MGD77LIST(1) Generic Mapping Tools MGD77LIST(1)NAMEmgd77list - A data-extractor for MGD77[+] files
SYNOPSISmgd77list 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] ] [ -Sastart‐
dist[unit] ] [ -Sbstopdist[unit] ] [ -T[m|e] ] [ -V ] [ -Wweight ] [
-Z+|- ] [ -bo[s|S|d|D[ncol]|c[var1/...]] ] [ -m[flag] ]
DESCRIPTIONmgd77list reads <NGDC-id>.[mgd77|nc] files and produces an ASCII [or
binary] table. The <NGDC-id>.[mgd77|nc] files contain track informa‐
tion 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 avail‐
able 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 dic‐
tated 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 OUT‐
PUT_DEGREE_FORMAT.
lat Longitude in the format dictated by the GMT parameter OUT‐
PUT_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 sec‐
tions, 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 calcula‐
tion, see -C [spherical great circle distances], and for dis‐
tance 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 Theo‐
retical Formula Code in the cruise's MGD77 header. If this is
not set or is invalid we default to the IGF 1980. Alterna‐
tively, 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 observa‐
tions 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 oper‐
ator (<, <=, =, !=, >=, >, |), and value is a constant used in
the comparison. Floating point parameters are compared numeri‐
cally; character parameters are compared lexically (after lead‐
ing 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 parame‐
ters 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 spe‐
cial 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 observa‐
tions 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 proce‐
dure 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 (pre‐
sumably) 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 "nor‐
mal 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. Alterna‐
tively, 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 direc‐
tory]. 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 insti‐
tution 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 dou‐
ble 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 > all‐
grav.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 shal‐
lower 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 abbrevia‐
tions for geophysical observations listed under -F above, and correc‐
tion consists of one or more terms that will be summed up and then sub‐
tracted 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 mul‐
tiplying 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), mag‐
netics (mqc), and gravity (gqc). They are not present in the original
MGD77 format, and if requested will return 9 or NULL.
SEE ALSOmgd77convert(1), mgd77info(1), mgd77manage(1), mgd77track(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
IGRF, see http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html
GMT 4.5.14 1 Nov 2015 MGD77LIST(1)
