X2SYS_INIT(1) Generic Mapping Tools X2SYS_INIT(1)NAMEx2sys_init - Initialize x2sys data base for track data files
SYNOPSISx2sys_init TAG -Ddeffile [ -Cc|f|g|e ] [ -Esuffix ] [ -F ] [ -Gd|g ] [
-Idx[/dy] ] [ -Nd|sunit ] [ -Rwest/east/south/north[r] ] [ -V ] [
-Wt|dgap ] [ -m[i|o][flag] ]
DESCRIPTIONx2sys_init is the starting point for anyone wishing to use x2sys; it
initializes a set of data bases that are particular to one kind of
track data. These data, their associated data bases, and key parame‐
ters are given a short-hand notation called an x2sys TAG. The TAG
keeps track of settings such as file format, whether the data are geo‐
graphic or not, and the binning resolution for track indices. Running
x2sys_init is a prerequisite to running any of the other x2sys pro‐
grams, such as x2sys_binlist, which will create a crude representation
of where each data track go within the domain and which observations
are available; this information serves as input to x2sys_put which
updates the track data base. Then, x2sys_get can be used to find which
tracks and data are available inside a given region. With that list of
tracks you can use x2sys_cross to calculate track crossovers, use
x2sys_report to report crossover statistics or x2sys_list to pull out
selected crossover information that x2sys_solve can use to determine
track-specific systematic corrections. These corrections may be used
with x2sys_datalist to extract corrected data values for use in subse‐
quent work.
TAG The unique name of this data type x2sys TAG.
-C Select procedure for along-track distance calculation when
needed by other programs:
c Cartesian distances [Default, unless -G is set].
f Flat Earth distances.
g Great circle distances [Default if -G is set].
e Geodesic distances on current GMT ellipsoid.
-D Definition file prefix for this data set [See DEFINITION FILES
below for more information]. Specify full path if the file is
not in the current directory.
OPTIONS
No space between the option flag and the associated arguments.
-E Specifies the file extension (suffix) for these data files. If
not given we use the definition file prefix as the suffix (see
-D).
-F Force creating new files if old ones are present [Default will
abort if old TAG files are found].
-G Selects geographical coordinates. Append d for discontinuity at
the Dateline (makes longitude go from -180 to + 180) or g for
discontinuity at Greenwich (makes longitude go from 0 to 360
[Default]). If not given we assume the data are Cartesian.
-I x_inc [and optionally y_inc] is the grid spacing. Append m to
indicate minutes or c to indicate seconds for geographic data.
These spacings refer to the binning used in the track bin-index
data base.
-m Multiple segment file(s). Segments are separated by a special
record. For ASCII files the first character must be flag
[Default is '>']. For binary files all fields must be NaN and
-b must set the number of output columns explicitly. By default
the -m setting applies to both input and output. Use -mi and
-mo to give separate settings to input and output.
-N Sets the units used for distance and speed when requested by
other programs. Append d for distance or s for speed, then give
the desired unit as c (Cartesian userdist or userdist/usertime),
e (meter or m/s), k (km or km/hr), m (miles or miles/hr), or n
(nautical miles or knots). [Default is -Ndk -Nse (km and m/s)
if -G is set and -Ndc and -Nsc otherwise (Cartesian units)].
-R west, east, south, and north specify the Region of interest, and
you may specify them in decimal degrees or in
[+-]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, specify the name of an existing grid file and the
-R settings (and grid spacing, if applicable) are copied from
the grid. For Cartesian data just give xin/xmax/ymin/ymax.
This sets the complete domain for the relevant track data set.
-V Selects verbose mode, which will send progress reports to stderr
[Default runs "silently"].
-W Give t or d and append the corresponding maximum time gap (in
user units; this is typically seconds [Infinity]), or distance
(for units, see -N) gap [Infinity]) allowed between the two data
points immediately on either side of a crossover. If these lim‐
its are exceeded then a data gap is assumed and no COE will be
determined.
