1MGD77LIST(1) Generic Mapping Tools MGD77LIST(1)
2
6 mgd77list - A data-extractor for MGD77[+] files
7
9 mgd77list NGDC-ids -Fcolumns[,logic][:bittests] [ -Ac|d|f|mcode ] [
10 -Cf|g|e ] [ -Dastartdate ] [ -Dbstopdate ] [ -E ] [ -Gastartrec ] [
11 -Gbstoprec ] [ -H[i][nrec] ] [ -Iignore ] [ -X[corrtable] ] [ -M[flag]
12 ] [ -Nd|sunit ] [ -Qa|vmin/max ] [ -Rwest/east/south/north[r] ] [ -Sas‐
13 tartdist[unit] ] [ -Sbstopdist[unit] ] [ -T[m|e] ] [ -V ] [ -Wweight ]
14 [ -Z+|- ] [ -bo[s|S|d|D[ncol]|c[var1/...]] ]
15
17 mgd77list reads <NGDC-id>.[mgd77|nc] files and produces an ASCII [or
18 binary] table. The <NGDC-id>.[mgd77|nc] files contain track informa‐
19 tion such as leg-id, time and position, geophysical observables such as
20 gravity, magnetics, and bathymetry, and control codes and corrections
21 such as Eotvos and diurnal corrections. The MGD77+ extended netCDF
22 files may also contain additional user columns (for a listing of avail‐
23 able columns, use mgd77info -C, and to learn how to add your own custom
24 columns, see mgd77manage). The user may extract any combination of
25 these parameters, any of six computed quantities (distance, heading,
26 velocity, Carter correction, and gravity and magnetic global reference
27 fields), calendar sub-units of time (year, month, day, hour, min, sec),
28 the NGDC id, and finally a preset weight (see -W). A sub-section can
29 be specified by passing time- or distance-intervals along track or by
30 selecting a geographical region. Finally, each output record may be
31 required to pass any number of logical tests involving data values or
32 bit flags.
33 NGDC-ids
36 Can be one or more of five kinds of specifiers:
37 1) 8-character NGDC IDs, e.g., 01010083, JA010010etc., etc.
38 2) 2-character <agency> codes which will return all cruises from
39 each agency.
40 3) 4-character <agency><vessel> codes, which will return all
41 cruises from those vessels.
42 4) =<list>, where <list> is a table with NGDC IDs, one per line.
43 5) If nothing is specified we return all cruises in the data
44 base.
45 (See mgd77info -F for agency and vessel codes). The ".mgd77" or
46 ".nc" extensions will automatically be appended, if needed (use
47 -I to ignore certain file types). Cruise files will be looked
48 for first in the current directory and second in all directories
49 listed in $MGD77_HOME/mgd77_paths.txt [If $MGD77_HOME is not set
50 it will default to $GMT_SHAREDIR/mgd77].
51 -F The required columns string must be a comma-separated list of
53 parameter abbreviations given in the desired output order. Any
54 parameters given in UPPER case must not be NaN in a record for
55 output to occur. Unless specified separately, the output format
56 (if ASCII) is controlled by the GMT parameter D_FORMAT. The
57 available abbreviations are:
58 drt The digital record type, usually 3 or 5 (for Y2K-compliant
60 cruises).
61 id The survey ID string (leg name).
63 ngdcid The 8-character NGDC cruise ID string (usually the file prefix).
65 time Choose between Absolute calendar time (atime, the default) in
67 the format dictated by the GMT parameters OUTPUT_DATE_FORMAT
68 and OUTPUT_CLOCK_FORMAT, or Relative time (rtime) in the format
69 dictated by the GMT parameters D_FORMAT and TIME_SYSTEM (or
70 TIME_EPOCH and TIME_UNIT). Note that if -b is used then time is
71 written as seconds since 1970 (i.e., you ust select TIME_SYSTEM
72 UNIX to process this data further).
73 lon Longitude in the format dictated by the GMT parameter OUT‐
75 PUT_DEGREE_FORMAT.
76 lat Longitude in the format dictated by the GMT parameter OUT‐
78 PUT_DEGREE_FORMAT.
79 twt Two-Way Travel time (in s).
81 depth Corrected bathymetry (in m, positive below sealevel).
83 mtf1 Magnetic Total Field intensity from sensor 1 (in nTesla).
85 mtf2 Magnetic Total Field intensity from sensor 2 (in nTesla).
