MGD77MANAGE(1) Generic Mapping Tools MGD77MANAGE(1)NAMEmgd77manage - Manage extra columns in MGD77+ files
SYNOPSISmgd77manage NGDC-ids [ -A[+]a|c|d|D|e|E|g|i|n|t|Tfileinfo ] [ -Cf|g|e ]
[ -Dabbrev1,abbrev2,... ] [ -Eempty ] [ -F ] [ -Iab‐
brev/name/unit/t/scale/offset/comment ] [ -Ne|k|m|n ] [
-Q[b|c|l|n][[/]threshold] ] [ -V ] [ -bi[s|S|d|D[ncol]|c[var1/...]] ]
DESCRIPTIONmgd77manage deals with maintaining extra custom columns in MGD77+
netCDF files. You can either delete one or more columns, add a new
column, update an existing column with new data, or supply error cor‐
rection information (*.e77 files). New data may come from a table
(ASCII unless -b is used), be based on existing columns and certain
theoretical expressions, or they may be obtained by sampling a grid
(choose between GMT grid or a Sandwell/Smith Mercator *.img grid) along
track. The new data will be appended to the MGD77+ file in the form of
an extra data column of specified type. The data file will be modi‐
fied; no new file will be created. For the big issues, see the DISCUS‐
SION section below.
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). The ".mgd77" or
".nc" extensions will automatically be appended, if needed (use
-I to ignore certain 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].
OPTIONS
No space between the option flag and the associated arguments
-A Add a new data column. If an existing column with the same
abbreviation already exists in the file we will cowardly refuse
to update the file. Specifying -A+ overcomes this reluctance
(However, sometimes an existing column cannot be upgraded with‐
out first deleting it; if so you will be warned). Select a col‐
umn source code among a, c, d, D, e, g, i, n, t, or T; detailed
descriptions for each choice follow:
a Append filename of a single column table to add. File must
have the same number of rows as the MGD77+ file. If no file is
given we read from stdin instead.
c Create a new column that derives from existing data or formu‐
las for corrections and reference fields. Append c for the
Carter corrections subtracted from uncorrected depths, g for the
IGF gravity reference field (a.k.a "normal gravity"), m for the
IGRF total field magnetic reference field, and r for recomputed
magnetic anomaly (append 1 or 2 to specify which total field
column to use [1]). For gravity we choose the reference field
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. You can override this behaviour by
appending the desired code: 1 = Heiskanen 1924, 2 = Interna‐
tional 1930, 3 = IGF1967, or 4 = IGF1980.
d Append filename of a two-column table with the first column
holding distances along track and the second column holding data
values. If no file is given we read from stdin instead.
Records with matching distances in the MGD77+ file will be
assigned the new values; at other distances we set them to NaN.
Alternatively, give upper case D instead and we will interpolate
the column at all record distances. See -N for choosing dis‐
tance units and -C for choosing how distances are calculated.
e Expects to find an e77 error/correction log from mgd77sniffer
with the name NGDC_ID.e77 in the current directory or in
$MGD77_HOME/E77; this file will examined and used to make modi‐
fications to the header values, specify a systematic correction
for certain columns (such as scale and offset), specify that a
certain anomaly should be recalculated from the observations
(e.g., recalculate mag from mtf1 and the latest IGRF), and add
or update the special column flag which may hold bitflags (0 =
GOOD, 1 = BAD) for each data field in the standard MGD77 data
set. Any fixed correction terms found (such as needing to scale
a field by 0.1 or 10 because the source agency used incorrect
units) will be written as attributes to the netCDF MGD77+ file
and applied when the data are read by mgd77list. Ephemeral cor‐
rections such as those determined by crossover analysis are not
kept in the data files but reside in correction tables (see
mgd77list for details). By default, the first character of each
header line in the e77 file (which is ?, Y or N) will be con‐
sulted to see if the corresponding adjustment should be applied.
