1MGD77SNIFFER(1) Generic Mapping Tools MGD77SNIFFER(1)
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6 mgd77sniffer - Scan for errors in MGD77 data
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9 mgd77sniffer NGDC-ids [ -Afieldabbrev,scale,offset ] [ -Cmaxspd ] [
10 -Dd|e|f|l|m|s|v ][r] [ -gfieldabbrev,imggrid,scale,mode ] [ -Gfieldab‐
11 brev,grid ] [ -H[i][nrec] ] [ -Ifieldabbrev,rec1,recN ] [ -K ] [ -Lcus‐
12 tom limits file ] [ -N ] [ -Q[b|c|l|n][[/]threshold] ] [
13 -Rwest/east/south/north[r] ] [ -Sd|s|t ] [ -Tgap ] [ -V ] [
14 -Wc|g|o|s|t|v|x ] [ -bo[s|S|d|D[ncol]|c[var1/...]] ]
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17 mgd77sniffer scans old (pre-Y2K) and new format MGD77 files for errors
18 using point-by-point sanity checking, along-track detection of exces‐
19 sive slopes, and optional comparison of cruise data with global gravity
20 and predicted bathymetry grids. Detected data problems are output by
21 default as verbose descriptions of each detected error, often resulting
22 in multiple messages per scanned record. Data problems are optionally
23 output (-De option) using a computer-parseable format (see E77 ERROR
24 FORMAT description below). Default error thresholds are derived from
25 histograms of all MGD77 geophysical data collected between 1952 and
26 January, 2006. Thresholds are adjustable with the -L option.
27 NGDC-ids
29 Can be one or more of five kinds of specifiers:
30 1) 8-character NGDC IDs, e.g., 01010083, JA010010etc., etc.
31 2) 2-character <agency> codes which will return all cruises from
32 each agency.
33 3) 4-character <agency><vessel> codes, which will return all
34 cruises from those vessels.
35 4) =<list>, where <list> is a table with NGDC IDs, one per line.
36 5) If nothing is specified we return all cruises in the data
37 base.
38 (See mgd77info -F for agency and vessel codes). The ".mgd77" or
39 ".nc" extensions will automatically be appended, if needed (use
40 -I to ignore certain file types). Cruise files will be looked
41 for first in the current directory and second in all directories
42 listed in $MGD77_HOME/mgd77_paths.txt [If $MGD77_HOME is not set
43 it will default to $GMT_SHAREDIR/mgd77].
44
46 The mgd77sniffer links with Generic Mapping Tools 4.0 or later along
47 with the supplemental GMT packages x2sys and mgd77. See
48 http://gmt.soest.hawaii.edu for GMT details. Grids for comparison with
49 cruise data may be downloaded via the web.
50
52 -A Apply scale factor and DC adjustment to specified data field.
53 Allows adjustment of cruise data prior to along-track analysis.
54 CAUTION: data must be thoroughly examined before applying these
55 global data adjustments. May not be used for multiple cruises.
56 -C Set maximum ship speed in m/s, or knots with -N option. Ship
58 speeds exceeding 10 m/s (~20 knots) are flagged as excessive by
59 default.
60 -D Suppress default warning output and only dump cruise data row-
62 by-row such as values, gradients, grid-cruise differences, E77
63 error summaries for each record, re-created MGD77 records or
64 sniffer limits. Append r to include all records (default omits
65 records where navigation errors were detected).
66 -Dd output differences between cruise and grid data. Requires -G
68 option. Output columns include:
69 lat lon dist cruiseZ gridZ diff [cruiseZ2 gridZ2 diff2 ...]
71 Note: grid values are subtracted from cruise data so a positive
73 difference implies cruise > grid. For multiple grid comparison,
74 cruiseZ gridZ diff are repeated for each grid comparison in com‐
75 mand line order.
