"""
Defines the Session class to create and destroy a GMT API session and provides access to
the API functions.
Uses ctypes to wrap most of the core functions from the C API.
"""
import contextlib
import ctypes as ctp
import pathlib
import sys
import warnings
from collections.abc import Generator, Sequence
from typing import Literal
import numpy as np
import pandas as pd
import xarray as xr
from packaging.version import Version
from pygmt.clib.conversion import (
array_to_datetime,
as_c_contiguous,
dataarray_to_matrix,
sequence_to_ctypes_array,
strings_to_ctypes_array,
vectors_to_arrays,
)
from pygmt.clib.loading import get_gmt_version, load_libgmt
from pygmt.datatypes import _GMT_DATASET, _GMT_GRID, _GMT_IMAGE
from pygmt.exceptions import GMTCLibError, GMTCLibNoSessionError, GMTInvalidInput
from pygmt.helpers import (
_validate_data_input,
data_kind,
tempfile_from_geojson,
tempfile_from_image,
)
FAMILIES = [
"GMT_IS_DATASET", # Entity is a data table
"GMT_IS_GRID", # Entity is a grid
"GMT_IS_IMAGE", # Entity is a 1- or 3-band unsigned char image
"GMT_IS_PALETTE", # Entity is a color palette table
"GMT_IS_POSTSCRIPT", # Entity is a PostScript content struct
"GMT_IS_MATRIX", # Entity is a user matrix
"GMT_IS_VECTOR", # Entity is a set of user vectors
"GMT_IS_CUBE", # Entity is a 3-D data cube
]
VIAS = [
"GMT_VIA_MATRIX", # dataset is passed as a matrix
"GMT_VIA_VECTOR", # dataset is passed as a set of vectors
]
GEOMETRIES = [
"GMT_IS_NONE", # items without geometry (e.g., CPT)
"GMT_IS_POINT", # items are points
"GMT_IS_LINE", # items are lines
"GMT_IS_POLY", # items are polygons
"GMT_IS_LP", # items could be any one of LINE or POLY
"GMT_IS_PLP", # items could be any one of POINT, LINE, or POLY
"GMT_IS_SURFACE", # items are 2-D grid
"GMT_IS_VOLUME", # items are 3-D grid
]
METHODS = [
"GMT_IS_DUPLICATE", # tell GMT the data are read-only
"GMT_IS_REFERENCE", # tell GMT to duplicate the data
]
DIRECTIONS = ["GMT_IN", "GMT_OUT"]
MODES = ["GMT_CONTAINER_ONLY", "GMT_IS_OUTPUT"]
REGISTRATIONS = ["GMT_GRID_PIXEL_REG", "GMT_GRID_NODE_REG"]
DTYPES = {
np.int8: "GMT_CHAR",
np.int16: "GMT_SHORT",
np.int32: "GMT_INT",
np.int64: "GMT_LONG",
np.uint8: "GMT_UCHAR",
np.uint16: "GMT_USHORT",
np.uint32: "GMT_UINT",
np.uint64: "GMT_ULONG",
np.float32: "GMT_FLOAT",
np.float64: "GMT_DOUBLE",
np.str_: "GMT_TEXT",
np.datetime64: "GMT_DATETIME",
np.timedelta64: "GMT_LONG",
}
# Dictionary for storing the values of GMT constants.
GMT_CONSTANTS = {}
# Load the GMT library outside the Session class to avoid repeated loading.
_libgmt = load_libgmt()
__gmt_version__ = get_gmt_version(_libgmt)
[docs]
class Session:
"""
A GMT API session where most operations involving the C API happen.
Works as a context manager (for use in a ``with`` block) to create a GMT C
API session and destroy it in the end to clean up memory.
Functions of the shared library are exposed as methods of this class. Most
methods MUST be used with an open session (inside a ``with`` block). If
creating GMT data structures to communicate data, put that code inside the
same ``with`` block as the API calls that will use the data.
By default, will let :mod:`ctypes` try to find the GMT shared library
(``libgmt``). If the environment variable ``GMT_LIBRARY_PATH`` is set, will
look for the shared library in the directory specified by it.
A ``GMTVersionError`` exception will be raised if the GMT shared library
reports a version older than the required minimum GMT version.
The ``session_pointer`` attribute holds a ctypes pointer to the currently
open session.
Raises
------
GMTCLibNotFoundError
If there was any problem loading the library (couldn't find it or
couldn't access the functions).
GMTCLibNoSessionError
If you try to call a method outside of a 'with' block.
GMTVersionError
If the minimum required version of GMT is not found.
Examples
--------
>>> from pygmt.helpers.testing import load_static_earth_relief
>>> from pygmt.helpers import GMTTempFile
>>> grid = load_static_earth_relief()
>>> type(grid)
<class 'xarray.core.dataarray.DataArray'>
>>> # Create a session and destroy it automatically when exiting the "with"
>>> # block.
>>> with Session() as ses:
... # Create a virtual file and link to the memory block of the grid.
... with ses.virtualfile_from_grid(grid) as fin:
... # Create a temp file to use as output.
... with GMTTempFile() as fout:
... # Call the grdinfo module with the virtual file as input
... # and the temp file as output.
... ses.call_module("grdinfo", [fin, "-C", f"->{fout.name}"])
... # Read the contents of the temp file before it's deleted.
... print(fout.read().strip())
-55 -47 -24 -10 190 981 1 1 8 14 1 1
"""
@property
def session_pointer(self):
"""
The :class:`ctypes.c_void_p` pointer to the current open GMT session.
Raises
------
GMTCLibNoSessionError
If trying to access without a currently open GMT session (i.e.,
outside of the context manager).
"""
if not hasattr(self, "_session_pointer") or self._session_pointer is None:
raise GMTCLibNoSessionError("No currently open GMT API session.")
return self._session_pointer
@session_pointer.setter
def session_pointer(self, session):
"""
Set the session void pointer.
"""
self._session_pointer = session
@property
def info(self):
"""
Dictionary with the GMT version and default paths and parameters.
"""
if not hasattr(self, "_info"):
self._info = {
"version": self.get_default("API_VERSION"),
"padding": self.get_default("API_PAD"),
# API_BINDIR points to the directory of the Python interpreter
# "binary dir": self.get_default("API_BINDIR"),
"share dir": self.get_default("API_SHAREDIR"),
# This segfaults for some reason
# 'data dir': self.get_default("API_DATADIR"),
"plugin dir": self.get_default("API_PLUGINDIR"),
"library path": self.get_default("API_LIBRARY"),
"cores": self.get_default("API_CORES"),
"grid layout": self.get_default("API_GRID_LAYOUT"),
}
# For GMT<6.4.0, API_IMAGE_LAYOUT is not defined if GMT is not
# compiled with GDAL. Since GMT 6.4.0, GDAL is a required GMT
# dependency. The code block can be refactored after we bump
# the minimum required GMT version to 6.4.0.
with contextlib.suppress(GMTCLibError):
self._info["image layout"] = self.get_default("API_IMAGE_LAYOUT")
# API_BIN_VERSION is new in GMT 6.4.0.
if Version(self._info["version"]) >= Version("6.4.0"):
self._info["binary version"] = self.get_default("API_BIN_VERSION")
return self._info
[docs]
def __enter__(self):
"""
Create a GMT API session.
Calls :meth:`pygmt.clib.Session.create`.
"""
self.create("pygmt-session")
return self
[docs]
def __exit__(self, exc_type, exc_value, traceback):
"""
Destroy the currently open GMT API session.
Calls :meth:`pygmt.clib.Session.destroy`.
"""
self.destroy()
[docs]
def __getitem__(self, name: str) -> int:
"""
Get the value of a GMT constant.
Parameters
----------
name
The name of the constant (e.g., ``"GMT_SESSION_EXTERNAL"``).
Returns
-------
value
Integer value of the constant. Do not rely on this value because it might
change.
"""
if name not in GMT_CONSTANTS:
GMT_CONSTANTS[name] = self.get_enum(name)
return GMT_CONSTANTS[name]
def get_enum(self, name: str) -> int:
"""
Get the value of a GMT constant (C enum) from ``gmt_resources.h``.
Used to set configuration values for other API calls. Wraps ``GMT_Get_Enum``.
Parameters
----------
name
The name of the constant (e.g., ``"GMT_SESSION_EXTERNAL"``).
Returns
-------
value
Integer value of the constant. Do not rely on this value because it might
change.
Raises
------
GMTCLibError
If the constant doesn't exist.
"""
c_get_enum = self.get_libgmt_func(
"GMT_Get_Enum", argtypes=[ctp.c_void_p, ctp.c_char_p], restype=ctp.c_int
)
# The C library introduced the void API pointer to GMT_Get_Enum so that it's
# consistent with other functions. It doesn't use the pointer so we can pass
# in None (NULL pointer). We can't give it the actual pointer because we need
# to call GMT_Get_Enum when creating a new API session pointer (chicken-and-egg
# type of thing).
session = None
value = c_get_enum(session, name.encode())
if value is None or value == -99999:
raise GMTCLibError(f"Constant '{name}' doesn't exist in libgmt.")
return value
[docs]
def get_libgmt_func(self, name, argtypes=None, restype=None):
"""
Get a ctypes function from the libgmt shared library.