If any undecided settings are found (i.i, ?) we will abort and
make no changes. Only records marked Y will be processed. You
can override this behavior by appending one or more modifiers to
the -Ae command: h will ignore all header corrections, f will
ignore all fixed systematic trend corrections, n, v, and s will
ignore bitflags pertaining to navigation, data values, and data
slopes, respectively. Use -A+e to replace any existing E77 cor‐
rections in the file with the new values. Finally, e77 correc‐
tions will not be applied if the E77 file has not been verified.
Use -AE to ignore the verification status.
g Sample a GMT geographic (lon, lat) grid along the track given
by the MGD77+ file using bicubic interpolation (however, see
-Q). Append name of a GMT grid file.
i Sample a Sandwell/Smith Mercator *.img grid along the track
given by the MGD77+ file using bicubic interpolation (however,
see -Q). Append the img grid filename, followed by the comma-
separated data scale (typically 1 or 0.1), the IMG file mode
(0-3), and optionally the img grid max latitude [80.738]. The
modes 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.
n Append filename of a two-column table with the first column
holding the record number (0 to nrows - 1) and the second column
holding data values. If no file is given we read from stdin
instead. Records with matching record numbers in the MGD77+
file will be assigned the new values; at other records we set
them to NaN.
t Append filename of a two-column table with the first column
holding absolute times along track and the second column holding
data values. If no file is given we read from stdin instead.
Records with matching times in the MGD77+ file will be assigned
the new values; at other times we set them to NaN. Alterna‐
tively, give upper case T instead and we will interpolate the
column at all record times.
-C Append a one-letter code to select the procedure for along-track
distance calculation when using -Ad|D (see -N for selecting dis‐
tance units):
f Flat Earth distances.
g Great circle distances [Default].
e Geodesic distances on current GMT ellipsoid.
-D Give a comma-separated list of column abbreviations that you
want to delete from the MGD77+ files. Do NOT use this option to
remove columns that you are replacing with new data (use -A+
instead). Because we cannot remove variables from netCDF files
we must create a new file without the columns to be deleted.
Once the file is successfully created we temporarily rename the
old file, change the new filename to the old filename, and
finally remove the old, renamed file.
-E Give a single character that will be repeated to fill empty
string values, e.g., '9' will yield a string like "99999..."
[9].
-F Force mode. When this mode is active you are empowered to
delete or replace even the standard MGD77 set of columns. You
better know what you are doing!
-I In addition to file information we must specify additional
information about the extra column. Specify a short (16 char or
less, using lower case letters, digits, or underscores only)
abbreviation for the selected data, its more descriptive name,
the data unit, the data type 1-character code (byte, short,
float, int, double, or text) you want used for storage in the
netCDF file, any scale and offset we should apply to the data to
make them fit inside the range implied by the chosen storage
type, and a general comment (< 128 characters) regarding what
these data represent. Note: If text data type is selected then
the terms "values" in the -A discussion refer to your text data.
Furthermore, the discussion on interpolation does not apply and
the NaN value becomes a "no string" value (see -E for what this
is). Place quotes around terms with more than one word (e.g.,
"Corrected Depth").
-N Specify the distance unit used when using -Ad|D by appending e
(meter), k (km), m (miles), or n (nautical miles). [Default is
-Nk (km)].
-Q Quick mode, use bilinear rather than bicubic interpolation
[Default]. Alternatively, select the interpolation mode by
adding b for B-spline smoothing, c for bicubic interpolation, l
for bilinear interpolation or n for nearest-neighbor value.
Optionally, append threshold in the range [0,1]. This parameter
controls how close to nodes with NaN values the interpolation
will go. E.g., a threshold of 0.5 will interpolate about half
way from a non-NaN to a NaN node, whereas 0.1 will go about 90%
of the way, etc. [Default is 1, which means none of the (4 or
16) nearby nodes may be NaN]. -Q0 will just return the value of
the nearest node instead of interpolating. This is the same as
using -Qn. Only relevant when -Ag|i is selected.
-V Selects verbose mode, which will send progress reports to stderr
[Default runs "silently"].
-bi Selects binary input. Append s for single precision [Default is
d (double)]. Uppercase S or D will force byte-swapping.