76 -De output E77 error classification format. Error output is
78 divided into (1) a header containing information globally appli‐
79 cable to the cruise and (2) individual error records summarizing
80 all errors encountered in each cruise record. mgd77sniffer
81 writes E77 directly to <ngdc_id.e77> file handle. See E77 ERROR
82 FORMAT below for additional details.
83 -Df output delta Z (change in geophysical field) column and
85 delta S (change in distance) for each geophysical field. Dis‐
86 tance between observations often differ for different fields
87 depending on instrument sampling rate, so ds is included for
88 each geophysical observation. Output columns include:
89 d[twt] ds d[depth] ds d[mtf1] ds d[mtf2] ds d[mag] ds d[diur] ds
91 d[msd] ds d[gobs] ds d[eot] ds d[faa] ds
92 -Dl display mgd77sniffer limits. Customize this output to create
94 a custom limits file for the -L option. No additional arguments
95 are required. Output columns include:
96 fieldabbrev min max maxSlope maxArea
98 -Dm output MGD77 format records in Y2K-compliant MGD77 format
100 -Ds output calculated gradients for speed and geophysical
102 fields. Gradients correspond to the gradient type selected in
103 the -S option (spatial derivatives by default). Output columns
104 include:
105 speed d[twt] d[depth] d[mtf1] d[mtf2] d[mag] d[diur] d[msd]
107 d[gobs] d[eot] d[faa]
108 See MGD77 FIELD INFO below for field and abbreviations descrip‐
110 tions.
111 -Dv display values for the twelve position and geophysical
113 fields for each MGD77 data record (in this order):
114 lat lon twt depth mtf1 mtf2 mag diur msens gobs eot faa
116 See below for MGD77 FIELD INFO.
118 -g Compare cruise data to the specified grid in Sandwell/Smith Mer‐
120 cator format. Requires a valid MGD77 field abbreviation (see
121 MGD77 FIELD INFO below) followed by a comma, the path (if not in
122 current directory) and grid filename, a scale to multiply the
123 data (1 or 0.1), and mode which stand for the following: (0) Img
124 files with no constraint code, returns data at all points, (1)
125 Img file with constraints coded, return data at all points, (2)
126 Img file with constraints coded, return data only at constrained
127 points and NaN elsewhere, and (3) Img file with constraints
128 coded, return 1 at constraints and 0 elsewhere.
129 -G Compare cruise data to the specified grid. Requires a valid
131 MGD77 field abbreviation (see MGD77 FIELD INFO below) followed
132 by a comma, then the path (if not in current directory) and grid
133 filename. Multiple grid comparison is supported by using sepa‐
134 rate -g or -G calls for each grid. See GRID FILE INFO below.
135 Grid comparison activates several additional error checks. (1)
137 Re-weighted Least Squares Regression of ship versus grid data
138 determines slope and DC shift, which when differing from
139 expected 1 and 0, respectively, may indicate incorrectly scaled
140 ship data, including incorrect units or instrument drift as well
141 as erroneous gravity tie-in. (2) Accumulated ship grid offsets
142 are computed along-track and excessive offsets are flagged
143 according to maxArea threshold (use -L option to adjust
144 maxArea). Warning: predicted bathymetry grids are constrained by
145 cruise data so grids and cruise data are not always independent.
146 Comparison of cruise bathymetry with predicted bathymetry grids
147 also activates a "navigation crossing over land" check.
148 -H (with -G|g only) disable (or force) decimation during RLS analy‐
151 sis of ship and gridded data. By default mgd77sniffer analyses
152 both the full and decimated data sets then reports RLS statis‐
153 tics for the higher correlation regression.
154 -Hb analyze both (default), report better of two.
156 -Hd to disable data decimation (equivalent to -H with no argu‐
158 ment).
159 -Hf to force data decimation.
161 -I Append a field abbreviation and the first and last record in a
163 range of records that should be flagged as bad (and set to NaN
164 prior to the analysis). Repeat as many times as needed. May not
165 be used for multiple cruises.
166 -K Reverse navigation quality flags (good to bad and vice versa).
168 May be necessary when a majority of navigation fixes are erro‐
169 neously flagged bad, which can happen when a cruise's first nav‐
170 igation fix is extremely erroneous. Caution! This will affect
171 sniffer output and should only be attempted after careful manual
172 navigation review.
173 -L Override mgd77sniffer default error detection limits. Supply
175 path and filename to the custom limits file. Rows not beginning
176 with a valid MGD77 field abbreviation are ignored. Field abbre‐
177 viations are listed below in exact form under MGD77 FIELD INFO.
178 Multiple field limits may be modified using one default file,
179 one field per line. Field min, max, max slope and max area may
180 be changed for each field. Max slope pertains to the gradient
181 type selected using the -S option. Max area is used by the -G
182 option as the threshold for flagging excessive offsets from the
183 specified grid. Dump defaults -Dl to view syntax or to quickly
184 create an editable custom limits file.