Assigns the argument and return type conversions for the function.
Use this method to access a C function from libgmt.
Parameters
----------
name : str
The name of the GMT API function.
argtypes : list
List of ctypes types used to convert the Python input arguments for
the API function.
restype : ctypes type
The ctypes type used to convert the input returned by the function
into a Python type.
Returns
-------
function
The GMT API function.
Examples
--------
>>> from ctypes import c_void_p, c_int
>>> with Session() as lib:
... func = lib.get_libgmt_func(
... "GMT_Destroy_Session", argtypes=[c_void_p], restype=c_int
... )
>>> type(func)
<class 'ctypes.CDLL.__init__.<locals>._FuncPtr'>
"""
if not hasattr(self, "_libgmt"):
self._libgmt = _libgmt
function = getattr(self._libgmt, name)
if argtypes is not None:
function.argtypes = argtypes
if restype is not None:
function.restype = restype
return function
[docs]
def create(self, name):
"""
Create a new GMT C API session.
This is required before most other methods of
:class:`pygmt.clib.Session` can be called.
.. warning::
Usage of :class:`pygmt.clib.Session` as a context manager in a
``with`` block is preferred over calling
:meth:`pygmt.clib.Session.create` and
:meth:`pygmt.clib.Session.destroy` manually.
Calls ``GMT_Create_Session`` and generates a new ``GMTAPI_CTRL``
struct, which is a :class:`ctypes.c_void_p` pointer. Sets the
``session_pointer`` attribute to this pointer.
Remember to terminate the current session using
:meth:`pygmt.clib.Session.destroy` before creating a new one.
Parameters
----------
name : str
A name for this session. Doesn't really affect the outcome.
"""
try:
# Won't raise an exception if there is a currently open session
_ = self.session_pointer
# In this case, fail to create a new session until the old one is
# destroyed
raise GMTCLibError(
"Failed to create a GMT API session: There is a currently open session."
" Must destroy it first."
)
# If the exception is raised, this means that there is no open session
# and we're free to create a new one.
except GMTCLibNoSessionError:
pass
c_create_session = self.get_libgmt_func(
"GMT_Create_Session",
argtypes=[ctp.c_char_p, ctp.c_uint, ctp.c_uint, ctp.c_void_p],
restype=ctp.c_void_p,
)
# Capture the output printed by GMT into this list. Will use it later
# to generate error messages for the exceptions raised by API calls.
self._error_log = []
@ctp.CFUNCTYPE(ctp.c_int, ctp.c_void_p, ctp.c_char_p)
def print_func(file_pointer, message): # noqa: ARG001
"""
Callback function that the GMT C API will use to print log and error
messages.
We'll capture the messages and print them to stderr so that they will show
up on the Jupyter notebook.
"""
# Have to use try..except due to upstream GMT bug in GMT <= 6.5.0.
# See https://github.com/GenericMappingTools/pygmt/issues/3205.
try:
message = message.decode().strip()
except UnicodeDecodeError:
return 0
self._error_log.append(message)
# Flush to make sure the messages are printed even if we have a crash.
print(message, file=sys.stderr, flush=True) # noqa: T201
return 0
# Need to store a copy of the function because ctypes doesn't and it
# will be garbage collected otherwise
self._print_callback = print_func
padding = self["GMT_PAD_DEFAULT"]
session_type = self["GMT_SESSION_EXTERNAL"]
session = c_create_session(name.encode(), padding, session_type, print_func)
if session is None:
raise GMTCLibError(
f"Failed to create a GMT API session:\n{self._error_message}"
)
self.session_pointer = session
@property
def _error_message(self):
"""
A string with all error messages emitted by the C API.
Only includes messages with the string ``"[ERROR]"`` in them.
"""
msg = ""
if hasattr(self, "_error_log"):
msg = "\n".join(line for line in self._error_log if "[ERROR]" in line)
return msg
[docs]
def destroy(self):
"""
Destroy the currently open GMT API session.
.. warning::
Usage of :class:`pygmt.clib.Session` as a context manager in a
``with`` block is preferred over calling
:meth:`pygmt.clib.Session.create` and
:meth:`pygmt.clib.Session.destroy` manually.
Calls ``GMT_Destroy_Session`` to terminate and free the memory of a
registered ``GMTAPI_CTRL`` session (the pointer for this struct is
stored in the ``session_pointer`` attribute).
Always use this method after you are done using a C API session. The
session needs to be destroyed before creating a new one. Otherwise,
some of the configuration files might be left behind and can influence
subsequent API calls.
Sets the ``session_pointer`` attribute to ``None``.
"""
c_destroy_session = self.get_libgmt_func(
"GMT_Destroy_Session", argtypes=[ctp.c_void_p], restype=ctp.c_int
)
status = c_destroy_session(self.session_pointer)
if status:
raise GMTCLibError(
f"Failed to destroy GMT API session:\n{self._error_message}"
)
self.session_pointer = None
[docs]
def get_default(self, name: str) -> str:
"""
Get the value of a GMT configuration parameter or a GMT API parameter.
In addition to the long list of GMT configuration parameters, the following API
parameter names are also supported:
* ``"API_VERSION"``: The GMT API version
* ``"API_PAD"``: The grid padding setting
* ``"API_BINDIR"``: The binary file directory
* ``"API_SHAREDIR"``: The share directory
* ``"API_DATADIR"``: The data directory
* ``"API_PLUGINDIR"``: The plugin directory
* ``"API_LIBRARY"``: The core library path
* ``"API_CORES"``: The number of cores
* ``"API_IMAGE_LAYOUT"``: The image/band layout
* ``"API_GRID_LAYOUT"``: The grid layout
* ``"API_BIN_VERSION"``: The GMT binary version (with git information)
Parameters
----------
name
The name of the GMT configuration parameter (e.g., ``"PROJ_LENGTH_UNIT"``)
or a GMT API parameter (e.g., ``"API_VERSION"``).
Returns
-------
value
The current value for the parameter.
Raises
------
GMTCLibError
If the parameter doesn't exist.
"""
c_get_default = self.get_libgmt_func(
"GMT_Get_Default",
argtypes=[ctp.c_void_p, ctp.c_char_p, ctp.c_char_p],
restype=ctp.c_int,
)
# Make a string buffer to get a return value
value = ctp.create_string_buffer(4096)
status = c_get_default(self.session_pointer, name.encode(), value)
if status != 0:
msg = f"Error getting value for '{name}' (error code {status})."
raise GMTCLibError(msg)
return value.value.decode()
[docs]
def get_common(self, option: str) -> bool | int | float | np.ndarray:
"""
Inquire if a GMT common option has been set and return its current value if
possible.
Parameters
----------
option
The GMT common option to check. Valid options are ``"B"``, ``"I"``, ``"J"``,
``"R"``, ``"U"``, ``"V"``, ``"X"``, ``"Y"``, ``"a"``, ``"b"``, ``"f"``,
``"g"``, ``"h"``, ``"i"``, ``"n"``, ``"o"``, ``"p"``, ``"r"``, ``"s"``,
``"t"``, and ``":"``.
Returns
-------
value
Whether the option was set or its value. If the option was not set, return
``False``. Otherwise, the return value depends on the choice of the option.
- options ``"B"``, ``"J"``, ``"U"``, ``"g"``, ``"n"``, ``"p"``, and ``"s"``:
return ``True`` if set, else ``False`` (bool)
- ``"I"``: 2-element array for the increments (float)
- ``"R"``: 4-element array for the region (float)
- ``"V"``: the verbose level (int)
- ``"X"``: the xshift (float)
- ``"Y"``: the yshift (float)
- ``"a"``: geometry of the dataset (int)
- ``"b"``: return 0 if ``-bi`` was set and 1 if ``-bo`` was set (int)
- ``"f"``: return 0 if ``-fi`` was set and 1 if ``-fo`` was set (int)
- ``"h"``: whether to delete existing header records (int)
- ``"i"``: number of input columns (int)
- ``"o"``: number of output columns (int)
- ``"r"``: registration type (int)
- ``"t"``: 2-element array for the transparency (float)
- ``":"``: return 0 if ``-:i`` was set and 1 if ``-:o`` was set (int)
Examples
--------
>>> with Session() as lib:
... lib.call_module(
... "basemap", ["-R0/10/10/15", "-JX5i/2.5i", "-Baf", "-Ve"]
... )
... region = lib.get_common("R")
... projection = lib.get_common("J")
... timestamp = lib.get_common("U")
... verbose = lib.get_common("V")
... lib.call_module("plot", ["-T", "-Xw+1i", "-Yh-1i"])
... xshift = lib.get_common("X") # xshift/yshift are in inches
... yshift = lib.get_common("Y")
>>> print(region, projection, timestamp, verbose, xshift, yshift)
[ 0. 10. 10. 15.] True False 3 6.0 1.5
>>> with Session() as lib:
... lib.call_module("basemap", ["-R0/10/10/15", "-JX5i/2.5i", "-Baf"])
... lib.get_common("A")
Traceback (most recent call last):
...
pygmt.exceptions.GMTInvalidInput: Unknown GMT common option flag 'A'.
