"""
GMT supplementary X2SYS module for crossover analysis.
"""
import contextlib
import os
from pathlib import Path
import pandas as pd
from pygmt.clib import Session
from pygmt.exceptions import GMTInvalidInput
from pygmt.helpers import (
GMTTempFile,
build_arg_string,
data_kind,
dummy_context,
fmt_docstring,
kwargs_to_strings,
unique_name,
use_alias,
)
@contextlib.contextmanager
def tempfile_from_dftrack(track, suffix):
"""
Saves pandas.DataFrame track table to a temporary tab-separated ASCII text
file with a unique name (to prevent clashes when running x2sys_cross),
adding a suffix extension to the end.
Parameters
----------
track : pandas.DataFrame
A table holding track data with coordinate (x, y) or (lon, lat) values,
and (optionally) time (t).
suffix : str
File extension, e.g. xyz, tsv, etc.
Yields
------
tmpfilename : str
A temporary tab-separated value file with a unique name holding the
track data. E.g. 'track-1a2b3c4.tsv'.
"""
try:
tmpfilename = f"track-{unique_name()[:7]}.{suffix}"
track.to_csv(
path_or_buf=tmpfilename,
sep="\t",
index=False,
date_format="%Y-%m-%dT%H:%M:%S.%fZ",
)
yield tmpfilename
finally:
os.remove(tmpfilename)
[docs]@fmt_docstring
@use_alias(
D="fmtfile",
E="suffix",
F="force",
G="discontinuity",
I="spacing",
N="units",
R="region",
V="verbose",
W="gap",
j="distcalc",
)
@kwargs_to_strings(I="sequence", R="sequence")
def x2sys_init(tag, **kwargs):
r"""
Initialize a new x2sys track database.
Serves as the starting point for x2sys and 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.
Before you can run :meth:`pygmt.x2sys_init` you must set the environmental
parameter X2SYS_HOME to a directory where you have write permission, which
is where x2sys can keep track of your settings.
Full option list at :gmt-docs:`supplements/x2sys/x2sys_init.html`
{aliases}
Parameters
----------
tag : str
The unique name of this data type x2sys TAG.
fmtfile : str
Format definition file prefix for this data set (see
:gmt-docs:`GMT's Format Definition Files
<supplements/x2sys/x2sys_init.html#format-definition-files>`
for more information). Specify full path if the file is not in the
current directory.
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)
- **geoz** (same, with one z-column).
suffix : str
Specifies the file extension (suffix) for these data files. If not
given we use the format definition file prefix as the suffix (see
``fmtfile``).
discontinuity : str
**d**\|\ **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.
spacing : str or list
*dx*\[/*dy*].
*dx* and optionally *dy* is the grid spacing. Append **m** to
indicate minutes or **s** to indicate seconds for geographic data.
These spacings refer to the binning used in the track bin-index data
base.
units : str or list
**d**\|\ **s**\ *unit*.
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** - meters or m/s
- **f** - feet or feet/s
- **k** - km or km/hr
- **m** - miles or miles/hr
- **n** - nautical miles or knots
- **u** - survey feet or survey feet/s
[Default is ``units=["dk", "se"]`` (km and m/s) if ``discontinuity`` is
set, and ``units=["dc", "sc"]`` otherwise (e.g., for Cartesian units)].
{R}
{V}
gap : str or list
**t**\|\ **d**\ *gap*.
Give **t** or **d** and append the corresponding maximum time gap (in
user units; this is typically seconds [Default is infinity]), or
distance (for units, see ``units``) gap [Default is 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.
{j}
"""
with Session() as lib:
arg_str = " ".join([tag, build_arg_string(kwargs)])
lib.call_module(module="x2sys_init", args=arg_str)
[docs]@fmt_docstring
@use_alias(
A="combitable",
C="runtimes",
D="override",
I="interpolation",
R="region",
S="speed",
T="tag",
Q="coe",
V="verbose",
W="numpoints",
Z="trackvalues",
)
@kwargs_to_strings(R="sequence")
def x2sys_cross(tracks=None, outfile=None, **kwargs):
r"""
Calculate crossovers between track data files.
Determines all intersections between ("external cross-overs") or within
("internal cross-overs") tracks (Cartesian or geographic), and report the
time, position, distance along track, heading and speed along each track
segment, and the crossover error (COE) and mean values for all observables.
By default, :meth:`pygmt.x2sys_cross` will look for both external and
internal COEs. As an option, you may choose to project all data using one
of the map projections prior to calculating the COE.
Full option list at :gmt-docs:`supplements/x2sys/x2sys_cross.html`
{aliases}
Parameters
----------
tracks : pandas.DataFrame or str or list
A table or a list of tables with (x, y) or (lon, lat) values in the
first two columns. Track(s) can be provided as pandas DataFrame tables
or file names. Supported file formats are ASCII, native binary, or
COARDS netCDF 1-D data. More columns may also be present.
