Provided by: gmt_4.5.11-1build1_amd64 
NAME
mgd77list - A data-extractor for MGD77[+] files
SYNOPSIS
mgd77list NGDC-ids -Fcolumns[,logic][:bittests] [ -A[+]c|d|f|m|tcode ] [ -Cf|g|e ] [
-DA|astartdate ] [ -DB|bstopdate ] [ -E ] [ -Gastartrec ] [ -Gbstoprec ] [ -H[i][nrec] ] [
-Iignore ] [ -L[corrtable] ] [ -Nd|sunit ] [ -Qa|vmin/max ] [ -Rwest/east/south/north[r] ]
[ -Sastartdist[unit] ] [ -Sbstopdist[unit] ] [ -T[m|e] ] [ -V ] [ -Wweight ] [ -Z+|- ] [
-bo[s|S|d|D[ncol]|c[var1/...]] ] [ -m[flag] ]
DESCRIPTION
mgd77list reads <NGDC-id>.[mgd77|nc] files and produces an ASCII [or binary] table. The
<NGDC-id>.[mgd77|nc] files contain track information such as leg-id, time and position,
geophysical observables such as gravity, magnetics, and bathymetry, and control codes and
corrections such as Eotvos and diurnal corrections. The MGD77+ extended netCDF files may
also contain additional user columns (for a listing of available columns, use mgd77info
-C, and to learn how to add your own custom columns, see mgd77manage). The user may
extract any combination of these parameters, any of six computed quantities (distance,
heading, velocity, Carter correction, and gravity and magnetic global reference fields),
calendar sub-units of time (year, month, day, hour, min, sec), the NGDC id, and finally a
preset weight (see -W). A sub-section can be specified by passing time- or distance-
intervals along track or by selecting a geographical region. Finally, each output record
may be required to pass any number of logical tests involving data values or bit flags.
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].
-F The required columns string must be a comma-separated list of parameter
abbreviations given in the desired output order. Any parameters given in UPPER
case must not be NaN in a record for output to occur. Unless specified separately,
the output format (if ASCII) is controlled by the GMT parameter D_FORMAT. The
available abbreviations are:
drt The digital record type, usually 3 or 5 (for Y2K-compliant cruises).
id The survey ID string (leg name).
tz The time zone adjustment (in hours from -13 to +12)
ngdcid The 8-character NGDC cruise ID string (usually the file prefix).
time Choose between Absolute calendar time (atime, the default) in the format dictated
by the GMT parameters OUTPUT_DATE_FORMAT and OUTPUT_CLOCK_FORMAT, Relative time
(rtime) in the format dictated by the GMT parameters D_FORMAT and TIME_SYSTEM (or
TIME_EPOCH and TIME_UNIT)), or Fractional year (ytime) in the format dictated by
D_FORMAT.
lon Longitude in the format dictated by the GMT parameter OUTPUT_DEGREE_FORMAT.
lat Longitude in the format dictated by the GMT parameter OUTPUT_DEGREE_FORMAT.
twt Two-Way Travel time (in s).
depth Corrected bathymetry (in m, positive below sealevel).
mtf1 Magnetic Total Field intensity from sensor 1 (in nTesla).
mtf2 Magnetic Total Field intensity from sensor 2 (in nTesla).
mag Residual magnetic anomaly (in nTesla).
gobs Observed gravity (in mGal).
faa Free-air gravity anomaly (in mGal).
ptc Position Type Code (1 = fix, 3 = interpolated, 9 = unspecified).
bcc Bathymetric Correction Code, indicating the procedure used to convert travel time
to depth. (01-55 = Matthews' zone used to correct the depth, 59 = Matthews'
corrections used but the zones is unspecified in the data record, 60 = S. Kuwahara
formula for T-S, 61 = Wilson formula for T-S, 62 = Del Grosso formula for T-S, 63 =
Carter's tables, 88 = Other, described in header sections, 99 = unspecified).
btc Bathymetric Type Code, indicating how the bathymetry value was obtained (1 =
observed, 3 = interpolated, 9 = unspecified).