"""
if option not in "BIJRUVXYabfghinoprst:":
raise GMTInvalidInput(f"Unknown GMT common option flag '{option}'.")
c_get_common = self.get_libgmt_func(
"GMT_Get_Common",
argtypes=[ctp.c_void_p, ctp.c_uint, ctp.POINTER(ctp.c_double)],
restype=ctp.c_int,
)
value = np.empty(6, np.float64) # numpy array to store the value of the option
status = c_get_common(
self.session_pointer,
ord(option),
value.ctypes.data_as(ctp.POINTER(ctp.c_double)),
)
if status == self["GMT_NOTSET"]: # GMT_NOTSET (-1) means the option is not set
return False
if status == 0: # Option is set and no other value is returned.
return True
# Otherwise, option is set and values are returned.
match option:
case "I" | "R" | "t":
# Option values (in double type) are returned via the 'value' array.
# 'status' is number of valid values in the array.
return value[:status]
case "X" | "Y": # Only one valid element in the array.
return value[0]
case _: # 'status' is the option value (in integer type).
return status
[docs]
def call_module(self, module: str, args: str | list[str]):
"""
Call a GMT module with the given arguments.
Wraps ``GMT_Call_Module``.
The ``GMT_Call_Module`` API function supports passing module arguments in three
different ways:
1. Pass a single string that contains whitespace-separated module arguments.
2. Pass a list of strings and each string contains a module argument.
3. Pass a list of ``GMT_OPTION`` data structure.
Both options 1 and 2 are implemented in this function, but option 2 is preferred
because it can correctly handle special characters like whitespaces and
quotation marks in module arguments.
Parameters
----------
module
The GMT module name to be called (``"coast"``, ``"basemap"``, etc).
args
Module arguments that will be passed to the GMT module. It can be either
a single string (e.g., ``"-R0/5/0/10 -JX10c -BWSen+t'My Title'"``) or a list
of strings (e.g., ``["-R0/5/0/10", "-JX10c", "-BWSEN+tMy Title"]``).
Raises
------
GMTInvalidInput
If the ``args`` argument is not a string or a list of strings.
GMTCLibError
If the returned status code of the function is non-zero.
"""
c_call_module = self.get_libgmt_func(
"GMT_Call_Module",
argtypes=[ctp.c_void_p, ctp.c_char_p, ctp.c_int, ctp.c_void_p],
restype=ctp.c_int,
)
# 'args' can be (1) a single string or (2) a list of strings.
argv: bytes | ctp.Array[ctp.c_char_p] | None
if isinstance(args, str):
# 'args' is a single string that contains whitespace-separated arguments.
# In this way, we need to correctly handle option arguments that contain
# whitespaces or quotation marks. It's used in PyGMT <= v0.11.0 but is no
# longer recommended.
mode = self["GMT_MODULE_CMD"]
argv = args.encode()
elif isinstance(args, list):
# 'args' is a list of strings and each string contains a module argument.
# In this way, GMT can correctly handle option arguments with whitespaces or
# quotation marks. This is the preferred way to pass arguments to the GMT
# API and is used for PyGMT >= v0.12.0.
mode = len(args) # 'mode' is the number of arguments.
# Pass a null pointer if no arguments are specified.
argv = strings_to_ctypes_array(args) if mode != 0 else None
else:
raise GMTInvalidInput(
"'args' must be either a string or a list of strings."
)
status = c_call_module(self.session_pointer, module.encode(), mode, argv)
if status != 0:
raise GMTCLibError(
f"Module '{module}' failed with status code {status}:\n{self._error_message}"
)
[docs]
def create_data(
self,
family,
geometry,
mode,
dim=None,
ranges=None,
inc=None,
registration="GMT_GRID_NODE_REG",
pad=None,
):
"""
Create an empty GMT data container.
Parameters
----------
family : str
A valid GMT data family name (e.g., ``'GMT_IS_DATASET'``). See the
``FAMILIES`` attribute for valid names.
geometry : str
A valid GMT data geometry name (e.g., ``'GMT_IS_POINT'``). See the
``GEOMETRIES`` attribute for valid names.
mode : str
A valid GMT data mode (e.g., ``'GMT_IS_OUTPUT'``). See the
``MODES`` attribute for valid names.
dim : list of 4 integers
The dimensions of the dataset. See the documentation for the GMT C
API function ``GMT_Create_Data`` (``src/gmt_api.c``) for the full
range of options regarding 'dim'. If ``None``, will pass in the
NULL pointer.
ranges : list of 4 floats
The dataset extent. Also a bit of a complicated argument. See the C
function documentation. It's called ``range`` in the C function but
it would conflict with the Python built-in ``range`` function.
inc : list of 2 floats
The increments between points of the dataset. See the C function
documentation.
registration : str
The node registration (what the coordinates mean). Can be
``'GMT_GRID_PIXEL_REG'`` or ``'GMT_GRID_NODE_REG'``. Defaults to
``'GMT_GRID_NODE_REG'``.
pad : int
The grid padding. Defaults to ``GMT_PAD_DEFAULT``.
Returns
-------
data_ptr : int
A ctypes pointer (an integer) to the allocated ``GMT_Dataset``
object.
"""
c_create_data = self.get_libgmt_func(
"GMT_Create_Data",
argtypes=[
ctp.c_void_p, # API
ctp.c_uint, # family
ctp.c_uint, # geometry
ctp.c_uint, # mode
ctp.POINTER(ctp.c_uint64), # dim
ctp.POINTER(ctp.c_double), # range
ctp.POINTER(ctp.c_double), # inc
ctp.c_uint, # registration
ctp.c_int, # pad
ctp.c_void_p,
], # data
restype=ctp.c_void_p,
)
family_int = self._parse_constant(family, valid=FAMILIES, valid_modifiers=VIAS)
mode_int = self._parse_constant(
mode,
valid=MODES,
valid_modifiers=["GMT_GRID_IS_CARTESIAN", "GMT_GRID_IS_GEO"],
)
geometry_int = self._parse_constant(geometry, valid=GEOMETRIES)
registration_int = self._parse_constant(registration, valid=REGISTRATIONS)
# Convert dim, ranges, and inc to ctypes arrays if given (will be None
# if not given to represent NULL pointers)
dim = sequence_to_ctypes_array(dim, ctp.c_uint64, 4)
ranges = sequence_to_ctypes_array(ranges, ctp.c_double, 4)
inc = sequence_to_ctypes_array(inc, ctp.c_double, 2)
# Use a NULL pointer (None) for existing data to indicate that the
# container should be created empty. Fill it in later using put_vector
# and put_matrix.
data_ptr = c_create_data(
self.session_pointer,
family_int,
geometry_int,
mode_int,
dim,
ranges,
inc,
registration_int,
self._parse_pad(family, pad),
None,
)
if data_ptr is None:
raise GMTCLibError("Failed to create an empty GMT data pointer.")
return data_ptr
def _parse_pad(self, family, pad):
"""
Parse and return an appropriate value for pad if none is given.
Pad is a bit tricky because, for matrix types, pad control the matrix ordering
(row or column major). Using the default pad will set it to column major and
mess things up with the numpy arrays.
"""
if pad is None:
pad = 0 if "MATRIX" in family else self["GMT_PAD_DEFAULT"]
return pad
def _parse_constant(self, constant, valid, valid_modifiers=None):
"""
Parse a constant, convert it to an int, and validate it.
The GMT C API takes certain defined constants, like ``'GMT_IS_GRID'``,
that need to be validated and converted to integer values using
:meth:`pygmt.clib.Session.__getitem__`.
The constants can also take a modifier by appending another constant
name, e.g. ``'GMT_IS_GRID|GMT_VIA_MATRIX'``. The two parts must be
converted separately and their values are added.
If valid modifiers are not given, then will assume that modifiers are
not allowed. In this case, will raise a
:class:`pygmt.exceptions.GMTInvalidInput` exception if given a
modifier.
Parameters
----------
constant : str
The name of a valid GMT API constant, with an optional modifier.
valid : list of str
A list of valid values for the constant. Will raise a
:class:`pygmt.exceptions.GMTInvalidInput` exception if the given
value is not on the list.
"""
parts = constant.split("|")
name = parts[0]
nmodifiers = len(parts) - 1
if nmodifiers > 1:
raise GMTInvalidInput(
f"Only one modifier is allowed in constants, {nmodifiers} given: '{constant}'"
)
if nmodifiers > 0 and valid_modifiers is None:
raise GMTInvalidInput(
"Constant modifiers are not allowed since valid values were not given: '{constant}'"
)
if name not in valid:
raise GMTInvalidInput(
f"Invalid constant argument '{name}'. Must be one of {valid}."
)
if (
nmodifiers > 0
and valid_modifiers is not None
and parts[1] not in valid_modifiers
):
raise GMTInvalidInput(
f"Invalid constant modifier '{parts[1]}'. Must be one of {valid_modifiers}."
