"""
Non-plot GMT modules.
"""
import numpy as np
import xarray as xr
from .clib import Session
from .helpers import (
build_arg_string,
fmt_docstring,
GMTTempFile,
use_alias,
data_kind,
dummy_context,
)
from .exceptions import GMTInvalidInput
[docs]@fmt_docstring
@use_alias(V="verbose")
def grdinfo(grid, **kwargs):
"""
Get information about a grid.
Can read the grid from a file or given as an xarray.DataArray grid.
Full option list at :gmt-docs:`grdinfo.html`
Parameters
----------
grid : str or xarray.DataArray
The file name of the input grid or the grid loaded as a DataArray.
{V}
Returns
-------
info : str
A string with information about the grid.
"""
kind = data_kind(grid, None, None)
with GMTTempFile() as outfile:
with Session() as lib:
if kind == "file":
file_context = dummy_context(grid)
elif kind == "grid":
file_context = lib.virtualfile_from_grid(grid)
else:
raise GMTInvalidInput("Unrecognized data type: {}".format(type(grid)))
with file_context as infile:
arg_str = " ".join(
[infile, build_arg_string(kwargs), "->" + outfile.name]
)
lib.call_module("grdinfo", arg_str)
result = outfile.read()
return result
[docs]@fmt_docstring
@use_alias(C="per_column", I="spacing", T="nearest_multiple", V="verbose")
def info(table, **kwargs):
"""
Get information about data tables.
Reads from files and finds the extreme values in each of the columns
reported as min/max pairs. It recognizes NaNs and will print warnings if
the number of columns vary from record to record. As an option, it will
find the extent of the first two columns rounded up and down to the nearest
multiple of the supplied increments given by *spacing*. Such output will be
in a numpy.ndarray form ``[w, e, s, n]``, which can be used directly as the
*region* argument for other modules (hence only dx and dy are needed). If
the *per_column* option is combined with *spacing*, then the numpy.ndarray
output will be rounded up/down for as many columns as there are increments
provided in *spacing*. A similar option *nearest_multiple* option will
provide a numpy.ndarray in the form of ``[zmin, zmax, dz]`` for makecpt.
Full option list at :gmt-docs:`gmtinfo.html`
{aliases}
Parameters
----------
table : str or np.ndarray or pandas.DataFrame or xarray.Dataset
Pass in either a file name to an ASCII data table, a 1D/2D numpy array,
a pandas dataframe, or an xarray dataset made up of 1D xarray.DataArray
data variables.
per_column : bool
Report the min/max values per column in separate columns.
spacing : str
``'[b|p|f|s]dx[/dy[/dz...]]'``.
Report the min/max of the first n columns to the nearest multiple of
the provided increments and output results in the form
``[w, e, s, n]``.
nearest_multiple : str
``'dz[+ccol]'``
Report the min/max of the first (0'th) column to the nearest multiple
of dz and output this in the form ``[zmin, zmax, dz]``.
{V}
Returns
-------
output : np.ndarray or str
Return type depends on whether any of the 'per_column', 'spacing', or
'nearest_multiple' parameters are set.
- np.ndarray if either of the above parameters are used.
- str if none of the above parameters are used.
"""
kind = data_kind(table)
with Session() as lib:
if kind == "file":
file_context = dummy_context(table)
elif kind == "matrix":
try:
# pandas.DataFrame and xarray.Dataset types
arrays = [array for _, array in table.items()]
except AttributeError:
# Python lists, tuples, and numpy ndarray types
arrays = np.atleast_2d(np.asanyarray(table).T)
file_context = lib.virtualfile_from_vectors(*arrays)
else:
raise GMTInvalidInput(f"Unrecognized data type: {type(table)}")
with GMTTempFile() as tmpfile:
with file_context as fname:
arg_str = " ".join(
[fname, build_arg_string(kwargs), "->" + tmpfile.name]
)
lib.call_module("info", arg_str)
result = tmpfile.read()
if any(arg in kwargs for arg in ["C", "I", "T"]):
# Converts certain output types into a numpy array
# instead of a raw string that is less useful.
if result.startswith(("-R", "-T")): # e.g. -R0/1/2/3 or -T0/9/1
result = result[2:].replace("/", " ")
result = np.loadtxt(result.splitlines())
return result
[docs]@fmt_docstring
@use_alias(G="download", V="verbose")
def which(fname, **kwargs):
"""
Find the full path to specified files.
Reports the full paths to the files given through *fname*. We look for
the file in (1) the current directory, (2) in $GMT_USERDIR (if defined),
(3) in $GMT_DATADIR (if defined), or (4) in $GMT_CACHEDIR (if defined).
*fname* can also be a downloadable file (either a full URL, a
`@file` special file for downloading from the GMT Site Cache, or
`@earth_relief_*` topography grids). In these cases, use option *download*
to set the desired behavior. If *download* is not used (or False), the file
will not be found.