185 Example custom default file contents (see below for units):
187 # abbrev min max maxSlope maxArea
188 twt 0 15 1 0
189 depth 0 11000 500 5000
190 mag -800 800 - -
191 faa -300 300 100 2500
192 Use a dash '-' to retain a default limit. Hint: to test your
194 custom limits, try: mgd77sniffer -Dl -L<yourlimitsfile>
195 -N Use nautical units.
197 -P Flag regression statistics that are outside the specified confi‐
199 dence level. (i.e., -P5 flags coefficients m, b, rms, and r
200 that fall outside 95%.)
201 -Q Quick mode, use bilinear rather than bicubic interpolation
203 [Default]. Alternatively, select the interpolation mode by
204 adding b for B-spline smooting, c for bicubic interpolation, l
205 for bilinear interpolation or n for nearest-neighbor value.
206 Optionally, append threshold in the range [0,1]. This parameter
207 controls how close to nodes with NaN values the interpolation
208 will go. E.g., a threshold of 0.5 will interpolate about half
209 way from a non-NaN to a NaN node, whereas 0.1 will go about 90%
210 of the way, etc. [Default is 1, which means none of the (4 or
211 16) nearby nodes may be NaN]. -Q0 will just return the value of
212 the nearest node instead of interpolating. This is the same as
213 using -Qn.
214 -R west, east, south, and north specify the Region of interest, and
216 you may specify them in decimal degrees or in
217 [+-]dd:mm[:ss.xxx][W|E|S|N] format. Append r if lower left and
218 upper right map coordinates are given instead of w/e/s/n. The
219 two shorthands -Rg and -Rd stand for global domain (0/360 and
220 -180/+180 in longitude respectively, with -90/+90 in latitude).
221 -S Specify gradient type for along-track excessive slope checking.
223 -Sd Calculate change in z values along track (dz). Output is
224 given in geophysical units, e.g. mGal.
225 -Ss Calculate spatial gradients (dz/ds). Output is given in geo‐
226 physical units per km along the survey track, e.g. mGal/km.
227 -St Calculate time gradients (dz/dt) [default]. Output is given
228 in geophysical units per second along the survey track, e.g.
229 mGal/sec.
230 -T Adjusts mgd77sniffer gap handling. By default, data gaps greater
232 than 5 km are skipped. Set to zero to de-activate gap skipping.
233 -W Print out only certain warning types for verbose error messages.
235 Comma delimit any combination of c|g|o|s|t|v|x: where (c) type
236 code warnings, (g)radient out of range, (o)ffsets from grid
237 (requires -G|g), (s)peed out of range, (t)ime warnings, (v)alue
238 out of range, (x) warning summaries. By default ALL warning mes‐
239 sages are printed.Not compatible with any -D options.
240 -V runs in verbose mode.
242 -b output binary data for -Dd|f|s|v option. Append s for single
244 and d for double precision [Default is double].
245
247 Field Abbreviation Units
248 Two-way Travel Time twt sec
249 Corrected Depth depth m
250 Mag Total Field1 mtf1 nT
251 Mag Total Field2 mtf2 nT
252 Residual Magnetic mag nT
253 Diurnal Correction diur nT
254 Mag Sensor Depth/Alt msens m
255 Observed Gravity gobs mGal
256 Eotvos Correction eot mGal
257 Free Air Anomaly faa mGal
258
260 For -g the grids must be in the format used by Sandwell & Smith, which
261 is a spherical Mercator 2-byte grid with no header. For -G the grid
262 files can be of any grid type supported by GMT and therefore must con‐
263 tain a GMT header. A correctly formatted *.i2 grid file can be gener‐
264 ated using grdraster as shown below.
265 gmtset GRIDFILE_SHORTHAND TRUE
267 Create/edit .gmt_io file to include the following rows:
269 # GMT I/O shorthand file
270 # suffix format_id scale offset NaN
271 grd 0 - - -
272 i2 2 - - 32767
273 grdraster 1 -R0/359:55/-90/90 -Getopo5_hdr.i2
275 The new grid, etopo5_hdr.i2 in this example, contains a GMT header and
277 can be used in the -G option to compare cruise depth with grid values.
