# mgd77sniffer

Along-track quality control of MGD77 cruises

## Synopsis

gmt mgd77sniffer GEODAS-ids [ -A fieldabbrev,scale,offset ] [ -C maxspd ] [ -D d|e|E|f|l|m|s|v[r] ] [ -E ] [ -G fieldabbrev,imggrid,scale,mode or -G fieldabbrev,grid ] [ -H ] [ -I fieldabbrev,rec1,recN ] [ -L custom-limits-file ] [ -M ] [ -N ] [ -R region ] [ -S d|s|t ] [ -T gap ] [ -V[level] ] [ -W c|g|o|s|t|v|x ] [ -Z level ] [ -bo binary ] [ -do nodata[+c col] ] [ -n flags ] [ --PAR=value ]

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

## Description

mgd77sniffer scans old (pre-Y2K) and new format ASCII MGD77 files for errors using point-by-point sanity checking, along-track detection of excessive slopes, and optional comparison of cruise data with global gravity and predicted bathymetry grids. Detected data problems are output by default as verbose descriptions of each detected error, often resulting in multiple messages per scanned record. Data problems are optionally output (-De option) using a computer-parseable format (see E77 ERROR FORMAT description below). Default error thresholds are derived from histograms of all MGD77 geophysical data collected between 1952 and January, 2006. Thresholds are adjustable with the -L option. Grids for comparison with cruise data may be downloaded via the web.

## Required Arguments

NGDC-ids

  Can be one or more of five kinds of specifiers:

  1. 8-character GEODAS 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 GEODAS 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). 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].

## Optional Arguments

-A fieldabbrev,scale,offset

  Apply scale factor and offset adjustment to specified data field. Allows adjustment of cruise data prior to along-track analysis. CAUTION: data must be thoroughly examined before applying these global data adjustments. May not be used for multiple cruises.

-C maxspd

  Set maximum ship speed in m/s, or knots with -N option. Ship speeds exceeding 10 m/s (~20 knots) are flagged as excessive by default.

-Dd|e|E|f|l|m|s|v[r]

  Suppress default warning output and only dump cruise data row-by-row such as values, gradients, grid-cruise differences, E77 error summaries for each record, re-created MGD77 records or sniffer limits. Append r to include all records (default omits records where navigation errors were detected).

  -Dd output differences between cruise and grid data. Requires -G option. Output columns include:

  lat lon dist cruiseZ gridZ diff [cruiseZ2 gridZ2 diff2 …]

  Note: Grid values are subtracted from cruise data so a positive difference implies cruise > grid. For multiple grid comparison, cruiseZ gridZ diff are repeated for each grid comparison in command line order.

  -De output E77 error classification format. Error output is divided into (1) a header containing information globally applicable to the cruise and (2) individual error records summarizing all errors encountered in each cruise record. mgd77sniffer writes E77 directly to <geodas_id.e77> file handle. See E77 ERROR FORMAT below for additional details.

  -DE Same as -De but no regression tests will be carried out.

  -Df output delta Z (change in geophysical field) column and delta S (change in distance) for each geophysical field. Distance between observations often differ for different fields depending on instrument sampling rate, so ds is included for each geophysical observation. Output columns include:

  d[twt] ds d[depth] ds d[mtf1] ds d[mtf2] ds d[mag] ds d[diur] ds d[msd] ds d[gobs] ds d[eot] ds d[faa] ds

  -Dl display mgd77sniffer limits. Customize this output to create a custom limits file for the -L option. No additional arguments are required. Output columns include:

  fieldabbrev min max maxSlope maxArea

  -Dm output MGD77 format records in Y2K-compliant MGD77 format

  -Dn output distance to coast for each record. Requires the -Gnav option. Output columns include:

  lat lon dist distToCoast

  -Ds output calculated gradients for speed and geophysical fields. Gradients correspond to the gradient type selected in the -S option (spatial derivatives by default). Output columns include:

  speed d[twt] d[depth] d[mtf1] d[mtf2] d[mag] d[diur] d[msd] d[gobs] d[eot] d[faa]

  See MGD77 FIELD INFO below for field and abbreviations descriptions.

  -Dv display values for the twelve position and geophysical fields for each MGD77 data record (in this order):

  lat lon twt depth mtf1 mtf2 mag diur msens gobs eot faa

  See below for MGD77 FIELD INFO.

-E

  Reverse navigation quality flags (good to bad and vice versa). May be necessary when a majority of navigation fixes are erroneously flagged bad, which can happen when a cruise’s first navigation fix is extremely erroneous. Caution! This will affect sniffer output and should only be attempted after careful manual navigation review.