Optionally, append ncol, the number of columns in your binary
input file if it exceeds the columns needed by the program. Or
append c if the input file is netCDF. Optionally, append
var1/var2/... to specify the variables to be read. This applies
to the input 1- or 2-column data files specified under some of
the -A options. The binary input option is only available for
numerical data columns.
EXAMPLES
To append Geosat/ERS-1 gravity version 11.2 as an extra data column in
the cruises 01010047.nc and 01010008.nc, storing the values as mGal*10
in a 2-byte short integer, try
mgd77manage 01010047 01010008 -Ai 10/1/grav.11.2.img -I sat‐
grav/"Geosat/ERS-1 gravity"/"mGal"/s/10/0/"Sandwell/Smith version 11.2"
-V
To append a filtered version of magnetics as an extra data column of
type float for the cruise 01010047.nc, and interpolate the filtered
data at the times given in the MGD77+ file, try
mgd77manage 01010047 -AT mymag.tm -I filtmag/"Intermediate-wavelength
magnetic residuals"/"nTesla"/f/1/0/"Useful for looking for isochrons"
-V
To delete the existing extra columns satfaa, coastdist, and satvgg from
all MGD77+ files, try
mgd77manage `cat allmgd77.lis` -D satfaa,coastdist,satvgg -V
To create a 4-byte float column with the correct IGRF reference field
in all MGD77+ files, try
mgd77manage `cat allmgd77.lis` -Acm-I igrf/"IGRF reference
field"/"nTesla"/f/1/0/"IGRF version 10 for 1990-2010" -V
DISCUSSION
1. Preamble
The mgd77 supplement is an attempt to (1) improve on the limited func‐
tionality of the existing mgg supplement, (2) incorporate some of the
ideas from Scripps' gmt+ supplement by allowing extra data columns, and
(3) add new capabilities for managing marine geophysical trackline data
stored in an architecture-independent CF-1.0- and COARDS-compliant
netCDF file format. Here are some of the underlying ideas and steps
you need to take to maintain your files.
2. Introduction
Our starting point is the MGD77 ASCII data files distributed from NGDC
on CD-ROMS, DVD-ROMS, and via FTP. Using Geodas to install the files
locally we choose the "Carter corrected depth" option which will fill
in the depth column using the two-way traveltimes and the Carter tables
if twt is present. This step yields ~5000 individual cruise files.
Place these in one or more sub-directories of your choice, list these
sub-directories (one per line) in the file mgd77_paths.txt, and place
that file in the directory pointed to by $MGD77_HOME; if not set this
variable defaults to $GMT_SHAREDIR/mgd77.
3. Conversion
Convert the ASCII MGD77 files to the new netCDF MGD77+ format using
mgd77convert. Typically, you will make a list of all the cruises to be
converted (with or without extension), and you then run
mgd77convert -Fa -Tc -V -Lwe+ `cat cruises.lis` > log.txt
The verbose settings will ensure that all problems found during conver‐
sion will be reported. The new *.nc files may also be placed in one or
more separate sub-directories and these should also be listed in the
mgd77_paths.txt file. We suggest you place the directories with *.nc
files ahead of the *.mgd77 directories. When you later want to limit a
search to files of a certain extension you should use the -I option.
4. Adding new columns
mgd77manage will allow you to add additional data columns to your *.nc
files. These can be anything, including text strings, but most likely
are numerical values sampled along the track from a supplied grid or an
existing column that have been filtered or manipulated for a particular
purpose. The format supports up to 32 such extra columns. See this
man page for how to add columns. You may later decide to remove some
of these columns or update the data associated with a certain column.
Data extraction tools such as mgd77list can be used to extract a mix of
standard MGD77 columns (navigation, time, and the usual geophysical
observations) and your custom columns.