msens Magnetic sensor for used to evaluate the residual field (1 = 1st or leading sensor,
2 = 2nd or trailing sensor, 9 = unspecified).
msd Depth (or altitude) of the magnetic sensor (in m, positive below sealevel).
diur Magnetic diurnal correction (in nTesla).
eot Eotvos correction (in mGal).
sln Seismic Line Number string.
sspn Seismic Shot Point Number string.
nqc Navigation Quality Code (5 = suspected, by source institution, 6 = suspected, by
NGDC, 9 = no problems identified).
bqc Bathymetry Quality Code (1 = good, 2 = fair, 3 = poor, 4 = bad, 5 = bad, suspected
by source institution, 6 = bad, suspected by NGDC, 9 = not set).
mqc Magnetics Quality Code (1 = good, 2 = fair, 3 = poor, 4 = bad, 5 = bad, suspected
by source institution, 6 = bad, suspected by NGDC, 9 = not set).
gqc Gravity Quality Code (1 = good, 2 = fair, 3 = poor, 4 = bad, 5 = bad, suspected by
source institution, 6 = bad, suspected by NGDC, 9 = not set).
In addition, the following derived quantities can be requested:
year The year of each record.
month The month of each record.
day The day of the month of each record.
hour The hour of each record.
min The minutes of each record.
sec The decimal seconds of each record.
date The date in yyyymmdd string format.
hhmm The clock in hhmm.xxxx format (0-2359.xxxx).
dmin The decimal minutes of each record (0-59.xxxx).
dist Along-track distance from start of leg. For method of calculation, see -C
[spherical great circle distances], and for distance units, see -N [km].
az Ship azimuth (heading) measured clockwise from north (in degrees).
vel Ship speed; see -N for units [m/s].
weight Weight assigned to this data set (see -W).
carter Carter depth correction, if twt is present in file (in m). Sign: Correction is to
be subtracted from uncorrected depths to yield a corrected depth.
igrf International geomagnetic reference field (total field) (in nTesla).
ngrav International Gravity reference Field ("normal gravity") (in mGal). Field is
selected based on the parameter Gravity Theoretical Formula Code in the cruise's
MGD77 header. If this is not set or is invalid we default to the IGF 1980.
Alternatively, specify the field directly using -Af (see that option for more
details).
The following short-hand flags are also recognized:
mgd77 This results in all 27 MGD77 fields being written out in the official MGD77 order.
mgd77t This results in all 26 MGD77T fields being written out in the official MGD77T
order.
all as mgd77 or mgd77t but time is written as a single date-time string.
geo This limits the output to 10 fields (time, lon, lat plus the seven geophysical
observations twt, depth, mtf1, mtf2, mag, gobs, and faa). By appending + to either
of these set we will also append dist, azim, vel, and weight as listed above.
As an option, logical tests may be added for any of the observations by appending
,logic, which is itself composed of one or more comma-separated instructions of the
form parOPvalue, where par is one of the parameters listed above, OP is a logical
operator (<, <=, =, !=, >=, >, |), and value is a constant used in the comparison.
Floating point parameters are compared numerically; character parameters are
compared lexically (after leading and trailing blanks have been removed). The bit
comparison (|) means that at least one of the bits in value must be turned on in
par. At least one of the tests must be true for the record to be output, except
for tests using UPPER case parameters which all must be true for output to occur.
Note that specifying a test does not imply that the corresponding column will be
included in the output stream; it must be present in columns for that to occur.
Note: some of the operators are special UNIX characters and you are advised to
place quotes around the entire argument to -F.
Finally, for MGD77+ files you may optionally append :bittests which is : (a colon)
followed by one or more comma-separated +-col terms. This compares specific
bitflags only for each listed column. Here, + means the chosen bit must be 1 (ON)
whereas - means it must be 0 (OFF). All bit tests given must be passed. By
default, MGD77+ files that have the special MGD77_flags column present will use
those flags, and observations associated with ON-bits (meaning they are flagged as
bad) will be set to NaN; append : with no trailing information to turn this
behavior off (i.e., no bit flags will be consulted).
