Provided by: gmt-common_5.2.1+dfsg-3build1_all 
NAME
mgd77sniffer - Along-track quality control of MGD77 cruises
SYNOPSIS
mgd77sniffer NGDC-ids [ fieldabbrev,scale,offset ] [ maxspd ] [ d|e|E|f|l|m|s|v[r] ] [
fieldabbrev,imggrid,scale,mode or fieldabbrev,grid ] [ ] [ fieldabbrev,rec1,recN ] [ ] [
custom-limits-file ] [ ] [ region ] [ d|s|t ] [ gap ] [ [level] ] [ c|g|o|s|t|v|x ] [ -bo<binary> ] [
-do<nodata> ] [ -n<flags> ]
Note: No space is allowed between the option flag and the associated arguments.
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.
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.
REQUIRED ARGUMENTS
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].
OPTIONAL ARGUMENTS
-Afieldabbrev,scale,offset
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.
-Cmaxspd
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.
-Dd|e|E|f|l|m|s|v[r]
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 the -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.
-Ginformation
Compare cruise data to GMT or IMG grids. Use one of the formats below.
-Gfieldabbrev,imggrid,scale,mode 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. -Gfieldabbrev,grid 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 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.
-Ifieldabbrev,rec1,recN
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.
-Lcustom-limits-file
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%.)
-R[unit]west/east/south/north[/zmin/zmax][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 for grid
creation, give Rcodelon/lat/nx/ny, where code is a 2-character combination of L, C, R (for left,
center, or right) and T, M, B for top, middle, or bottom. e.g., BL for lower left. This indicates
which point on a rectangular region the lon/lat coordinate refers to, and the grid dimensions nx
and ny with grid spacings via -I is used to create the corresponding region. Alternatively,
specify the name of an existing grid file and the -R settings (and grid spacing, if applicable)
are copied from the grid. Using -Runit expects projected (Cartesian) coordinates compatible with
chosen -J and we inversely project to determine actual rectangular geographic region. For
perspective view (-p), optionally append /zmin/zmax. In case of perspective view (-p), a z-range
(zmin, zmax) can be appended to indicate the third dimension. This needs to be done only when
using the -Jz option, not when using only the -p option. In the latter case a perspective view of
the plane is plotted, with no third dimension.
-Sd|s|t
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.
-Tgap Adjusts mgd77sniffer gap handling. By default, data gaps greater than 5 km are skipped. Set to
zero to de-activate gap skipping.
-Wc|g|o|s|t|v|x
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[level] (more ...)
Select verbosity level [c].
-bo[ncols][type] (more ...)
Select native binary output. Output binary data for -Dd|f|s|v option.
-donodata (more ...)
Replace output columns that equal NaN with nodata.
-n[b|c|l|n][+a][+bBC][+c][+tthreshold] (more ...)
Select interpolation mode for grids.
-^ or just -
Print a short message about the syntax of the command, then exits (NOTE: on Windows use just -).
-+ or just +
Print an extensive usage (help) message, including the explanation of any module-specific option
(but not the GMT common options), then exits.
-? or no arguments
Print a complete usage (help) message, including the explanation of options, then exits.
--version
Print GMT version and exit.
--show-datadir
Print full path to GMT share directory and exit.
CONSEQUENCES OF GRID RESAMPLING
Resample or sampling of grids will use various algorithms (see -n) that may lead to possible distortions
or unexpected results in the resampled values. One expected effect of resampling with splines is the
tendency for the new resampled values to slightly exceed the global min/max limits of the original grid.
If this is unacceptable, you can impose clipping of the resampled values values so they do not exceed the
input min/max values by adding +c to your -n option.
MGD77 FIELD INFO
────────────────────────────────────────
Field Abbreviation Units
────────────────────────────────────────
Two-way Travel Time
────────────────────────────────────────
Corrected Depth depth
────────────────────────────────────────
Mag Total Field1
────────────────────────────────────────
Mag Total Field2
────────────────────────────────────────
Residual Magnetic mag
────────────────────────────────────────
Diurnal Correction diur
────────────────────────────────────────
Mag Sensor Depth/Alt
────────────────────────────────────────
Observed Gravity gobs
────────────────────────────────────────
Eotvos Correction eot
────────────────────────────────────────
Free Air Anomaly
┌───────────┬──────────────┬───────────┐
│ │ │ │
GRID FILE INFO │ │ │ │
--
E77 ERROR FORMAT │ │ │ │
--
EXAMPLES
To scan for excessive values or gradients, try
gmt mgd77sniffer 08010001
To dump cruise gradients, try
gmt mgd77sniffer 08010001 -Ds
To compare cruise depth with ETOPO5 bathymetry and gravity with Sandwell/Smith 2 min gravity version 11,
try
mgd77sniffer 08010001 -Gdepth,/data/GRIDS/etopo5_hdr.i2 \
-Gfaa,/data/GRIDS/grav.11.2.img,0.1,1
SEE ALSO
mgd77list, mgd77track x2sys_init
REFERENCES
The Marine Geophysical Data Exchange Format - MGD77, see
http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt.
COPYRIGHT
2015, P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis, and F. Wobbe
5.2.1 January 28, 2016 MGD77SNIFFER(1gmt)