)
integer_value = sum(self[part] for part in parts)
return integer_value
def _check_dtype_and_dim(self, array, ndim):
"""
Check that a numpy array has the given number of dimensions and is a valid data
type.
Parameters
----------
array : numpy.ndarray
The array to be tested.
ndim : int
The desired number of array dimensions.
Returns
-------
gmt_type : int
The GMT constant value representing this data type.
Raises
------
GMTInvalidInput
If the array has the wrong number of dimensions or
is an unsupported data type.
Examples
--------
>>> import numpy as np
>>> data = np.array([1, 2, 3], dtype="float64")
>>> with Session() as ses:
... gmttype = ses._check_dtype_and_dim(data, ndim=1)
... gmttype == ses["GMT_DOUBLE"]
True
>>> data = np.ones((5, 2), dtype="float32")
>>> with Session() as ses:
... gmttype = ses._check_dtype_and_dim(data, ndim=2)
... gmttype == ses["GMT_FLOAT"]
True
"""
# Check that the array has the given number of dimensions
if array.ndim != ndim:
raise GMTInvalidInput(
f"Expected a numpy {ndim}-D array, got {array.ndim}-D."
)
# Check that the array has a valid/known data type
if array.dtype.type not in DTYPES:
try:
if array.dtype.type is np.object_:
# Try to convert unknown object type to np.datetime64
array = array_to_datetime(array)
else:
raise ValueError
except ValueError as e:
raise GMTInvalidInput(
f"Unsupported numpy data type '{array.dtype.type}'."
) from e
return self[DTYPES[array.dtype.type]]
[docs]
def put_vector(self, dataset, column, vector):
r"""
Attach a numpy 1-D array as a column on a GMT dataset.
Use this function to attach numpy array data to a GMT dataset and pass
it to GMT modules. Wraps ``GMT_Put_Vector``.
The dataset must be created by :meth:`pygmt.clib.Session.create_data`
first. Use ``family='GMT_IS_DATASET|GMT_VIA_VECTOR'``.
Not all numpy dtypes are supported, only: int8, int16, int32, int64,
uint8, uint16, uint32, uint64, float32, float64, str\_, and datetime64.
.. warning::
The numpy array must be C contiguous in memory. If it comes from a
column slice of a 2-D array, for example, you will have to make a
copy. Use :func:`numpy.ascontiguousarray` to make sure your vector
is contiguous (it won't copy if it already is).
Parameters
----------
dataset : :class:`ctypes.c_void_p`
The ctypes void pointer to a ``GMT_Dataset``. Create it with
:meth:`pygmt.clib.Session.create_data`.
column : int
The column number of this vector in the dataset (starting from 0).
vector : numpy 1-D array
The array that will be attached to the dataset. Must be a 1-D C
contiguous array.
Raises
------
GMTCLibError
If given invalid input or ``GMT_Put_Vector`` exits with
status != 0.
"""
c_put_vector = self.get_libgmt_func(
"GMT_Put_Vector",
argtypes=[ctp.c_void_p, ctp.c_void_p, ctp.c_uint, ctp.c_uint, ctp.c_void_p],
restype=ctp.c_int,
)
gmt_type = self._check_dtype_and_dim(vector, ndim=1)
if gmt_type in {self["GMT_TEXT"], self["GMT_DATETIME"]}:
if gmt_type == self["GMT_DATETIME"]:
vector = np.datetime_as_string(array_to_datetime(vector))
vector_pointer = strings_to_ctypes_array(vector)
else:
vector_pointer = vector.ctypes.data_as(ctp.c_void_p)
status = c_put_vector(
self.session_pointer, dataset, column, gmt_type, vector_pointer
)
if status != 0:
raise GMTCLibError(
f"Failed to put vector of type {vector.dtype} "
f"in column {column} of dataset."
)
[docs]
def put_strings(self, dataset, family, strings):
"""
Attach a numpy 1-D array of dtype str as a column on a GMT dataset.
Use this function to attach string type numpy array data to a GMT
dataset and pass it to GMT modules. Wraps ``GMT_Put_Strings``.
The dataset must be created by :meth:`pygmt.clib.Session.create_data`
first.
.. warning::
The numpy array must be C contiguous in memory. If it comes from a
column slice of a 2-D array, for example, you will have to make a
copy. Use :func:`numpy.ascontiguousarray` to make sure your vector
is contiguous (it won't copy if it already is).
Parameters
----------
dataset : :class:`ctypes.c_void_p`
The ctypes void pointer to a ``GMT_Dataset``. Create it with
:meth:`pygmt.clib.Session.create_data`.
family : str
The family type of the dataset. Can be either ``GMT_IS_VECTOR`` or
``GMT_IS_MATRIX``.
strings : numpy 1-D array
The array that will be attached to the dataset. Must be a 1-D C
contiguous array.
Raises
------
GMTCLibError
If given invalid input or ``GMT_Put_Strings`` exits with
status != 0.
"""
c_put_strings = self.get_libgmt_func(
"GMT_Put_Strings",
argtypes=[
ctp.c_void_p,
ctp.c_uint,
ctp.c_void_p,
ctp.POINTER(ctp.c_char_p),
],
restype=ctp.c_int,
)
family_int = self._parse_constant(
family, valid=FAMILIES, valid_modifiers=METHODS
)
strings_pointer = strings_to_ctypes_array(strings)
status = c_put_strings(
self.session_pointer, family_int, dataset, strings_pointer
)
if status != 0:
raise GMTCLibError(
f"Failed to put strings of type {strings.dtype} into dataset"
)
[docs]
def put_matrix(self, dataset, matrix, pad=0):
"""
Attach a numpy 2-D array to a GMT dataset.
Use this function to attach numpy array data to a GMT dataset and pass
it to GMT modules. Wraps ``GMT_Put_Matrix``.
The dataset must be created by :meth:`pygmt.clib.Session.create_data`
first. Use ``|GMT_VIA_MATRIX'`` in the family.
Not all numpy dtypes are supported, only: int8, int16, int32, int64,
uint8, uint16, uint32, uint64, float32, and float64.
.. warning::
The numpy array must be C contiguous in memory. Use
:func:`numpy.ascontiguousarray` to make sure your vector is
contiguous (it won't copy if it already is).
Parameters
----------
dataset : :class:`ctypes.c_void_p`
The ctypes void pointer to a ``GMT_Dataset``. Create it with
:meth:`pygmt.clib.Session.create_data`.
matrix : numpy 2-D array
The array that will be attached to the dataset. Must be a 2-D C
contiguous array.
pad : int
The amount of padding that should be added to the matrix. Use when
creating grids for modules that require padding.
Raises
------
GMTCLibError
If given invalid input or ``GMT_Put_Matrix`` exits with
status != 0.
"""
c_put_matrix = self.get_libgmt_func(
"GMT_Put_Matrix",
argtypes=[ctp.c_void_p, ctp.c_void_p, ctp.c_uint, ctp.c_int, ctp.c_void_p],
restype=ctp.c_int,
)
gmt_type = self._check_dtype_and_dim(matrix, ndim=2)
matrix_pointer = matrix.ctypes.data_as(ctp.c_void_p)
status = c_put_matrix(
self.session_pointer, dataset, gmt_type, pad, matrix_pointer
)
if status != 0:
raise GMTCLibError(f"Failed to put matrix of type {matrix.dtype}.")
[docs]
def read_data(
self,
infile: str,
kind: Literal["dataset", "grid", "image"],
family: str | None = None,
geometry: str | None = None,
mode: str = "GMT_READ_NORMAL",
region: Sequence[float] | None = None,
data=None,
):
"""
Read a data file into a GMT data container.
Wraps ``GMT_Read_Data`` but only allows reading from a file. The function
definition is different from the original C API function.
Parameters
----------
infile
The input file name.
kind
The data kind of the input file. Valid values are ``"dataset"``, ``"grid"``
and ``"image"``.
family
A valid GMT data family name (e.g., ``"GMT_IS_DATASET"``). See the
``FAMILIES`` attribute for valid names. If ``None``, will determine the data
family from the ``kind`` parameter.
geometry
A valid GMT data geometry name (e.g., ``"GMT_IS_POINT"``). See the
``GEOMETRIES`` attribute for valid names. If ``None``, will determine the
data geometry from the ``kind`` parameter.
mode
How the data is to be read from the file. This option varies depending on
the given family. See the
:gmt-docs:`GMT API documentation <devdocs/api.html#import-from-a-file-stream-or-handle>`
for details. Default is ``GMT_READ_NORMAL`` which corresponds to the default
read mode value of 0 in the ``GMT_enum_read`` enum.
region
Subregion of the data, in the form of [xmin, xmax, ymin, ymax, zmin, zmax].
If ``None``, the whole data is read.
data
``None`` or the pointer returned by this function after a first call. It's
useful when reading grids/images/cubes in two steps (get a grid/image/cube
structure with a header, then read the data).
Returns
-------
Pointer to the data container, or ``None`` if there were errors.