DEFINITION FILES
These *.def files contain information about the data file format and
have two sections: (1) header information and (2) column information.
All header information starts with the character # in the first column,
immediately followed by an upper-case directive. If the directive
takes an argument it is separated by white-space. You may append a
trailing # comments. Five directives are recognized:
ASCII states that the data files are in ASCII format.
BINARY states that the data files are native binary files.
NETCDF states that the data files are COARDS-compliant 1-D netCDF
files.
SKIP takes an integer argument which is either the number of lines to
skip (when reading ASCII files) or the number of bytes to skip (when
reading native binary files). Not used with netCDF files.
GEO indicates that these files are geographic data sets, with periodic‐
ities in the x-coordinate (longitudes). Alternatively, use -G.
MULTISEG means each track consists of multiple segments separated by a
GMT multisegment header (alternatively, use -m when defining the system
TAG). Not used with netCDF files.
The column information consists of one line per column in the order the
columns appear in the data file. For each column you must provide
seven attributes:
name type NaN NaN-proxy scale offset oformat
name is the name of the column variable. It is expected that you will
use the special names lon (or x if Cartesian) and lat (or y) for the
two required coordinate columns, and time when optional time data are
present.
type is always a for ASCII representations of numbers, whereas for
binary files you may choose among c for signed 1-byte character
(-127,+128), u for unsigned byte (0-255), h for signed 2-byte integers
(-32768,+32767), i for signed 4-byte integers
(-2,147,483,648,+2,147,483,647), f for 4-byte floating points and d for
8-byte double precision floating points. For netCDF, simply use d as
netCDF will automatically handle type-conversions during reading.
NaN is Y if certain values (e.g, -9999) are to be replaced by NAN, and
N otherwise.
NaN-proxy is that special value (e.g., -9999).
scale is used to multiply the data after reading.
offset is used to add to the scaled data.
oformat is a C-style format string used to print values from this col‐
umn.
If you give - as the oformat then GMT's formatting machinery will be
used instead (i.e., D_FORMAT, PLOT_DEGREE_FORMAT, PLOT_DATE_FORMAT,
PLOT_CLOCK_FORMAT). Some file formats already have definition files
premade. These include mgd77 (for plain ASCII MGD77 data files),
mgd77+ (for enhanced MGD77+ netCDF files), gmt (for old mgg supplement
binary files), xy (for plain ASCII x, y tables), xyz (same, with one z-
column), geo (for plain ASCII longitude, latitude files), and geoz
(same, with one z-column).
EXAMPLES
If you have a large set of track data files you can organize them using
the x2sys tools. Here we will outline the steps. Let us assume that
your track data file format consist of 2 header records with text
information followed by any number of identically formatted data
records with 6 columns (lat, lon, time, obs1, obs2, obs3) and that
files are called *.trk. We will call this the "line" format. First, we
create the line.def file:
# Define file for the line format
#ASCII # File is ASCII
#SKIP 2 # Skip 2 header records
#GEO # Data are geographic
#name type NaN NaN-proxy scale offset oformat
lat a N 0 1 0 %9.5f
lon a N 0 1 0 %10.5f
time a N 0 1 0 %7.1f
obs1 a N 0 1 0 %7.2f
obs2 a N 0 1 0 %7.2f
obs3 a N 0 1 0 %7.2f
Next we create the TAG and the TAG directory with the databases for
these line track files. Assuming these contain geographic data and
that we want to keep track of the data distribution at a 1 x 1 degree
resolution, with distances in km calculated along geodesics and with
speeds given in knots, we may run
x2sys_init LINE -V -G -D line -Rg -Ce -Ndk -NsN -I 1/1 -E trk
where we have selected LINE to be our x2sys tag. When x2sys tools try
to read your line data files they will first look in the current direc‐
tory and second look in the file TAG_paths.txt for a list of additional
directories to examine. Therefore, create such a file (here
LINE_paths.txt) and stick the full paths to your data directories
there. All TAG-related files (definition files, tag files, and track
data bases created) will be expected to be in the directory pointed to
by $X2SYS_HOME/TAG (in our case $X2SYS_HOME/LINE). Note that the argu‐
ment to -D must contain the full path if the *.def file is not in the
current directory. x2sys_init will copy this file to the
$X2SYS_HOME/TAG directory where all other x2sys tools will expect to
find it.
