Extract data from MGD77 files
gmt mgd77list GEODAS-ids -Fcolumns[,logic][:bittests] [ -Ac|d|f|m|tcode[+f] ] [ -DA|astartdate ] [ -DB|bstopdate ] [ -E ] [ -Gastartrec ] [ -Gbstoprec ] [ -Ia|c|m|t ] [ -L[corrtable] ] [ -Nd|sunit ] [ -Qa|c|vmin/max ] [ -Rregion ] [ -Sastartdist ] [ -Sbstopdist ] [ -T[m|e] ] [ -V[level] ] [ -Wweight ] [ -Zn|p ] [ -bobinary ] [ -hheaders ] [ -jflags ] [ --PAR=value ]
Note: No space is allowed between the option flag and the associated arguments.
mgd77list reads MGD77 files and produces an ASCII [or binary] table. The MGD77 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 GEODAS 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.
Can be one or more of five kinds of specifiers:
8-character GEODAS IDs, e.g., 01010083, JA010010etc., etc.
2-character agency codes which will return all cruises from each agency.
4-character <agency><vessel> codes, which will return all cruises from those vessels.
=list, where list is a table with GEODAS IDs, one per line.
If nothing is specified we return all cruises in the data base.
(See mgd77info -L for agency and vessel codes). If no file extension is given then we search for files with one of the four known extensions. The search order (and the extensions) tried is MGD77+ (“.nc”), MGD77T (“.m77t”), MGD77 (“.mgd77” ) and plain text file (“.dat”). Use -I to ignore one or more of these 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].
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:
The record number counter.
The digital record type, usually 3 or 5 (for Y2K-compliant cruises).
The survey ID string (leg name).
The 8-character NGDC (now NCEI) cruise ID string (usually the file prefix).
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.
Longitude in the format dictated by the GMT parameter FORMAT_GEO_OUT.
Longitude in the format dictated by the GMT parameter FORMAT_GEO_OUT.
Two-Way Travel time (in s).
Corrected bathymetry (in m, positive below sea level).
Magnetic Total Field intensity from sensor 1 (in nTesla).
Magnetic Total Field intensity from sensor 2 (in nTesla).
Residual magnetic anomaly (in nTesla).
Observed gravity (in mGal).
Free-air gravity anomaly (in mGal).
Position Type Code (1 = fix, 3 = interpolated, 9 = unspecified).
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).
Bathymetric Type Code, indicating how the bathymetry value was obtained (1 = observed, 3 = interpolated, 9 = unspecified).
Magnetic sensor for used to evaluate the residual field (1 = 1st or leading sensor, 2 = 2nd or trailing sensor, 9 = unspecified).
Depth (or altitude) of the magnetic sensor (in m, positive below sealevel).
Magnetic diurnal correction (in nTesla).
Eotvos correction (in mGal).
Seismic Line Number string.
Seismic Shot Point Number string.
Navigation Quality Code (5 = suspected, by source institution, 6 = suspected, by NCEI, 9 = no problems identified).
In addition, the following derived navigational quantities can be requested:
The year of each record.
The month of each record.
The day of the month of each record.
The hour of each record.
The minutes of each record.
The decimal seconds of each record.
Along-track distance from start of leg. For method of calculation, see -j [spherical great circle distances], and for distance units, see -N [km].
Ship azimuth (heading) measured clockwise from north (in degrees).
Ship course change (change in heading) measured clockwise from north (in degrees).
Ship speed; see -N for units [m/s].
Finally, the following computed quantities can be requested:
Weight assigned to this data set (see -W).
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.
International geomagnetic reference field (total field) (in nTesla).
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).
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:
This results in all 27 MGD77 fields being written out in the official MGD77 order.
The full set of all 26 columns in the MGD77T specification.
This limits the output to 10 fields (time, lon, lat plus the seven geophysical observations twt, depth, mtf1, mtf2, mag, gobs, and faa).
As mgd77t but in plain table order.
This returns all data columns in the file.
As mgd77t but with time items written as a date-time string.
By appending + to any of these set we will also append dist, azim, cc, 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. Notes: (1) 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. (2) Some of the operators are special UNIX characters and you are advised to place quotes around the entire argument to -F. (3) The logical tests only apply to observed data; derived data (such as distances, velocities, etc.) must be limited using program options such as -D, -Q, -S, etc.
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). Note that these record-based flags are different from any systematic corrections along track; the latter are deactivated by -T.
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. Append +f 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.
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.
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).
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).
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).
-Amcoffset applies a correction to compensate for the fact that the magnetic field was not acquired at the same position as the ship’s position [i.e., the navigation]. This is accomplished by re-interpolating the total magnetic field to what it would have been if it were 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 trouble. Measures are taken to minimize this effect but they aren’t 100% fool proof. 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)].
Compute fake times for cruises with known duration but lacking individual record times.
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].
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].
Exact match: Only output records that match all the requested geophysical columns [Default outputs records that matches at least one of the observed columns].
Do not list records before startrec [Default is 0, the first record].