Raises
------
GMTCLibError
If the GMT API function fails to read the data.
""" # noqa: W505
c_read_data = self.get_libgmt_func(
"GMT_Read_Data",
argtypes=[
ctp.c_void_p, # V_API
ctp.c_uint, # family
ctp.c_uint, # method
ctp.c_uint, # geometry
ctp.c_uint, # mode
ctp.POINTER(ctp.c_double), # wesn
ctp.c_char_p, # infile
ctp.c_void_p, # data
],
restype=ctp.c_void_p, # data_ptr
)
# Determine the family, geometry and data container from kind
_family, _geometry, dtype = {
"dataset": ("GMT_IS_DATASET", "GMT_IS_PLP", _GMT_DATASET),
"grid": ("GMT_IS_GRID", "GMT_IS_SURFACE", _GMT_GRID),
"image": ("GMT_IS_IMAGE", "GMT_IS_SURFACE", _GMT_IMAGE),
}[kind]
if family is None:
family = _family
if geometry is None:
geometry = _geometry
data_ptr = c_read_data(
self.session_pointer,
self[family],
self["GMT_IS_FILE"], # Reading from a file
self[geometry],
self[mode],
sequence_to_ctypes_array(region, ctp.c_double, 6),
infile.encode(),
data,
)
if data_ptr is None:
raise GMTCLibError(f"Failed to read dataset from '{infile}'.")
return ctp.cast(data_ptr, ctp.POINTER(dtype))
[docs]
def write_data(self, family, geometry, mode, wesn, output, data):
"""
Write a GMT data container to a file.
The data container should be created by
:meth:`pygmt.clib.Session.create_data`.
Wraps ``GMT_Write_Data`` but only allows writing to a file. So the
``method`` argument is omitted.
Parameters
----------
family : str
A valid GMT data family name (e.g., ``'GMT_IS_DATASET'``). See the
``FAMILIES`` attribute for valid names. Don't use the
``GMT_VIA_VECTOR`` or ``GMT_VIA_MATRIX`` constructs for this. Use
``GMT_IS_VECTOR`` and ``GMT_IS_MATRIX`` instead.
geometry : str
A valid GMT data geometry name (e.g., ``'GMT_IS_POINT'``). See the
``GEOMETRIES`` attribute for valid names.
mode : str
How the data is to be written to the file. This option varies
depending on the given family. See the GMT API documentation for
details.
wesn : list or numpy array
[xmin, xmax, ymin, ymax, zmin, zmax] of the data. Must have 6
elements.
output : str
The output file name.
data : :class:`ctypes.c_void_p`
Pointer to the data container created by
:meth:`pygmt.clib.Session.create_data`.
Raises
------
GMTCLibError
For invalid input arguments or if the GMT API functions returns a
non-zero status code.
"""
c_write_data = self.get_libgmt_func(
"GMT_Write_Data",
argtypes=[
ctp.c_void_p,
ctp.c_uint,
ctp.c_uint,
ctp.c_uint,
ctp.c_uint,
ctp.POINTER(ctp.c_double),
ctp.c_char_p,
ctp.c_void_p,
],
restype=ctp.c_int,
)
family_int = self._parse_constant(family, valid=FAMILIES, valid_modifiers=VIAS)
geometry_int = self._parse_constant(geometry, valid=GEOMETRIES)
status = c_write_data(
self.session_pointer,
family_int,
self["GMT_IS_FILE"],
geometry_int,
self[mode],
sequence_to_ctypes_array(wesn, ctp.c_double, 6),
output.encode(),
data,
)
if status != 0:
raise GMTCLibError(f"Failed to write dataset to '{output}'")
[docs]
@contextlib.contextmanager
def open_virtualfile(self, family, geometry, direction, data):
"""
Open a GMT virtual file to pass data to and from a module.
GMT uses a virtual file scheme to pass in data or get data from API
modules. Use it to pass in your GMT data structure (created using
:meth:`pygmt.clib.Session.create_data`) to a module that expects an
input file, or get the output from a module that writes to a file.
Use in a ``with`` block. Will automatically close the virtual file when
leaving the ``with`` block. Because of this, no wrapper for
``GMT_Close_VirtualFile`` is provided.
Parameters
----------
family : str
A valid GMT data family name (e.g., ``"GMT_IS_DATASET"``). Should
be the same as the one you used to create your data structure.
geometry : str
A valid GMT data geometry name (e.g., ``"GMT_IS_POINT"``). Should
be the same as the one you used to create your data structure.
direction : str
Either ``"GMT_IN"`` or ``"GMT_OUT"`` to indicate if passing data to
GMT or getting it out of GMT, respectively.
By default, GMT can modify the data you pass in. Add modifier
``"GMT_IS_REFERENCE"`` to tell GMT the data are read-only, or
``"GMT_IS_DUPLICATE"`` to tell GMT to duplicate the data.
data : int or None
The ctypes void pointer to your GMT data structure. For output
(i.e., ``direction="GMT_OUT"``), it can be ``None`` to have GMT
automatically allocate the output GMT data structure.
Yields
------
vfname : str
The name of the virtual file that you can pass to a GMT module.
Examples
--------
>>> from pygmt.helpers import GMTTempFile
>>> import numpy as np
>>> x = np.array([0, 1, 2, 3, 4])
>>> y = np.array([5, 6, 7, 8, 9])
>>> with Session() as lib:
... family = "GMT_IS_DATASET|GMT_VIA_VECTOR"
... geometry = "GMT_IS_POINT"
... dataset = lib.create_data(
... family=family,
... geometry=geometry,
... mode="GMT_CONTAINER_ONLY",
... dim=[2, 5, 1, 0], # columns, lines, segments, type
... )
... lib.put_vector(dataset, column=0, vector=x)
... lib.put_vector(dataset, column=1, vector=y)
... # Add the dataset to a virtual file
... vfargs = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset)
... with lib.open_virtualfile(*vfargs) as vfile:
... # Send the output to a temp file so that we can read it
... with GMTTempFile() as ofile:
... lib.call_module("info", [vfile, f"->{ofile.name}"])
... print(ofile.read().strip())
<vector memory>: N = 5 <0/4> <5/9>
"""
c_open_virtualfile = self.get_libgmt_func(
"GMT_Open_VirtualFile",
argtypes=[
ctp.c_void_p,
ctp.c_uint,
ctp.c_uint,
ctp.c_uint,
ctp.c_void_p,
ctp.c_char_p,
],
restype=ctp.c_int,
)
c_close_virtualfile = self.get_libgmt_func(
"GMT_Close_VirtualFile",
argtypes=[ctp.c_void_p, ctp.c_char_p],
restype=ctp.c_int,
)
family_int = self._parse_constant(family, valid=FAMILIES, valid_modifiers=VIAS)
geometry_int = self._parse_constant(geometry, valid=GEOMETRIES)
direction_int = self._parse_constant(
direction, valid=DIRECTIONS, valid_modifiers=METHODS
)
buff = ctp.create_string_buffer(self["GMT_VF_LEN"])
status = c_open_virtualfile(
self.session_pointer, family_int, geometry_int, direction_int, data, buff
)
if status != 0:
raise GMTCLibError("Failed to create a virtual file.")
vfname = buff.value.decode()
try:
yield vfname
finally:
status = c_close_virtualfile(self.session_pointer, vfname.encode())
if status != 0:
raise GMTCLibError(f"Failed to close virtual file '{vfname}'.")
def open_virtual_file(self, family, geometry, direction, data):
"""
Open a GMT virtual file to pass data to and from a module.
.. deprecated: 0.11.0
Will be removed in v0.15.0. Use :meth:`pygmt.clib.Session.open_virtualfile`
instead.
"""
msg = (
"API function `Session.open_virtual_file()' has been deprecated "
"since v0.11.0 and will be removed in v0.15.0. "
"Use `Session.open_virtualfile()' instead."
)
warnings.warn(msg, category=FutureWarning, stacklevel=2)
return self.open_virtualfile(family, geometry, direction, data)
[docs]
@contextlib.contextmanager
def virtualfile_from_vectors(self, *vectors):
"""
Store 1-D arrays as columns of a table inside a virtual file.
Use the virtual file name to pass in the data in your vectors to a GMT
module.
Context manager (use in a ``with`` block). Yields the virtual file name
that you can pass as an argument to a GMT module call. Closes the
virtual file upon exit of the ``with`` block.
Use this instead of creating the data container and virtual file by
hand with :meth:`pygmt.clib.Session.create_data`,
:meth:`pygmt.clib.Session.put_vector`, and
:meth:`pygmt.clib.Session.open_virtualfile`.
If the arrays are C contiguous blocks of memory, they will be passed
without copying to GMT. If they are not (e.g., they are columns of a
2-D array), they will need to be copied to a contiguous block.
Parameters
----------
vectors : 1-D arrays
The vectors that will be included in the array. All must be of the
same size.
Yields
------
fname : str
The name of virtual file. Pass this as a file name argument to a
GMT module.