-G information

  Compare cruise data to GMT or IMG grids. Use one of the formats below. -G fieldabbrev,imggrid,scale,mode Compare cruise data to the specified grid in Sandwell/Smith Mercator format. Requires a valid MGD77 field abbreviation (see MGD77 FIELD INFO below) followed by a comma, the path (if not in current directory) and grid filename, a scale to multiply the data (1 or 0.1), and mode which stand for the following: (0) Img files with no constraint code, returns data at all points, (1) Img file with constraints coded, return data at all points, (2) Img file with constraints coded, return data only at constrained points and NaN elsewhere, and (3) Img file with constraints coded, return 1 at constraints and 0 elsewhere. -G fieldabbrev,grid Compare cruise data to the specified grid. Requires a valid MGD77 field abbreviation (see MGD77 FIELD INFO below) followed by a comma, then the path (if not in current directory) and grid filename. Multiple grid comparison is supported by using separate -G calls for each grid. See GRID FILE INFO below.

  Grid comparison activates several additional error checks. (1) Re-weighted Least Squares Regression of ship versus grid data determines slope and intercept shift, which when differing from expected 1 and 0, respectively, may indicate incorrectly scaled ship data, including incorrect units or instrument drift as well as erroneous gravity tie-in. (2) Accumulated ship grid offsets are computed along-track and excessive offsets are flagged according to maxArea threshold (use -L option to adjust maxArea). Warning: predicted bathymetry grids are constrained by cruise data so grids and cruise data are not always independent. Comparison of cruise bathymetry with predicted bathymetry grids also activates a “navigation crossing over land” check.

-H

  (with -G|g only) disable (or force) decimation during RLS analysis of ship and gridded data. By default mgd77sniffer analyses both the full and decimated data sets then reports RLS statistics for the higher correlation regression.

  -Hb analyze both (default), report better of two.

  -Hd to disable data decimation (equivalent to -H with no argument).

  -Hf to force data decimation.

-I fieldabbrev,rec1,recN

  Append a field abbreviation and the first and last record in a range of records that should be flagged as bad (and set to NaN prior to the analysis). Repeat as many times as needed. May not be used for multiple cruises.

-L custom-limits-file

  Override mgd77sniffer default error detection limits. Supply path and filename to the custom limits file. Rows not beginning with a valid MGD77 field abbreviation are ignored. Field abbreviations are listed below in exact form under MGD77 FIELD INFO. Multiple field limits may be modified using one default file, one field per line. Field min, max, max slope and max area may be changed for each field. Max slope pertains to the gradient type selected using the -S option. Max area is used by the -G option as the threshold for flagging excessive offsets from the specified grid. Dump defaults -Dl to view syntax or to quickly create an editable custom limits file.

  Example custom default file contents (see below for units):

  # abbrev | min | max | maxSlope | maxArea
  twt | 0 | 15 | 1 | 0
  depth | 0 | 11000 | 500 | 5000
  mag | -800 | 800 | -- | --
  faa | -300 | 300 | 100 | 2500

  Use a dash ‘-’ to retain a default limit. Hint: to test your custom limits, try: mgd77sniffer -Dl -L<yourlimitsfile>

-M

  Adjust navigation on land threshold (meters inland) [100].

-N

  Use nautical units.

-R west/east/south/north[/zmin/zmax][+r][+u unit]

> Specify the region of interest.

> The region may be specified in one of several ways:

> 1. -R west/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.

> 2. -R west/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.

> 3. -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).

> 4. -R code1,code2,…[+e|r|R incs]. 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, -R FR+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.

> 5. -R xmin/xmax/ymin/ymax[+u unit] 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 -R halfwidth[/halfheight]+u unit, where halfheight defaults to halfwidth if not given. This short-hand requires the +u modifier.

> 6. -R justifylon0/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, -RCM 25/25/50/50 specifies a 50x50 grid centered on 25,25.

> 7. -R gridfile. 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).

> 8. -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.

-Sd|s|t

  Specify gradient type for along-track excessive slope checking. -Sd Calculate change in z values along track (dz). Output is given in geophysical units, e.g., mGal. -Ss Calculate spatial gradients (dz/ds). Output is given in geophysical units per km along the survey track, e.g., mGal/km. -St Calculate time gradients (dz/dt) [default]. Output is given in geophysical units per second along the survey track, e.g., mGal/sec.

-T gap

  Adjusts mgd77sniffer gap handling. By default, data gaps greater than 5 km are skipped. Set to zero to de-activate gap skipping.

-Wc|g|o|s|t|v|x

  Print out only certain warning types for verbose error messages. Comma delimit any combination of c|g|o|s|t|v|x: where (c) type code warnings, (g)radient out of range, (o)ffsets from grid (requires -G|g), (s)peed out of range, (t)ime warnings, (v)alue out of range, (x) warning summaries. By default ALL warning messages are printed.Not compatible with any -D options.

-V[level]

  Select verbosity level [w]. (See full description) (See cookbook information).

-Z

  Flag regression statistics that are outside the specified confidence level. (i.e., -Z5 flags coefficients m, b, rms, and r that fall outside 95%.)

-bo record[+b|l] (more …)

  Select native binary format for table output. Output binary data for -Dd|f|s|v option.

-do nodata[+c col] (more …)

  Replace output columns that equal NaN with nodata.

-n[b|c|l|n][+a][+b BC][+c][+t threshold] (more …)

  Select interpolation mode for grids.

