Y2K-compliant MGD77 format
-Dn output distance to coast for each record. Requires -Gnav or
-gnav option. Output columns include:
lat lon dist distToCoast
-Ds output calculated gradients for speed and geophysical
fields. Gradients correspond to the gradient type selected in
the -S option (spatial derivatives by default). Output columns
include:
speed d[twt] d[depth] d[mtf1] d[mtf2] d[mag] d[diur] d[msd]
d[gobs] d[eot] d[faa]
See MGD77 FIELD INFO below for field and abbreviations descrip‐
tions.
-Dv display values for the twelve position and geophysical
fields for each MGD77 data record (in this order):
lat lon twt depth mtf1 mtf2 mag diur msens gobs eot faa
See below for MGD77 FIELD INFO.
-g Compare cruise data to the specified grid in Sandwell/Smith Mer‐
cator format. Requires a valid MGD77 field abbreviation (see
MGD77 FIELD INFO below) followed by a comma, the path (if not in
current directory) and grid filename, a scale to multiply the
data (1 or 0.1), and mode which stand for the following: (0) Img
files with no constraint code, returns data at all points, (1)
Img file with constraints coded, return data at all points, (2)
Img file with constraints coded, return data only at constrained
points and NaN elsewhere, and (3) Img file with constraints
coded, return 1 at constraints and 0 elsewhere.
-G Compare cruise data to the specified grid. Requires a valid
MGD77 field abbreviation (see MGD77 FIELD INFO below) followed
by a comma, then the path (if not in current directory) and grid
filename. Multiple grid comparison is supported by using sepa‐
rate -g or -G calls for each grid. See GRID FILE INFO below.
Grid comparison activates several additional error checks. (1)
Re-weighted Least Squares Regression of ship versus grid data
determines slope and DC shift, which when differing from
expected 1 and 0, respectively, may indicate incorrectly scaled
ship data, including incorrect units or instrument drift as well
as erroneous gravity tie-in. (2) Accumulated ship grid offsets
are computed along-track and excessive offsets are flagged
according to maxArea threshold (use -L option to adjust
maxArea). Warning: predicted bathymetry grids are constrained by
cruise data so grids and cruise data are not always independent.
Comparison of cruise bathymetry with predicted bathymetry grids
also activates a "navigation crossing over land" check.
-H (with -G|g only) disable (or force) decimation during RLS analy‐
sis of ship and gridded data. By default mgd77sniffer analyses
both the full and decimated data sets then reports RLS statis‐
tics for the higher correlation regression.
-Hb analyze both (default), report better of two.
-Hd to disable data decimation (equivalent to -H with no argu‐
ment).
-Hf to force data decimation.
-I Append a field abbreviation and the first and last record in a
range of records that should be flagged as bad (and set to NaN
prior to the analysis). Repeat as many times as needed. May not
be used for multiple cruises.
-K Reverse navigation quality flags (good to bad and vice versa).
May be necessary when a majority of navigation fixes are erro‐
neously flagged bad, which can happen when a cruise's first nav‐
igation fix is extremely erroneous. Caution! This will affect
sniffer output and should only be attempted after careful manual
navigation review.
-L Override mgd77sniffer default error detection limits. Supply
path and filename to the custom limits file. Rows not beginning
with a valid MGD77 field abbreviation are ignored. Field abbre‐
viations are listed below in exact form under MGD77 FIELD INFO.
Multiple field limits may be modified using one default file,
one field per line. Field min, max, max slope and max area may
be changed for each field. Max slope pertains to the gradient
type selected using the -S option. Max area is used by the -G
option as the threshold for flagging excessive offsets from the
specified grid. Dump defaults -Dl to view syntax or to quickly
create an editable custom limits file.
Example custom default file contents (see below for units):
# abbrev min max maxSlope maxArea
twt 0 15 1 0
depth 0 11000 500 5000
mag -800 800 - -
faa -300 300 100 2500
Use a dash '-' to retain a default limit. Hint: to test your
custom limits, try: mgd77sniffer-Dl -L<yourlimitsfile>
-N Use nautical units.
-P Flag regression statistics that are outside the specified confi‐
dence level. (i.e., -P5 flags coefficients m, b, rms, and r
that fall outside 95%.)