Examples
--------
>>> from pygmt.helpers import GMTTempFile
>>> import numpy as np
>>> import pandas as pd
>>> x = [1, 2, 3]
>>> y = np.array([4, 5, 6])
>>> z = pd.Series([7, 8, 9])
>>> with Session() as ses:
... with ses.virtualfile_from_vectors(x, y, z) as fin:
... # Send the output to a file so that we can read it
... with GMTTempFile() as fout:
... ses.call_module("info", [fin, f"->{fout.name}"])
... print(fout.read().strip())
<vector memory>: N = 3 <1/3> <4/6> <7/9>
"""
# Conversion to a C-contiguous array needs to be done here and not in
# put_vector or put_strings because we need to maintain a reference to
# the copy while it is being used by the C API. Otherwise, the array
# would be garbage collected and the memory freed. Creating it in this
# context manager guarantees that the copy will be around until the
# virtual file is closed. The conversion is implicit in
# vectors_to_arrays.
arrays = vectors_to_arrays(vectors)
columns = len(arrays)
# Find arrays that are of string dtype from column 3 onwards
# Assumes that first 2 columns contains coordinates like longitude
# latitude, or datetime string types.
for col, array in enumerate(arrays[2:]):
if pd.api.types.is_string_dtype(array.dtype):
columns = col + 2
break
rows = len(arrays[0])
if not all(len(i) == rows for i in arrays):
raise GMTInvalidInput("All arrays must have same size.")
family = "GMT_IS_DATASET|GMT_VIA_VECTOR"
geometry = "GMT_IS_POINT"
dataset = self.create_data(
family, geometry, mode="GMT_CONTAINER_ONLY", dim=[columns, rows, 1, 0]
)
# Use put_vector for columns with numerical type data
for col, array in enumerate(arrays[:columns]):
self.put_vector(dataset, column=col, vector=array)
# Use put_strings for last column(s) with string type data
# Have to use modifier "GMT_IS_DUPLICATE" to duplicate the strings
string_arrays = arrays[columns:]
if string_arrays:
if len(string_arrays) == 1:
strings = string_arrays[0]
elif len(string_arrays) > 1:
strings = np.array(
[" ".join(vals) for vals in zip(*string_arrays, strict=True)]
)
strings = np.asanyarray(a=strings, dtype=str)
self.put_strings(
dataset, family="GMT_IS_VECTOR|GMT_IS_DUPLICATE", strings=strings
)
with self.open_virtualfile(
family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset
) as vfile:
yield vfile
[docs]
@contextlib.contextmanager
def virtualfile_from_matrix(self, matrix):
"""
Store a 2-D array as a table inside a virtual file.
Use the virtual file name to pass in the data in your matrix to a GMT
module.
Context manager (use in a ``with`` block). Yields the virtual file name
that you can pass as an argument to a GMT module call. Closes the
virtual file upon exit of the ``with`` block.
The virtual file will contain the array as a ``GMT_MATRIX`` pretending
to be a ``GMT_DATASET``.
**Not meant for creating ``GMT_GRID``**. The grid requires more
metadata than just the data matrix. Use
:meth:`pygmt.clib.Session.virtualfile_from_grid` instead.
Use this instead of creating the data container and virtual file by
hand with :meth:`pygmt.clib.Session.create_data`,
:meth:`pygmt.clib.Session.put_matrix`, and
:meth:`pygmt.clib.Session.open_virtualfile`
The matrix must be C contiguous in memory. If it is not (e.g., it is a
slice of a larger array), the array will be copied to make sure it is.
Parameters
----------
matrix : 2-D array
The matrix that will be included in the GMT data container.
Yields
------
fname : str
The name of virtual file. Pass this as a file name argument to a
GMT module.
Examples
--------
>>> from pygmt.helpers import GMTTempFile
>>> import numpy as np
>>> data = np.arange(12).reshape((4, 3))
>>> print(data)
[[ 0 1 2]
[ 3 4 5]
[ 6 7 8]
[ 9 10 11]]
>>> with Session() as ses:
... with ses.virtualfile_from_matrix(data) as fin:
... # Send the output to a file so that we can read it
... with GMTTempFile() as fout:
... ses.call_module("info", [fin, f"->{fout.name}"])
... print(fout.read().strip())
<matrix memory>: N = 4 <0/9> <1/10> <2/11>
"""
# Conversion to a C-contiguous array needs to be done here and not in
# put_matrix because we need to maintain a reference to the copy while
# it is being used by the C API. Otherwise, the array would be garbage
# collected and the memory freed. Creating it in this context manager
# guarantees that the copy will be around until the virtual file is
# closed.
matrix = as_c_contiguous(matrix)
rows, columns = matrix.shape
family = "GMT_IS_DATASET|GMT_VIA_MATRIX"
geometry = "GMT_IS_POINT"
dataset = self.create_data(
family, geometry, mode="GMT_CONTAINER_ONLY", dim=[columns, rows, 1, 0]
)
self.put_matrix(dataset, matrix)
with self.open_virtualfile(
family, geometry, "GMT_IN|GMT_IS_REFERENCE", dataset
) as vfile:
yield vfile
[docs]
@contextlib.contextmanager
def virtualfile_from_grid(self, grid):
"""
Store a grid in a virtual file.
Use the virtual file name to pass in the data in your grid to a GMT
module. Grids must be :class:`xarray.DataArray` instances.
Context manager (use in a ``with`` block). Yields the virtual file name
that you can pass as an argument to a GMT module call. Closes the
virtual file upon exit of the ``with`` block.
The virtual file will contain the grid as a ``GMT_MATRIX`` with extra
metadata.
Use this instead of creating a data container and virtual file by hand
with :meth:`pygmt.clib.Session.create_data`,
:meth:`pygmt.clib.Session.put_matrix`, and
:meth:`pygmt.clib.Session.open_virtualfile`.
The grid data matrix must be C contiguous in memory. If it is not
(e.g., it is a slice of a larger array), the array will be copied to
make sure it is.
Parameters
----------
grid : :class:`xarray.DataArray`
The grid that will be included in the virtual file.
Yields
------
fname : str
The name of virtual file. Pass this as a file name argument to a
GMT module.
Examples
--------
>>> from pygmt.helpers.testing import load_static_earth_relief
>>> from pygmt.helpers import GMTTempFile
>>> data = load_static_earth_relief()
>>> print(data.shape)
(14, 8)
>>> print(data.lon.values.min(), data.lon.values.max())
-54.5 -47.5
>>> print(data.lat.values.min(), data.lat.values.max())
-23.5 -10.5
>>> print(data.values.min(), data.values.max())
190.0 981.0
>>> with Session() as ses:
... with ses.virtualfile_from_grid(data) as fin:
... # Send the output to a file so that we can read it
... with GMTTempFile() as fout:
... ses.call_module(
... "grdinfo", [fin, "-L0", "-Cn", f"->{fout.name}"]
... )
... print(fout.read().strip())
-55 -47 -24 -10 190 981 1 1 8 14 1 1
>>> # The output is: w e s n z0 z1 dx dy n_columns n_rows reg gtype
"""
_gtype = {0: "GMT_GRID_IS_CARTESIAN", 1: "GMT_GRID_IS_GEO"}[grid.gmt.gtype]
_reg = {0: "GMT_GRID_NODE_REG", 1: "GMT_GRID_PIXEL_REG"}[grid.gmt.registration]
# Conversion to a C-contiguous array needs to be done here and not in
# put_matrix because we need to maintain a reference to the copy while
# it is being used by the C API. Otherwise, the array would be garbage
# collected and the memory freed. Creating it in this context manager
# guarantees that the copy will be around until the virtual file is
# closed. The conversion is implicit in dataarray_to_matrix.
matrix, region, inc = dataarray_to_matrix(grid)
family = "GMT_IS_GRID|GMT_VIA_MATRIX"
geometry = "GMT_IS_SURFACE"
gmt_grid = self.create_data(
family,
geometry,
mode=f"GMT_CONTAINER_ONLY|{_gtype}",
ranges=region,
inc=inc,
registration=_reg,
)
self.put_matrix(gmt_grid, matrix)
args = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", gmt_grid)
with self.open_virtualfile(*args) as vfile:
yield vfile
[docs]
def virtualfile_in( # noqa: PLR0912
self,
check_kind=None,
data=None,
x=None,
y=None,
z=None,
extra_arrays=None,
required_z=False,
required_data=True,
):
"""
Store any data inside a virtual file.
This convenience function automatically detects the kind of data passed
into it, and produces a virtualfile that can be passed into GMT later
on.
Parameters
----------
check_kind : str or None
Used to validate the type of data that can be passed in. Choose
from 'raster', 'vector', or None. Default is None (no validation).
data : str or pathlib.Path or xarray.DataArray or {table-like} or None
Any raster or vector data format. This could be a file name or
path, a raster grid, a vector matrix/arrays, or other supported
data input.
x/y/z : 1-D arrays or None
x, y, and z columns as numpy arrays.
extra_arrays : list of 1-D arrays
Optional. A list of numpy arrays in addition to x, y, and z.
All of these arrays must be of the same size as the x/y/z arrays.
required_z : bool
State whether the 'z' column is required.
required_data : bool
Set to True when 'data' is required, or False when dealing with
optional virtual files. [Default is True].