Do not list data after stoprec. [Default is the last record].
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].
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.
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)].
Specify an accepted range (min/max) of azimuths. Records whose track azimuth falls outside this range are ignored [0/360].
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].
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].
Specify the region of interest.
The region may be specified in one of several ways:
-Rwest/east/south/north. This is the standard way to specify geographic regions when using map projections where meridians and parallels are rectilinear. The coordinates may be specified in decimal degrees or in [±]dd:mm[:ss.xxx][W|E|S|N] format.
-Rwest/south/east/north+r. This form is useful for map projections that are oblique, making meridians and parallels poor choices for map boundaries. Here, we instead specify the lower left corner and upper right corner geographic coordinates, followed by the modifier +r. This form guarantees a rectangular map even though lines of equal longitude and latitude are not straight lines.
-Rg or -Rd. These forms can be used to quickly specify the global domain (0/360 for -Rg and -180/+180 for -Rd in longitude, with -90/+90 in latitude).
-Rcode1,code2,…[+e|r|Rincs]. This indirectly supplies the region by consulting the DCW (Digital Chart of the World) database and derives the bounding regions for one or more countries given by the codes. Simply append one or more comma-separated countries using either the two-character ISO 3166-1 alpha-2 convention (e.g., NO) or the full country name (e.g., Norway). To select a state within a country (if available), append .state (e.g, US.TX), or the full state name (e.g., Texas). To specify a whole continent, spell out the full continent name (e.g., -RAfrica). Finally, append any DCW collection abbreviations or full names for the extent of the collection or named region. All names are case-insensitive. The following modifiers can be appended:
+r to adjust the region boundaries to be multiples of the steps indicated by inc, xinc/yinc, or winc/einc/sinc/ninc [default is no adjustment]. For example, -RFR+r1 will select the national bounding box of France rounded to nearest integer degree, where inc can be positive to expand the region or negative to shrink the region.
+R to adjust the region by adding the amounts specified by inc, xinc/yinc, or winc/einc/sinc/ninc [default is no extension], where inc can be positive to expand the region or negative to shrink the region.
+e to adjust the region boundaries to be multiples of the steps indicated by inc, xinc/yinc, or winc/einc/sinc/ninc, while ensuring that the bounding box is adjusted by at least 0.25 times the increment [default is no adjustment], where inc can be positive to expand the region or negative to shrink the region.
-Rxmin/xmax/ymin/ymax[+uunit] specifies a region in projected units (e.g., UTM meters) where xmin/xmax/ymin/ymax are Cartesian projected coordinates compatible with the chosen projection (-J) and unit is an allowable distance unit [e]; we inversely project to determine the actual rectangular geographic region. For projected regions centered on (0,0) you may use the short-hand -Rhalfwidth[/halfheight]+uunit, where halfheight defaults to halfwidth if not given. This short-hand requires the +u modifier.
-Rjustifylon0/lat0/nx/ny, where justify 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). The two character code justify indicates which point on a rectangular region region the lon0/lat0 coordinates refer to and the grid dimensions nx and ny are used with grid spacings given via -I to create the corresponding region. This method can be used when creating grids. For example, -RCM25/25/50/50 specifies a 50x50 grid centered on 25,25.
-Rgridfile. This will copy the domain settings found for the grid in specified file. Note that depending on the nature of the calling module, this mechanism will also set grid spacing and possibly the grid registration (see Grid registration: The -r option).
-Ra[uto] or -Re[xact]. Under modern mode, and for plotting modules only, you can automatically determine the region from the data used. You can either get the exact area using -Re [Default if no -R is given] or a slightly larger area sensibly rounded outwards to the next multiple of increments that depend on the data range using -Ra.
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)].
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].
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]. Note that record-based E77 flags (MGD77+ format only) are not considered systematic corrections. Instead, the application of these bit-flags can be controlled via the : (colon) modifier to OPT(F).
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 .
Append the sign you want for depth, carter, and msd values below sea level (-Zn gives negative bathymetry) [Default is -Zp for positive down].
- -borecord[+b|l] (more …)
Select native binary format for table 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][+msegheader][+rremark][+ttitle] (more …)
Skip or produce header record(s).
- -je|f|g (more …)
Determine how spherical distances are calculated.
- -^ or just -
Print a short message about the syntax of the command, then exit (Note: on Windows just use -).
- -+ or just +
Print an extensive usage (help) message, including the explanation of any module-specific option (but not the GMT common options), then exit.
- -? or no arguments
Print a complete usage (help) message, including the explanation of all options, then exit.
Temporarily override a GMT default setting; repeatable. See gmt.conf for parameters.
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.txt
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.txt
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.txt
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.txt
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.txt
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.
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.
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))]
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 NCEI 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:
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
The Marine Geophysical Data Exchange Format - MGD77, see http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt
Wessel, P., and Chandler, M. T., 2007, The mgd77 supplement to the Generic Mapping Tools, Comp. Geosci., 33(1), 62-75, https://doi.org/10.1023/A:1021744224009.