Source code for pygmt.clib.session

"""
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 sys
import ctypes as ctp
from contextlib import contextmanager

from packaging.version import Version
import numpy as np

from ..exceptions import (
    GMTCLibError,
    GMTCLibNoSessionError,
    GMTInvalidInput,
    GMTVersionError,
)
from .loading import load_libgmt
from .conversion import (
    kwargs_to_ctypes_array,
    vectors_to_arrays,
    dataarray_to_matrix,
    as_c_contiguous,
)

FAMILIES = [
    "GMT_IS_DATASET",
    "GMT_IS_GRID",
    "GMT_IS_PALETTE",
    "GMT_IS_MATRIX",
    "GMT_IS_VECTOR",
]

VIAS = ["GMT_VIA_MATRIX", "GMT_VIA_VECTOR"]

GEOMETRIES = [
    "GMT_IS_NONE",
    "GMT_IS_POINT",
    "GMT_IS_LINE",
    "GMT_IS_POLYGON",
    "GMT_IS_PLP",
    "GMT_IS_SURFACE",
]

MODES = ["GMT_CONTAINER_ONLY", "GMT_OUTPUT"]

REGISTRATIONS = ["GMT_GRID_PIXEL_REG", "GMT_GRID_NODE_REG"]

DTYPES = {
    "float64": "GMT_DOUBLE",
    "float32": "GMT_FLOAT",
    "int64": "GMT_LONG",
    "int32": "GMT_INT",
    "uint64": "GMT_ULONG",
    "uint32": "GMT_UINT",
}