Returns
-------
file_context : contextlib._GeneratorContextManager
The virtual file stored inside a context manager. Access the file
name of this virtualfile using ``with file_context as fname: ...``.
Examples
--------
>>> from pygmt.helpers import GMTTempFile
>>> import xarray as xr
>>> data = xr.Dataset(
... coords=dict(index=[0, 1, 2]),
... data_vars=dict(
... x=("index", [9, 8, 7]),
... y=("index", [6, 5, 4]),
... z=("index", [3, 2, 1]),
... ),
... )
>>> with Session() as ses:
... with ses.virtualfile_in(check_kind="vector", data=data) as fin:
... # Send the output to a file so that we can read it
... with GMTTempFile() as fout:
... ses.call_module("info", [fin, f"->{fout.name}"])
... print(fout.read().strip())
<vector memory>: N = 3 <7/9> <4/6> <1/3>
"""
kind = data_kind(data, required=required_data)
_validate_data_input(
data=data,
x=x,
y=y,
z=z,
required_z=required_z,
required_data=required_data,
kind=kind,
)
if check_kind:
valid_kinds = ("file", "arg") if required_data is False else ("file",)
if check_kind == "raster":
valid_kinds += ("grid", "image")
elif check_kind == "vector":
valid_kinds += ("matrix", "vectors", "geojson")
if kind not in valid_kinds:
raise GMTInvalidInput(
f"Unrecognized data type for {check_kind}: {type(data)}"
)
# Decide which virtualfile_from_ function to use
_virtualfile_from = {
"file": contextlib.nullcontext,
"arg": contextlib.nullcontext,
"geojson": tempfile_from_geojson,
"grid": self.virtualfile_from_grid,
"image": tempfile_from_image,
# Note: virtualfile_from_matrix is not used because a matrix can be
# converted to vectors instead, and using vectors allows for better
# handling of string type inputs (e.g. for datetime data types)
"matrix": self.virtualfile_from_vectors,
"vectors": self.virtualfile_from_vectors,
}[kind]
# Ensure the data is an iterable (Python list or tuple)
if kind in {"geojson", "grid", "image", "file", "arg"}:
if kind == "image" and data.dtype != "uint8":
msg = (
f"Input image has dtype: {data.dtype} which is unsupported, "
"and may result in an incorrect output. Please recast image "
"to a uint8 dtype and/or scale to 0-255 range, e.g. "
"using a histogram equalization function like "
"skimage.exposure.equalize_hist."
)
warnings.warn(message=msg, category=RuntimeWarning, stacklevel=2)
_data = (data,) if not isinstance(data, pathlib.PurePath) else (str(data),)
elif kind == "vectors":
_data = [np.atleast_1d(x), np.atleast_1d(y)]
if z is not None:
_data.append(np.atleast_1d(z))
if extra_arrays:
_data.extend(extra_arrays)
elif kind == "matrix": # turn 2-D arrays into list of vectors
if hasattr(data, "items") and not hasattr(data, "to_frame"):
# pandas.DataFrame or xarray.Dataset types.
# pandas.Series will be handled below like a 1-D numpy.ndarray.
_data = [array for _, array in data.items()]
elif hasattr(data, "ndim") and data.ndim == 2 and data.dtype.kind in "iuf":
# Just use virtualfile_from_matrix for 2-D numpy.ndarray
# which are signed integer (i), unsigned integer (u) or
# floating point (f) types
_virtualfile_from = self.virtualfile_from_matrix
_data = (data,)
else:
# Python list, tuple, numpy.ndarray, and pandas.Series types
_data = np.atleast_2d(np.asanyarray(data).T)
# Finally create the virtualfile from the data, to be passed into GMT
file_context = _virtualfile_from(*_data)
return file_context
[docs]
def virtualfile_from_data(
self,
check_kind=None,
data=None,
x=None,
y=None,
z=None,
extra_arrays=None,
required_z=False,
required_data=True,
):
"""
Store any data inside a virtual file.
.. deprecated: 0.13.0
Will be removed in v0.15.0. Use :meth:`pygmt.clib.Session.virtualfile_in`
instead.
"""
msg = (
"API function 'Session.virtualfile_from_datae()' has been deprecated since "
"v0.13.0 and will be removed in v0.15.0. Use 'Session.virtualfile_in()' "
"instead."
)
warnings.warn(msg, category=FutureWarning, stacklevel=2)
return self.virtualfile_in(
check_kind=check_kind,
data=data,
x=x,
y=y,
z=z,
extra_arrays=extra_arrays,
required_z=required_z,
required_data=required_data,
)
[docs]
@contextlib.contextmanager
def virtualfile_out(
self,
kind: Literal["dataset", "grid", "image"] = "dataset",
fname: str | None = None,
) -> Generator[str, None, None]:
r"""
Create a virtual file or an actual file for storing output data.
If ``fname`` is not given, a virtual file will be created to store the output
data into a GMT data container and the function yields the name of the virtual
file. Otherwise, the output data will be written into the specified file and the
function simply yields the actual file name.
Parameters
----------
kind
The data kind of the virtual file to create. Valid values are ``"dataset"``,
``"grid"``, and ``"image"``. Ignored if ``fname`` is specified.
fname
The name of the actual file to write the output data. No virtual file will
be created.
Yields
------
vfile
Name of the virtual file or the actual file.
Examples
--------
>>> from pathlib import Path
>>> from pygmt.clib import Session
>>> from pygmt.datatypes import _GMT_DATASET
>>> from pygmt.helpers import GMTTempFile
>>>
>>> with GMTTempFile(suffix=".txt") as tmpfile:
... with Path(tmpfile.name).open(mode="w") as fp:
... print("1.0 2.0 3.0 TEXT", file=fp)
...
... # Create a virtual file for storing the output table.
... with Session() as lib:
... with lib.virtualfile_out(kind="dataset") as vouttbl:
... lib.call_module("read", [tmpfile.name, vouttbl, "-Td"])
... ds = lib.read_virtualfile(vouttbl, kind="dataset")
... assert isinstance(ds.contents, _GMT_DATASET)
...
... # Write data to an actual file without creating a virtual file.
... with Session() as lib:
... with lib.virtualfile_out(fname=tmpfile.name) as vouttbl:
... assert vouttbl == tmpfile.name
... lib.call_module("read", [tmpfile.name, vouttbl, "-Td"])
... line = Path(vouttbl).read_text()
... assert line == "1\t2\t3\tTEXT\n"
"""
if fname is not None: # Yield the actual file name.
yield fname
else: # Create a virtual file for storing the output data.
# Determine the family and geometry from kind
family, geometry = {
"dataset": ("GMT_IS_DATASET", "GMT_IS_PLP"),
"grid": ("GMT_IS_GRID", "GMT_IS_SURFACE"),
"image": ("GMT_IS_IMAGE", "GMT_IS_SURFACE"),
}[kind]
direction = "GMT_OUT|GMT_IS_REFERENCE" if kind == "image" else "GMT_OUT"
with self.open_virtualfile(family, geometry, direction, None) as vfile:
yield vfile
def inquire_virtualfile(self, vfname: str) -> int:
"""
Get the family of a virtual file.
Parameters
----------
vfname
Name of the virtual file to inquire.
Returns
-------
family
The integer value for the family of the virtual file.
Examples
--------
>>> from pygmt.clib import Session
>>> with Session() as lib:
... with lib.virtualfile_out(kind="dataset") as vfile:
... family = lib.inquire_virtualfile(vfile)
... assert family == lib["GMT_IS_DATASET"]
"""
c_inquire_virtualfile = self.get_libgmt_func(
"GMT_Inquire_VirtualFile",
argtypes=[ctp.c_void_p, ctp.c_char_p],
restype=ctp.c_uint,
)
return c_inquire_virtualfile(self.session_pointer, vfname.encode())
[docs]
def read_virtualfile(
self,
vfname: str,
kind: Literal["dataset", "grid", "image", "cube", None] = None,
):
"""
Read data from a virtual file and optionally cast into a GMT data container.
Parameters
----------
vfname
Name of the virtual file to read.
kind
Cast the data into a GMT data container. Valid values are ``"dataset"``,
``"grid"``, ``"image"`` and ``None``. If ``None``, will return a ctypes void
pointer.
Returns
-------
pointer
Pointer to the GMT data container. If ``kind`` is ``None``, returns a ctypes
void pointer instead.