-Q Quick mode, use bilinear rather than bicubic interpolation
[Default]. Alternatively, select the interpolation mode by
adding b for B-spline smoothing, c for bicubic interpolation, l
for bilinear interpolation or n for nearest-neighbor value.
Optionally, append threshold in the range [0,1]. This parameter
controls how close to nodes with NaN values the interpolation
will go. E.g., a threshold of 0.5 will interpolate about half
way from a non-NaN to a NaN node, whereas 0.1 will go about 90%
of the way, etc. [Default is 1, which means none of the (4 or
16) nearby nodes may be NaN]. -Q0 will just return the value of
the nearest node instead of interpolating. This is the same as
using -Qn.
-R west, east, south, and north specify the Region of interest, and
you may specify them in decimal degrees or in
[+-]dd:mm[:ss.xxx][W|E|S|N] format. Append r if lower left and
upper right map coordinates are given instead of w/e/s/n. The
two shorthands -Rg and -Rd stand for global domain (0/360 and
-180/+180 in longitude respectively, with -90/+90 in latitude).
Alternatively, specify the name of an existing grid file and the
-R settings (and grid spacing, if applicable) are copied from
the grid.
-S Specify gradient type for along-track excessive slope checking.
-Sd Calculate change in z values along track (dz). Output is
given in geophysical units, e.g., mGal.
-Ss Calculate spatial gradients (dz/ds). Output is given in geo‐
physical units per km along the survey track, e.g., mGal/km.
-St Calculate time gradients (dz/dt) [default]. Output is given
in geophysical units per second along the survey track, e.g.,
mGal/sec.
-T Adjusts mgd77sniffer gap handling. By default, data gaps greater
than 5 km are skipped. Set to zero to de-activate gap skipping.
-W Print out only certain warning types for verbose error messages.
Comma delimit any combination of c|g|o|s|t|v|x: where (c) type
code warnings, (g)radient out of range, (o)ffsets from grid
(requires -G|g), (s)peed out of range, (t)ime warnings, (v)alue
out of range, (x) warning summaries. By default ALL warning mes‐
sages are printed.Not compatible with any -D options.
-V Selects verbose mode, which will send progress reports to stderr
[Default runs "silently"].
-b output binary data for -D d|f|s|v option. Append s for single
and d for double precision [Default is double].
MGD77 FIELD INFO
Field Abbreviation Units
Two-way Travel Time twt sec
Corrected Depth depth m
Mag Total Field1 mtf1 nT
Mag Total Field2 mtf2 nT
Residual Magnetic mag nT
Diurnal Correction diur nT
Mag Sensor Depth/Alt msens m
Observed Gravity gobs mGal
Eotvos Correction eot mGal
Free Air Anomaly faa mGal
GRID FILE INFO
For -g the grids must be in the format used by Sandwell & Smith, which
is a spherical Mercator 2-byte grid with no header. For -G the grid
files can be of any grid type supported by GMT and therefore must con‐
tain a GMT header. A correctly formatted *.i2 grid file can be gener‐
ated using grdraster as shown below.
gmtset GRIDFILE_SHORTHAND TRUE
Create/edit .gmt_io file to include the following rows:
# GMT I/O shorthand file
# suffix format_id scale offset NaN
grd 0 - - -
i2 2 - - 32767
grdraster 1 -R0/359:55/-90/90 -Getopo5_hdr.i2
The new grid, etopo5_hdr.i2 in this example, contains a GMT header and
can be used in the -G option to compare cruise depth with grid values.
E77 ERROR FORMAT
Header Information pertaining to an entire cruise, such as NGDC and
survey institution identification codes, cruise examination
time, two-way travel time corrector information, data precision
warnings, as well as systematic scales, DC shifts and correla‐
tion coefficients from global grid comparisons are reported as
E77 header information.