87 mag Residual magnetic anomaly (in nTesla).
89 gobs Observed gravity (in mGal).
91 faa Free-air gravity anomaly (in mGal).
93 ptc Position Type Code (1 = fix, 3 = interpolated, 9 = unspecified).
95 bcc Bathymetric Correction Code, indicating the procedure used to
97 convert travel time to depth. (01-55 = Matthews' zone used to
98 correct the depth, 59 = Matthews' corrections used but the zones
99 is unspecified in the data record, 60 = S. Kuwahara formula for
100 T-S, 61 = Wilson formula for T-S, 62 = Del Grosso formula for T-
101 S, 63 = Carter's tables, 88 = Other, described in header sec‐
102 tions, 99 = unspecified).
103 btc Bathymetric Type Code, indicating how the bathymetry value was
105 obtained (1 = observed, 3 = interpolated, 9 = unspecified).
106 msens Magnetic sensor for used to evaluate the residual field (1 = 1st
108 or leading sensor, 2 = 2nd or trailing sensor, 9 = unspecified).
109 msd Depth (or altitude) of the magnetic sensor (in m, positive below
111 sealevel).
112 diur Magnetic diurnal correction (in nTesla).
114 eot Eotvos correction (in mGal).
116 sln Seismic Line Number string.
118 sspn Seismic Shot Point Number string.
120 nqc Navigation Quality Code (5 = suspected, by source institution, 6
122 = suspected, by NGDC, 9 = no problems identified).
123 In addition, the following derived quantities can be requested:
125 year The year of each record.
127 month The month of each record.
129 day The day of the month of each record.
131 hour The hour of each record.
133 min The minutes of each record.
135 sec The decimal seconds of each record.
137 dist Along-track distance from start of leg. For method of calcula‐
139 tion, see -C [spherical great circle distances], and for dis‐
140 tance units, see -N [km].
141 az Ship azimuth (heading) measured clockwise from north (in
143 degrees).
144 vel Ship speed; see -N for units [m/s].
146 weight Weight assigned to this data set (see -W).
148 carter Carter depth correction, if twt is present in file (in m).
150 Sign: Correction is to be subtracted from uncorrected depths to
151 yield a corrected depth.
152 igrf International geomagnetic reference field (total field) (in
154 nTesla).
155 ngrav International Gravity reference Field ("normal gravity") (in
157 mGal). Field is selected based on the parameter Gravity Theo‐
158 retical Formula Code in the cruise's MGD77 header. If this is
159 not set or is invalid we default to the IGF 1980. Alterna‐
160 tively, specify the field directly using -Af (see that option
161 for more details).
162 The following short-hand flags are also recognized:
164 all This returns all data columns in the file.
166 mgd77 This results in all 27 MGD77 fields being written out in the
168 offical MGD77 order.
169 geo This limits the output to 10 fields (time, lon, lat plus the
171 seven geophysical observations twt, depth, mtf1, mtf2, mag,
172 gobs, and faa). By appending + to either of these set we will
173 also append dist, azim, vel, and weight as listed above.
174 As an option, logical tests may be added for any of the observa‐
176 tions by appending ,logic, which is itself composed of one or
177 more comma-separated instructions of the form parOPvalue, where
178 par is one of the parameters listed above, OP is a logical oper‐
179 ator (<, <=, =, !=, >=, >, |), and value is a constant used in
180 the comparison. Floating point parameters are compared numeri‐
181 cally; character parameters are compared lexically (after lead‐
182 ing and trailing blanks have been removed). The bit comparison
183 (|) means that at least one of the bits in value must be turned
184 on in par. At least one of the tests must be true for the
185 record to be output, except for tests using UPPER case parame‐
186 ters which all must be true for output to occur. Note that
187 specifying a test does not imply that the corresponding column
188 will be included in the output stream; it must be present in
189 columns for that to occur. Note: some of the operators are spe‐
190 cial UNIX characters and you are advised to place quotes around
191 the entire argument to -F.
192 Finally, for MGD77+ files you may optionally append :bittests
194 which is : (a colon) followed by one or more comma-separated
195 +-col terms. This compares specific bitflags only for each
196 listed column. Here, + means the chosen bit must be 1 (ON)
197 whereas - means it must be 0 (OFF). All bit tests given must be
198 passed. By default, MGD77+ files that have the special
199 MGD77_flags column present will use those flags, and observa‐
200 tions associated with ON-bits (meaning they are flagged as bad)
201 will be set to NaN; append : with no trailing information to
202 turn this behavior off (i.e., no bit flags will be consulted).