OPTIONS
No space between the option flag and the associated arguments.
-A By default, corrected depth (depth), magnetic residual anomaly (mag), free-air
gravity anomaly (faa), and the derived quantity Carter depth correction (carter)
are all output as is (if selected in -F); this option adjusts that behavior. For
each of these columns there are 2-4 ways to adjust the data. Append c(arter),
d(epth), f(aa), or m(ag) and select the code for the procedure you want applied.
You may select more than one procedure for a data column by summing their numerical
codes (1, 2, 4, and 8). E.g., -Ac 3 will first try method -Ac 1 to estimate a
Carter correction but if depth is NaN we will next try -Ac 2 which only uses twt.
In all cases, if any of the values required by an adjustment procedure is NaN then
the result will be NaN. This is also true if the original anomaly is NaN. Specify
-A+ to recalculate anomalies even if the anomaly in the file is NaN. Additionally,
you can use -At to create fake times for cruises that has no time; these are based
on distances and cruise duration.
-Ac Determines how the carter correction term is calculated. Below, C(twt) stands for
the Carter-corrected depth (it also depends on lon, lat), U(twt, v) is the
uncorrected depth (= twt * v / 2) using as v the "Assumed Sound Velocity" parameter
in the MGD77 header (if it is a valid velocity, otherwise we default to 1500 m/s);
alternatively, append your preferred velocity v in m/s, TU(depth, v) is the 2-way
travel time estimated from the (presumably) uncorrected depth, and TC(depth) is the
2-way travel time obtained by inverting the (presumably) corrected depth using the
Carter correction formula. Select from
-Ac1[,v] returns difference between U(twt, v) and depth [Default].
-Ac2[,v] returns difference between U(twt, v) and Carter (twt).
-Ac4[,v] returns difference between (assumed uncorrected) depth and Carter
(TU(depth)).
-Ac8[,v] returns difference between U(TC(depth), v) and depth.
-Ad Determines how the depth column output is obtained:
-Ad1 returns depth as stored in the data set [Default].
-Ad2[,v] returns calculated uncorrected depth U(twt, v).
-Ad4 returns calculated corrected depth C(twt).
-Af Determines how the faa column output is obtained. If ngrav (i.e., the International
Gravity reference Field (IGF), or "normal gravity") is required it is selected
based on the MGD77 header parameter "Theoretical Gravity Formula Code"; if this
code is not present or is invalid we default to 4. Alternatively, append the
preferred field (1-4) to select 1 (Heiskanen 1924), 2 (IGF 1930), 3 (IGF 1967) or 4
(IGF 1980). Select from
-Af1[,field] returns faa as stored in the data set [Default]. Optionally, sets the
IGF field to use if you also have requested ngrav as an output column in -F.
-Af2[,field] returns the difference between gobs and ngrav (with optional field
directive).
-Af3[,field] returns the combination of gobs + eot - ngrav (with optional field
directive).
-Am Determines how the mag column output is obtained. There may be one or two total
field measurements in the file (mtf1 and mtf2), and the column msens may state
which one is the leading sensor (1 or 2; it may also be undefined). Select from
-Am1 returns mag as stored in the data set [Default].
-Am2 returns the difference between mgfx and igrf, where x is the leading sensor (1
or 2) indicated by the msens data field (defaults to 1 if unspecified).
-Am4 returns the difference between mgfx and igrf, where x is the sensor (2 or 1)
not indicated by the msens data field (defaults to 2 if unspecified).
-C Append a one-letter code to select the procedure for along-track distance
calculation (see -N for selecting units):
f Flat Earth distances.
g Great circle distances [Default].
e Geodesic distances on current GMT ellipsoid.
-Da Do not list data collected before startdate (yyyy-mm-ddT[hh:mm:ss]) [Default is
start of cruise]. Use -DA to exclude records whose time is undefined (i.e., NaN).
[Default reports those records].
