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mgd77sniffer(1)                       GMT                      mgd77sniffer(1)




NAME

       mgd77sniffer - Along-track quality control of MGD77 cruises


SYNOPSIS

       mgd77sniffer  NGDC-ids  [  -Afieldabbrev,scale,offset ] [  -Cmaxspd ] [
       -Dd|e|E|f|l|m|s|v[r] ] [  -E ] [   -Gfieldabbrev,imggrid,scale,mode  or
       -Gfieldabbrev,grid  ]  [   -H  ] [  -Ifieldabbrev,rec1,recN ] [  -Lcus-
       tom-limits-file ] [  -M ] [  -N ] [  -Rregion ] [  -Sd|s|t ] [  -Tgap ]
       [  -V[level] ] [  -Wc|g|o|s|t|v|x ] [  -Zlevel ] [ -bobinary ] [ -dono-
       data ] [ -nflags ]

       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 out-
       put  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.


REQUIREMENTS

       The mgd77sniffer links with Generic Mapping Tools 4.0  or  later  along
       with   the   supplemental   GMT   packages   x2sys   and   mgd77.   See
       http://gmt.soest.hawaii.edu for GMT details. 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 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).  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+ (a.nca), MGD77T (a.m77ta), MGD77 (a.mgd77a ) and plain
              text file (a.data).  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

       -Afieldabbrev,scale,offset
              Apply scale factor and DC 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.

       -Cmaxspd
              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 ^<i>a|]

              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 com-
              mand line order.

              -De  output  E77  error  classification  format. Error output is
              divided into (1) a header containing information globally appli-
              cable to the cruise and (2) individual error records summarizing
              all errors  encountered  in  each  cruise  record.  mgd77sniffer
              writes  E77 directly to <ngdc_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. Dis-
              tance 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  descrip-
              tions.

              -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 erro-
              neously flagged bad, which can happen when a cruiseas first nav-
              igation  fix  is  extremely erroneous. Caution! This will affect
              sniffer output and should only be attempted after careful manual
              navigation review.

       -Ginformation
              Compare  cruise data to GMT or IMG grids. Use one of the formats
              below.  -Gfieldabbrev,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) fol-
              lowed  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.  -Gfieldabbrev,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 com-
              parison 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  DC  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 anavigation crossing over landa check.

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

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

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

              -Hf to force data decimation.

       -Ifieldabbrev,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.

       -Lcustom-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 abbre-
              viations 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   | a        | a       |
                       +---------+------+-------+----------+---------+
                       |faa      | -300 | 300   | 100      | 2500    |
                       +---------+------+-------+----------+---------+

              Use  a  dash  a-a  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.

       -Rwest/east/south/north[/zmin/zmax][+r][+uunit]
              west, east, south, and north specify the region of interest, and
              you    may    specify    them   in   decimal   degrees   or   in
              [A+-]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. Appending +uunit expects projected (Carte-
              sian)  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.

       -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  gra-
              dients  (dz/dt)  [default]. Output is given in geophysical units
              per second along the survey track, e.g., mGal/sec.

       -Tgap  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 mes-
              sages are printed.Not compatible with any -D options.

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

       -V[level] (more a|)
              Select verbosity level [c].

       -bo[ncols][type] (more a|)
              Select  native  binary  output. Output binary data for -Dd|f|s|v
              option.

       -donodata (more a|)
              Replace output columns that equal NaN with nodata.

       -n[b|c|l|n][+a][+bBC][+c][+tthreshold] (more a|)
              Select interpolation mode for grids.

       -^ or just -
              Print a short message about the  syntax  of  the  command,  then
              exits (NOTE: on Windows just use -).

       -+ or just +
              Print  an extensive usage (help) message, including the explana-
              tion 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 all options, then exits.


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 lim-
       its 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 eitehr be in  the  format  used  by  Sandwell  &
       Smith, which is a spherical Mercator 2-byte grid with no header, or any
       grid type supported by GMT and therefore must contain a GMT  header.  A
       correctly  formatted *.i2 grid file can be generated using grdraster as
       shown below.

       gmtset GRIDFILE_SHORTHAND TRUE

       Create/edit .gmt_io file to include the following rows:

       # GMT I/O shorthand file

       # suffix  format_id  scale  offset  NaN

       grd 0  -  -  -  -

       i2  2  -  -  32767

              gmt grdraster 1 -R0/359:55/-90/90 -Getopo5_hdr.i2

       The new grid, etopo5_hdr.i2 in this example, contains a GMT header  and
       can  be used in the -G option to compare cruise depth with grid values.


E77 ERROR FORMAT

       Header Information pertaining to an entire cruise,  such  as  NGDC  and
              survey  institution  identification  codes,  cruise  examination
              time, two-way travel time corrector information, data  precision
              warnings,  as  well as systematic scales, DC shifts and correla-
              tion 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  veri-
              fied (toggle aNa above to aYa 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  refer-
              ence 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 repre-
              senting 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  signi-
              fying 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

              |aaaaaaaaaaaaaaaa-|aaa-|

              | 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 |

              |aaaaaaaaaaaaaaaa-|aaa-|

              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

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


SEE ALSO

       grdraster(1), mgd77list(1), mgd77track(1), x2sys_init(1)


REFERENCES

       The  Marine   Geophysical   Data   Exchange   Format   -   MGD77,   see
       http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt.


COPYRIGHT

       2017, P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis, and F. Wobbe



5.4.2                            Jun 24, 2017                  mgd77sniffer(1)

gmt5 5.4.2 - Generated Thu Jun 29 14:50:36 CDT 2017
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