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] ] [
-Sa startdist[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, 2014, The Generic Mapping Tools (GMT) version
4.5.12 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