[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 < 6.0.0rc1. 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.datasets import load_earth_relief >>> from pygmt.helpers import GMTTempFile >>> grid = load_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", "{} -C ->{}".format(fin, fout.name)) ... # Read the contents of the temp file before it's deleted. ... print(fout.read().strip()) -180 180 -90 90 -8425 5551 1 1 361 181 """ # The minimum version of GMT required required_version = "6.0.0rc1" @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"), "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"), # API_IMAGE_LAYOUT not defined if GMT is not compiled with GDAL # "image layout": self.get_default("API_IMAGE_LAYOUT"), "grid layout": self.get_default("API_GRID_LAYOUT"), } return self._info
[docs] def __enter__(self): """ Create a GMT API session and check the libgmt version. Calls :meth:`~gmt.clib.Session.create`. Raises ------ GMTVersionError If the version reported by libgmt is less than ``Session.required_version``. Will destroy the session before raising the exception. """ self.create("pygmt-session") # Need to store the version info because 'get_default' won't work after the # session is destroyed. version = self.info["version"] if Version(version) < Version(self.required_version): self.destroy() raise GMTVersionError( "Using an incompatible GMT version {}. Must be equal or newer than {}.".format( version, self.required_version ) ) return self
[docs] def __exit__(self, exc_type, exc_value, traceback): """ Destroy the currently open GMT API session. Calls :meth:`~gmt.clib.Session.destroy`. """ self.destroy()
[docs] def __getitem__(self, name): """ 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 : str The name of the constant (e.g., ``"GMT_SESSION_EXTERNAL"``) Returns ------- constant : int 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 lib 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("Constant '{}' doesn't exits in libgmt.".format(name)) 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 = load_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:`~gmt.clib.Session` as a context manager in a ``with`` block is preferred over calling :meth:`~gmt.clib.Session.create` and :meth:`~gmt.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 # pylint: disable=pointless-statement # 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 fist." ) # 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): # pylint: disable=unused-argument """ 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. """ message = message.decode().strip() 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) 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( "Failed to create a GMT API session:\n{}".format(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:`~gmt.clib.Session` as a context manager in a ``with`` block is preferred over calling :meth:`~gmt.clib.Session.create` and :meth:`~gmt.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( "Failed to destroy GMT API session:\n{}".format(self._error_message) ) self.session_pointer = None
[docs] def get_default(self, name): """ Get the value of a GMT default parameter (library version, paths, etc). Possible default parameter names include: * ``"API_VERSION"``: The GMT 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 Parameters ---------- name : str The name of the default parameter (e.g., ``"API_VERSION"``) Returns ------- value : str The default 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(10000) status = c_get_default(self.session_pointer, name.encode(), value) if status != 0: raise GMTCLibError( "Error getting default value for '{}' (error code {}).".format( name, status ) ) return value.value.decode()
[docs] def call_module(self, module, args): """ Call a GMT module with the given arguments. Makes a call to ``GMT_Call_Module`` from the C API using mode ``GMT_MODULE_CMD`` (arguments passed as a single string). Most interactions with the C API are done through this function. Parameters ---------- module : str Module name (``'pscoast'``, ``'psbasemap'``, etc). args : str String with the command line arguments that will be passed to the module (for example, ``'-R0/5/0/10 -JM'``). Raises ------ 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, ) mode = self["GMT_MODULE_CMD"] status = c_call_module( self.session_pointer, module.encode(), mode, args.encode() ) if status != 0: raise GMTCLibError( "Module '{}' failed with status code {}:\n{}".format( module, status, self._error_message ) )
[docs] def create_data(self, family, geometry, mode, **kwargs): """ Create an empty GMT data container. Parameters ---------- family : str A valid GMT data family name (e.g., ``'GMT_IS_DATASET'``). See the ``data_families`` attribute for valid names. geometry : str A valid GMT data geometry name (e.g., ``'GMT_IS_POINT'``). See the ``data_geometries`` attribute for valid names. mode : str A valid GMT data mode (e.g., ``'GMT_OUTPUT'``). See the ``data_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 : int 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_GEO"] ) geometry_int = self._parse_constant(geometry, valid=GEOMETRIES) registration_int = self._parse_constant( kwargs.get("registration", "GMT_GRID_NODE_REG"), valid=REGISTRATIONS ) # Convert dim, ranges, and inc to ctypes arrays if given (will be None # if not given to represent NULL pointers) dim = kwargs_to_ctypes_array("dim", kwargs, ctp.c_uint64 * 4) ranges = kwargs_to_ctypes_array("ranges", kwargs, ctp.c_double * 4) inc = kwargs_to_ctypes_array("inc", kwargs, 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, kwargs), None, ) if data_ptr is None: raise GMTCLibError("Failed to create an empty GMT data pointer.") return data_ptr
def _parse_pad(self, family, kwargs): """ 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. """ pad = kwargs.get("pad", None) if pad is None: if "MATRIX" in family: pad = 0 else: pad = 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:`~gmt.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:`~gmt.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( "Only one modifier is allowed in constants, {} given: '{}'".format( nmodifiers, constant ) ) if nmodifiers > 0 and valid_modifiers is None: raise GMTInvalidInput( "Constant modifiers not allowed since valid values were not " + "given: '{}'".format(constant) ) if name not in valid: raise GMTInvalidInput( "Invalid constant argument '{}'. Must be one of {}.".format( name, str(valid) ) ) if ( nmodifiers > 0 and valid_modifiers is not None and parts[1] not in valid_modifiers ): raise GMTInvalidInput( "Invalid constant modifier '{}'. Must be one of {}.".format( parts[1], str(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 dimensions and is a valid data type. Parameters ---------- array : numpy array The array to be tested. ndim : int The desired dimension of the array. Returns ------- gmt_type : int The GMT constant value representing this data type. Raises ------ GMTCLibError If the array has the wrong 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 """ if array.dtype.name not in DTYPES: raise GMTInvalidInput( "Unsupported numpy data type '{}'.".format(array.dtype.name) ) if array.ndim != ndim: raise GMTInvalidInput( "Expected a numpy 1d array, got {}d.".format(array.ndim) ) return self[DTYPES[array.dtype.name]]