5. Error sources
Before we discuss how to correct errors we will first list the differ‐
ent classes of errors associated with MGD77 data: (1) Header record
errors occur when some of the information fields in the header do not
comply with the MGD77 specification or required information is missing.
mgd77convert will list these errors when the extended verbose setting
is selected. These errors typically do not affect the data and are
instead errors in the meta-data (2) Fixed systematic errors occur when
a particular data column, despite the MGD77 specification, has been
encoded incorrectly. This usually means the data will be off by a con‐
stant factor such as 10 or 0.1, or in some cases even 1.8288 which con‐
verts fathoms to meters. (3) Unknown systematic errors occur when the
instrument that recorded the data or the processing that followed
introduced signals that appear to be systematic functions of time along
track, latitude, heading, or some other combination of terms that have
a physical or logical explanation. These terms may sometimes be
resolved by data analysis techniques such as along-track and across-
track investigations, and will result in correction terms that when
applied to the data will remove these unwanted signals in an optimal
way. Because these correction terms may change when new data are con‐
sidered in their determination, such corrections are considered to be
ephemeral. (4) Individual data points or sequences of data may violate
rules such as being outside of possible ranges or in other ways violate
sanity. Furthermore, sequences of points that may be within valid
ranges may give rise to data gradients that are unreasonable. The sta‐
tus of every point can therefore be determined and this gives rise to
bitflags GOOD or BAD. Our policy is that error sources 1, 2, and 4
will be corrected by supplying the information as meta-data in the rel‐
evant *.nc files, whereas the corrections for error source 3 (because
they will constantly be improved) will be maintained in a separate list
of corrections.
6. Finding errors
The mgd77sniffer is a tool that does a thorough along-track sanity
check of the original MGD77 ASCII files and produces a corresponding
*.e77 error log. All problems found are encoded in the error log, and
recommended fixed correction terms are given, if needed. An analyst
may verify that the suggested corrections are indeed valid (we only
want to correct truly obvious unit errors), edit these error logs and
modify such correction terms and activate them by changing the relevant
code key (see mgd77sniffer for more details). mgd77manage can ingest
these error logs and (1) correct bad header records given the sugges‐
tions in the log, (2) insert scale/offset correction terms to be used
when reading certain columns, and (3) insert any bit-flags found.
Rerun this step if you later find other problems as all E77 settings or
flags will be recreated based on the latest E77 log.
7. Error corrections
The extraction program mgd77list allows for corrections to be applied
on-the-fly when data are requested. First, data with BAD bitflags are
suppressed. Second, data with fixed systematic correction terms are
corrected accordingly. Third, data with ephemeral correction terms
will have those corrections applied (if a correction table is sup‐
plied). All of these steps require the presence of the relevant meta-
data and all can be overruled by the user. In addition, users may add
their own bitflags as separate data columns and use mgd77list's logical
tests to further dictate which data are suppressed from output.
CREDITS
The IGRF calculations are based on a Fortran program written by Susan
Macmillan, British Geological Survey, translated to C via f2c by
Joaquim Luis, and adapted to GMT style by Paul Wessel.
SEE ALSOmgd77convert(1), mgd77list(1), mgd77info(1), mgd77sniffer(1)mgd77track(1)x2sys_init(1)REFERENCES
Wessel, P., and W. H. F. Smith, 2015, The Generic Mapping Tools (GMT)
version 4.5.14 Technical Reference & Cookbook, SOEST/NOAA.
Wessel, P., and W. H. F. Smith, 1998, New, Improved Version of Generic
Mapping Tools Released, EOS Trans., AGU, 79 (47), p. 579.
Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Map‐
ping Tools Released, EOS Trans., AGU, 76 (33), p. 329.
Wessel, P., and W. H. F. Smith, 1995, New Version of the Generic Map‐
ping Tools Released, http://www.agu.org/eos_elec/95154e.html, Copyright
1995 by the American Geophysical Union.
Wessel, P., and W. H. F. Smith, 1991, Free Software Helps Map and Dis‐
play Data, EOS Trans., AGU, 72 (41), p. 441.
The Marine Geophysical Data Exchange Format - "MGD77", see
http://www.ngdc.noaa.gov/mgg/dat/geodas/docs/mgd77.txt
IGRF, see http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html
GMT 4.5.14 1 Nov 2015 MGD77MANAGE(1)