203
205 No space between the option flag and the associated arguments.
206 -A By default, corrected depth (depth), magnetic residual anomaly
208 (mag), free-air gravity anomaly (faa), and the derived quantity
209 Carter depth correction (carter) are all output as is (if
210 selected in -F); this option adjusts that behavior. For each of
211 these columns there are 2-4 ways to adjust the data. Append
212 c(arter), d(epth), f(aa), or m(ag) and select the code for the
213 procedure you want applied. You may select more than one proce‐
214 dure for a data column by summing their numerical codes (1, 2,
215 4, and 8). E.g., -Ac3 will first try method -Ac1 to estimate a
216 Carter correction but if depth is NaN we will next try -Ac2
217 which only uses twt. In all cases, if any of the values
218 required by an adjustment procedure is NaN then the result will
219 be NaN.
220 -Ac Determines how the carter correction term is calculated. Below,
222 C(twt) stands for the Carter-corrected depth (it also depends on
223 lon, lat), U(twt, v) is the uncorrected depth (= twt * v / 2)
224 using as v the "Assumed Sound Velocity" parameter in the MGD77
225 header (if it is a valid velocity, otherwise we default to 1500
226 m/s); alternatively, append your preferred velocity v in m/s,
227 TU(depth, v) is the 2-way travel time estimated from the (pre‐
228 sumably) uncorrected depth, and TC(depth) is the 2-way travel
229 time obtained by inverting the (presumably) corrected depth
230 using the Carter correction formula. Select from
231 -Ac1[,v] returns difference between U(twt, v) and depth
232 [Default].
233 -Ac2[,v] returns difference between U(twt, v) and Carter (twt).
234 -Ac4[,v] returns difference between (assumed uncorrected) depth
235 and Carter (TU(depth)).
236 -Ac8[,v] returns difference between U(TC(depth), v) and depth.
237 -Ad Determines how the depth column output is obtained:
239 -Ad1 returns depth as stored in the data set [Default].
240 -Ad2[,v] returns calculated uncorrected depth U(twt, v).
241 -Ad4 returns calculated corrected depth C(twt).
242 -Af Determines how the faa column output is obtained. If ngrav
244 (i.e., the International Gravity reference Field (IGF), or "nor‐
245 mal gravity") is required it is selected based on the MGD77
246 header parameter "Theoretical Gravity Formula Code"; if this
247 code is not present or is invalid we default to 4. Alterna‐
248 tively, append the preferred field (1-4) to select 1 (Heiskanen
249 1924), 2 (IGF 1930), 3 (IGF 1967) or 4 (IGF 1980). Select from
250 -Af1[,field] returns faa as stored in the data set [Default].
251 Optionally, sets the IGF field to use if you also have requested
252 ngrav as an output column in -F.
253 -Af2[,field] returns the difference between gobs and ngrav (with
254 optional field directive).
255 -Am Determines how the mag column output is obtained. There may be
257 one or two total field measurements in the file (mtf1 and mtf2),
258 and the column msens may state which one is the leading sensor
259 (1 or 2; it may also be undefined). Select from
260 -Am1 returns mag as stored in the data set [Default].
261 -Am2 returns the difference between mgfx and igrf, where x is
262 the leading sensor (1 or 2) indicated by the msens data field
263 (defaults to 1 if unspecified).
264 -Am4 returns the difference between mgfx and igrf, where x is
265 the sensor (2 or 1) not indicated by the msens data field
266 (defaults to 2 if unspecified).
267 -C Append a one-letter code to select the procedure for along-track
269 distance calculation (see -N for selecting units):
270 f Flat Earth distances.
271 g Great circle distances [Default].
272 e Geodesic distances on current GMT ellipsoid.
273 -Da Do not list data collected before startdate (yyyy-mm-
275 ddT[hh:mm:ss]) [Default is start of cruise].
276 -Db Do not list data collected after stopdate (yyyy-mm-
278 ddT[hh:mm:ss]). [Default is end of cruise].
279 -E Exact match: Only output records that match all the requested
281 geophysical columns [Default outputs records that matches at
282 least one of the observed columns].
283 -Ga Do not list records before startrec [Default is 0, the first
285 record].
286 -Gb Do not list data after stoprec. [Default is the last record].