[docs] def put_vector(self, dataset, column, vector): """ Attach a numpy 1D array as a column on a GMT dataset. Use this functions 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:`~gmt.clib.Session.create_data` first. Use ``family='GMT_IS_DATASET|GMT_VIA_VECTOR'``. Not at all numpy dtypes are supported, only: float64, float32, int64, int32, uint64, and uint32. .. warning:: The numpy array must be C contiguous in memory. If it comes from a column slice of a 2d 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:`~gmt.clib.Session.create_data`. column : int The column number of this vector in the dataset (starting from 0). vector : numpy 1d-array The array that will be attached to the dataset. Must be a 1d 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) 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( " ".join( [ "Failed to put vector of type {}".format(vector.dtype), "in column {} of dataset.".format(column), ] ) )
[docs] def put_matrix(self, dataset, matrix, pad=0): """ Attach a numpy 2D array to a GMT dataset. Use this functions 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:`~gmt.clib.Session.create_data` first. Use ``|GMT_VIA_MATRIX'`` in the family. Not at all numpy dtypes are supported, only: float64, float32, int64, int32, uint64, and uint32. .. 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:`~gmt.clib.Session.create_data`. matrix : numpy 2d-array The array that will be attached to the dataset. Must be a 2d 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("Failed to put matrix of type {}.".format(matrix.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:`~gmt.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 ``data_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 ``data_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:`~gmt.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], (ctp.c_double * 6)(*wesn), output.encode(), data, ) if status != 0: raise GMTCLibError("Failed to write dataset to '{}'".format(output))
[docs] @contextmanager def open_virtual_file(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 to API modules. Use it to pass in your GMT data structure (created using :meth:`~gmt.clib.Session.create_data`) to a module that expects an input or output 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. data : int The ctypes void pointer to your 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 os >>> 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', dataset) ... with lib.open_virtual_file(*vfargs) as vfile: ... # Send the output to a temp file so that we can read it ... with GMTTempFile() as ofile: ... args = '{} ->{}'.format(vfile, ofile.name) ... lib.call_module('info', args) ... 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=["GMT_IN", "GMT_OUT"], valid_modifiers=["GMT_IS_REFERENCE", "GMT_IS_DUPLICATE"], ) buff = ctp.create_string_buffer(self["GMT_STR16"]) 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("Failed to close virtual file '{}'.".format(vfname))
[docs] @contextmanager def virtualfile_from_vectors(self, *vectors): """ Store 1d 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:`~gmt.clib.Session.create_data`, :meth:`~gmt.clib.Session.put_vector`, and :meth:`~gmt.clib.Session.open_virtual_file`. 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 2D array), they will need to be copied to a contiguous block. Parameters ---------- vectors : 1d 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', '{} ->{}'.format(fin, 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_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 # vectors_to_arrays. arrays = vectors_to_arrays(vectors) columns = len(arrays) 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] ) for col, array in enumerate(arrays): self.put_vector(dataset, column=col, vector=array) with self.open_virtual_file(family, geometry, "GMT_IN", dataset) as vfile: yield vfile
[docs] @contextmanager def virtualfile_from_matrix(self, matrix): """ Store a 2d 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:`~gmt.clib.Session.virtualfile_from_grid` instead. Use this instead of creating the data container and virtual file by hand with :meth:`~gmt.clib.Session.create_data`, :meth:`~gmt.clib.Session.put_matrix`, and :meth:`~gmt.clib.Session.open_virtual_file` 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 : 2d 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', '{} ->{}'.format(fin, 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_virtual_file(family, geometry, "GMT_IN", dataset) as vfile: yield vfile
[docs] @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:`~gmt.clib.Session.create_data`, :meth:`~gmt.clib.Session.put_matrix`, and :meth:`~gmt.clib.Session.open_virtual_file` 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.datasets import load_earth_relief >>> from pygmt.helpers import GMTTempFile >>> data = load_earth_relief(resolution='60m') >>> print(data.shape) (181, 361) >>> print(data.lon.values.min(), data.lon.values.max()) -180.0 180.0 >>> print(data.lat.values.min(), data.lat.values.max()) -90.0 90.0 >>> print(data.values.min(), data.values.max()) -8425.0 5551.0 >>> 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: ... args = '{} -L0 -Cn ->{}'.format(fin, fout.name) ... ses.call_module('grdinfo', args) ... print(fout.read().strip()) -180 180 -90 90 -8425 5551 1 1 361 181 >>> # The output is: w e s n z0 z1 dx dy n_columns n_rows """ # 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="GMT_CONTAINER_ONLY", ranges=region, inc=inc ) self.put_matrix(gmt_grid, matrix) args = (family, geometry, "GMT_IN|GMT_IS_REFERENCE", gmt_grid) with self.open_virtual_file(*args) as vfile: yield vfile
[docs] def extract_region(self): """ Extract the WESN bounding box of the currently active figure. Retrieves the information from the PostScript file, so it works for country codes as well. Returns ------- * wesn : 1d array A 1D numpy array with the west, east, south, and north dimensions of the current figure. Examples -------- >>> import pygmt >>> fig = pygmt.Figure() >>> fig.coast(region=[0, 10, -20, -10], projection="M6i", frame=True, ... land='black') >>> with Session() as lib: ... wesn = lib.extract_region() >>> print(', '.join(['{:.2f}'.format(x) for x in wesn])) 0.00, 10.00, -20.00, -10.00 Using ISO country codes for the regions (for example ``'US.HI'`` for Hawaii): >>> fig = pygmt.Figure() >>> fig.coast(region='US.HI', projection="M6i", frame=True, ... land='black') >>> with Session() as lib: ... wesn = lib.extract_region() >>> print(', '.join(['{:.2f}'.format(x) for x in wesn])) -164.71, -154.81, 18.91, 23.58 The country codes can have an extra argument that rounds the region a multiple of the argument (for example, ``'US.HI+r5'`` will round the region to multiples of 5): >>> fig = pygmt.Figure() >>> fig.coast(region='US.HI+r5', projection="M6i", frame=True, ... land='black') >>> with Session() as lib: ... wesn = lib.extract_region() >>> print(', '.join(['{:.2f}'.format(x) for x in wesn])) -165.00, -150.00, 15.00, 25.00 """ c_extract_region = self.get_libgmt_func( "GMT_Extract_Region", argtypes=[ctp.c_void_p, ctp.c_char_p, ctp.POINTER(ctp.c_double)], restype=ctp.c_int, ) wesn = np.empty(4, dtype=np.float64) wesn_pointer = wesn.ctypes.data_as(ctp.POINTER(ctp.c_double)) # The second argument to GMT_Extract_Region is a file pointer to a # PostScript file. It's only valid in classic mode. Use None to get a # NULL pointer instead. status = c_extract_region(self.session_pointer, None, wesn_pointer) if status != 0: raise GMTCLibError("Failed to extract region from current figure.") return wesn