NAME¶
x2sys_init - Initialize x2sys data base for track data files
SYNOPSIS¶
x2sys_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] ]
DESCRIPTION¶
x2sys_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 parameters are given a
short-hand notation called an x2sys TAG. The TAG keeps track of settings such
as file format, whether the data are geographic or not, and the binning
resolution for track indices. Running
x2sys_init is a prerequisite to
running any of the other x2sys programs, 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 subsequent 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 limits 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
periodicities 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 column.
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 directory 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 argument 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 information 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 certain
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 numbers
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 ALSO¶
x2sys_binlist(1),
x2sys_datalist(1),
x2sys_get(1),
x2sys_list(1),
x2sys_put(1),
x2sys_report(1),
x2sys_solve(1)