Sample
# Cruise 08010039 ID 74010908 MGD77 FILE VERSION: 19801230
N_RECS: 3066
# Examined: Wed Oct 3 16:30:13 2007 by mtchandl
# Arguments: -De -Gdepth,/data/GRIDS/etopo5_hdr.i2
N Errata table verification status
# mgd77manage applies corrections if the errata table is veri‐
fied (toggle 'N' above to 'Y' after review)
# For instructions on E77 format and usage, see
http://gmt.soest.hawaii.edu/mgd77/errata.php
# Verified by:
# Comments:
# Errata: Header
Y-E-08010039-H13-02: Invalid Magnetics Sampling Rate: (99) [ ]
Y-W-08010039-H13-10: Survey year (1975) outside magnetic refer‐
ence field IGRF 1965 time range (1965-1970)
Y-I-08010039-depth-00: RLS m: 1.00053 b: 0 rms: 127.851 r:
0.973422 significant: 1 decimation: 0
Y-W-08010039-twt-09: More recent bathymetry correction table
available
Y-W-08010039-mtf1-10: Integer precision
Y-W-08010039-mag-10: Integer precision
Error Record
Individual error records have strict format. Included is a time
or distance column followed by record number, a formatted error
code string, and finally a verbose description of errors
detected in the record. Three error classes are encoded into the
error code string with different alphabetic characters repre‐
senting unique error types. See below for error code format
description.
Format
<time/distance> <record number> <error code string> <descrip‐
tion>
Sample
# Errata: Data
Y 08010039 1975-05-10T22:16:05.88 74 C-0-0 NAV:
excessive speed
Error Code Description
Each of the three error classes is separated by a dash '-' and
described by a combination of alphabetic characters or 0 signi‐
fying no detected problems.
Error classes: NAV-VAL-GRAD
Error Class Descriptions
NAV (navigation):
0 - fine
A - time out of range
B - time decreasing
C - excessive speed
D - above sea level
E - lat undefined
F - lon undefined
VAL (value):
0 - fine
K - twt invalid
L - depth invalid
O - mtf1 invalid
etc.
GRAD (gradient):
0 - fine
K - d[twt] excessive
L - d[depth] excessive
O - d[mtf1] excessive
etc.
The NAV error class has unique cases while VAL and GRAD classes
are described by alphabetic characters for each of the 24
numeric fields in MGD77 format order.
MGD77 bit-pattern w/ E77 alpha characters
|-------------------------------------------------|----------|
| X W V U T S R Q P O N M L K J I H G F E D C B A | E77 Code |
| - - - - - - - - - - - - - - - - - - - - - - - - | - - - - -|
| n f e g m d m m m m b b d t p l l m h d m y t d | F I |
| q a o o s i s a t t t c e w t o a i o a o e z r | i D |
| c a t b d u e g f f c c p t c n t n u y n a t | e |
| s r n 2 1 t r t r | l |
| s h h | d |
| - - - - - - - - - - - - - - - - - - - - - - - - | - - - - -|
| 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | Bit place|
| - G C G C C - G G G - - G G - - - T T T T T - - | Bit type |
|-------------------------------------------------|----------|
Bit types: (G)eophysical, (C)orrection, (T)ime
EXAMPLES
To scan for excessive values or gradients, try
mgd77sniffer 08010001
To dump cruise gradients, try
mgd77sniffer 08010001 -Ds
To compare cruise depth with ETOPO5 bathymetry and gravity with
Sandwell/Smith 2 min gravity version 11, try
mgd77sniffer 08010001 -G depth,/data/GRIDS/etopo5_hdr.i2 -g
faa,/data/GRIDS/grav.11.2.img,0.1,1
SEE ALSOmgd77list(1), mgd77track(1)x2sys_init(1)REFERENCES
Wessel, P., and W. H. F. Smith, 2015, The Generic Mapping Tools (GMT)
version 4.5.14 Technical Reference & Cookbook, SOEST/NOAA.
Wessel, P., and W. H. F. Smith, 1998, New, Improved Version of Generic
Mapping Tools Released, EOS Trans., AGU, 79 (47), p. 579.
Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Map‐
ping Tools Released, EOS Trans., AGU, 76 (33), p. 329.
Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Map‐
ping Tools Released, http://www.agu.org/eos_elec/95154e.html, Copyright
1995 by the American Geophysical Union.
Wessel, P., and W. H. F. Smith, 1991, Free Software Helps Map and Dis‐
play Data, EOS Trans., AGU, 72 (41), p. 441.
The Marine Geophysical Data Exchange Format - "MGD77", see
http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt
GMT 4.5.14 1 Nov 2015 MGD77SNIFFER(1)