-Db Do not list data collected on or after stopdate (yyyy-mm-ddT[hh:mm:ss]). [Default
is end of cruise]. Use -DB to exclude records whose time is undefined (i.e., NaN).
[Default reports those records].
-E Exact match: Only output records that match all the requested geophysical columns
[Default outputs records that matches at least one of the observed columns].
-Ga Do not list records before startrec [Default is 0, the first record].
-Gb Do not list data after stoprec. [Default is the last record].
-H Issue a header record with names for each data field.
-I Ignore certain data file formats from consideration. Append a|c|m|t to ignore MGD77
ASCII, MGD77+ netCDF, MGD77T ASCII or plain tab-separated ASCII table files,
respectively. The option may be repeated to ignore more than one format. [Default
ignores none].
-L Apply optimal corrections to columns where such corrections are available. Append
the correction table to use [Default uses the correction table
mgd77_corrections.txt in the $MGD77_HOME directory]. For the format of this file,
see CORRECTIONS below.
-N Append d for distance or s for speed, then give the desired unit as e (meter or
m/s), k (km or km/hr), m (miles or miles/hr), or n (nautical miles or knots).
[Default is -Ndk -Nse (km and m/s)].
-Qa Specify an accepted range (min/max) of azimuths. Records whose track azimuth falls
outside this range are ignored [0-360].
-Qv Specify an accepted range (min/max; or just min if there is no upper limit) of
velocities. Records whose track speed falls outside this range are ignored
[0-infinity].
-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.
-Sa Do not list data that are less than startdist meter along track from port of
departure. Append k for km, m for miles, or n for nautical miles [Default is 0
meters].
-Sb Do not list data that are stopdist or more meters along track from port of
departure. Append k for km, m for miles, or n for nautical miles [Default is end
of track].
-T Turns OFF the otherwise automatic adjustment of values based on correction terms
that are stored in the MGD77+ file and used to counteract such things as wrong
units used by the source institution when creating the original MGD77 file from
which the MGD77+ file derives (the option has no effect on plain MGD77 ASCII
files). Append m or e to limit the option to the MGD77 or extended columns set
only [Default applies to both].
-V Selects verbose mode, which will send progress reports to stderr [Default runs
"silently"].
-W Set the weight for these data. Weight output option must be set in -F. This is
useful if the data are to be processed with the weighted averaging techniques
offered by blockmean, blockmedian, and blockmode [1].
-Z Append the sign you want for depth, carter, and msd values below sea level (-Z-
gives negative bathymetry) [Default is positive down].
-bo Selects binary output mode (single precision; append d for double precision, or use
S|D to swap bytes on output) [Default is ASCII]. -H is ignored if -bo is selected.
Likewise, string-fields cannot be selected. Note that if time is one of the binary
output columns it will be stored as Unix-time (seconds since 1970). To read this
information in GMT to obtain absolute calendar time will require you to use
--TIME_SYSTEM=unix.
-m[flag]
Issue a multi-segment header record with cruise ID for each cruise.