Full option list at :gmt-docs:`gmtwhich.html`
{aliases}
Parameters
----------
fname : str
The file name that you want to check.
download : bool or str
If the file is downloadable and not found, we will try to download the
it. Use True or 'l' (default) to download to the current directory. Use
'c' to place in the user cache directory or 'u' user data directory
instead.
{V}
Returns
-------
path : str
The path of the file, depending on the options used.
Raises
------
FileNotFoundError
If the file is not found.
"""
with GMTTempFile() as tmpfile:
arg_str = " ".join([fname, build_arg_string(kwargs), "->" + tmpfile.name])
with Session() as lib:
lib.call_module("which", arg_str)
path = tmpfile.read().strip()
if not path:
raise FileNotFoundError("File '{}' not found.".format(fname))
return path
[docs]class config: # pylint: disable=invalid-name
"""
Set GMT defaults globally or locally.
Change GMT defaults globally::
pygmt.config(PARAMETER=value)
Change GMT defaults locally by using it as a context manager::
with pygmt.config(PARAMETER=value):
...
Full GMT defaults list at :gmt-docs:`gmt.conf.html`
"""
def __init__(self, **kwargs):
# Save values so that we can revert to their initial values
self.old_defaults = {}
self.special_params = {
"FONT": [
"FONT_ANNOT_PRIMARY",
"FONT_ANNOT_SECONDARY",
"FONT_HEADING",
"FONT_LABEL",
"FONT_TAG",
"FONT_TITLE",
],
"FONT_ANNOT": ["FONT_ANNOT_PRIMARY", "FONT_ANNOT_SECONDARY"],
"FORMAT_TIME_MAP": ["FORMAT_TIME_PRIMARY_MAP", "FORMAT_TIME_SECONDARY_MAP"],
"MAP_ANNOT_OFFSET": [
"MAP_ANNOT_OFFSET_PRIMARY",
"MAP_ANNOT_OFFSET_SECONDARY",
],
"MAP_GRID_CROSS_SIZE": [
"MAP_GRID_CROSS_SIZE_PRIMARY",
"MAP_GRID_CROSS_SIZE_SECONDARY",
],
"MAP_GRID_PEN": ["MAP_GRID_PEN_PRIMARY", "MAP_GRID_PEN_SECONDARY"],
"MAP_TICK_LENGTH": ["MAP_TICK_LENGTH_PRIMARY", "MAP_TICK_LENGTH_SECONDARY"],
"MAP_TICK_PEN": ["MAP_TICK_PEN_PRIMARY", "MAP_TICK_PEN_SECONDARY"],
}
with Session() as lib:
for key in kwargs:
if key in self.special_params:
for k in self.special_params[key]:
self.old_defaults[k] = lib.get_default(k)
else:
self.old_defaults[key] = lib.get_default(key)
# call gmt set to change GMT defaults
arg_str = " ".join(
["{}={}".format(key, value) for key, value in kwargs.items()]
)
with Session() as lib:
lib.call_module("set", arg_str)
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
# revert to initial values
arg_str = " ".join(
["{}={}".format(key, value) for key, value in self.old_defaults.items()]
)
with Session() as lib:
lib.call_module("set", arg_str)
[docs]@xr.register_dataarray_accessor("gmt")
class GMTDataArrayAccessor:
"""
This is the GMT extension for :class:`xarray.DataArray`.
You can access various GMT specific metadata about your grid as follows:
>>> from pygmt.datasets import load_earth_relief
>>> # Use the global Earth relief grid with 1 degree spacing
>>> grid = load_earth_relief(resolution="01d")
>>> # See if grid uses Gridline (0) or Pixel (1) registration
>>> grid.gmt.registration
1
>>> # See if grid uses Cartesian (0) or Geographic (1) coordinate system
>>> grid.gmt.gtype
1
"""
def __init__(self, xarray_obj):
self._obj = xarray_obj
try:
self._source = self._obj.encoding["source"] # filepath to NetCDF source
# From the shortened summary information of `grdinfo`,
# get grid registration in column 10, and grid type in column 11
self._registration, self._gtype = map(
int, grdinfo(self._source, C="n", o="10,11").split()
)
except KeyError:
self._registration = 0 # Default to Gridline registration
self._gtype = 0 # Default to Cartesian grid type
@property
def registration(self):
"""
Registration type of the grid, either Gridline (0) or Pixel (1).
"""
return self._registration
@registration.setter
def registration(self, value):
if value in (0, 1):
self._registration = value
else:
raise GMTInvalidInput(
f"Invalid grid registration value: {value}, should be a boolean of "
"either 0 for Gridline registration or 1 for Pixel registration"
)
@property
def gtype(self):
"""
Coordinate system type of the grid, either Cartesian (0) or Geographic
(1).
"""
return self._gtype
@gtype.setter
def gtype(self, value):
if value in (0, 1):
self._gtype = value
else:
raise GMTInvalidInput(
f"Invalid coordinate system type: {value}, should be a boolean of "
"either 0 for Cartesian or 1 for Geographic"
)