288 -H Issue a header record with names for each data field.
290 -I Ignore certain data file formats from consideration. Append
292 a|c|t to ignore MGD77 ASCII, MGD77+ netCDF, or plain tab-sepa‐
293 rated ASCII table files, respectively. The option may be
294 repreated to ignore more than one format. [Default ignores
295 none].
296 -L Apply optimal corrections to columns where such corrections are
298 available. Append the correction table to use [Default uses the
299 correction table mgd77_corrections.d in the $MGD77_HOME direc‐
300 tory]. For the format of this file, see CORRECTIONS below.
301 -M Issue a multi-segment header record with cruise ID for each
303 cruise.
304 -N Append d for distance or s for speed, then give the desired unit
306 as e (meter or m/s), k (km or km/hr), m (miles or miles/hr), or
307 n (nautical miles or knots). [Default is -Ndk -Nse (km and
308 m/s)].
309 -Qa Specify an accepted range (min/max) of azimuths. Records whose
311 track azimuth falls outside this range are ignored [0-360].
312 -Qv Specify an accepted range (min/max; or just min if there is no
314 upper limit) of velocities. Records whose track speed falls
315 outside this range are ignored [0-infinity].
316 -R west, east, south, and north specify the Region of interest, and
318 you may specify them in decimal degrees or in
319 [+-]dd:mm[:ss.xxx][W|E|S|N] format. Append r if lower left and
320 upper right map coordinates are given instead of w/e/s/n. The
321 two shorthands -Rg and -Rd stand for global domain (0/360 and
322 -180/+180 in longitude respectively, with -90/+90 in latitude).
323 -Sa Do not list data that are less than startdist meter along track
325 from port of departure. Append k for km, m for miles, or n for
326 nautical miles [Default is 0 meters].
327 -Sb Do not list data that are more than stopdist meters along track
329 from port of departure. Append k for km, m for miles, or n for
330 nautical miles [Default is end of track].
331 -T Turns OFF the otherwise automatic adjustment of values based on
333 correction terms that are stored in the MGD77+ file and used to
334 counteract such things as wrong units used by the source insti‐
335 tution when creating the original MGD77 file from which the
336 MGD77+ file derives (the option has no effect on plain MGD77
337 ASCII files). Append m or e to limit the option to the MGD77 or
338 extended columns set only [Default applies to both].
339 -V Selects verbose mode, which will send progress reports to stderr
341 [Default runs "silently"].
342 -W Set the weight for these data. Weight output option must be set
344 in -F. This is useful if the data are to be processed with the
345 weighted averaging techniques offered by blockmean, blockmedian,
346 and blockmode [1].
347 -Z Append the sign you want for depth, carter, and msd values below
349 sea level (-Z- gives negative bathymetry) [Default is positive
350 down].
351 -bo Selects binary output mode (single precision; append d for dou‐
353 ble precision, or use S|D to swap bytes on output) [Default is
354 ASCII]. -H is ignored if -bo is selected. Likewise, string-
355 fields cannot be selected.
356
358 To get a (distance, heading, gravity, bathymetry) listing from
359 01010047.mgd77, starting at June 3 1971 20:45 and ending at distance =
360 5000 km, use the following command:
361 mgd77list 01010047 -Da1971-06-03T20:45 -Sb5000 -Fdist,azim,faa,depth >
363 myfile.d
364 To make input for blockmean and surface using free-air anomalies from
366 all the cruises listed in the file cruises.lis, but only the data that
367 are inside the specified area, and make the output binary:
368 mgd77list `cat cruises.lis` -Flon,lat,faa -R-40/-30/25/35 -bo > all‐
370 grav.b
371 To extract the locations of depths exceeding 9000 meter that were not
373 interpolated (btc != 1) from all the cruises listed in the file
374 cruises.lis:
375 mgd77list `cat cruises.lis` -F"depth,DEPTH>9000,BTC!=1" > really_deep.d
377 To extract dist, faa, and grav12_2 from records whose depths are shal‐
379 lower than 3 km and where none of the requested fields are NaN, from
380 all the MGD77+ netCDF files whose cruise ids are listed in the file
381 cruises.lis, we try
382 mgd77list `cat cruises.lis` -E -Ia -F"dist,faa,grav12_2,depth<3000" >
384 shallow_grav.d
385 To extract dist, faa, and grav12_2 from all the MGD77+ netCDF files
387 whose cruise ids are listed in the file cruises.lis, but only retrieve
388 records whose bitflag for faa indicates BAD values, we try
389 mgd77list `cat cruises.lis` -E -Ia -F"dist,faa,grav12_2:+faa" >
391 bad_grav.d
392 To output lon, lat, mag, and faa from all the cruises listed in the
394 file cruises.lis, but recalculate the two residuals based on the latest
395 reference fields, try:
