
README file for GMT supplemental x2sys programs
Distributed under the GNU Lesser Public License; see file
LICENSE.TXT in main GMT directory.

AUTHOR:		Paul Wessel
DATE:		1-JAN-2011
INSTALL INFO:	Installed as part of GMT5 supplements

The notes below are mostly for historical references

1.4 UPDATE [3-AUG-2010]

Modularized as part of new GMT5-style design.
Make any old mgg .gmt involvement subject to GMT_COMPATIBILITY setting

1.3 UPDATE [24-JULY-2009]

Added x2sys_merge.c which merges an updated COEs table (smaller) into
a main one (bigger). The new COEs should only contain updated values
of already existing tracks crossings.

1.2 UPDATE [1-OCT-2008]

Added x2sys_list.c which replaces the purpose of old x_list,
x2sys_solve.c which replaces x_solve_dc_drift.c, and
x2sys_report which replaces x_report.c.  These are all
experimental and should not be relied upon; syntax and use may
change without notice!  Furthermore, x2sys can now read COARDS
1-D netCDF data files.

1.1 UPDATE
Added x2sys_binlist.c which replicates the purpose of the old gmt2bin.c
program, but this version is data-format independent.  Also added are
x2sys_put.c (old binlegs functionality) and x2sys_get.c (old gmtlegs.c
functionality) as well as x2sys_init.c (initializes a track data base
and eventually a crossover database).  x2sys is actively undergoing
revisions and will be unstable for a while.

1.0 INFORMATION

X2SYS is a set of tools for the calculation of track crossovers.
Crossovers occur when spatial time-series tracks intersect themselves or
other tracks.  At these crossover points one would ideally find that
the data measurements agree, but due to navigational uncertainties,
instrument imprecision or drift, or temporal changes in the fields,
this is rarely the case.  Studying these discrepancies, then, may allow
one to learn more about the processes that causes these errors (and possibly
allow one to reduce them) and about the precision of the observed data.

X2SYS is built from scratch but inherits much philosophy from its
predecessor, the XSYSTEM [Wessel, 1989].  Unlike XSYSTEM, X2SYS was written
to meet additional criteria:

* It should be POSIX, ANSI-C, and Y2K compliant.

* It should take advantage of the GMT libraries.

* It should be released under the GNU Public License.

* It should be abstracted away from the underlying track data structure.

* It should be backwards compatible with the old XOVER.

Advantages of the new tools derive from these criteria: X2SYS is easy to
install on a wide range of computers, it can be used with any type of data
file structure (within reason), may produce the same output as the old XOVER
program, and is freely distributable yet covered by copyright.  The core
algorithm for calculating crossovers have been replaced with the principles
discussed in the book on C algorithms by Sedgewick [1990].  The result is
that X2SYS calculates crossovers faster than its predecessor, although this
may be to some extend dependent on the track layout.

Input data and description files
--------------------------------

The data files that can be understood by X2SYS can either be ASCII
or binary files.  Common for both formats is the need for a logical
structure.  Data files may consist of a header block that can be
any number of ASCII record or BINARY bytes, followed by any number
of data records.  For ASCII files, the data columns are separated
by tabs, spaces, or commas, or they are given in the old-style FORTRAN
card format.  In that format, all the columns are given back to back
with no intervening spaces (Such files were usually written
back in the dark ages when nobody put much emphasis on human
readability).  One example of such a format is the MGD-77 format for
marine underway geophysical data from NGDC.  For BINARY files,
each column can be of stored as any of the standard data types
(e.g., int, char, short int, double, float).  Regardless of format,
the structure of the input spatial time-series track data files
must be conveyed to the X2SYS programs (using the -D switch) via
an X2SYS definition file.  A few definition files are provided with
the package; from these, users can design their own based on the format
of their particular data sets.  Definition files should be given
the suffix .def and must be prepared according to the following
specifications:

1. You may have any number of comment lines starting with #.  They
   can appear anywhere in the file.

2. Three special comments are defined:

  a) #ASCII   The track data file is an ASCII file.
  b) #BINARY  The track data file is a binary file.
  c) #SKIP n  Here, n is the number of header records (if ASCII)
     or header bytes (if BINARY) to skip before reading data records.