Create tbf file(s):
Once the (empty) TAG databases have been initialized we go
through a two-step process to populate them. First we run
x2sys_binlist on all our track files to create one (or more)
multi-segment track bin-index files (tbf). These contain infor‐
mation on which 1 x 1 degree bins (or any other blocksize; see
-I) each track has visited and which observations (in your case
obs1, obs2, obs3) were actually observed (not all tracks may
have all three kinds of observations everywhere). For instance,
if your tracks are listed in the file tracks.lis we may run this
command:
x2sys_binlist -V -T LINE :tracks.lis > tracks.tbf
Update index data base:
Next, the track bin-index files are fed to x2sys_put which will
insert the information into the TAG databases:
x2sys_put -V -T LINE tracks.tbf
Search for data:
You may now use x2sys_get to find all the tracks within a cer‐
tain sub-region, and optionally limit the search to those tracks
that have a particular combination of observables. E.g., to
find all the tracks which has both obs1 and obs3 inside the
specified region, run
x2sys_get -V -T LINE -R 20/40/-40/-20 -F obs1,obs3 > tracks.tbf
MGD77[+] or GMT:
Definition files already exist for MGD77 files (both standard
ASCII and enhanced netCDF-based MGD77+ files) and the old *.gmt
files manipulated by the mgg supplements; for these data sets
the -C and -N will default to great circle distance calculation
in km and speed in m/s. There are also definition files for
plain x,y[,z] and lon,lat[,z] tracks. To initiate new track
databases to be used with MGD77 data from NGDC, try
x2sys_init MGD77 -V-D mgd77 -E mgd77 -Rd -Gd -Nsn -I 1/1 -Wt
900 -Wd 5
where we have chosen a 15 minute (900 sec) or 5 km threshold to
indicate a data gap and selected knots as the speed; the other
steps are similar.
Binary files:
Let us pretend that your line files actually are binary files
with a 128-byte header structure (to be skipped) followed by the
data records and where lon, lat, time are double precision num‐
bers while the three observations are 2-byte integers which must
be multiplied by 0.1. Finally, the first two observations may
be -32768 which means there is no data available. All that is
needed is a different line.def file:
# Define file for the binary line format
#BINARY # File is now binary
#SKIP 128 # Skip 128 bytes
#GEO # Data are geographic
#name type NaN? NaN-proxy scale offset oformat
lon d N 0 1 0 %10.5f
lat d N 0 1 0 %9.5f
time d N 0 1 0 %7.1f
obs1 h Y -32768 0.1 0 %6.1f
obs2 h Y -32768 0.1 0 %6.1f
obs3 h N 0 0.1 0 %6.1f
The rest of the steps are identical.
COARDS 1-D netCDF files:
Finally, suppose that your line files actually are netCDF files
that conform to the COARDS convention, with data columns named
lon, lat, time, obs1, obs2, and obs3. All that is needed is a
different line.def file:
# Define file for the netCDF COARDS line format
#NETCDF # File is now netCDF
#GEO # Data are geographic
#name type NaN? NaN-proxy scale offset oformat
lon d N 0 1 0 %10.5f
lat d N 0 1 0 %9.5f
time d N 0 1 0 %7.1f
obs1 d N 0 1 0 %6.1f
obs2 d N 0 1 0 %6.1f
obs3 d N 0 1 0 %6.1f
Note we use no scaling or NAN proxies since those issues are
usually handled internally in the netCDF format description.
SEE ALSOx2sys_binlist(1), x2sys_datalist(1), x2sys_get(1), x2sys_list(1),
x2sys_put(1), x2sys_report(1), x2sys_solve(1)GMT 4.5.14 1 Nov 2015 X2SYS_INIT(1)