If the filenames are missing their file extension, we will append the
suffix specified for this TAG. Track files will be searched for first
in the current directory and second in all directories listed in
$X2SYS_HOME/TAG/TAG_paths.txt (if it exists). [If $X2SYS_HOME is not
set it will default to $GMT_SHAREDIR/x2sys]. (Note: MGD77 files will
also be looked for via $MGD77_HOME/mgd77_paths.txt and .gmt files
will be searched for via $GMT_SHAREDIR/mgg/gmtfile_paths).
outfile : str
Optional. The file name for the output ASCII txt file to store the
table in.
tag : str
Specify the x2sys TAG which identifies the attributes of this data
type.
combitable : str
Only process the pair-combinations found in the file *combitable*
[Default process all possible combinations among the specified files].
The file *combitable* is created by :gmt-docs:`x2sys_get's -L option
<supplements/x2sys/x2sys_get.html#l>`.
runtimes : bool or str
Compute and append the processing run-time for each pair to the
progress message (use ``runtimes=True``). Pass in a filename (e.g.
``runtimes="file.txt"``) to save these run-times to file. The idea here
is to use the knowledge of run-times to split the main process in a
number of sub-processes that can each be launched in a different
processor of your multi-core machine. See the MATLAB function
`split_file4coes.m
<https://github.com/GenericMappingTools/gmt/blob/master/src/x2sys/>`_.
override : bool or str
**S**\|\ **N**.
Control how geographic coordinates are handled (Cartesian data are
unaffected). By default, we determine if the data are closer to one
pole than the other, and then we use a cylindrical polar conversion to
avoid problems with longitude jumps. You can turn this off entirely
with ``override`` and then the calculations uses the original data (we
have protections against longitude jumps). However, you can force the
selection of the pole for the projection by appending **S** or **N**
for the south or north pole, respectively. The conversion is used
because the algorithm used to find crossovers is inherently a
Cartesian algorithm that can run into trouble with data that has large
longitudinal range at higher latitudes.
interpolation : str
**l**\|\ **a**\|\ **c**.
Sets the interpolation mode for estimating values at the crossover.
Choose among:
- **l** - Linear interpolation [Default].
- **a** - Akima spline interpolation.
- **c** - Cubic spline interpolation.
coe : str
Use **e** for external COEs only, and **i** for internal COEs only
[Default is all COEs].
{R}
speed : str or list
**l**\|\ **u**\|\ **h**\ *speed*.
Defines window of track speeds. If speeds are outside this window we do
not calculate a COE. Specify:
- **l** sets lower speed [Default is 0].
- **u** sets upper speed [Default is infinity].
- **h** does not limit the speed but sets a lower speed below which
headings will not be computed (i.e., set to NaN) [Default
calculates headings regardless of speed].
For example, you can use ``speed=["l0", "u10", "h5"]`` to set a lower
speed of 0, upper speed of 10, and disable heading calculations for
speeds below 5.
{V}
numpoints : int
Give the maximum number of data points on either side of the crossover
to use in the spline interpolation [Default is 3].
trackvalues : bool
Report the values of each track at the crossover [Default reports the
crossover value and the mean value].
Returns
-------
crossover_errors : :class:`pandas.DataFrame` or None
Table containing crossover error information.
Return type depends on whether the ``outfile`` parameter is set:
- :class:`pandas.DataFrame` with (x, y, ..., etc) if ``outfile`` is not
set
- None if ``outfile`` is set (track output will be stored in the set in
``outfile``)
"""
with Session() as lib:
file_contexts = []
for track in tracks:
kind = data_kind(track)
if kind == "file":
file_contexts.append(dummy_context(track))
elif kind == "matrix":
# find suffix (-E) of trackfiles used (e.g. xyz, csv, etc) from
# $X2SYS_HOME/TAGNAME/TAGNAME.tag file
lastline = (
Path(os.environ["X2SYS_HOME"], kwargs["T"], f"{kwargs['T']}.tag")
.read_text()
.strip()
.split("\n")[-1]
) # e.g. "-Dxyz -Etsv -I1/1"
for item in sorted(lastline.split()): # sort list alphabetically
if item.startswith(("-E", "-D")): # prefer -Etsv over -Dxyz
suffix = item[2:] # e.g. tsv (1st choice) or xyz (2nd choice)
# Save pandas.DataFrame track data to temporary file
file_contexts.append(tempfile_from_dftrack(track=track, suffix=suffix))
else:
raise GMTInvalidInput(f"Unrecognized data type: {type(track)}")
with GMTTempFile(suffix=".txt") as tmpfile:
with contextlib.ExitStack() as stack:
fnames = [stack.enter_context(c) for c in file_contexts]
if outfile is None:
outfile = tmpfile.name
arg_str = " ".join([*fnames, build_arg_string(kwargs), "->" + outfile])
lib.call_module(module="x2sys_cross", args=arg_str)
# Read temporary csv output to a pandas table
if outfile == tmpfile.name: # if outfile isn't set, return pd.DataFrame
# Read the tab-separated ASCII table
table = pd.read_csv(
tmpfile.name,
sep="\t",
header=2, # Column names are on 2nd row
comment=">", # Skip the 3rd row with a ">"
parse_dates=[2, 3], # Datetimes on 3rd and 4th column
)
# Remove the "# " from "# x" in the first column
table = table.rename(columns={table.columns[0]: table.columns[0][2:]})
elif outfile != tmpfile.name: # if outfile is set, output in outfile only
table = None
return table