Wrap GMT's standard data type GMT_CUBE for cubes

pygmt/clib/session.py

@@ -27,7 +27,7 @@
     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.datatypes import _GMT_CUBE, _GMT_DATASET, _GMT_GRID, _GMT_IMAGE
 from pygmt.exceptions import GMTCLibError, GMTCLibNoSessionError, GMTInvalidInput
 from pygmt.helpers import (
     _validate_data_input,
@@ -1059,7 +1059,7 @@ def put_matrix(self, dataset, matrix, pad=0):
     def read_data(
         self,
         infile: str,
-        kind: Literal["dataset", "grid", "image"],
+        kind: Literal["dataset", "grid", "image", "cube"],
         family: str | None = None,
         geometry: str | None = None,
         mode: str = "GMT_READ_NORMAL",
@@ -1077,8 +1077,8 @@ def read_data(
         infile
             The input file name.
         kind
-            The data kind of the input file. Valid values are ``"dataset"``, ``"grid"``
-            and ``"image"``.
+            The data kind of the input file. Valid values are ``"dataset"``, ``"grid"``,
+            ``"image"`` and ``"cube"``.
         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
@@ -1130,6 +1130,7 @@ def read_data(
             "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),
+            "cube": ("GMT_IS_CUBE", "GMT_IS_VOLUME", _GMT_CUBE),
         }[kind]
         if family is None:
             family = _family
@@ -1882,7 +1883,7 @@ def virtualfile_from_data(
     @contextlib.contextmanager
     def virtualfile_out(
         self,
-        kind: Literal["dataset", "grid", "image"] = "dataset",
+        kind: Literal["dataset", "grid", "image", "cube"] = "dataset",
         fname: str | None = None,
     ) -> Generator[str, None, None]:
         r"""
@@ -1897,7 +1898,7 @@ def virtualfile_out(
         ----------
         kind
             The data kind of the virtual file to create. Valid values are ``"dataset"``,
-            ``"grid"``, and ``"image"``. Ignored if ``fname`` is specified.
+            ``"grid"``, ``"image"`` and ``"cube"``. Ignored if ``fname`` is specified.
         fname
             The name of the actual file to write the output data. No virtual file will
             be created.
@@ -1941,6 +1942,7 @@ def virtualfile_out(
                 "dataset": ("GMT_IS_DATASET", "GMT_IS_PLP"),
                 "grid": ("GMT_IS_GRID", "GMT_IS_SURFACE"),
                 "image": ("GMT_IS_IMAGE", "GMT_IS_SURFACE"),
+                "cube": ("GMT_IS_CUBE", "GMT_IS_VOLUME"),
             }[kind]
             direction = "GMT_OUT|GMT_IS_REFERENCE" if kind == "image" else "GMT_OUT"
             with self.open_virtualfile(family, geometry, direction, None) as vfile:
@@ -1989,8 +1991,8 @@ def read_virtualfile(
             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.
+            ``"grid"``, ``"image"``, ``"cube"`` and ``None``. If ``None``, will return
+            a ctypes void pointer.
 
         Returns
         -------
@@ -2040,9 +2042,12 @@ def read_virtualfile(
         # _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]
+        dtype = {
+            "dataset": _GMT_DATASET,
+            "grid": _GMT_GRID,
+            "image": _GMT_IMAGE,
+            "cube": _GMT_CUBE,
+        }[kind]
         return ctp.cast(pointer, ctp.POINTER(dtype))
 
     def virtualfile_to_dataset(

pygmt/datatypes/__init__.py

@@ -2,6 +2,7 @@
 Wrappers for GMT data types.
 """
 
+from pygmt.datatypes.cube import _GMT_CUBE
 from pygmt.datatypes.dataset import _GMT_DATASET
 from pygmt.datatypes.grid import _GMT_GRID
 from pygmt.datatypes.image import _GMT_IMAGE