Examples
--------
>>> from pathlib import Path
>>> from pygmt.clib import Session
>>> from pygmt.helpers import GMTTempFile
>>>
>>> # Read dataset from a virtual file
>>> with Session() as lib:
... with GMTTempFile(suffix=".txt") as tmpfile:
... with Path(tmpfile.name).open(mode="w") as fp:
... print("1.0 2.0 3.0 TEXT", file=fp)
... with lib.virtualfile_out(kind="dataset") as vouttbl:
... lib.call_module("read", [tmpfile.name, vouttbl, "-Td"])
... # Read the virtual file as a void pointer
... void_pointer = lib.read_virtualfile(vouttbl)
... assert isinstance(void_pointer, int) # void pointer is an int
... # Read the virtual file as a dataset
... data_pointer = lib.read_virtualfile(vouttbl, kind="dataset")
... assert isinstance(data_pointer, ctp.POINTER(_GMT_DATASET))
>>>
>>> # Read grid from a virtual file
>>> with Session() as lib:
... with lib.virtualfile_out(kind="grid") as voutgrd:
... lib.call_module("read", ["@earth_relief_01d_g", voutgrd, "-Tg"])
... # Read the virtual file as a void pointer
... void_pointer = lib.read_virtualfile(voutgrd)
... assert isinstance(void_pointer, int) # void pointer is an int
... data_pointer = lib.read_virtualfile(voutgrd, kind="grid")
... assert isinstance(data_pointer, ctp.POINTER(_GMT_GRID))
"""
c_read_virtualfile = self.get_libgmt_func(
"GMT_Read_VirtualFile",
argtypes=[ctp.c_void_p, ctp.c_char_p],
restype=ctp.c_void_p,
)
pointer = c_read_virtualfile(self.session_pointer, vfname.encode())
# The GMT C API function GMT_Read_VirtualFile returns a void pointer. It usually
# needs to be cast into a pointer to a GMT data container (e.g., _GMT_GRID or
# _GMT_DATASET).
if kind is None: # Return the ctypes void pointer
return pointer
if kind == "cube":
raise NotImplementedError(f"kind={kind} is not supported yet.")
dtype = {"dataset": _GMT_DATASET, "grid": _GMT_GRID, "image": _GMT_IMAGE}[kind]
return ctp.cast(pointer, ctp.POINTER(dtype))
[docs]
def virtualfile_to_dataset(
self,
vfname: str,
output_type: Literal["pandas", "numpy", "file", "strings"] = "pandas",
header: int | None = None,
column_names: list[str] | None = None,
dtype: type | dict[str, type] | None = None,
index_col: str | int | None = None,
) -> pd.DataFrame | np.ndarray | None:
"""
Output a tabular dataset stored in a virtual file to a different format.
The format of the dataset is determined by the ``output_type`` parameter.
Parameters
----------
vfname
The virtual file name that stores the result data.
output_type
Desired output type of the result data.
- ``"pandas"`` will return a :class:`pandas.DataFrame` object.
- ``"numpy"`` will return a :class:`numpy.ndarray` object.
- ``"file"`` means the result was saved to a file and will return ``None``.
- ``"strings"`` will return the trailing text only as an array of strings.
header
Row number containing column names for the :class:`pandas.DataFrame` output.
``header=None`` means not to parse the column names from table header.
Ignored if the row number is larger than the number of headers in the table.
column_names
The column names for the :class:`pandas.DataFrame` output.
dtype
Data type for the columns of the :class:`pandas.DataFrame` output. Can be a
single type for all columns or a dictionary mapping column names to types.
index_col
Column to set as the index of the :class:`pandas.DataFrame` output.
Returns
-------
result
The result dataset. If ``output_type="file"`` returns ``None``.
Examples
--------
>>> from pathlib import Path
>>> import numpy as np
>>> import pandas as pd
>>>
>>> from pygmt.helpers import GMTTempFile
>>> from pygmt.clib import Session
>>>
>>> with GMTTempFile(suffix=".txt") as tmpfile:
... # prepare the sample data file
... with Path(tmpfile.name).open(mode="w") as fp:
... print(">", file=fp)
... print("1.0 2.0 3.0 TEXT1 TEXT23", file=fp)
... print("4.0 5.0 6.0 TEXT4 TEXT567", file=fp)
... print(">", file=fp)
... print("7.0 8.0 9.0 TEXT8 TEXT90", file=fp)
... print("10.0 11.0 12.0 TEXT123 TEXT456789", file=fp)
...
... # file output
... with Session() as lib:
... with GMTTempFile(suffix=".txt") as outtmp:
... with lib.virtualfile_out(
... kind="dataset", fname=outtmp.name
... ) as vouttbl:
... lib.call_module("read", [tmpfile.name, vouttbl, "-Td"])
... result = lib.virtualfile_to_dataset(
... vfname=vouttbl, output_type="file"
... )
... assert result is None
... assert Path(outtmp.name).stat().st_size > 0
...
... # strings, numpy and pandas outputs
... with Session() as lib:
... with lib.virtualfile_out(kind="dataset") as vouttbl:
... lib.call_module("read", [tmpfile.name, vouttbl, "-Td"])
...
... # strings output
... outstr = lib.virtualfile_to_dataset(
... vfname=vouttbl, output_type="strings"
... )
... assert isinstance(outstr, np.ndarray)
... assert outstr.dtype.kind in ("S", "U")
...
... # numpy output
... outnp = lib.virtualfile_to_dataset(
... vfname=vouttbl, output_type="numpy"
... )
... assert isinstance(outnp, np.ndarray)
...
... # pandas output
... outpd = lib.virtualfile_to_dataset(
... vfname=vouttbl, output_type="pandas"
... )
... assert isinstance(outpd, pd.DataFrame)
...
... # pandas output with specified column names
... outpd2 = lib.virtualfile_to_dataset(
... vfname=vouttbl,
... output_type="pandas",
... column_names=["col1", "col2", "col3", "coltext"],
... )
... assert isinstance(outpd2, pd.DataFrame)
>>> outstr
array(['TEXT1 TEXT23', 'TEXT4 TEXT567', 'TEXT8 TEXT90',
'TEXT123 TEXT456789'], dtype='<U18')
>>> outnp
array([[1.0, 2.0, 3.0, 'TEXT1 TEXT23'],
[4.0, 5.0, 6.0, 'TEXT4 TEXT567'],
[7.0, 8.0, 9.0, 'TEXT8 TEXT90'],
[10.0, 11.0, 12.0, 'TEXT123 TEXT456789']], dtype=object)
>>> outpd
0 1 2 3
0 1.0 2.0 3.0 TEXT1 TEXT23
1 4.0 5.0 6.0 TEXT4 TEXT567
2 7.0 8.0 9.0 TEXT8 TEXT90
3 10.0 11.0 12.0 TEXT123 TEXT456789
>>> outpd2
col1 col2 col3 coltext
0 1.0 2.0 3.0 TEXT1 TEXT23
1 4.0 5.0 6.0 TEXT4 TEXT567
2 7.0 8.0 9.0 TEXT8 TEXT90
3 10.0 11.0 12.0 TEXT123 TEXT456789
"""
if output_type == "file": # Already written to file, so return None
return None
# Read the virtual file as a _GMT_DATASET object
result = self.read_virtualfile(vfname, kind="dataset").contents
if output_type == "strings": # strings output
return result.to_strings()
result = result.to_dataframe(
header=header, column_names=column_names, dtype=dtype, index_col=index_col
)
if output_type == "numpy": # numpy.ndarray output
return result.to_numpy()
return result # pandas.DataFrame output
[docs]
def virtualfile_to_raster(
self,
vfname: str,
kind: Literal["grid", "image", "cube", None] = "grid",
outgrid: str | None = None,
) -> xr.DataArray | None:
"""
Output raster data stored in a virtual file to an :class:`xarray.DataArray`
object.
The raster data can be a grid, an image or a cube.
Parameters
----------
vfname
The virtual file name that stores the result grid/image/cube.
kind
Type of the raster data. Valid values are ``"grid"``, ``"image"``,
``"cube"`` or ``None``. If ``None``, will inquire the data type from the
virtual file name.
outgrid
Name of the output grid/image/cube. If specified, it means the raster data
was already saved into an actual file and will return ``None``.
Returns
-------
result
The result grid/image/cube. If ``outgrid`` is specified, return ``None``.
Examples
--------
>>> from pathlib import Path
>>> from pygmt.clib import Session
>>> from pygmt.helpers import GMTTempFile
>>> with Session() as lib:
... # file output
... with GMTTempFile(suffix=".nc") as tmpfile:
... outgrid = tmpfile.name
... with lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd:
... lib.call_module("read", ["@earth_relief_01d_g", voutgrd, "-Tg"])
... result = lib.virtualfile_to_raster(
... vfname=voutgrd, outgrid=outgrid
... )
... assert result == None
... assert Path(outgrid).stat().st_size > 0
...
... # xarray.DataArray output
... outgrid = None
... with lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd:
... lib.call_module("read", ["@earth_relief_01d_g", voutgrd, "-Tg"])
... result = lib.virtualfile_to_raster(vfname=voutgrd, outgrid=outgrid)
... assert isinstance(result, xr.DataArray)
"""
if outgrid is not None: # Already written to file, so return None
return None
if kind is None: # Inquire the data family from the virtualfile
family = self.inquire_virtualfile(vfname)
kind = { # type: ignore[assignment]
self["GMT_IS_GRID"]: "grid",
self["GMT_IS_IMAGE"]: "image",
self["GMT_IS_CUBE"]: "cube",
}[family]
return self.read_virtualfile(vfname, kind=kind).contents.to_dataarray()