     Default values are ASCII format with no header records.

3. Each data column must have a record describing the data type.
   You may have any number of column descriptors records.  Each record
   must have the following entries separated by spaces or tabs:

name	The actual name of each data column.  Some names are
	given special meaning.  For instance, use lon and lat for
	geographic coordinates, x and y for Cartesian coordinates,
	and time for the time column.  Other column names have no
	restrictions.

type	A 1-char code to indicate what data type we have.  Choose
	among:

	ASCII data:

	a	ASCII word
	A	ASCII word in FORTRAN card format (all columns must have A)

	BINARY data:

	c	signed 1-byte character
	u	unsigned 1-byte character
	h	signed 2-byte integer
	i	signed 4-byte integer
	l	signed 4- or 8-byte integer (long)
	f	4-byte floating point single precision
	d	8-byte floating point double precision

Note that a/A is the only type used when the file format is ASCII,
and that only the other types are allowed with BINARY files.

NaN-proxy?	This is either Y or N, indicating whether this column
	has a special value that should be treated as a NaN (Not-a-Number
	or missing value).  For instance, if your data uses -99999 to
	indicate lack of data, then this flag should be Y.

NaN-proxy	The special value that represents NaN for this column.
	It is only used if NaN-proxy? is set to Y. Then, all occurrences
	of column values that equal the proxy are reset to NaN.

scale	Factor to multiply each value with.

offset	Amount to subtract from the column value after scaling.

oformat	C-style format statement describing how you want this column
	to be formatted when ASCII output has been selected.

cardform	This optional entry is only used with FORTRAN card formats
	and is necessary to describe which positional columns in the input
	record constitute this logical column.  The entry is given as a
	range of position.  For instance, 15-24 indicates that this data
	column are to be decoded from the FORTRAN card record from column
	position 15 through 24.

Below is an example of a definition file that describes the data format of
the old Lamont GMT MGG binary files:

#
# Define file for X2SYS processing of GMT/MGG files
#
# This file applies to the GMT MGG file format.
# This format was developed by P. Wessel and
# Walter H.F. Smith at Lamont in the late 1980ies
# Utilities to deal with these files are supplied
# in the GMT supplemental package mgg.
#
#---------------------------------------------------------------------
#BINARY		# The input file is binary
#SKIP 18	# The number of header bytes to skip
#---------------------------------------------------------------------
#name	intype	NaN-proxy?	NaN-proxy	scale	offset	oformat
time	i	N		0		1	0	%10.0lf
lat	i	N		0		1.0e-6	0	%9.5lf
lon	i	N		0		1.0e-6	0	%10.5lf
faa	h	Y		-32000		0.1	0	%6.1lf
mag	h	Y		-32000		1	32000	%6.0lf
top	h	Y		-32000		1	0	%6.0lf
#---------------------------------------------------------------------

Note, however, that due to the wide use of the MGD77 and GMT MGG formats,
specifying -Dgmt or -Dmgd77 will bypass the generic reading routines and
use special i/o-functions that knows about these formats.

The program x2sys_datalist will simply produce a listing of the
contents of your data file.  Your first step after designing a definition
file is to try it out with x2sys_datalist to make sure it is correct.

The program x2sys_cross calculates crossovers between tracks and within
tracks.  The -O option ensures that output is compatible with that of the
old XOVER program.

References:

Sedgewick, R., 1990, Algorithms in C. Addison-Wesley.
Wessel, P. 1989, XOVER: A Cross-over Error Detector for Track Data, Computers
   & Geosciences, 15, 333-346.