EXAMPLES
To get a (distance, heading, gravity, bathymetry) listing from 01010047.mgd77, starting at
June 3 1971 20:45 and ending at distance = 5000 km, use the following command:
mgd77list 01010047 -Da 1971-06-03T20:45 -Sb 5000 -F dist,azim,faa,depth > myfile.d
To make input for blockmean and surface using free-air anomalies from all the cruises
listed in the file cruises.lis, but only the data that are inside the specified area, and
make the output binary:
mgd77list `cat cruises.lis` -F lon,lat,faa -R-40/-30/25/35 -bo > allgrav.b
To extract the locations of depths exceeding 9000 meter that were not interpolated (btc !=
1) from all the cruises listed in the file cruises.lis:
mgd77list `cat cruises.lis` -F"depth,DEPTH>9000,BTC!=1" > really_deep.d
To extract dist, faa, and grav12_2 from records whose depths are shallower than 3 km and
where none of the requested fields are NaN, from all the MGD77+ netCDF files whose cruise
ids are listed in the file cruises.lis, we try
mgd77list `cat cruises.lis` -E -Ia -F"dist,faa,grav12_2,depth<3000" > shallow_grav.d
To extract dist, faa, and grav12_2 from all the MGD77+ netCDF files whose cruise ids are
listed in the file cruises.lis, but only retrieve records whose bitflag for faa indicates
BAD values, we try
mgd77list `cat cruises.lis` -E -Ia -F"dist,faa,grav12_2:+faa" > bad_grav.d
To output lon, lat, mag, and faa from all the cruises listed in the file cruises.lis, but
recalculate the two residuals based on the latest reference fields, try:
mgd77list `cat cruises.lis` -F lon,lat,mag,faa -Af 2,4 -Am 2 > data.d
RECALCULATED ANOMALIES
When recalculated anomalies are requested (either explicitly via the -A option or
implicitly via E77 metadata in the MGD77+ file) we only do so for the records whose
original anomaly was not a NaN. This restriction is implemented since many anomaly
columns contains corrections, usually in the form of hand-edited changes, that cannot be
duplicated from the corresponding observation.
IGRF
The IGRF calculations are based on a Fortran program written by Susan Macmillan, British
Geological Survey, translated to C via f2c by Joaquim Luis, U Algarve, and adapted to GMT-
style by Paul Wessel.
IGF
The equations used are reproduced here using coefficients extracted directly from the
source code (let us know if you find errors):
(1) g = 978052.0 * [1 + 0.005285 * sin^2(lat) - 7e-6 * sin^2(2*lat) + 27e-6 * cos^2(lat) *
cos^2(lon-18)]
(2) g = 978049.0 * [1 + 0.0052884 * sin^2(lat) - 0.0000059 * sin^2(2*lat)]
(3) g = 978031.846 * [1 + 0.0053024 * sin^2(lat) - 0.0000058 * sin^2(2*lat)]
(4) g = 978032.67714 * [(1 + 0.00193185138639 * sin^2(lat)) / sqrt (1 - 0.00669437999013 *
sin^2(lat))]
CORRECTIONS
The correction table is an ASCII file with coefficients and parameters needed to carry out
corrections. Comment records beginning with # are allowed. All correction records are of
the form
cruiseID observation correction
where cruiseID is a NGDC prefix, observation is one of the abbreviations for geophysical
observations listed under -F above, and correction consists of one or more terms that will
be summed up and then subtracted from the observation before output. Each term must have
this exact syntax:
factor[*[function]([scale](abbrev[-origin]))[^power]]
where terms in brackets are optional (the brackets themselves are not used but regular
parentheses must be used as indicated). No spaces are allowed except between terms. The
factor is the amplitude of the basis function, while the optional function can be one of
sin, cos, or exp. The optional scale and origin can be used to translate the argument
(before giving it to the optional function). The argument abbrev is one of the
abbreviations for observations listed above. If origin is given as T it means that we
should replace it with the value of abbrev for the very first record in the file (this is
usually only done for time). If the first record entry is NaN we revert origin to zero.
Optionally, raise the entire expression to the given power, before multiplying by the
amplitude. The following is an example of fictitious corrections to the cruise 99999999,
implying the depth should have the Carter correction removed, faa should have a linear
trend removed, the magnetic anomaly (mag) should be corrected by a strange dependency on
ship heading and latitude, and gobs needs to have 10 mGal added (hence given as -10):
99999999 depth 1.0*((carter))
99999999 faa 14.1 1e-5*((time-T))
99999999 mag 0.5*cos(0.5*(azim-19))^2 1.0*exp(-1e-3(lat))^1.5
99999999 gobs -10
QUALITY CODES
The MGD77T format added three quality codes for bathymetry (bqc), magnetics (mqc), and
gravity (gqc). They are not present in the original MGD77 format, and if requested will
return 9 or NULL.
SEE ALSO
mgd77convert(1), mgd77info(1), mgd77manage(1), mgd77track(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
IGRF, see http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html