mgd77listgmt - Online in the Cloud

PROGRAM:

NAME

mgd77list - Extract data from MGD77 files

SYNOPSIS

mgd77list NGDC-ids columns[,logic][:bittests] [ [+]c|d|f|m|tcode ] [ f|g|e ] [
A|astartdate ] [ B|bstopdate ] [ ] [ astartrec ] [ bstoprec ] [ ignore ] [ [corrtable] ]
[ d|sunit ] [ a|c|vmin/max ] [ region ] [ astartdist[unit] ] [ bstopdist[unit] ] [ [m|e] ]
[ [level] ] [ weight ] [ +|- ] [ -bo<binary> ] [ -h<headers> ]

Note: No space is allowed between the option flag and the associated arguments.

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 8 computed quantities (distance,
heading, course-change, velocity, Carter correction, Eotvos 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. If multiple cruises are requested then
they are separated by segment headers.

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].

-Fcolumns[,logic][:bittests]
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 FORMAT_FLOAT_OUT. The
available column abbreviations for information stored in the files (some columns
may be NaN) are:

recno The record number counter.

drt The digital record type, usually 3 or 5 (for Y2K-compliant cruises).

id The survey ID string (leg name).

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 FORMAT_DATE_OUT and FORMAT_CLOCK_OUT,
Relative time (rtime) in the format dictated by the GMT parameters
FORMAT_FLOAT_OUT and TIME_SYSTEM (or TIME_EPOCH and TIME_UNIT)), or
Fractional year (ytime) in the format dictated by FORMAT_FLOAT_OUT.

lon Longitude in the format dictated by the GMT parameter FORMAT_GEO_OUT.

lat Longitude in the format dictated by the GMT parameter FORMAT_GEO_OUT.

twt Two-Way Travel time (in s).

depth Corrected bathymetry (in m, positive below sea level).

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).

In addition, the following derived navigational 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.

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).

cc Ship course change (change in heading) measured clockwise from north (in
degrees).

vel Ship speed; see -N for units [m/s].

Finally, the following computed quantities can be requested:

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 added to 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).

ceot Calculated Eotvos correction from navigation, using E = 7.5038 * V *
cos(lat) * sin(az) + 0.004154 * V^2 (in mGal). Sign: Correction is to be
added to uncorrected faa to yield a corrected faa.

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 The full set of all 26 columns in the MGD77T specification.

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, cc, vel,
and weight as listed above.

all This returns all data columns in the file.

allt As mgd77t but with time items written as a date-time string.

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).

OPTIONAL ARGUMENTS

-A[+]c|d|f|m|tcode
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., -Ac3 will first try method -Ac1 to estimate a Carter
correction but if depth is NaN we will next try -Ac2 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).

-Af4[,field] returns the combination of gobs + eot - ngrav (with optional field
directive).

-Af8[,field] returns the combination of gobs + pred_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).

-Amc<offset>[unit] Apply a correction that tries to compensate the fact that the
magnetic field was not acquired at the same position as the navigation refer
(ship's position). This is accomplished by re-interpolating the total magnetic
field to what it would have had if it was measured at the ship's position
(remember, it probably was measured <offset> meters behind). Due to this
interpolation step, bad navigation, namely too many repeated points, may cause
troubles. Measures are taken to minimize this effect but they aren't 100% full
prof. The interpolation method is controlled by the GMT default GMT_INTERPOLANT.
Append e for meter, f for feet, k for km, m for miles, n for nautical miles, or u
for survey feet [Default is e (meters)].

-Cf|g|e
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.

-Dastartdate
Do not list data collected before startdate (yyyy-mm-ddBD(T)[hh:mm:ss]) [Default is
start of cruise]. Use -DA to exclude records whose time is undefined (i.e., NaN).
[Default reports those records].

-Dbstopdate
Do not list data collected on or after stopdate (yyyy-mm-ddBD(T)[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].

-Gastartrec
Do not list records before startrec [Default is 0, the first record].

-Gbstoprec
Do not list data after stoprec. [Default is the last record].

-Iignore
Ignore certain data file formats from consideration. Append a|c|t to ignore MGD77
ASCII, MGD77+ netCDF, or plain tab-separated ASCII table files, respectively. The
option may be repeated to ignore more than one format. [Default ignores none].

-L[corrtable]
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 Issue a segment header record with cruise ID for each cruise.

-Nd|sunit
Append d for distance or s for speed, then give the desired unit as e (meter or
m/s), f (feet or feet/s), k (km or km/hr), m (miles or miles/hr), n (nautical miles
or knots), or u (survey feet or sfeet/s). [Default is -Ndk -Nse (km and m/s)].

-Qamin/max
Specify an accepted range (min/max) of azimuths. Records whose track azimuth falls
outside this range are ignored [0/360].

-Qcmin/max
Specify an accepted range (min/max) of course changes. Records whose track course
change falls outside this range are ignored [-360/+360]. Use -QC to take the
absolute value of the course change before the test [Default uses signed course
changes].

-Qvmin/max
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[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.

-Sastartdist[unit]
Do not list data that are less than startdist meter along track from port of
departure. Append e for meter, f for feet, k for km, m for miles, n for nautical
miles, or u for survey feet [Default is 0e (meters)].

-Sbstopdist[unit]
Do not list data that are stopdist or more meters along track from port of
departure. Append e for meter, f for feet, k for km, m for miles, n for nautical
miles, or u for survey feet [Default is end of track].

-T[m|e]
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[level] (more ...)
Select verbosity level [c].

-Wweight
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[ncols][type] (more ...)
Select native binary output. 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=1.

-h[i|o][n][+c][+d][+rremark][+rtitle] (more ...)
Skip or produce header record(s).

-^ 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.

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:

gmt mgd77list 01010047 -Da1971-06-03T20:45 -Sb5000 -Fdist,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:

gmt mgd77list `cat cruises.lis` -Flon,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:

gmt 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

gmt 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

gmt 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:

gmt mgd77list `cat cruises.lis` -Flon,lat,mag,faa -Af2,4 -Am2 > 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

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