-^ 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.

--PAR=value

  Temporarily override a GMT default setting; repeatable. See gmt.conf for parameters.

## Consequences of grid resampling

Resample or sampling of grids will use various algorithms (see -n) that may lead to possible distortions or unexpected results in the resampled values. One expected effect of resampling with splines is the tendency for the new resampled values to slightly exceed the global min/max limits of the original grid. If this is unacceptable, you can impose clipping of the resampled values values so they do not exceed the input min/max values by adding +c to your -n option.

## Mgd77 Field Info

Field | Abbreviation | Units
Two-way | Travel | Time
Corrected | Depth | depth
Mag | Total | Field1
Mag | Total | Field2
Residual | Magnetic | mag
Diurnal | Correction | diur
Mag | Sensor | Depth/Alt
Observed | Gravity | gobs
Eotvos | Correction | eot
Free | Air | Anomaly

## Grid File Info

For -G the grids must either be in the img format used by Sandwell & Smith, which is a spherical Mercator 2-byte grid with no header, or any regular grid type supported by GMT.

## E77 Error Format

Header

  Information pertaining to an entire cruise, such as NCEI and survey institution identification codes, cruise examination time, two-way travel time corrector information, data precision warnings, as well as systematic scales, constant offsets and correlation coefficients from global grid comparisons are reported as E77 header information.

  Sample

  # Cruise 08010039 ID 74010908 MGD77 FILE VERSION: 19801230 N_RECS: 3066

  # Examined: Wed Oct 3 16:30:13 2007 by mtchandl

  # Arguments: -De -Gdepth,/data/GRIDS/etopo5_hdr.i2

  N Errata table verification status

  # mgd77manage applies corrections if the errata table is verified (toggle ‘N’ above to ‘Y’ after review)

  # For instructions on E77 format and usage, see http://gmt.soest.hawaii.edu/mgd77/errata.php

  # Verified by:

  # Comments:

  # Errata: Header

  Y-E-08010039-H13-02: Invalid Magnetics Sampling Rate: (99) [ ]

  Y-W-08010039-H13-10: Survey year (1975) outside magnetic reference field IGRF 1965 time range (1965-1970)

  Y-I-08010039-depth-00: RLS m: 1.00053 b: 0 rms: 127.851 r: 0.973422 significant: 1 decimation: 0

  Y-W-08010039-twt-09: More recent bathymetry correction table available

  Y-W-08010039-mtf1-10: Integer precision

  Y-W-08010039-mag-10: Integer precision

Error Record

  Individual error records have strict format. Included is a time or distance column followed by record number, a formatted error code string, and finally a verbose description of errors detected in the record. Three error classes are encoded into the error code string with different alphabetic characters representing unique error types. See below for error code format description.

  Format <time/distance> <record number> <error code string> <description>

  Sample

  # Errata: Data

  Y 08010039 1975-05-10T22:16:05.88 74 C-0-0 NAV: excessive speed

Error Code Description

  Each of the three error classes is separated by a dash - and described by a combination of alphabetic characters or 0 signifying no detected problems.

  Error classes: NAV-VAL-GRAD

  Error Class Descriptions

  NAV (navigation):

  0 - fine

  A - time out of range

  B - time decreasing

  C - excessive speed

  D - above sea level

  E - lat undefined

  F - lon undefined

  VAL (value):

  0 - fine

  K - twt invalid

  L - depth invalid

  O - mtf1 invalid

  etc.

  GRAD (gradient):

  0 - fine

  K - d[twt] excessive

  L - d[depth] excessive

  O - d[mtf1] excessive

    etc.

  The NAV error class has unique cases while VAL and GRAD classes are described by alphabetic characters for each of the 24 numeric fields in MGD77 format order.

  MGD77 bit-pattern w/ E77 alpha characters

  |-------------------------------------------------|----------|

  | 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 |

  | - - - - - - - - - - - - - - - - - - - - - - - - | - - - - -|

  | 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 |

  | 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 |

  | c a t b d u e g f f c c p t c n t n u y n a t | e |

  | s r n 2 1 t r t r | l |

  | s h h | d |

  | - - - - - - - - - - - - - - - - - - - - - - - - | - - - - -|

  | 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|

  | - G C G C C - G G G - - G G - - - T T T T T - - | Bit type |

  |-------------------------------------------------|----------|

  Bit types: (G)eophysical, (C)orrection, (T)ime

## Examples

To scan for excessive values or gradients, try

    gmt mgd77sniffer 08010001

To dump cruise gradients, try

    gmt mgd77sniffer 08010001 -Ds

To compare cruise depth with ETOPO5 bathymetry and gravity with Sandwell/Smith 2 min gravity version 11, try

    gmt mgd77sniffer 08010001 -Gdepth,/data/GRIDS/etopo5_hdr.i2 \
                 -Gfaa,/data/GRIDS/grav.11.2.img,0.1,1

## See Also

mgd77list, mgd77track x2sys_init

## References

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/10.1016/j.cageo.2006.05.006.