pygmt/datatypes/cube.py

@@ -0,0 +1,105 @@
+"""
+Wrapper for the GMT_CUBE data type.
+"""
+
+import ctypes as ctp
+from typing import ClassVar
+
+from pygmt.datatypes.header import (
+    _GMT_GRID_HEADER,
+    GMT_GRID_UNIT_LEN80,
+    GMT_GRID_VARNAME_LEN80,
+    gmt_grdfloat,
+)
+
+
+class _GMT_CUBE(ctp.Structure):  # noqa: N801
+    """
+    GMT cube data structure for 3-D data.
+
+    The GMT_CUBE structure is a extension of the GMT_GRID structure to handle 3-D data
+    cubes. It requires a 2-D grid header and extended parameters for the 3rd dimension.
+
+    header->n_bands is used for the number of layers in 3-D cubes.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from pygmt import which
+    >>> from pygmt.clib import Session
+    >>> cubefile = which("@cube.nc", download="c")
+    >>> with Session() as lib:
+    ...     with lib.virtualfile_out(kind="cube") as voutcube:
+    ...         lib.call_module("read", [cubefile, voutcube, "-Tu", "-Vd"])
+    ...         # Read the cube from the virtual file
+    ...         cube = lib.read_virtualfile(vfname=voutcube, kind="cube").contents
+    ...         # The cube header
+    ...         header = cube.header.contents
+    ...         # Access the header properties
+    ...         print(header.n_rows, header.n_columns, header.registration)
+    ...         print(header.wesn[:], header.inc[:])
+    ...         print(header.z_scale_factor, header.z_add_offset)
+    ...         print(header.x_units, header.y_units, header.z_units)
+    ...         print(header.nm, header.size, header.complex_mode)
+    ...         print(header.type, header.n_bands, header.mx, header.my)
+    ...         print(header.pad[:])
+    ...         print(header.mem_layout, header.xy_off)
+    ...         # Cube-specific attributes.
+    ...         print(cube.mode, cube.z_range[:], cube.z_inc, cube.name, cube.units)
+    ...         # The x, y, and z coordinates
+    ...         x = np.ctypeslib.as_array(cube.x, shape=(header.n_columns,)).copy()
+    ...         y = np.ctypeslib.as_array(cube.y, shape=(header.n_rows,)).copy()
+    ...         z = np.ctypeslib.as_array(cube.z, shape=(header.n_bands,)).copy()
+    ...         # The data array (with paddings)
+    ...         data = np.ctypeslib.as_array(
+    ...             cube.data, shape=(header.my, header.mx, header.n_bands)
+    ...         ).copy()
+    ...         # The data array (without paddings)
+    ...         pad = header.pad[:]
+    ...         data = data[pad[2] : header.my - pad[3], pad[0] : header.mx - pad[1], :]
+    11 11 0
+    [0.0, 10.0, 0.0, 10.0] [1.0, 1.0]
+    1.0 0.0
+    b'x' b'y' b'cube'
+    121 226 0
+    18 4 15 15
+    [2, 2, 2, 2]
+    b'' 0.0
+    0 [1.0, 5.0] 0.0 b'' b'z'
+    >>> x
+    array([ 0.,  1.,  2.,  3.,  4.,  5.,  6.,  7.,  8.,  9., 10.])
+    >>> y
+    array([10.,  9.,  8.,  7.,  6.,  5.,  4.,  3.,  2.,  1.,  0.])
+    >>> z
+    array([1., 2., 3., 5.])
+    >>> data.shape
+    (11, 11, 4)
+    >>> # data.min(), data.max()  # The min/max are wrong. Upstream bug?
+    >>> # (-29.4, 169.4)
+    """
+
+    _fields_: ClassVar = [
+        # Pointer to full GMT 2-D header for a layer (common to all layers)
+        ("header", ctp.POINTER(_GMT_GRID_HEADER)),
+        # Pointer to the gmt_grdfloat 3-D cube - a stack of 2-D padded grids
+        ("data", ctp.POINTER(gmt_grdfloat)),
+        # Vector of x coordinates common to all layers
+        ("x", ctp.POINTER(ctp.c_double)),
+        # Vector of y coordinates common to all layers
+        ("y", ctp.POINTER(ctp.c_double)),
+        # Low-level information for GMT use only
+        ("hidden", ctp.c_void_p),
+        # mode=GMT_CUBE_IS_STACK means the input dataset was a list of 2-D grids, rather
+        # than a single cube.
+        ("mode", ctp.c_uint),
+        # Minimum/maximum z values (complements header->wesn[4])
+        ("z_range", ctp.c_double * 2),
+        # z increment (complements inc[2]) (0 if variable z spacing)
+        ("z_inc", ctp.c_double),
+        # Array of z values (complements x, y)
+        ("z", ctp.POINTER(ctp.c_double)),
+        # Name of the 3-D variable, if read from file (or empty if just one)
+        ("name", ctp.c_char * GMT_GRID_VARNAME_LEN80),
+        # Units in 3rd direction (complements x_units, y_units, z_units)
+        ("units", ctp.c_char * GMT_GRID_UNIT_LEN80),
+    ]

pygmt/helpers/caching.py

@@ -75,6 +75,7 @@ def cache_data():
         "@Table_5_11_mean.xyz",
         "@capitals.gmt",
         "@circuit.png",
+        "@cube.nc",
         "@earth_relief_20m_holes.grd",
         "@fractures_06.txt",
         "@hotspots.txt",

pygmt/tests/test_clib_read_data.py

@@ -201,6 +201,24 @@ def test_clib_read_data_image_two_steps(expected_xrimage):
             xr.testing.assert_equal(xrimage, expected_xrimage)
 
 
+def test_clib_read_data_cube_actual_grid():
+    """
+    Test the Session.read_data method for cube, but actually the file is a grid.
+    """
+    with Session() as lib:
+        with pytest.raises(GMTCLibError):
+            lib.read_data("@earth_relief_01d_p", kind="cube", mode="GMT_CONTAINER_ONLY")
+
+
+def test_clib_read_data_cube_actual_image():
+    """
+    Test the Session.read_data method for cube, but actually the file is an image.
+    """
+    with Session() as lib:
+        with pytest.raises(GMTCLibError):
+            lib.read_data("@earth_day_01d", kind="cube", mode="GMT_CONTAINER_ONLY")
+
+
 def test_clib_read_data_fails():
     """
     Test that the Session.read_data method raises an exception if there are errors.