Provided by: gmt_4.5.11-1build1_amd64 
NAME
mgd77sniffer - Scan for errors in MGD77 data
SYNOPSIS
mgd77sniffer NGDC-ids [ -Afieldabbrev,scale,offset ] [ -Cmaxspd ] [ -Dd|e|E|f|l|m|s|v[r] ] [
-gfieldabbrev,imggrid,scale,mode ] [ -Gfieldabbrev,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/...]] ]
DESCRIPTION
mgd77sniffer 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 output 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 command
line order.
-De output E77 error classification format. Error output is divided into (1) a header containing
information globally applicable 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. Distance 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 descriptions.
-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 Mercator 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 separate -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 analysis of ship and gridded data. By
default mgd77sniffer analyses both the full and decimated data sets then reports RLS statistics
for the higher correlation regression.
-Hb analyze both (default), report better of two.
-Hd to disable data decimation (equivalent to -H with no argument).
-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 erroneously flagged bad, which can happen when a cruise's first navigation
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
abbreviations 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 confidence 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 geophysical 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 messages 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
contain a GMT header. A correctly formatted *.i2 grid file can be generated 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 correlation 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 verified (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 reference 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 representing unique error types. See below for error code format
description.
Format
<time/distance> <record number> <error code string> <description>
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 signifying 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 ALSO
mgd77list(1), mgd77track(1) x2sys_init(1)
REFERENCES
Wessel, P., and W. H. F. Smith, 2013, The Generic Mapping Tools (GMT) version 4.5.11 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 Mapping Tools Released, EOS Trans., AGU,
76 (33), p. 329.
Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Mapping 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 Display 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 4.5.11 5 Nov 2013 MGD77SNIFFER(1gmt)