396 mgd77list `cat cruises.lis` -Flon,lat,mag,faa -Af2,4 -Am2 > data.d
398
400 The IGRF calculations are based on a Fortran program written by Susan
401 Macmillan, British Geological Survey, translated to C via f2c by
402 Joaquim Luis, U Algarve, and adapted to GMT-style by Paul Wessel.
403
405 The equations used are reproduced here using coefficients extracted
406 directly from the source code (let us know if you find errors):
407 (1) g = 978052.0 * [1 + 0.005285 * sin^2(lat) - 7e-6 * sin^2(2*lat) +
408 27e-6 * cos^2(lat) * cos^2(lon-18)]
409 (2) g = 978049.0 * [1 + 0.0052884 * sin^2(lat) - 0.0000059 *
410 sin^2(2*lat)]
411 (3) g = 978031.846 * [1 + 0.0053024 * sin^2(lat) - 0.0000058 *
412 sin^2(2*lat)]
413 (4) g = 978032.67714 * [(1 + 0.00193185138639 * sin^2(lat)) / sqrt (1 -
414 0.00669437999013 * sin^2(lat))]
415
417 The correction table is an ASCII file with coefficients and parameters
418 needed to carry out corrections. Comment records beginning with # are
419 allowed. All correction records are of the form
420 cruiseID observation correction
422 where cruiseID is a NGDC prefix, observation is one of the abbrevia‐
424 tions for geophysical observations listed under -F above, and correc‐
425 tion consists of one or more terms that will be summed up and then sub‐
426 tracted from the observation before output. Each term must have this
427 exact syntax:
428 factor[*[function]([scale](abbrev[-origin]))[^power]]
430 where terms in brackets are optional (the brackets themselves are not
432 used but regular parentheses must be used as indicated). No spaces are
433 allowed except between terms. The factor is the amplitude of the basis
434 function, while the optional function can be one of sin, cos, or exp.
435 The optional scale and origin can be used to translate the argument
436 (before giving it to the optional function). The argument abbrev is
437 one of the abbreviations for observations listed above. If origin is
438 given as T it means that we should replace it with the value of abbrev
439 for the very first record in the file (this is usually only done for
440 time). If the first record entry is NaN we revert origin to zero.
441 Optionally, raise the entire expression to the given power, before mul‐
442 tiplying by the amplitude. The following is an example of ficticious
443 corrections to the cruise 99999999, implying the depth should have the
444 Carter correction removed, faa should have a linear trend removed, the
445 magnetic anomaly (mag) should be corrected by a strange dependency on
446 ship heading and latitude, and gobs needs to have 10 mGal added (hence
447 given as -10):
448 99999999 depth 1.0*((carter))
450 99999999 faa 14.1 1e-5*((time-T))
451 99999999 mag 0.5*cos(0.5*(azim-19))^2 1.0*exp(-1e-3(lat))^1.5
452 99999999 gobs -10
453
455 mgd77convert(1), mgd77info(1), mgd77manage(1), mgd77track(1)
456
458 Wessel, P., and W. H. F. Smith, 2005, The Generic Mapping Tools (GMT)
459 version 4.1 Technical Reference & Cookbook, SOEST/NOAA.
460 Wessel, P., and W. H. F. Smith, 1998, New, Improved Version of Generic
461 Mapping Tools Released, EOS Trans., AGU, 79 (47), p. 579.
462 Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Map‐
463 ping Tools Released, EOS Trans., AGU, 76 (33), p. 329.
464 Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Map‐
465 ping Tools Released, http://www.agu.org/eos_elec/95154e.html, Copyright
466 1995 by the American Geophysical Union.
467 Wessel, P., and W. H. F. Smith, 1991, Free Software Helps Map and Dis‐
468 play Data, EOS Trans., AGU, 72 (41), p. 441.
469 The Marine Geophysical Data Exchange Format - "MGD77", see
470 http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt
471 IGRF, see http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html
472GMT 4.3.1 15 May 2008 MGD77LIST(1)