278
280 Header Information pertaining to an entire cruise, such as NGDC and
281 survey institution identification codes, cruise examination
282 time, two-way travel time corrector information, data precision
283 warnings, as well as systematic scales, DC shifts and correla‐
284 tion coefficients from global grid comparisons are reported as
285 E77 header information.
286 Sample
288 # Cruise 08010039 ID 74010908 MGD77 FILE VERSION: 19801230
289 N_RECS: 3066
290 # Examined: Wed Oct 3 16:30:13 2007 by mtchandl
291 # Arguments: -De -Gdepth,/data/GRIDS/etopo5_hdr.i2
292 N Errata table verification status
293 # mgd77manage applies corrections if the errata table is veri‐
294 fied (toggle 'N' above to 'Y' after review)
295 # For instructions on E77 format and usage, see
296 http://gmt.soest.hawaii.edu/mgd77/errata.php
297 # Verified by:
298 # Comments:
299 # Errata: Header
300 Y-E-08010039-H13-02: Invalid Magnetics Sampling Rate: (99) [ ]
301 Y-W-08010039-H13-10: Survey year (1975) outside magnetic refer‐
302 ence field IGRF 1965 time range (1965-1970)
303 Y-I-08010039-depth-00: RLS m: 1.00053 b: 0 rms: 127.851 r:
304 0.973422 significant: 1 decimation: 0
305 Y-W-08010039-twt-09: More recent bathymetry correction table
306 available
307 Y-W-08010039-mtf1-10: Integer precision
308 Y-W-08010039-mag-10: Integer precision
309 Error Record
312 Individual error records have strict format. Included is a time
313 or distance column followed by record number, a formatted error
314 code string, and finally a verbose description of errors
315 detected in the record. Three error classes are encoded into the
316 error code string with different alphabetic characters repre‐
317 senting unique error types. See below for error code format
318 description.
319 Format
321 <time/distance> <record number> <error code string> <descrip‐
322 tion>
323 Sample
325 # Errata: Data
326 Y 08010039 1975-05-10T22:16:05.88 74 C-0-0 NAV:
327 excessive speed
328 Error Code Description
331 Each of the three error classes is separated by a dash '-' and
332 described by a combination of alphabetic characters or 0 signi‐
333 fying no detected problems.
334 Error classes: NAV-VAL-GRAD
336 Error Class Descriptions
338 NAV (navigation):
339 0 - fine
340 A - time out of range
341 B - time decreasing
342 C - excessive speed
343 D - above sea level
344 E - lat undefined
345 F - lon undefined
346 VAL (value):
348 0 - fine
349 K - twt invalid
350 L - depth invalid
351 O - mtf1 invalid
352 etc.
353 GRAD (gradient):
355 0 - fine
356 K - d[twt] excessive
357 L - d[depth] excessive
358 O - d[mtf1] excessive
359 etc.
360 The NAV error class has unique cases while VAL and GRAD classes
362 are described by alphabetic characters for each of the 24
363 numeric fields in MGD77 format order.
364 MGD77 bit-pattern w/ E77 alpha characters
366 |-------------------------------------------------|----------|
367 | X W V U T S R Q P O N M L K J I H G F E D C B A | E77 Code |
368 | - - - - - - - - - - - - - - - - - - - - - - - - | - - - - -|
369 | n f e g m d m m m m b b d t p l l m h d m y t d | F I |
370 | q a o o s i s a t t t c e w t o a i o a o e z r | i D |
371 | c a t b d u e g f f c c p t c n t n u y n a t | e |
372 | s r n 2 1 t r t r | l |
373 | s h h | d |
374 | - - - - - - - - - - - - - - - - - - - - - - - - | - - - - -|
375 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | Bit place|
376 | - G C G C C - G G G - - G G - - - T T T T T - - | Bit type |
377 |-------------------------------------------------|----------|
378 Bit types: (G)eophysical, (C)orrection, (T)ime
379
382 To scan for excessive values or gradients, try
383 mgd77sniffer 08010001
385 To dump cruise gradients, try
387 mgd77sniffer 08010001 -Ds
389 To compare cruise depth with ETOPO5 bathymetry and gravity with
391 Sandwell/Smith 2 min gravity version 11, try
392 mgd77sniffer 08010001 -Gdepth,/data/GRIDS/etopo5_hdr.i2
394 -gfaa,/data/GRIDS/grav.11.2.img,0.1,1
395
398 mgd77list(1), mgd77track(1) x2sys_init(1)
399
401 The Marine Geophysical Data Exchange Format - "MGD77", see
402 http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt
403 Wessel, P., and W. H. F. Smith, 2006, The Generic Mapping Tools (GMT)
405 version 4.1.1 Technical Reference & Cookbook, SOEST/NOAA.
406GMT 4.3.1 15 May 2008 MGD77SNIFFER(1)